title: ALDH+_DMSO_T47D_Exp_7

source_name: Aldefluor+ cells from T47D cell line treated with DMSO, experiment 7

tag: cell line

tag: treatment

tag: fraction

tag: experiment

tag: collected cells (x10^6)

tag: collected rna (ng)


title: 343723

status: Public on Nov 01 2016

type: protein

city: Seattle

first: Paul

last: Lampe

state: WA

address: 1100 Fairview Ave. N., Mail Stop M5-C800

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Labeled lysates were incubated on arrays for 90 minutes, washed serially to remove excess dye.

scan_protocol: Slides were scanned in an Axon GenePix 4000B microarray scanner and data extracted using GenePix Pro 6.0 software.

data_processing: For fold change of signal compared to reference, the M value, was calculated as log2(Rc/Gc); where Rc is red corrected and Gc is green corrected for each antibody spot. Technical sources of variation were normalized using loess procedures developed for microarrays. Following normalization, triplicate features were summarized using their median. M values were further normalized using linear regression to remove the systematic bias due to experimental factors.

molecule: protein

organism: Homo sapiens

source_name: Depleted Plasma

label_protocol: The depleted plasma was concentrated to its original volume, measured for total protein concentration, labeled with the amine reactive dyes Cy3- and Cy5-maleimide and unincorporated dye was removed. Individual Cy5-labeled subject samples were incubated with an equal amount of Cy3-labeled reference (a common pool of plasma comprised of samples collected from 7 women aged 45–72 years was used as a reference for all samples).

extract_protocol: Albumin and IgG were depleted from plasma.

tag: age

tag: hormone replacement therapy

value: No

tag: bmi

tag: tissue

value: Depleted Plasma


title: UPittTumor4_copy_number

type: genomic

city: Boston

first: Tony

middle: Edward

last: Godfrey

state: Massachusetts

address: 700 Albany Street

department: Surgery

institute: Boston University

description: Pittsburgh patient tumor

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were washed on an Affymetrix wash station and scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 3.0 and Affymetrix Copy Number Analysis Tool (CNAT 5.0) softwares. DNA copy number analysis was performed in Nexus 6.0 Copy Number Analysis software (BioDiscovery, CA) using NCBI Build 36.1 (hg18).  The UPMC data was normalized to a baseline reference file created using DNA isolated from white blood cells from 15 individuals in the same patient population and the UM dataset was normalized to a reference file created using DNA from 72 matched normal squamous esophageal epithelium specimens.  The two datasets were independently pre-processed and the SNP-Rank Segmentation algorithm was used to segment the normalized data with a minimum requirement of 8 probe-sets and a significance threshold p-value of 10-6.  Log2 copy number thresholds for gains and losses were set at +0.15 (~2.2 copies) and -0.2 (~1.7 copies) respectively while high level gains and homozygous loss were set at +0.5 (~2.8 copies) and -0.8 (~1.1 copies) respectively for both datasets.

label: Biotin

molecule: genomic DNA

source_name: Esophagus tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was obtained from white blood cells,  tumors or normal esophageal epithelium frozen at the time of surgical dissection and maintained at -80C until use.

value: Esophagus tumor tissue

tag: gender

value: Female

tag: diagnosis

value: Cancer

tag: tumor histology

value: Adeno

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

value: I

tag: neoadjuvant therapy

tag: perioperative death

value: FALSE

tag: vital status

value: Alive

tag: OS time

tag: recurrence status

value: Yes

tag: dfs time


title: UPittTumor8_copy_number

description: Pittsburgh patient tumor

value: Male


title: UPittTumor3_copy_number

description: Pittsburgh patient tumor

value: IIB


title: 345

tag: age

tag: ethnicity

value: White (not of Hispanic origin)


