title: IMR91L Apoptosis

description: Regional preferences in apoptotic DNA degradation were determined by co-hybridizing high molecular (> 48 kb) and degraded apoptotic DNA (~4 kb), which we have extracted from 1% low melting agarose and amplified by means of the GenomePlex Whole Genome Amplification Kit.


title: 22A2

status: Public on Jul 01 2014

type: RNA

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: carcinoma

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalised using lumi library in R 3.0.2

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: prostate

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted with MirVana Isolation Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: malignacy type

value: Prostate carcinoma

tag: carcinoma percentage

tag: paired sample status

value: control


title: 5B

description: carcinoma


title: 18-RP

description: control

value: Bladder carcinoma


title: 28-RP

description: control


title: 27A2

description: carcinoma


title: 22A1

description: carcinoma

value: carcinoma


title: 27A1

description: carcinoma


title: 19A1

description: carcinoma


title: 23-h

description: control

value: benign prostatic hyperplasia


title: 26-RP

description: control


title: 19A2

description: carcinoma


title: 1-RP

description: control


title: 12-h

description: control


title: 17-RP

description: control


title: 6-h

description: control


title: 2-RP

description: control


title: 31-h

description: control


title: 18B

description: carcinoma


title: 10-h

description: control


title: 24-h

description: control


title: 30-h

description: control


title: 25-h

description: control


title: RABL6A Knock Down #1-3

city: Iowa City

first: Benjamin

middle: W

last: Darbro

state: IA

address: 200 Hawkins Drive

country: USA

institute: University of Iowa

description: KD1 replicate 3

data_processing: The data were normalised using quantile normalisation with GenomeStudio Software from Illumina

source_name: Pancreatic Neuroendocrine Tumor Cell Line

label_protocol: Briefly, 100 nanograms total RNA was converted to amplified Biotin-aRNA using the Epicentre Target Amp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924) according to the manufacturer’s recommended protocol. The amplified Biotin-aRNA product was purified through a QIAGEN RNeasy MinElute cleanup column (QIAGEN Cat #74204) according to modifications from Epicentre.  Illumina hybridization buffer was mixed with 750ng of this product, placed onto Illumina-Human H12 v4 BeadChips (Part No. BD-103-0204), and incubated at 58º C for 17h, with rocking.  Following hybridization, the arrays were washed, blocked used the Illumina Direct Hybridization Kit, and then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.

growth_protocol: Human BON-1 PNET cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) / F12 containing 10% fetal bovine serum (FBS), 4 mM glutamine, and 100 mg/mL penicillin / streptomycin. Human embryonic kidney (HEK) 293T cells were maintained in standard DMEM containing the same supplements.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen) from 3 separately generated sets of BON-1 cells expressing RABL6A shRNAs or control vector. RNA preparation for hybridization to Illumina-Human H12 v4 BeadChips (BD-103-0204) was performed at the University of Iowa DNA Facility using the manufacturer’s recommended protocol

treatment_protocol: RABL6A and p53 shRNA constructs in the pLKO.1 lentiviral vector (Open Biosytems, Huntsville, AL) have been described (27, 29).

tag: treatment

value: RABL6A shRNA #1

tag: cell line

value: BON-1 PNET


title: RABL6A Knock Down #2-2

description: KD2 replicate 2

value: RABL6A shRNA #2


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 337

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

hyb_protocol: Illumina's BeadArray protocol

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

data_processing: The raw log2 transformed 14,111 probes that are expressed in both phase of CDGY studies were normalized utilizing Supervised Normalization of Microarray algorithm (SNM package is downloadable from bioconductor) fitting technical effects of plate and RNA quality, adjusting BMI, gender, ethnicity, and Age. CVD_TYPE was considered as a biological variable.

source_name: Whole peripheral blood

label_protocol: Illumina's BeadArray protocol

extract_protocol: Total RNA was extracted from Whole peripheral blood using Paxgene Blood RNA kit. Quality control was performed using Agilent's Bioanalyzer.

tag: gender

value: FEM

tag: ethnicity

value: CAU

tag: plate

value: F

tag: rna integrity score

tag: phase of study


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 335

value: MAL


title: Vector control #2

description: Vector replicate 2

value: Vector


title: RABL6A Knock Down #2-1

description: KD2 replicate 1


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 336


title: RABL6A Knock Down #1-1

description: KD1 replicate 1


title: RABL6A Knock Down #2-3

description: KD2 replicate 3


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 328


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 326


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 324


title: RABL6A Knock Down #1-2

description: KD1 replicate 2


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 338


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 321


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 333


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 334


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 322


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 330


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 329


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 332


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 323


title: Vector control #1

description: Vector replicate 1


title: 8BK

description: carcinoma


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 331


title: Vector control #3

description: Vector replicate 3


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 327


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 320


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 319


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 311


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 309


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 314


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 317


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 313


title: 5-h

description: control


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 315


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 316


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 305


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 303


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 304


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 318


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 302


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 308


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 307


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 300


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 298


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 299


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 312


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 296


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 297


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 310


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 295


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 294


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 306


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 301


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 292


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 291


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 293


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 286


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 287


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 282

value: E


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 281


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 283


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 285


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 280


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 276


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 284


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 273


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 274


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 275


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 279


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 277


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 290


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 289


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 278


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 271


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 272


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 270


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 269


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 288


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 263


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 266


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 261


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 262


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 267


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 265


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 258


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 260


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 259


title: 7-h

description: control


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 268


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 256


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 257


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 252


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 253


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 264


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 251


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 244


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 254


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 249


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 243


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 255


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 250


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 248


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 242


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 241


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 240


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 239


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 247


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 245


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 231


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 236


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 232


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 235


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 237


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 233


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 230


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 224


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 238


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 234


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 325


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 222


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 220


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 221


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 219


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 225


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 223


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 218


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 217


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 226


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 229


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 214


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 227


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 228


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 213


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 215


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 216


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 212


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 211


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 210


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 204


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 205


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 209


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 207


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 206


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 203


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 202


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 201


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 197


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 196


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 198


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 195


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 199


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 200


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 208


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 189


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 188

value: D


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 191


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 193


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 192


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 187


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 190


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 186


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 194


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 185


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 184


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 183


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 182


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 181


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 180


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 179


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 176


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 170

value: B


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 178


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 173


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 169


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 177


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 171


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 172


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 174


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 168


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 175


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 167


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 163


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 166


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 159


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 164


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 157


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 156


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 161


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 160


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 165


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 158


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 155


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 154


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 153


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 162


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 152


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 151


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 147


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 148


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 246


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 143


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 146


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 149


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 144


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 141


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 142

value: AFA


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 145


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 150


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 135


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 133


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 132


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 127


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 139


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 131


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 134


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 130

value: SAS


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 128


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 137


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 136


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 129


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 126


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 140


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 138


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 119


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 120


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 125


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 118


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 115


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 122


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 114


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 116


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 111


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 123


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 124


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 121


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 112


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 113


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 105


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 106


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 103


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 110


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 104


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 109


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 108


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 117


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 99


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 102


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 98


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 100


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 101


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 97


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 107


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 95


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 96


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 89


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 90


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 88


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 94


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 85

value: A


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 93


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 86


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 84


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 81


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 87


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 83


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 92


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 82


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 79


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 78


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 75


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 74


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 76


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 91


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 80


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 70


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 71


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 68


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 67


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 72


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 69


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 66


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 77


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 65


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 73


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 64


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 62


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 59


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 56


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 57


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 58


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 60


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 63


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 61


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 54


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 51


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 47


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 50


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 49


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 46


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 48


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 55


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 44


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 43


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 42


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 34


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 39


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 36


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 40


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 41


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 35


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 38


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 37


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 52


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 33


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 28


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 45


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 26


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 29


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 31


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 32


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 30


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 27


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 25


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 19


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 24


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 17


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 22


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 12


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 20


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 21


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 16


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 23


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 18


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 11


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 14


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 6


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 10


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 7


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 13


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 4


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 9


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 15


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 3


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 1


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 8


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 5


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 2


title: Blood Control individualHFS172

city: Montreal

first: Jacklyn

last: Quinlan

state: Qc

address: 3175 Cote Ste-Catherine

department: Pediatrics

country: Canada

institute: CHU Ste-Justine Hospital

description:
Sample310
globin mRNA-depleted total RNA

data_processing: The data was log2 transfromed and normalised using quantile normalisation with JMP Genomics

label: Biotin

source_name: whole blood

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

extract_protocol: RNA was extracted from whole blood collected in Tempus tubes using the Tempus Spin RNA Isolation kit (Applied Biosystems). Total RNA was then globin-mRNA-depleted using GlobinClear kit (Ambion). Quality control was performed with Agilent Bioanalyser.