title: UPittTumor2_copy_number

description: Pittsburgh patient tumor

value: IIA


title: UPittTumor1_copy_number

description: Pittsburgh patient tumor

value: IV

value: Dead


title: 342

value: Black or African-American

tag: hormone replacement therapy

tag: bmi


title: 343711

tag: tissue


title: 343719

value: No


title: ALDH+_DMSO_T47D_Exp_6

type: RNA

city: Ann Arbor

first: Sean

middle: Patrick

last: McDermott

state: MI

address: 2800 Plymouth Rd

department: Internal Medicine - Hem/Onc

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 2.5 ug of cDNA were hybridized at [48C – 3’; 48C – WT] on Human Gene ST 2.1 plates, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515)

data_processing: CEL files processed using R and Bioconductor after loading the following, and associated, packages: oligo, genefilter, affycoretools, limma, ReportingTools, sva, gplots, hwriter, pd.hugene.2.1.st, hugene21sttranscriptcluster.db. Files were preprocessed by Robust Multiarray Average (RMA) with background substraction, quantile normalization, and median polish. Data was fitted with robust probe level linear models to all the probesets for quality control analysis. Since flow cytometry was performed on 6 separate days, batch effects (sorts) were accounted for using ComBat in the sva package. Differentially expressed genes were identified using univariate comparisons. First, the relative reliability of each array is estimated by measuring how well the expression values for that array follow the linear model. Second, data is fitted to a linear model (limma package). Third, the estimated coefficients and standard errors are computed. Finally, initial statistics are determined using an empirical Bayesian model. Multiple testing comparisons were adjusted using Benjamini and Hochberg (aka FDR). Probes with an adjusted p-value <0.05 were considered statistically significant.

label: biotin

molecule: total RNA

source_name: Aldefluor+ cells from T47D cell line treated with DMSO, experiment 6

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 10 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 2.5 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

growth_protocol: SUM159 cells were cultured in F12 media supplemented with 5% FBS, 5 μg/mL insulin, 1 μg/mL hydrocortisone, 50 units/mL Penicillin, and 50μg/mL Streptomycin. T47D cells were cultured in RPMI-1640 media supplemented with 10% FBS, 50 units/mL Penicillin, and 50μg/mL Streptomycin.

extract_protocol: Collected cells from flow cytometry were centrifuged at 337g for 5min at 4C. Excess volume was removed with a p1000 pipette and the remaining sample transferred to 1.5mL microcentrifuge tube. Tubes were centrifuged at 300g for 5min at 4C. Supernatant was removed with a p200 pipette until <30μL sample remained. RNA was extracted using the Qiagen RNeasy Mini Kit following the manufacturer instructions. Briefly, 350μL RLT was added to cell pellets (in <30μL) and vortexed for 30sec. 350μL 70% EtOH was added to each sample and mixed until no viscosity remained. 700uL of each sample was transferred to spin column, centrifuged 10,000g x 15sec. Flow-through was removed. Then 700μL RW1 was added to spin column, centrifuged 10,000g x 15sec. Flow-through was removed. Then 500μL RPE buffer was added to spin column, centrifuged 10,000g x 15sec. Flow-through was removed. Then 500μL RPE buffer to spin column, centrifuged 10,000g x 2min. Flow-through was removed. Spin columns were placed on new 1.5mL RNAse-free centrifuge tubes. 50μL of RNAse-free water was added to membrane and then centrifuged 10,000g x 1min.

treatment_protocol: 0.75x10^6 SUM159 cells or 1.5x10^6 T47D cells were plated in 6 T75 flasks with 20mL media per flask. 5μM (micromolar) ID8 (or DMSO) was added to 3 T75 flasks with 20mL fresh media after 4 days. Cells were treated for 72 hours. Cells from 3 T75 flasks were collected with 0.05% trypsin/0.53mM EDTA and counted. 5x10^6 cells were filtered through 35μm membranes into three separate 5mL FACS tubes, and centrifuged at 337g for 5min at 4C. Cell pellets were suspended in 985μL Aldefluor Assay Buffer. 10μL of 0.1mg/mL DAPI was added. 5μL of DEAB, as an inhibitor of the Aldefluor reaction, was added to a separate 5mL FACS tube. 5μL of activated Aldefluor reagent was added to 995μL of cells/DAPI. 500μL of this solution was immediately transferred to the tube containing DEAB. Cells were incubated for 30min at 37C. Tubes were centrifuged at 337g for 5min at 4C,  suspended in Aldefluor Assay Buffer at 2.5x10^6 cells/mL, and placed on ice. Cell sorting was performed using a Beckman Coulter MoFlo XDP with 355nm, 488nm, and 633nm lasers with appropriate filters. Gating for Aldefluor+ events were determined using the DEAB sample and was set at 0.1%. ALDH+ and ALDH- cells from DMSO and ID8 groups were collected into separate 5mL FACS tubes containing 1mL of PBS/3% FBS.