tag: age (years)

tag: clinical status

value: C

tag: severity score

tag: Sex

tag: hb phenotype

value: AA

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood Control individualHFS168

description:
Sample306
globin mRNA-depleted total RNA

value: M


title: Blood Control individualHFS170

description:
Sample308
globin mRNA-depleted total RNA

value: AS


title: Blood Control individualHFS166

description:
Sample304
globin mRNA-depleted total RNA


title: Blood Control individualHFS169

description:
Sample307
globin mRNA-depleted total RNA


title: Blood Control individualHFS164

description:
Sample302
globin mRNA-depleted total RNA


title: Blood Control individualHFS162

description:
Sample300
globin mRNA-depleted total RNA


title: Blood Control individualHFS160

description:
Sample298
globin mRNA-depleted total RNA


title: Blood Control individualHFS173

description:
Sample311
globin mRNA-depleted total RNA


title: Blood Control individualHFS171

description:
Sample309
globin mRNA-depleted total RNA


title: Blood Control individualHFS158

description:
Sample296
globin mRNA-depleted total RNA


title: Blood Control individualHFS167

description:
Sample305
globin mRNA-depleted total RNA


title: Blood Control individualHFS156

description:
Sample294
globin mRNA-depleted total RNA


title: Blood Control individualHFS145

description:
Sample284
globin mRNA-depleted total RNA


title: Blood Control individualHFS149

description:
Sample288
globin mRNA-depleted total RNA


title: Blood Control individualHFS159

description:
Sample297
globin mRNA-depleted total RNA


title: Blood Control individualHFS163

description:
Sample301
globin mRNA-depleted total RNA


title: Blood Control individualHFS161

description:
Sample299
globin mRNA-depleted total RNA


title: Whole peripheral blood_PaxGene Blood RNATube, Sample 53


title: Blood Control individualHFS165

description:
Sample303
globin mRNA-depleted total RNA


title: Blood Control individualHFS157

description:
Sample295
globin mRNA-depleted total RNA


title: Blood Control individualHFS151

description:
Sample290
globin mRNA-depleted total RNA


title: Blood Control individualHFS154

description:
Sample293
globin mRNA-depleted total RNA


title: Blood Control individualHFS138

description:
Sample278
globin mRNA-depleted total RNA


title: Blood Control individualHFS140

description:
Sample280
globin mRNA-depleted total RNA


title: Blood Control individualHFS143

description:
Sample282
globin mRNA-depleted total RNA


title: Blood Control individualHFS147

description:
Sample286
globin mRNA-depleted total RNA


title: Blood Control individualHFS139

description:
Sample279
globin mRNA-depleted total RNA


title: Blood Control individualHFS153

description:
Sample292
globin mRNA-depleted total RNA


title: Blood Control individualHFS137

description:
Sample277
globin mRNA-depleted total RNA


title: Blood Control individualHFS134

description:
Sample274
globin mRNA-depleted total RNA


title: Blood Control individualHFS136

description:
Sample276
globin mRNA-depleted total RNA


title: Blood Control individualHFS129

description:
Sample270
globin mRNA-depleted total RNA


title: Blood Control individualHFS122

description:
Sample266
globin mRNA-depleted total RNA


title: Blood Control individualHFS150

description:
Sample289
globin mRNA-depleted total RNA


title: Blood Control individualHFS148

description:
Sample287
globin mRNA-depleted total RNA


title: Blood Control individualHFS144

description:
Sample283
globin mRNA-depleted total RNA


title: Blood Control individualHFS131

description:
Sample272
globin mRNA-depleted total RNA


title: Blood Control individualHFS135

description:
Sample275
globin mRNA-depleted total RNA


title: Blood Control individualHFS109

description:
Sample254
globin mRNA-depleted total RNA


title: Blood Control individualHFS115

description:
Sample260
globin mRNA-depleted total RNA


title: Blood Control individualHFS152

description:
Sample291
globin mRNA-depleted total RNA


title: Blood Control individualHFS130

description:
Sample271
globin mRNA-depleted total RNA


title: Blood Control individualHFS141

description:
Sample281
globin mRNA-depleted total RNA


title: Blood Control individualHFS146

description:
Sample285
globin mRNA-depleted total RNA


title: Blood Control individualHFS113

description:
Sample258
globin mRNA-depleted total RNA


title: Blood Control individualHFS127

description:
Sample269
globin mRNA-depleted total RNA


title: Blood Control individualHFS119

description:
Sample264
globin mRNA-depleted total RNA


title: Blood Control individualHFS120

description:
Sample265
globin mRNA-depleted total RNA


title: Blood Control individualHFS111

description:
Sample256
globin mRNA-depleted total RNA


title: Blood Control individualHFS132

description:
Sample273
globin mRNA-depleted total RNA


title: Blood Control individualHFS126

description:
Sample268
globin mRNA-depleted total RNA


title: Blood Control individualHFS117

description:
Sample262
globin mRNA-depleted total RNA


title: LA_02.Early.CON

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

hyb_protocol: Nimblegen Hybridication Protocol

scan_protocol: Default scan parameters

data_processing: Nimblegen Signal Processing Software

organism: Macaca mulatta

source_name: LA

label_protocol: Nimblegen Labeling Protocol

extract_protocol: Tissues were pulverized under liquid N2. Total RNA was extracted using TRIzol reagent following manufacturer's protocol (Invitrogen Life Technologies). RNA quantififcation was performed using Nanodrop sepctrophotometer, and RNA qulaity was assessed using denaturing formaldehyde agarose gel.

treatment_protocol: Pregnant rhesus monkey were exposed daily to oral Bisphenol A (400 μg/kg. body weight/day) or vehicle during early (50–100 ± 2 days) or late (100 ± 2 days–term) gestation.

tag: treatment

value: vehicle control

tag: time point

value: Early gestation

tag: sample id


title: Blood Control individualHFS118

description:
Sample263
globin mRNA-depleted total RNA


title: Blood Control individualHFS124

description:
Sample267
globin mRNA-depleted total RNA


title: Blood Control individualHFS116

description:
Sample261
globin mRNA-depleted total RNA


title: Blood Control individualHFS112

description:
Sample257
globin mRNA-depleted total RNA


title: LA_09.Late.CON

value: Late gestation


title: Blood Control individualHFS110

description:
Sample255
globin mRNA-depleted total RNA


title: Blood Control individualHFS114

description:
Sample259
globin mRNA-depleted total RNA


title: LA_08.Late.CON


title: Blood Control individualHFS105

description:
Sample252
globin mRNA-depleted total RNA


title: Blood SCD patientA0396

description:
Sample250
globin mRNA-depleted total RNA

value: FU

value: SS


title: LA_12.Late.BPA

value: Bisphenol A


title: Blood Control individualHFS101

description:
Sample251
globin mRNA-depleted total RNA


title: Blood Control individualHFS106

description:
Sample253
globin mRNA-depleted total RNA

value: F


title: Blood SCD patientA0395

description:
Sample249
globin mRNA-depleted total RNA

value: E


title: Tumor_intact_2

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

description: Intact animal, no surgery.

hyb_protocol: Following fragmentation, 20 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS 1.4 (MAS 5.0 algorithm) using Affymetrix default analysis settings and global scaling as normalization method. The 2% trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Mus musculus

source_name: Tumor-bearing eyeball of intact mouse

label_protocol: Biotinylated cRNAs (aRNAs) were prepared from 500 ng of total RNA using an Affymetrix 3'-IVT Express kit, following the manufacturer's instructions.

growth_protocol: Male and female mice (C57BL/6 strain) were used, at greater than seven weeks of age.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Mini kit, according to the manufacturer's instructions.

treatment_protocol: Mice were splenectomized or received no surgery, then were challenged by injection of 10^4 luciferase-expressing E.G7-OVA cells injected into the anterior chamber of the eye. Fifteen days later, the animals were euthanized and tumor-bearing eyes were removed.

tag: strain/background

tag: surgery

value: injection of luciferase-expressing E.G7-OVA cells into anterior chamber of eye

tag: tissue

value: tumor-bearing eyeball


title: LA_05.Early.BPA


title: LA_04.Early.BPA


title: Tumor_splnx_2

description: Splenectomized animal.

source_name: Tumor-bearing eyeball of splenectomized mouse

value: splenectomy


title: Blood SCD patientA0392

description:
Sample247
globin mRNA-depleted total RNA


title: Blood SCD patientA0390

description:
Sample245
globin mRNA-depleted total RNA


title: Blood SCD patientA0388

description:
Sample243
globin mRNA-depleted total RNA


title: Blood SCD patientA0391

description:
Sample246
globin mRNA-depleted total RNA


title: Tumor_intact_1

description: Intact animal, no surgery.


title: LA_06.Early.BPA


title: Blood SCD patientA0393

description:
Sample248
globin mRNA-depleted total RNA


title: Blood SCD patientA0386

description:
Sample241
globin mRNA-depleted total RNA


title: LA_01.Early.CON


title: Blood SCD patientA0382

description:
Sample239
globin mRNA-depleted total RNA


title: Blood SCD patientA0379

description:
Sample237
globin mRNA-depleted total RNA


title: WT-B

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. Arrays were washed and stained by streptavidin-phycoerythrin conjugate in the Affymetrix Fluidics Station 400.