tag: cell line

tag: treatment

value: DMSO

tag: fraction

value: Aldefluor+

tag: experiment

tag: collected cells (x10^6)

tag: collected rna (ng)


title: ALDH-_ID8_SUM159_Exp_4

source_name: Aldefluor- cells from SUM159 cell line treated with ID8, experiment 4

value: Aldefluor-


title: 340

value: Depleted Plasma


title: 347


title: ALDH-_ID8_SUM159_Exp_3

source_name: Aldefluor- cells from SUM159 cell line treated with ID8, experiment 3


title: 343720


title: ALDH+_ID8_SUM159_Exp_3

source_name: Aldefluor+ cells from SUM159 cell line treated with ID8, experiment 3


title: ALDH+_ID8_SUM159_Exp_2

source_name: Aldefluor+ cells from SUM159 cell line treated with ID8, experiment 2


title: ALDH-_DMSO_SUM159_Exp_2

source_name: Aldefluor- cells from SUM159 cell line treated with DMSO, experiment 2


title: ALDH-_DMSO_SUM159_Exp_4

source_name: Aldefluor- cells from SUM159 cell line treated with DMSO, experiment 4


title: ALDH-_ID8_SUM159_Exp_2

source_name: Aldefluor- cells from SUM159 cell line treated with ID8, experiment 2


title: 338


title: ALDH+_ID8_SUM159_Exp_4

source_name: Aldefluor+ cells from SUM159 cell line treated with ID8, experiment 4


title: ALDH+_DMSO_SUM159_Exp_4

source_name: Aldefluor+ cells from SUM159 cell line treated with DMSO, experiment 4


title: 343721


title: 336


title: ALDH-_DMSO_SUM159_Exp_3

source_name: Aldefluor- cells from SUM159 cell line treated with DMSO, experiment 3


title: ALDH+_DMSO_SUM159_Exp_3

source_name: Aldefluor+ cells from SUM159 cell line treated with DMSO, experiment 3


title: 334


title: 343701


title: 343


title: 330


title: 343643


title: 343636


title: 343703


title: 343640


title: 343637


title: 343621


title: 329


title: 327


title: B2_Beer_102_tEAC

first: Derek

middle: John

last: Nancarrow

address: 1500 E. Medical Center Dr.

department: Department of Surgery

description: Esophagectomy specimen with no preoperative chemoradiation therapy.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 20 hr at 48C on GeneChip Human Gene 2.1 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed with R/Bioconductor software and normalized using RMA. The arrays were run in two batches, the first batch holding 8 NE, 5 NG, and 35 GEJAC, while the second batch consisted of 52 tEAC and an additional 35 GEJAC. We adjusted log2-transformed data for batch effects by adding constants (one per probe-set) to the values of each probe-set in the second batch to make the mean for the GEJAC's in batch 2 agree with the GEJAC mean in batch 1. When fitting a one-way analysis of variance (ANOVA) model with means for each of the four tissue types, we reduce the degrees of freedom in the mean-squared-error and F-tests by 1 to account for this batch adjustment. Analyses were restricted to the 26,613 coding and non-coding genes for which annotation details were available, including HUGO Gene Nomenclature Committee (HGNC) approved gene symbol and Entrez Gene ID.

source_name: tubular esophagus adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT Expression Kit User Manual, 2010, Affymetrix).

extract_protocol: Total RNAs from primary tissues were isolated using Trizol reagent from Invitrogen and the RNeasy mini kit from QIAGEN following the manufacturers' instructions.

treatment_protocol: Samples were immediately fresh-frozen in liquid nitrogen and stored at -80oC until use.

tag: patient disease state

value: esophageal adenocarcinoma

tag: sample type

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

tag: tumor stage

value: 57 yr

tag: gender

value: male

tag: racial group

value: white American


title: ALDH+_DMSO_SUM159_Exp_2

source_name: Aldefluor+ cells from SUM159 cell line treated with DMSO, experiment 2


title: 343624

value: Yes


title: B2_Beer_092_tEAC

value: III

value: 81 yr


title: B2_Beer_098_tEAC

value: 77 yr


title: 343619


title: B2_Beer_094_tEAC


title: 343623


title: 16_BA25

city: Exeter

first: Therese

middle: M

last: Murphy

address: RILD building

department: University of Exeter Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).  Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on Illumina's database and probes identified by Chen et al. (Epigenetics 2013, 8:203-209) were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3 and Cy5

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer's standard protocol.

extract_protocol: Genomic DNA was isolated from ~50 mg of each dissected brain region using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

value: cortex, Brodmann area 25

tag: groupid

value: non-psychiatric sudden death

value: M


title: 325

tag: age

value: White (not of Hispanic origin)


title: B2_Beer_101_tEAC

value: 69 yr


title: 324

tag: ethnicity

value: No


title: B2_Beer_090_tEAC

value: 70 yr

value: female

value: unknown


title: 343616

tag: hormone replacement therapy

value: Depleted Plasma


title: 173_BA25


title: B2_Beer_084_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

value: 68 yr


title: 167_BA25

value: MDD suicide case


title: 321

value: Yes

tag: bmi


title: 322

tag: tissue


title: 158_BA25


title: 319


title: 162_BA25

value: F


title: B2_Beer_086_tEAC

value: III

value: 89 yr

value: male

value: white American


title: B2_Beer_087_tEAC

value: I

value: 46 yr


title: 314

value: White (not of Hispanic origin)


title: 153_BA25

value: cortex, Brodmann area 25


title: B2_Beer_078_tEAC

value: 56 yr


title: 317

value: No

value: Depleted Plasma


title: 343493


title: 313


title: 343490


title: 343484


title: 312


title: 309


title: B2_Beer_076_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 85 yr

value: female


title: B2_Beer_077_tEAC

value: tubular esophagus adenocarcinoma

value: unknown

value: 58 yr


title: 177_BA25

value: non-psychiatric sudden death

value: F


title: 343473

value: Yes


title: B2_Beer_074_tEAC

value: IIA

value: 63 yr

value: white American


title: 305

value: White (not of Hispanic origin)


title: B2_Beer_075_tEAC

value: IIB

value: 69 yr

value: male


title: 15_BA25

value: cortex, Brodmann area 25

value: M


title: 302

value: No

value: Depleted Plasma


title: B2_Beer_073_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

value: 80 yr


title: 343469


title: 343536


title: 343474


title: 49_BA11

value: cortex, Brodmann area 11

value: MDD suicide case


title: 190_BA25


title: B2_Beer_071_tEAC

value: III

value: 73 yr


title: 281


title: 282


title: 343467

value: Yes


title: 52_BA11


title: 280

value: White (not of Hispanic origin)