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.

source_name: Colonic mucosa

label_protocol: GeneChip 3' IVT Express Labeling Kit was used to prepare biotinylated cRNA according to the standard Affymetrix protocol from 0.2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse colonic mucosa was isolated.

extract_protocol: Total RNA was extracted by using Trizol (Invitrogen) and then purified by using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: strain

tag: cell type

value: intestinal epithelial cells (IECs)

tag: genotype/variation

value: wildtype


title: Tumor_splnx_1

description: Splenectomized animal.


title: LA_11.Late.BPA


title: Blood SCD patientA0376

description:
Sample235
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score


title: KO-C


title: WT-C


title: Blood SCD patientA0387

description:
Sample242
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype

value: SC

tag: white blood cells


title: Blood SCD patientA0384

description:
Sample240
globin mRNA-depleted total RNA

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1


title: LA_10.Late.BPA

tag: treatment

tag: time point


title: LA_03.Early.CON

tag: sample id


title: LA_07.Late.CON


title: Blood SCD patientA0389

description:
Sample244
globin mRNA-depleted total RNA


title: Blood SCD patientA0381

description:
Sample238
globin mRNA-depleted total RNA

tag: genotypic pc2


title: Blood SCD patientA0373

description:
Sample233
globin mRNA-depleted total RNA


title: RA_10.Late.BPA

source_name: RA


title: Blood SCD patientA0377

description:
Sample236
globin mRNA-depleted total RNA


title: KO-B


title: Blood SCD patientA0371

description:
Sample231
globin mRNA-depleted total RNA


title: WT-A


title: ureter tumor biological replicate 2

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Gene expression data from urothelial carcinoma

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

data_processing: DNA microarray analyses were performed with R. MAS5.0 background correction was performed and arrays were median normlalized. Differentially expressed genes were called if fold change (FC) FC ≥1.5 and p<0.05 (student's t-test).

source_name: C57Bl/6, 6-8 weeks

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: Ureter epithelium from 6-8 week old mice was isolated.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified with the RNAeasy kit from QIAGEN

treatment_protocol: Three-week old mice were administered Doxycycline for 1 week to induce recombination in R26rtTA;teto-Cre;Ncstnf/f mice.

tag: genetic background

tag: tissue

value: ureter tumor


title: Blood SCD patientA0374

description:
Sample234
globin mRNA-depleted total RNA


title: Blood SCD patientA0370

description:
Sample230
globin mRNA-depleted total RNA


title: KO-A

tag: strain

tag: cell type


title: RA_07.Late.CON


title: Blood SCD patientA0372

description:
Sample232
globin mRNA-depleted total RNA

tag: age (years)


title: RA_12.Late.BPA


title: Blood SCD patientA0369

description:
Sample229
globin mRNA-depleted total RNA

tag: clinical status


title: Blood SCD patientA0364

description:
Sample227
globin mRNA-depleted total RNA

tag: severity score


title: normal ureter  biological replicate 1

description: Gene expression data from normal urothelial tissue

value: normal ureter


title: normal ureter  biological replicate 2


title: Blood SCD patientA0360

description:
Sample225
globin mRNA-depleted total RNA

tag: Sex

value: M


title: RA_08.Late.CON

value: vehicle control


title: ureter tumor biological replicate 1


title: Blood SCD patientA0354

description:
Sample221
globin mRNA-depleted total RNA

tag: hb phenotype


title: Blood SCD patientA0366

description:
Sample228
globin mRNA-depleted total RNA

tag: white blood cells


title: Blood SCD patientA0358

description:
Sample224
globin mRNA-depleted total RNA

tag: mean corpuscular volume


title: Blood SCD patientA0363

description:
Sample226
globin mRNA-depleted total RNA

tag: red blood cells


title: Blood SCD patientA0357

description:
Sample223
globin mRNA-depleted total RNA


title: RA_09.Late.CON


title: RA_06.Early.BPA

value: Early gestation


title: Blood SCD patientA0355

description:
Sample222
globin mRNA-depleted total RNA


title: RA_02.Early.CON


title: 0404_AC(3)17_M2_MAGIC67

city: San Diego

first: Peter

middle: J

last: Belmont

address: 10724 Science Center Drive

institute: Pfizer

description: wildtype control colon

data_processing:
per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)
Normalized signal intensity. The normalized matrix contains two datasets - the training set normalized by RMA with batch effect removed by ComBat and validation set normalized by RMA

source_name: normal colon control

growth_protocol: Approximately 10mg of primary tumor tissue was excised for RNA extraction

extract_protocol: Qiagen RNEasy kit

treatment_protocol: No treatment

tag: genotype code

value: WT

tag: genotype

value: wild type

tag: data set

value: Validation set

tag: batch

value: wildtype control colon

value: C57BL6/129 mixed


title: 0704_AC(3)30_M_MY395

description: wildtype control colon

hyb_protocol: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)


title: Blood SCD patientA0351

description:
Sample219
globin mRNA-depleted total RNA

value: E

value: SS


title: 1111_OS(18)6_nu_M_N6_Vilard_111068_SFV

description: APC,KRAS mutant tumor validation set

scan_protocol: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)

source_name: primary colon cancer

value: AK

value: APC KRAS mutant

value: APC,KRAS mutant tumor


title: RA_01.Early.CON

tag: treatment

tag: time point

tag: sample id


title: RA_05.Early.BPA

value: Bisphenol A


title: 0404_AC(3)15_M2_MAGIC93

description: wildtype control colon

label_protocol: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)

tag: tissue

tag: genetic background


title: Blood SCD patientA0350

description:
Sample218
globin mRNA-depleted total RNA

tag: age (years)

value: FU

value: F

tag: genotypic pc1

tag: genotypic pc2


title: RA_03.Early.CON


title: 1111_OS(18)5_nu_M_N5_Vilard_111068_CC

description: APC,KRAS mutant tumor validation set


title: Blood SCD patientA0344

description:
Sample213
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

tag: Sex


title: RA_04.Early.BPA


title: Blood SCD patientA0349

description:
Sample217
globin mRNA-depleted total RNA

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0346

description:
Sample214
globin mRNA-depleted total RNA

tag: red blood cells


title: Blood SCD patientA0348

description:
Sample216
globin mRNA-depleted total RNA


title: Blood SCD patientA0347

description:
Sample215
globin mRNA-depleted total RNA


title: Blood SCD patientA0353

description:
Sample220
globin mRNA-depleted total RNA


title: Blood SCD patientA0340

description:
Sample211
globin mRNA-depleted total RNA


title: RA_11.Late.BPA

value: Late gestation


title: 1111_OS(18)3_nu_M_N3_Vilard_122346_CC

description: APC,KRAS mutant tumor validation set

tag: genotype code

tag: genotype

tag: data set


title: Blood SCD patientA0339

description:
Sample210
globin mRNA-depleted total RNA


title: Blood SCD patientA0343

description:
Sample212
globin mRNA-depleted total RNA

value: M


title: Blood SCD patientA0338

description:
Sample209
globin mRNA-depleted total RNA


title: LV_04.Early.BPA

source_name: LV

tag: treatment

tag: time point


title: 1111_OS(18)2_nu_M_N2_Vilard_112912_SFV

description: APC,KRAS mutant tumor validation set

tag: batch

tag: tissue


title: Blood SCD patientA0337

description:
Sample208
globin mRNA-depleted total RNA

tag: age (years)

value: SC


title: Blood SCD patientA0336

description:
Sample207
globin mRNA-depleted total RNA

tag: genotypic pc1


title: Blood SCD patientA0331

description:
Sample203
globin mRNA-depleted total RNA

tag: genotypic pc2


title: 1011_OS(16)6_nu_M_LgrSCAPP53_GFP+3

description: APC,P53 mutant tumor validation set

value: AP

value: APC P53 mutant

value: APC,P53 mutant tumor

tag: genetic background


title: LV_10.Late.BPA

tag: sample id


title: Blood SCD patientA0329

description:
Sample201
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

tag: Sex


title: Blood SCD patientA0335

description:
Sample206
globin mRNA-depleted total RNA

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0332

description:
Sample204
globin mRNA-depleted total RNA

tag: red blood cells


title: LV_01.Early.CON

value: vehicle control

value: Early gestation


title: 1011_OS(16)3_nu_M_LgrSCAPP53_GFP-3

description: APC,P53 mutant tumor validation set

tag: genotype code

tag: genotype

tag: data set

value: Validation set

value: C57BL6/129 mixed


title: LV_08.Late.CON

tag: treatment

tag: time point


title: 1011_OS(16)2_nu_M_LgrSCAPP53_GFP-2

description: APC,P53 mutant tumor validation set

tag: batch

tag: tissue


title: LV_12.Late.BPA


title: 1111_OS(18)1_nu_M_N1_Vilard_112912_CC

description: APC,KRAS mutant tumor validation set


title: 1011_OS(16)5_nu_M_LgrSCAPP53_GFP+2

description: APC,P53 mutant tumor validation set


title: Blood SCD patientA0322

description:
Sample196
globin mRNA-depleted total RNA

tag: age (years)

value: A

value: SS

tag: genotypic pc1

tag: genotypic pc2


title: 1011_OS(16)4_nu_M_LgrSCAPP53_GFP+1

description: APC,P53 mutant tumor validation set

tag: genetic background


title: Blood SCD patientA0326

description:
Sample200
globin mRNA-depleted total RNA

tag: clinical status

value: E

tag: severity score


title: Blood SCD patientA0324

description:
Sample198
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype


title: LV_03.Early.CON

tag: sample id


title: Blood SCD patientA0325

description:
Sample199
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells


title: 1011_OS(16)1_nu_M_LgrSCAPP53_GFP-1

description: APC,P53 mutant tumor validation set

tag: genotype code

tag: genotype

tag: data set


title: Blood SCD patientA0330

description:
Sample202
globin mRNA-depleted total RNA


title: Blood SCD patientA0323

description:
Sample197
globin mRNA-depleted total RNA


title: Blood SCD patientA0320

description:
Sample195
globin mRNA-depleted total RNA


title: Blood SCD patientA0334

description:
Sample205
globin mRNA-depleted total RNA


title: LV_11.Late.BPA

tag: treatment

tag: time point


title: Blood SCD patientA0318

description:
Sample194
globin mRNA-depleted total RNA

tag: age (years)