title: 343465


title: 36_BA11

value: non-psychiatric sudden death


title: 343453


title: 28_BA11


title: 277


title: 343404


title: 343406


title: B2_Beer_070_tEAC

value: IV

value: 63 yr

value: unknown


title: 343402


title: 276


title: B2_Beer_062_tEAC

value: 52 yr

value: male

value: white American


title: 273

value: No

value: Depleted Plasma


title: 343381


title: B2_Beer_068_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

value: 45 yr


title: 272

value: Black or African-American


title: 133_BA25

value: cortex, Brodmann area 25

value: M


title: 138_BA25

value: F


title: 14_BA25

value: non-psychiatric sudden death


title: B2_Beer_063_tEAC

value: IV

value: 73 yr


title: B2_Beer_061_tEAC

value: III

value: 72 yr


title: B2_Beer_056_tEAC

value: 59 yr

value: male


title: B2_Beer_057_tEAC

value: 61 yr

value: white American


title: 127_BA25

value: MDD suicide case


title: 343379

value: No

value: Depleted Plasma


title: 343376


title: 270

value: Other

value: Yes


title: 90_BA25

value: cortex, Brodmann area 25


title: B2_Beer_054_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

value: IIA

value: 66 yr


title: 268

value: White (not of Hispanic origin)


title: 343348


title: 267


title: 343345


title: 265


title: B2_Beer_053_tEAC

value: III


title: 262


title: B2_Beer_051_tEAC

value: 70 yr


title: B2_Beer_050_tEAC

value: 63 yr

value: male


title: B2_Beer_048_tEAC

value: IIB

value: 64 yr

value: unknown


title: 343297

value: Depleted Plasma


title: 234_BA11

value: cortex, Brodmann area 11

value: non-psychiatric sudden death

value: M


title: 135_BA25

value: cortex, Brodmann area 25


title: 260

value: No


title: 343343

value: Yes


title: 343295


title: 8_BA11


title: B2_Beer_046_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

value: IIA

value: 78 yr

value: white American


title: 258

value: White (not of Hispanic origin)


title: 343294


title: 10_BA25

value: MDD suicide case


title: 25_BA11


title: 105_BA25


title: 72_BA11

value: F


title: B2_Beer_045_tEAC

value: I

value: 66 yr

value: male

value: unknown


title: 257

value: Depleted Plasma


title: B2_Beer_043_tEAC

value: IIB

value: 84 yr


title: 343292

value: Yes


title: 70_BA11

value: cortex, Brodmann area 11

value: non-psychiatric sudden death

value: M


title: 343195

value: No


title: B2_Beer_044_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: tubular esophagus adenocarcinoma

value: III

value: 70 yr


title: 256

value: Asian or Pacific Islander


title: 254

value: Other


title: 343171


title: 253

value: White (not of Hispanic origin)


title: B2_Beer_042_tEAC

value: 75 yr

value: male

value: white American


title: 221_BA11

value: F


title: 343167

value: Yes

value: Depleted Plasma


title: 252


title: 248


title: B2_Beer_041_tEAC

value: 67 yr


title: 343083


title: 67_BA11

value: cortex, Brodmann area 11

value: MDD suicide case

value: M


title: 343126


title: 56_BA11


title: B2_Beer_040_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 64 yr


title: 230_BA11

value: non-psychiatric sudden death


title: 90_BA11


title: 250

value: No


title: 343077


title: B2_Beer_036_tEAC

value: tubular esophagus adenocarcinoma

value: III

value: 62 yr


title: B2_Beer_038_tEAC

value: 71 yr

value: male


title: 342996


title: 81_BA11


title: 203_BA11

value: F


title: B2_Beer_033_tEAC

value: 61 yr

value: white American


title: 52_BA25

value: cortex, Brodmann area 25


title: B2_Beer_032_tEAC


title: 243

value: White (not of Hispanic origin)

value: Depleted Plasma


title: B2_Beer_035_tEAC

value: 83 yr

value: female


title: 342994


title: 245

value: Asian or Pacific Islander


title: 242


title: 342984


title: 342995


title: 247

value: Yes


title: B2_Beer_030_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: IV

value: 65 yr


title: 81_BA25

value: MDD suicide case

value: M


title: 342982

value: No


title: 56_BA25


title: 238


title: 241


title: 8_BA25

value: non-psychiatric sudden death


title: 342976


title: 237


title: B2_Beer_031_tEAC

value: tubular esophagus adenocarcinoma

value: III

value: 63 yr

value: male


title: B2_Beer_028_tEAC

value: IIA

value: 76 yr

value: white American


title: 235

value: White (not of Hispanic origin)