title: 0404_TH4_M2_MA1228u

description: APC mutant tumor validation set

value: APC mutant

tag: batch

tag: tissue

value: APC mutant tumor


title: LV_02.Early.CON


title: Blood SCD patientA0315

description:
Sample192
globin mRNA-depleted total RNA

tag: genotypic pc1

tag: genotypic pc2


title: 0404_TH2_M2_MY77u

description: APC mutant tumor validation set

tag: genetic background


title: LV_07.Late.CON


title: 0404_TH1_M2_MY74u

description: APC mutant tumor validation set


title: LV_05.Early.BPA

value: Bisphenol A


title: Blood SCD patientA0305

description:
Sample184
globin mRNA-depleted total RNA

tag: clinical status

value: FU

tag: severity score

tag: Sex


title: Blood SCD patientA0314

description:
Sample191
globin mRNA-depleted total RNA

value: F

tag: hb phenotype

tag: white blood cells


title: Blood SCD patientA0317

description:
Sample193
globin mRNA-depleted total RNA

value: M

tag: mean corpuscular volume

tag: red blood cells


title: LV_06.Early.BPA

tag: sample id


title: Blood SCD patientA0307

description:
Sample186
globin mRNA-depleted total RNA

value: SC


title: Blood SCD patientA0306

description:
Sample185
globin mRNA-depleted total RNA


title: ABPTUMOR10

description: APC,BRAF, P53 mutant tumor

tag: genotype code

value: ABP

tag: genotype

value: APC BRAF P53 mutant

tag: data set

value: Training set

value: APC,BRAF, P53 mutant tumor


title: Blood SCD patientA0308

description:
Sample187
globin mRNA-depleted total RNA

tag: age (years)


title: Blood SCD patientA0313

description:
Sample190
globin mRNA-depleted total RNA


title: Blood SCD patientA0311

description:
Sample189
globin mRNA-depleted total RNA


title: Blood SCD patientA0303

description:
Sample183
globin mRNA-depleted total RNA


title: ABPTUMOR6

description: APC,BRAF, P53 mutant tumor

tag: batch


title: Blood SCD patientA0310

description:
Sample188
globin mRNA-depleted total RNA


title: Blood SCD patientA0301

description:
Sample182
globin mRNA-depleted total RNA


title: Blood SCD patientA0300

description:
Sample181
globin mRNA-depleted total RNA


title: RV_04.Early.BPA

source_name: RV

tag: treatment

tag: time point

value: Early gestation


title: RV_11.Late.BPA

value: Late gestation


title: LV_09.Late.CON

value: vehicle control


title: ABPTUMOR5

description: APC,BRAF, P53 mutant tumor

tag: tissue

value: C57BL6/129 mixed


title: RV_08.Late.CON


title: Blood SCD patientA0296

description:
Sample178
globin mRNA-depleted total RNA

value: SS


title: Blood SCD patientA0299

description:
Sample180
globin mRNA-depleted total RNA

value: A

tag: genotypic pc1

tag: genotypic pc2


title: ABPTUMOR4

description: APC,BRAF, P53 mutant tumor

tag: genetic background


title: ABPCONTROL3

description: wildtype control colon

value: WT

value: wild type

value: wildtype control colon


title: Blood SCD patientA0298

description:
Sample179
globin mRNA-depleted total RNA

tag: clinical status

value: FU

tag: severity score

tag: Sex


title: 1111_OS(18)4_nu_M_N4_Vilard_122346_SFV

description: APC,KRAS mutant tumor validation set

value: AK

value: APC KRAS mutant

value: Validation set

value: APC,KRAS mutant tumor


title: ABPTUMOR3

description: APC,BRAF, P53 mutant tumor

value: ABP

value: APC BRAF P53 mutant


title: ABTUMOR4G178743

description: APC,BRAF mutant tumor

value: AB

value: APC BRAF mutant

value: Training set

value: APC,BRAF mutant tumor


title: Blood SCD patientA0286

description:
Sample172
globin mRNA-depleted total RNA

value: F

tag: hb phenotype

value: SC

tag: white blood cells

tag: mean corpuscular volume


title: RV_12.Late.BPA

value: Bisphenol A

value: Late gestation

tag: sample id


title: Blood SCD patientA0284

description:
Sample171
globin mRNA-depleted total RNA

value: SS

tag: red blood cells


title: Blood SCD patientA0295

description:
Sample177
globin mRNA-depleted total RNA

value: E

value: M


title: ABPCONTROL1

description: wildtype control colon

tag: genotype code

value: WT

tag: genotype

value: wild type

tag: data set

value: wildtype control colon

value: C57BL6/129 mixed


title: Blood SCD patientA0287

description:
Sample173
globin mRNA-depleted total RNA

tag: age (years)

value: FU


title: Blood SCD patientA0293

description:
Sample176
globin mRNA-depleted total RNA


title: RV_09.Late.CON

tag: treatment

value: vehicle control

tag: time point


title: Blood SCD patientA0282

description:
Sample169
globin mRNA-depleted total RNA

tag: genotypic pc1


title: RV_05.Early.BPA

value: Early gestation


title: RV_07.Late.CON


title: ABTUMOR2G178739

description: APC,BRAF mutant tumor

value: AB

value: APC BRAF mutant

tag: batch

tag: tissue


title: Blood SCD patientA0278

description:
Sample168
globin mRNA-depleted total RNA

tag: clinical status

value: A

tag: genotypic pc2


title: Blood SCD patientA0290

description:
Sample174
globin mRNA-depleted total RNA

tag: severity score

tag: Sex

value: F


title: Blood SCD patientA0291

description:
Sample175
globin mRNA-depleted total RNA

tag: hb phenotype

tag: white blood cells


title: RV_01.Early.CON

tag: sample id


title: ABTUMOR3G178740

description: APC,BRAF mutant tumor

value: Training set

value: APC,BRAF mutant tumor

tag: genetic background


title: Blood SCD patientA0283

description:
Sample170
globin mRNA-depleted total RNA

tag: mean corpuscular volume

tag: red blood cells


title: ABCONTROL3

description: wildtype control colon

tag: genotype code

tag: genotype

tag: data set


title: Blood SCD patientA0274

description:
Sample167
globin mRNA-depleted total RNA

tag: age (years)

value: SC


title: Blood SCD patientA0271

description:
Sample166
globin mRNA-depleted total RNA

value: SS


title: RV_06.Early.BPA

tag: treatment

value: Bisphenol A

tag: time point


title: ABTUMOR1G178735

description: APC,BRAF mutant tumor

tag: batch

tag: tissue


title: RV_02.Early.CON


title: ABCONTROL2

description: wildtype control colon


title: RV_10.Late.BPA

value: Late gestation


title: B17

description: APC,KRAS,P53 mutant tumor

value: AKP

value: APC KRAS P53 mutant

value: APC,KRAS,P53 mutant tumor


title: RV_03.Early.CON


title: Blood SCD patientA0269

description:
Sample165
globin mRNA-depleted total RNA

tag: clinical status

value: E

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0264

description:
Sample161
globin mRNA-depleted total RNA

value: FU

tag: severity score

tag: Sex

value: M

tag: hb phenotype


title: Blood SCD patientA0267

description:
Sample163
globin mRNA-depleted total RNA

tag: white blood cells


title: Blood SCD patientA0263

description:
Sample160
globin mRNA-depleted total RNA

tag: mean corpuscular volume


title: BFM_12.Late.BPA

source_name: BFM

tag: sample id


title: C76

description: APC mutant tumor

tag: genotype code

value: APC mutant

value: APC mutant tumor

tag: genetic background

value: C57BL6/129 mixed


title: BFM_06.Early.BPA

value: Early gestation


title: D84

description: wildtype control colon

value: WT

tag: genotype

value: wild type

tag: data set

value: wildtype control colon


title: D85

description: wildtype control colon

value: Training set


title: Blood SCD patientA0252

description:
Sample155
globin mRNA-depleted total RNA

tag: age (years)

value: F

value: SC

tag: red blood cells


title: BFM_11.Late.BPA

tag: treatment

value: Bisphenol A

tag: time point

value: Late gestation


title: J17

description: APC mutant tumor

value: A

tag: batch

tag: tissue


title: BFM_03.Early.CON

value: vehicle control


title: Blood SCD patientA0258

description:
Sample156
globin mRNA-depleted total RNA

tag: clinical status

value: E

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0268

description:
Sample164
globin mRNA-depleted total RNA

value: FU

tag: severity score

tag: Sex

tag: hb phenotype


title: BFM_10.Late.BPA

tag: sample id


title: Blood SCD patientA0259

description:
Sample157
globin mRNA-depleted total RNA

value: M

value: SS

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0260

description:
Sample158
globin mRNA-depleted total RNA


title: Blood SCD patientA0262

description:
Sample159
globin mRNA-depleted total RNA


title: D83

description: wildtype control colon

tag: genotype code

tag: genotype

tag: genetic background


title: Blood SCD patientA0251

description:
Sample154
globin mRNA-depleted total RNA

tag: age (years)

tag: red blood cells


title: Blood SCD patientA0244

description:
Sample152
globin mRNA-depleted total RNA


title: Blood SCD patientA0242

description:
Sample150
globin mRNA-depleted total RNA


title: Blood SCD patientA0243

description:
Sample151
globin mRNA-depleted total RNA


title: I71

description: APC mutant tumor

value: APC mutant

tag: data set

value: APC mutant tumor


title: Blood SCD patientA0249

description:
Sample153
globin mRNA-depleted total RNA


title: Blood SCD patientA0239

description:
Sample148
globin mRNA-depleted total RNA


title: Blood SCD patientA0240

description:
Sample149
globin mRNA-depleted total RNA


title: BFM_09.Late.CON

tag: treatment

tag: time point


title: BFM_07.Late.CON


title: Blood SCD patientA0236

description:
Sample146
globin mRNA-depleted total RNA

tag: clinical status


title: B95

description: APC mutant tumor

tag: batch

tag: tissue

value: C57BL6/129 mixed


title: BFM_08.Late.CON


title: Blood SCD patientA0235

description:
Sample145
globin mRNA-depleted total RNA

tag: severity score

tag: genotypic pc1

tag: genotypic pc2


title: B99

description: APC mutant tumor


title: Blood SCD patientA0237

description:
Sample147
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype


title: BFM_01.Early.CON

value: Early gestation

tag: sample id


title: Blood SCD patientA0230

description:
Sample143
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume


title: J23

description: APC mutant tumor

tag: genotype code

tag: genotype

tag: genetic background


title: BFM_02.Early.CON


title: C74

description: APC mutant tumor

tag: data set


title: BFM_05.Early.BPA

tag: treatment


title: BFM_04.Early.BPA

tag: time point


title: K83

description: APC,KRAS mutant tumor

value: AK

value: APC KRAS mutant

value: APC,KRAS mutant tumor


title: Blood SCD patientA0220

description:
Sample137
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: red blood cells


title: Blood SCD patientA0234

description:
Sample144
globin mRNA-depleted total RNA

tag: severity score


title: Blood SCD patientA0224

description:
Sample139
globin mRNA-depleted total RNA

value: F

tag: genotypic pc1


title: Blood SCD patientA0227

description:
Sample141
globin mRNA-depleted total RNA

value: SC

tag: genotypic pc2


title: Blood SCD patientA0223

description:
Sample138
globin mRNA-depleted total RNA

tag: Sex


title: Blood SCD patientA0219

description:
Sample136
globin mRNA-depleted total RNA

tag: hb phenotype


title: Blood SCD patientA0226

description:
Sample140
globin mRNA-depleted total RNA


title: Blood SCD patientA0218

description:
Sample135
globin mRNA-depleted total RNA


title: K77

description: APC,KRAS mutant tumor

value: Training set

tag: batch

tag: tissue


title: Blood SCD patientA0217

description:
Sample134
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume


title: 60m after CO2 depletion in 1st duplicate time series (3.3) vs 30m after CO2 depletion in 2nd duplicate time series

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description:
3.3 over 2.4
60 min after onset CO2 depletion in 1st of duplicate time series (3.3) vs 30 min after onset CO2 depletion in 2nd of duplicate time series

hyb_protocol: To the mixed cDNA's 25 µl Slidehyb #1 hybridization buffer (Ambion, Austin, USA) 2x Hi-RPM hyb. Buffer (Agilent) was added and 40 ul of the resulting solution was applied on the slides

scan_protocol: Slides were scanned with a ScanArray Express 4000 scanner (Perkin Elmer)

data_processing: Data were normalized using Lowess normalization as available in MicroPrep and corrected for inter-slide differences. Median intensity of the different probes per gene was selected as the gene expression intensity.

organism: Lactobacillus johnsonii

label_protocol: The Cyscribe Post-labeling kit was used to synthesize cDNA out of 5 µg of total RNA, which was subsequently labeled according to the manufacturer's protocol (Amersham Biosciences, Amersham, Uk).

growth_protocol: Cultures were grown in 400 ml batches with MRS at 37˚C under constant pH of 6.5,  sparged with gas mixtures 750 ml/min, stirring of ca. 200 rpm

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification

treatment_protocol: Cells were harvested at 0.15 OD600 from 50 ml of growth medium by cold centrifugation (5', 2600 * g, 4 C)

tag: strain

tag: culture condition

value: 60 min after onset CO2 depletion (3.3)

value: 30 min after onset CO2 depletion


title: Blood SCD patientA0266

description:
Sample162
globin mRNA-depleted total RNA


title: Blood SCD patientA0228

description:
Sample142
globin mRNA-depleted total RNA


title: 30m after CO2 depletion in 1st duplicate time series (2.3) vs CO2 supplemented (1.4) in 2nd duplicate time series

description:
2.3 over 1.4
30 min after onset CO2 depletion in 1st of duplicate time series (2.3) vs CO2 supplemented culture (1.4) in 2nd of duplicate time series

value: 30 min after onset CO2 depletion (2.3)

value: CO2 supplemented culture (1.4)


title: K71

description: APC,KRAS mutant tumor

tag: genotype code

tag: genotype

tag: data set

tag: genetic background


title: K43

description: APC,KRAS mutant tumor


title: B6_P2_1

description: wildtype control colon

value: WT

value: wild type

value: wildtype control colon


title: Blood SCD patientA0197

description:
Sample128
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

value: E

value: M

value: SS


title: CO2 supplemented logarithmic culture (1.4) vs 30 min after onset CO2 depletion (2.4) 2nd of duplicate time series

description:
1.4 over 2.4
2nd of duplicate time series

value: 30 min after onset CO2 depletion (2.4)


title: Blood SCD patientA0205

description:
Sample130
globin mRNA-depleted total RNA

value: FU

tag: severity score

tag: red blood cells


title: aerobic logarithmic culture (O1.4) vs anaerobic logarithmic culture (1.4) 2nd of duplicate comparison

description:
O1.4 over 1.4
2nd of duplicate comparison

value: aerobic logarithmic culture (O1.4)

value: anaerobic logarithmic culture (1.4)


title: K45

description: APC,KRAS mutant tumor

value: AK

value: APC KRAS mutant

value: APC,KRAS mutant tumor

value: C57BL6/129 mixed


title: B6_P2_3

description: wildtype control colon

value: Training set


title: 30 min after onset CO2 depletion (2.4) vs 60 min after onset CO2 depletion (3.4) 2nd of duplicate time series

description:
2.4 over 3.4
2nd of duplicate time series

value: 60 min after onset CO2 depletion (3.4)


description:
O1.3 over O1.4
duplicate of aerobic logarithmic culture

value: aerobic logarithmic culture


title: A88

description: APC,KRAS,P53 mutant tumor

value: AKP

value: APC KRAS P53 mutant

value: APC,KRAS,P53 mutant tumor


description:
4.4 over 4.3
duplicate 120 min after onset CO2 depletion

value: 120 min after onset CO2 depletion


title: Blood SCD patientA0190

description:
Sample124
globin mRNA-depleted total RNA

value: A

value: F

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0170

description:
Sample121
globin mRNA-depleted total RNA

tag: Sex

value: M

tag: hb phenotype

value: SS


title: Blood SCD patientA0196

description:
Sample127
globin mRNA-depleted total RNA


title: Blood SCD patientA0215

description:
Sample133
globin mRNA-depleted total RNA

value: FU


title: Blood SCD patientA0214

description:
Sample132
globin mRNA-depleted total RNA

value: E


title: Blood SCD patientA0192

description:
Sample125
globin mRNA-depleted total RNA

value: SC


title: Blood SCD patientA0210

description:
Sample131
globin mRNA-depleted total RNA


title: Blood SCD patientA0202

description:
Sample129
globin mRNA-depleted total RNA


title: Blood SCD patientA0174

description:
Sample122
globin mRNA-depleted total RNA


title: 60 min after onset CO2 depletion (3.4) vs 120 min after onset CO2 depletion (4.4) 2nd of duplicate time series

description:
3.4 over 4.4
2nd of duplicate time series

value: 120 min after onset CO2 depletion (4.4)


title: Blood SCD patientA0178

description:
Sample123
globin mRNA-depleted total RNA


title: Blood SCD patientA0193

description:
Sample126
globin mRNA-depleted total RNA


title: A03

description: APC,P53 mutant tumor

value: AP

value: APC P53 mutant

tag: batch

tag: tissue

value: APC,P53 mutant tumor


title: ASA3 (36 h)

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

hyb_protocol: The Hy3™-labeled samples and a Hy5™- labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno) (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE 16.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array instruction manual using a Tecan HS 4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing: The image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). Values in series supplementary file "normalized_data.txt" are all log2intensities (Hy3).

source_name: Endothelial RNA from Aorta

label_protocol: 100 ng total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Endothelial enriched RNA was collected from the suprarenal regions and abdominal aortic regions of C57BL6 mice

extract_protocol: The arotic regions were dissected out carefully and the lumen were quickly flushed with Qiazol and total RNA isolated using Qiagen miRNAeasy miRNA kit.

treatment_protocol: Mice were implanted with Osmotic minipump to infuse Ang2 for 12 hours and 36 hours, respectively

tag: treatment

value: 36 h Ang2 pump implantation

value: suprarenal region of the abdominal aorta


title: K104

description: APC,KRAS mutant tumor

value: AK

value: APC KRAS mutant

value: Training set

value: APC,KRAS mutant tumor

value: C57BL6/129 mixed


title: Blood SCD patientA0169

description:
Sample120
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume


title: 60 min after onset CO2 depletion (3.3) vs 30 min after onset CO2 depletion (2.3) 1st of duplicate time series

description:
3.3 over 2.3
1st of duplicate time series

tag: strain

tag: culture condition

value: 60 min after onset CO2 depletion (3.3)

value: 30 min after onset CO2 depletion (2.3)


title: Blood SCD patientA0150

description:
Sample114
globin mRNA-depleted total RNA

value: F

value: SS


title: anaerobic logarithmic culture (1.3) / aerobic logarithmic culture (O 1.3) 1st of duplicate comparison

description:
1.3 over O1.3
1st of duplicate comparison

value: anaerobic logarithmic culture (1.3)

value: aerobic logarithmic culture (O 1.3)


title: ASA2 (36 h)


title: Blood SCD patientA0163

description:
Sample117
globin mRNA-depleted total RNA

value: FU

value: M

value: SC


title: Blood SCD patientA0156

description:
Sample115
globin mRNA-depleted total RNA

value: A


title: Blood SCD patientA0160

description:
Sample116
globin mRNA-depleted total RNA


title: Blood SCD patientA0166

description:
Sample118
globin mRNA-depleted total RNA


title: ASA1 (36 h)

value: 36 h Ang2 pump implantation


title: 30 min after onset CO2 depletion (2.3) vs CO2 supplemented culture (1.3) 1st of duplicate time series

description:
2.3 over 1.3
1st of duplicate time series

value: CO2 supplemented culture (1.3)


title: H46

description: APC,P53 mutant tumor

tag: genotype code

value: AP

tag: genotype

value: APC P53 mutant

tag: data set

value: APC,P53 mutant tumor


title: Blood SCD patientA0168

description:
Sample119
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status


title: A85

description: APC,KRAS,P53 mutant tumor

value: AKP

value: APC KRAS P53 mutant

value: Training set

value: APC,KRAS,P53 mutant tumor

tag: genetic background


title: Blood SCD patientA0144

description:
Sample113
globin mRNA-depleted total RNA

tag: severity score

tag: red blood cells

tag: genotypic pc1


title: 120 min after onset CO2 depletion (4.3) vs 60 min after onset CO2 depletion (3.3) 1st of duplicate time series

description:
4.3 over 3.3
1st of duplicate time series

value: 120 min after onset CO2 depletion (4.3)

value: 60 min after onset CO2 depletion (3.3)


title: A89

description: APC,KRAS,P53 mutant tumor

value: C57BL6/129 mixed


title: Blood SCD patientA0141

description:
Sample112
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype

value: SS

tag: genotypic pc2


title: ASA3 (12 h)

tag: treatment

value: 12 h Ang2 pump implantation

tag: tissue

value: suprarenal region of the abdominal aorta


title: Blood SCD patientA0137

description:
Sample111
globin mRNA-depleted total RNA

value: E

value: F

tag: white blood cells

tag: mean corpuscular volume


title: A83

description: APC,KRAS,P53 mutant tumor

tag: batch


title: ASA2 (12 h)

tag: strain


title: G40

description: APC,P53 mutant tumor

tag: genotype code

tag: genotype


title: SA3 (0h)

value: 0 h Ang2 pump implantation


title: A90

description: APC,KRAS,P53 mutant tumor

tag: data set


title: SA2 (0h)


title: Blood SCD patientA0130

description:
Sample105
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

value: M


title: Blood SCD patientA0133

description:
Sample107
globin mRNA-depleted total RNA

tag: severity score


title: A65

description: APC,KRAS,P53 mutant tumor

tag: genetic background


title: ASA1 (12 h)


title: Blood SCD patientA0132

description:
Sample106
globin mRNA-depleted total RNA

value: FU

tag: red blood cells

tag: genotypic pc1


title: Blood SCD patientA0134

description:
Sample108
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype


title: Blood SCD patientA0135

description:
Sample109
globin mRNA-depleted total RNA

tag: genotypic pc2


title: SA1 (0h)

tag: treatment

tag: tissue


title: Blood SCD patientA0136

description:
Sample110
globin mRNA-depleted total RNA

value: A

tag: white blood cells

tag: mean corpuscular volume


title: A54

description: APC,KRAS,P53 mutant tumor

tag: batch


title: Blood SCD patientA0127

description:
Sample103
globin mRNA-depleted total RNA


title: Blood SCD patientA0125

description:
Sample101
globin mRNA-depleted total RNA


title: Blood SCD patientA0121

description:
Sample97
globin mRNA-depleted total RNA


title: Blood SCD patientA0123

description:
Sample99
globin mRNA-depleted total RNA


title: Blood SCD patientA0119

description:
Sample95
globin mRNA-depleted total RNA


title: Untreated or WT (DAP12+/+) control microglia at E17.5 UT4_2012

city: Rotterdam

first: Wouter

last: Beumer

address: Dr. Molenwaterplein 50

department: Immunology

institute: Erasmus MC

description: Gene expression data from CX3CR1+ microglia from WT mice at E17.5

hyb_protocol: After fragmentation the chips were hybridized for 18h at 45C according to the manufacturers protocol.

scan_protocol: Chips were scanned on a Affymetrix GeneChip Scanner 3000 7G according to the manufacturers protocol using the GeneChip® Command Console® Software (AGCC) v3.2.4

data_processing: Quality analysis of the CEL data was assessed by running a standardized workflow developed at the BiGCaT department of Maastricht University - The Netherlands (http://www.arrayanalysis.org/). The expression data containing .CEL files were imported and processed further with BRB-ArrayTools (R. Simon, http://linus.nci.nih.gov/BRB-ArrayTools.html). Gene expression data was normalized using  RMA (Robust Multichip Average)

label_protocol: The RNA was reverse transcribed, amplified, biotinylated and fragmented with the Ovation Pico WTA v2 and Encore Biotin Module (NuGEN Technologies) and subsequently hybridized on Mouse Genome 430 2.0 Arrays (Affymetrix) according to the manufacturers protocols.

growth_protocol: Cells were obtained from pooled embronic hippocampi after 1. enzymatic digestion of tissue by 0.25% trypsin and Dnase I, 2.  FACS sorting of CX3CR1-GFP+ microglia.

extract_protocol: RNA was iolated and Dnase treated with the MiRNeasy kit (Qiagen)

treatment_protocol: Maternal inflammation (LPS) or DAP12-/- mutants. PBS treatment or WT mice were used as control

tag: cell type

value: Microglia

tag: gender

value: unknown

tag: age

value: untreated

value: wild type


title: Blood SCD patientA0129

description:
Sample104
globin mRNA-depleted total RNA

tag: age (years)


title: CellsCan_rep4

city: Frankfurt

first: Daniela

middle: Jasmin

last: Näther

address: Max-von-Laue-Str. 9

department: Molecular Biosciences

country: Germany

institute: Goethe University Frankfurt

description: Gene expression of cells grown on canola

hyb_protocol: 600 ng of fluorescent labelled aRNA was hybridized to the microarray for 17h at 68 degree.

scan_protocol: Slides were scanned immediately after washing on Agilent DNA Microarray Scanner (G2565AA).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default values (protocol GE1_107_Sep07 _91).

organism: Alcanivorax borkumensis SK2

source_name: Cells on canola, replicate 4

label_protocol: 0,5 µg of total RNA were Cy3-labelled with Message AmpII Bacteria Kit according to the recommendations of the supplier Ambion.

growth_protocol: Cells were grown on ONR7 medium with either pyruvate, hexadecane, canola or diesel as carbon source to exponential growth phase.

extract_protocol: Total RNA was isolated with RiboPure Bacteria Kit following manufacturer Ambion recommendations

treatment_protocol: Samples were taken at exponential growth phase.

tag: agent

value: canola

tag: growth phase

value: exponential


title: Blood SCD patientA0126

description:
Sample102
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

value: SC


title: CellsDis_rep4

description: Gene expression of cells grown on diesel

source_name: Cells on diesel, replicate 4

value: diesel


title: Blood SCD patientA0117

description:
Sample93
globin mRNA-depleted total RNA

tag: red blood cells

tag: genotypic pc1


title: Blood SCD patientA0124

description:
Sample100
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype

value: SS


title: Untreated or WT (DAP12+/+) control microglia at E17.5 UT-3_2013

tag: treatment

tag: genotype

tag: genetic background


title: CellsDis_rep3

source_name: Cells on diesel, replicate 3


title: Untreated or WT (DAP12+/+) control microglia at E17.5 UT-1_2013


title: Untreated or WT (DAP12+/+) control microglia at E17.5 UT-6_2013


title: Blood SCD patientA0122

description:
Sample98
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume

tag: genotypic pc2


title: Blood SCD patientA0118

description:
Sample94
globin mRNA-depleted total RNA


title: Blood SCD patientA0120

description:
Sample96
globin mRNA-depleted total RNA


title: CellsDis_rep2

source_name: Cells on diesel, replicate 2


title: Blood SCD patientA0115

description:
Sample91
globin mRNA-depleted total RNA

source_name: whole blood


title: Control for maternally inflamed microglia (PBS) at E17.5 PBS4_2008

description: Gene expression data from CX3CR1+ microglia from control non-maternally inflamed (PBS) mice at E17.5

tag: cell type

tag: gender

value: PBS control for maternal inflammation


title: Blood SCD patientA0116

description:
Sample92
globin mRNA-depleted total RNA

tag: age (years)


title: Blood SCD patientA0114

description:
Sample90
globin mRNA-depleted total RNA


title: Blood SCD patientA0111

description:
Sample88
globin mRNA-depleted total RNA


title: Blood SCD patientA0108

description:
Sample86
globin mRNA-depleted total RNA


title: CellsPyr_rep4

description: Gene expression of cells grown on pyruvate

source_name: Cells on pyruvate, replicate 4

tag: agent

value: pyruvate


title: Untreated or WT (DAP12+/+) control microglia at E17.5 UT-2_2013

tag: age


title: Control for maternally inflamed microglia (PBS) at E17.5 PBS-2_2013


title: Blood SCD patientA0106

description:
Sample84
globin mRNA-depleted total RNA

tag: clinical status

value: E


title: Blood SCD patientA0109

description:
Sample87
globin mRNA-depleted total RNA

tag: severity score


title: Untreated or WT (DAP12+/+) control microglia at E17.5 UT3_2012


title: Control for maternally inflamed microglia (PBS) at E17.5 PBS1_2010


title: Blood SCD patientA0107

description:
Sample85
globin mRNA-depleted total RNA

tag: red blood cells


title: CellsHex_rep2

description: Gene expression of cells grown on hexadecane

source_name: Cells on hexadecane, replicate 2

value: hexadecane

tag: growth phase


title: Blood SCD patientA0105

description:
Sample83
globin mRNA-depleted total RNA

tag: Sex

tag: genotypic pc1


title: CellsHex_rep4

source_name: Cells on hexadecane, replicate 4


title: CellsHex_rep3

source_name: Cells on hexadecane, replicate 3


title: Maternally inflamed microglia (LPS) at E17.5 LPS3_2008

description: Gene expression data from CX3CR1+ microglia from maternally inflamed (LPS) mice at E17.5

tag: treatment

value: Maternal inflamtion by LPS


title: Blood SCD patientA0104

description:
Sample82
globin mRNA-depleted total RNA

value: M

tag: hb phenotype


title: Control for maternally inflamed microglia (PBS) at E17.5 PBS2_2010

tag: genotype

tag: genetic background


title: Maternally inflamed microglia (LPS) at E17.5 LPS2_2010


title: CellsDis_rep1

source_name: Cells on diesel, replicate 1


title: Blood SCD patientA0103

description:
Sample81
globin mRNA-depleted total RNA

value: FU

value: F

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0100

description:
Sample79
globin mRNA-depleted total RNA


title: Blood SCD patientA0113

description:
Sample89
globin mRNA-depleted total RNA

value: A

tag: genotypic pc2


title: CellsCan_rep2

source_name: Cells on canola, replicate 2


title: CellsCan_rep3

source_name: Cells on canola, replicate 3


title: Maternally inflamed microglia (LPS) at E17.5 LPS1_2010

tag: cell type

value: Microglia

tag: gender

value: unknown


title: Blood SCD patientA0101

description:
Sample80
globin mRNA-depleted total RNA

tag: age (years)


title: CellsCan_rep1

source_name: Cells on canola, replicate 1

tag: agent


title: CellsHex_rep1

source_name: Cells on hexadecane, replicate 1


title: Maternally inflamed microglia (LPS) at E17.5 LPS-3_2_2013

tag: age

value: wild type


title: Blood SCD patientA0094

description:
Sample74
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score


title: CellsPyr_rep3

source_name: Cells on pyruvate, replicate 3

tag: growth phase


title: Blood SCD patientA0095

description:
Sample75
globin mRNA-depleted total RNA

tag: Sex

tag: red blood cells


title: Blood SCD patientA0098

description:
Sample77
globin mRNA-depleted total RNA

tag: genotypic pc1


title: DAP12-/- microglia at E17.5 DAP12KO-4_2013

description: Gene expression data from CX3CR1+ microglia from DAP12-/- mice at E17.5

source_name: DAP12-/- microglia at E17.5

tag: treatment

value: untreated

value: DAP12-/- mutation


title: Blood SCD patientA0096

description:
Sample76
globin mRNA-depleted total RNA

tag: hb phenotype


title: DAP12-/- microglia at E17.5 DAP12KO-2_2013

tag: genotype

tag: genetic background


title: Blood SCD patientA0090

description:
Sample71
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0091

description:
Sample72
globin mRNA-depleted total RNA


title: Blood SCD patientA0089

description:
Sample70
globin mRNA-depleted total RNA

value: SC

tag: genotypic pc2


title: Blood SCD patientA0099

description:
Sample78
globin mRNA-depleted total RNA


title: Blood SCD patientA0086

description:
Sample68
globin mRNA-depleted total RNA


title: CellsPyr_rep1

source_name: Cells on pyruvate, replicate 1

value: exponential


title: DAP12-/- microglia at E17.5 DAP12KO-5_2013

tag: cell type

tag: gender


title: Blood SCD patientA0082

description:
Sample66
globin mRNA-depleted total RNA

tag: age (years)

value: SS


title: CellsPyr_rep2

source_name: Cells on pyruvate, replicate 2

tag: agent


title: Blood SCD patientA0085

description:
Sample67
globin mRNA-depleted total RNA

tag: clinical status


title: Blood SCD patientA0087

description:
Sample69
globin mRNA-depleted total RNA

tag: severity score


title: DAP12-/- microglia at E17.5 DAP12KO-1_2013

tag: age


title: Input RNA 6h, rep2

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

description:
6_input 6h Extract_2
Preparation of cytoplasmic extract.
Total RNA extraction.

hyb_protocol: Following fragmentation, 12.5 µg of aRNA were hybridized at 45°C with 60 rpm for 16 hrs on Affymetrix Mouse Genome 430 2.0 Array. Subsequently, GeneChips were washed and stained in the Affymetrics Fluidics Station 450 using the program: FS450_0001.

scan_protocol: Scan was performed using the Affymetrix 3000 7G Scanner.

data_processing: Data was analyzed using ArrayStar 4 (DNASTAR), RMA background correction, normalization method: quantile, summarization method: medium polish. Due to high variation of values from Luciferase control IP, values from hnRNP K IP were compared with mean of all Luc IP values. Genes were selected with > 2 FC up at 0h and < 2 FC up at 6h. To include gene expression data, same analysis was done comparing hnRNP K IP with input. Genes with input values below 20 were excluded. Described processing was done for the first and the second replicate alone and the mean of both replicates and data were combined. Genes with higher values in mean Luciferase control IP than in hnRNP K IP were excluded, as well as not annotated genes. Data processing revealed 2163 genes, corresponding to 1901 single entries.

source_name: RAW 264.7, LPS, input

label_protocol: Biotinylated aRNAs were prepared according to the messageAmp Premier Amplification Kit (Ambion) prototcol.

growth_protocol: DMEM, 10% FBS, penicillin, streptomycin.

extract_protocol: Preparation of cytoplasmic extract, immunoprecipitation with antibodies against hnRNP K or Luciferase as control, isolation of total/co-purified RNA with Trizol.

treatment_protocol: Untreated (0h) or 10 ng/ml Lipopolysaccharide for 6h.

tag: cell line

value: macrophage cell line

value: LPS for 6hr

tag: ip antibody


title: Input RNA 6h, rep1

description:
6_input 6h Extract
Preparation of cytoplasmic extract.
Total RNA extraction.


title: IP Luciferase 6h, rep2

description:
5_Luciferase 6h Extract_2
Preparation of cytoplasmic extract.
IP with Luciferase antibody, extraction of co-purified RNA.

source_name: RAW 264.7, LPS, Luciferase IP

value: Luciferase

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot #


title: Blood SCD patientA0079

description:
Sample64
globin mRNA-depleted total RNA

value: E

tag: Sex

tag: hb phenotype

tag: red blood cells

tag: genotypic pc1


title: Blood SCD patientA0077

description:
Sample63
globin mRNA-depleted total RNA


title: IP Luciferase 6h, rep1

description:
5_Luciferase 6h Extract
Preparation of cytoplasmic extract.
IP with Luciferase antibody, extraction of co-purified RNA.

tag: treatment


title: Blood SCD patientA0093

description:
Sample73
globin mRNA-depleted total RNA

value: M

tag: white blood cells

tag: mean corpuscular volume

tag: genotypic pc2


title: Blood SCD patientA0074

description:
Sample60
globin mRNA-depleted total RNA

tag: age (years)

value: FU


title: Blood SCD patientA0075

description:
Sample61
globin mRNA-depleted total RNA

tag: clinical status


title: Control 536438A12

city: Basel

first: Guido

last: Steiner

address: Grenzacher Str.

country: Switzerland

institute: F. Hoffmann-La Roche

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

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

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

source_name: Control 536438A12

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

growth_protocol: C57Bl/6J females and males (2.5 months) or the F1 generation breeding were obtained from Janvier (France) and maintained in a temperature- and humidity-controlled facility on a 12-hour reversed light–dark cycle with food and water ad libitum. All procedures were carried out in accordance with Swiss cantonal regulations for animal experimentation. Mice were killed by cervical dislocation either 45 min (acute stress condition) or 2 weeks (baseline resting condition) after exposure to forced swim stress (6 min, 18°C water). The brain was removed and the hippocampus was rapidly dissected on ice and stored at -80°C until processed.

extract_protocol: RNA was extracted from the hippocampus with Trizol (Invitrogen) and amplified using the Ovation RNA amplification kit V2 (Nugen Technologies).

tag: tissue

value: hippocampus

tag: group

value: Control

tag: phenotype

value: F2 control handling, after control handling in F1 generation

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: IP hnRNP K 6h, rep2

description:
4_hnRNP K 6h Extract_2
Preparation of cytoplasmic extract.
IP with hnRNP K antibody, extraction of co-purified RNA.

source_name: RAW 264.7, LPS, hnRNP K IP

tag: cell line

tag: cell type

tag: ip antibody

value: hnRNP K

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: Blood SCD patientA0072

description:
Sample59
globin mRNA-depleted total RNA

source_name: whole blood

tag: age (years)

tag: severity score

tag: Sex

value: F

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Input RNA 0h, rep1

description:
3_input 0h Extract
Preparation of cytoplasmic extract.
Total RNA extraction.

source_name: RAW 264.7, untreated, input

tag: treatment


title: Blood SCD patientA0071

description:
Sample58
globin mRNA-depleted total RNA

tag: clinical status


title: Blood SCD patientA0062

description:
Sample50
globin mRNA-depleted total RNA


title: Control 536438A11

source_name: Control 536438A11

tag: tissue

tag: group

tag: phenotype

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: IP Luciferase 0h, rep2

description:
2_IP Luciferase 0h Extract_2
Preparation of cytoplasmic extract.
IP with Luciferase antibody, extraction of co-purified RNA.

source_name: RAW 264.7, untreated, Luciferase IP

tag: cell line

tag: cell type

tag: ip antibody

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: Blood SCD patientA0065

description:
Sample52
globin mRNA-depleted total RNA

tag: age (years)

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Input RNA 0h, rep2

description:
3_input 0h Extract_2
Preparation of cytoplasmic extract.
Total RNA extraction.

tag: treatment


title: Blood SCD patientA0080

description:
Sample65
globin mRNA-depleted total RNA

tag: clinical status


title: IP Luciferase 0h, rep1

description:
2_IP Luciferase 0h Extract
Preparation of cytoplasmic extract.
IP with Luciferase antibody, extraction of co-purified RNA.

tag: cell line


title: Control 536438A06

source_name: Control 536438A06

tag: tissue

tag: group

tag: phenotype

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Blood SCD patientA0069

description:
Sample56
globin mRNA-depleted total RNA

tag: age (years)

value: A

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells


title: MSUS_&_AS 536438A10

value: F2 acute stress, after paternal stress in F1 generation


title: Blood SCD patientA0076

description:
Sample62
globin mRNA-depleted total RNA

value: SC

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0061

description:
Sample49
globin mRNA-depleted total RNA

tag: clinical status


title: Blood SCD patientA0068

description:
Sample55
globin mRNA-depleted total RNA


title: Control_&_AS 536438A08

tag: tissue

tag: group

tag: phenotype

value: F2 acute stress, after control handling in F1 generation


title: Blood SCD patientA0067

description:
Sample54
globin mRNA-depleted total RNA


title: Blood SCD patientA0070

description:
Sample57
globin mRNA-depleted total RNA

value: SS


title: IP hnRNP K 6h, rep1

description:
4_hnRNP K 6h Extract
Preparation of cytoplasmic extract.
IP with hnRNP K antibody, extraction of co-purified RNA.

tag: cell line

tag: cell type

value: macrophage cell line

tag: treatment

tag: ip antibody

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: MSUS_&_AS 536438A09

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Control_&_AS 536438A07


title: Blood SCD patientA0066

description:
Sample53
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: IP hnRNP K 0h, rep2

description:
1_IP hnRNP K 0h Extract_2
Preparation of cytoplasmic extract.
IP with hnRNP K antibody, extraction of co-purified RNA.

source_name: RAW 264.7, untreated, hnRNP K IP

tag: cell line

tag: cell type

tag: treatment

tag: ip antibody

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: Blood SCD patientA0059

description:
Sample48
globin mRNA-depleted total RNA

tag: age (years)


title: Control 536438A05

source_name: Control 536438A05

tag: tissue

tag: group

tag: phenotype

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Blood SCD patientA0058

description:
Sample47
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells


title: Blood SCD patientA0054

description:
Sample45
globin mRNA-depleted total RNA

tag: age (years)

tag: genotypic pc1

tag: genotypic pc2


title: MSUS_&_AS 536438A04

tag: tissue

tag: group

tag: phenotype


title: Blood SCD patientA0057

description:
Sample46
globin mRNA-depleted total RNA


title: Blood SCD patientA0052

description:
Sample44
globin mRNA-depleted total RNA


title: IP hnRNP K 0h, rep1

description:
1_IP hnRNP K 0h Extract
Preparation of cytoplasmic extract.
IP with hnRNP K antibody, extraction of co-purified RNA.

tag: cell line

tag: cell type

tag: treatment

tag: ip antibody

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: Control_&_AS 536438A01

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Blood SCD patientA0048

description:
Sample40
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells


title: MSUS_&_AS 536438A03

tag: tissue

tag: group

tag: phenotype


title: Control 536437A11

source_name: Control 536437A11

tag: cage


title: Blood SCD patientA0063

description:
Sample51
globin mRNA-depleted total RNA

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0047

description:
Sample39
globin mRNA-depleted total RNA


title: Blood SCD patientA0050

description:
Sample42
globin mRNA-depleted total RNA


title: NOD pancreas CD8α-DC LPS rep 4

description: Gene expression data from NOD pancreas CD11c+CD8α- DCs at 5 weeks of age in-vitro stimulated with LPS

source_name: NOD pancreas CD11c+CD8α- DCs at 5 weeks in-vitro after 18h LPS stimulation

growth_protocol: NA. Cells were obtained from pancreas tissue after 1. enzymatic digestion of tissue, single-cell suspension 2. pre-separation of CD45+ cells with magnetic beads 3. FACS sorting of CD11c+CD8α- DCs

extract_protocol: RNA was iolated and Dnase treated with the PicoPure RNA extraction kit according to the manufacturers protocol (Arcurus, Applied Biosystems)

treatment_protocol: steady-state (no treatment) or in-vitro PBS/LPS stimulation for 18h

value: Pancreas CD11c+CD8α- DCs

tag: gender

value: female

tag: age

value: 5 weeks

tag: treatment

value: in-vitro LPS stimulation 18 hours

tag: strain

value: NOD


title: NOD pancreas CD8α-DC LPS rep 3


title: Blood SCD patientA0046

description:
Sample38
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

value: E


title: Blood SCD patientA0051

description:
Sample43
globin mRNA-depleted total RNA

value: FU

tag: severity score

tag: Sex

value: M


title: Blood SCD patientA0049

description:
Sample41
globin mRNA-depleted total RNA

tag: hb phenotype

tag: white blood cells


title: C57BL6 pancreas CD8α-DC LPS rep 3

description: Gene expression data from C57BL6 pancreas CD11c+CD8α- DCs at 5 weeks of age in-vitro stimulated with LPS

source_name: C57BL6 pancreas CD11c+CD8α- DCs at 5 weeks in-vitro after 18h LPS stimulation


title: Blood SCD patientA0038

description:
Sample32
globin mRNA-depleted total RNA

tag: mean corpuscular volume

tag: red blood cells


title: Blood SCD patientA0045

description:
Sample37
globin mRNA-depleted total RNA


title: C57BL6 pancreas CD8α-DC LPS rep 2

tag: tissue


title: NOD pancreas CD8α-DC LPS rep 1


title: MSUS_&_AS 536437A09

value: hippocampus

tag: group

tag: phenotype

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Control 536437A12

source_name: Control 536437A12

value: Control

value: F2 control handling, after control handling in F1 generation

tag: cage


title: C57BL6 pancreas CD8α-DC LPS rep 4

tag: gender

tag: age

tag: treatment

tag: strain


title: Control_&_AS 536438A02


title: Blood SCD patientA0041

description:
Sample34
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score

tag: Sex

value: F

tag: hb phenotype

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0037

description:
Sample31
globin mRNA-depleted total RNA

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells


title: Blood SCD patientA0040

description:
Sample33
globin mRNA-depleted total RNA


title: NOD pancreas CD8α-DC LPS rep 2

tag: tissue


title: Blood SCD patientA0043

description:
Sample35
globin mRNA-depleted total RNA


title: Blood SCD patientA0044

description:
Sample36
globin mRNA-depleted total RNA