value: Depleted Plasma


title: 342960

value: Yes


title: 342959


title: 36_BA25

value: cortex, Brodmann area 25


title: B2_Beer_025_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: I

value: unknown


title: 234

value: No


title: 342958


title: 28_BA25

value: non-psychiatric sudden death

value: M


title: B2_Beer_024_tEAC

value: tubular esophagus adenocarcinoma

value: III

value: 70 yr


title: 342956


title: 232


title: 70_BA25


title: 25_BA25

value: MDD suicide case


title: B2_Beer_023_tEAC

value: 57 yr

value: male


title: 342955


title: 230

value: White (not of Hispanic origin)


title: 228

value: Depleted Plasma


title: 227


title: B2_Beer_009_tEAC

value: IV

value: 66 yr

value: white American


title: 67_BA25

value: cortex, Brodmann area 25


title: 342947


title: 190_BA11

value: cortex, Brodmann area 11


title: 234_BA25


title: 72_BA25

value: F


title: B2_Beer_022_tEAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 74 yr


title: B2_Beer_019_tEAC

value: tubular esophagus adenocarcinoma


title: B2_Beer_007_tEAC

value: III

value: 71 yr


title: 225

value: Yes


title: 342945

value: No


title: 342951


title: B2_Beer_005_tEAC

value: IIB

value: male


title: 221

value: White (not of Hispanic origin)

value: Depleted Plasma


title: 179_BA11

value: MDD suicide case

value: M


title: 220


title: 342937


title: 342935


title: B2_Beer_002_tEAC

value: 69 yr

value: white American


title: 217

value: Other


title: 342941


title: 342906


title: 20_BA11

value: cortex, Brodmann area 11

value: non-psychiatric sudden death


title: 216

value: Black or African-American


title: 184_BA11


title: 342898


title: B2_Beer_099_GEJAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 79 yr


title: 173_BA11


title: B2_Beer_097_GEJAC

value: 64 yr


title: 183_BA11


title: B2_Beer_096_GEJAC

value: III

value: 70 yr


title: 15_BA11


title: B2_Beer_100_GEJAC

value: I

value: 68 yr

value: male


title: 215

value: No

value: Depleted Plasma


title: B2_Beer_089_GEJAC

value: 78 yr

value: female


title: B2_Beer_088_GEJAC

value: 72 yr

value: white American


title: 177_BA11

value: cortex, Brodmann area 11

value: non-psychiatric sudden death

value: F


title: 207

value: White (not of Hispanic origin)

value: Yes


title: 342888


title: 162_BA11


title: 342871


title: 210


title: 206


title: 342870


title: 205


title: 202


title: 342865


title: B2_Beer_085_GEJAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 75 yr


title: 16_BA11

value: M


title: 219

value: Black or African-American


title: 342816


title: 200


title: 197

value: Asian or Pacific Islander


title: 138_BA11


title: 158_BA11


title: 153_BA11

value: MDD suicide case


title: B2_Beer_080_GEJAC

value: IIB

value: 67 yr

value: male


title: B2_Beer_072_GEJAC

value: III

value: 48 yr


title: B2_Beer_081_GEJAC

value: 79 yr

value: female

value: white American


title: 133_BA11

value: cortex, Brodmann area 11

value: non-psychiatric sudden death


title: 342814

value: Yes

value: Depleted Plasma


title: 13_BA11


title: 196


title: B2_Beer_067_GEJAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 75 yr


title: 152_BA11

value: F


title: B2_Beer_069_GEJAC

value: 77 yr


title: B2_Beer_066_GEJAC

value: 73 yr


title: 342796

value: No


title: 194

value: Other


title: 342786


title: 127_BA11

value: MDD suicide case

value: M


title: 191

value: White (not of Hispanic origin)


title: 342782


title: 167_BA11


title: 190


title: 189


title: 14_BA11


title: 342778


title: 11_BA11


title: 135_BA11


title: 185


title: 342748


title: 342746


title: 184


title: 342743


title: 342896


title: 134_BA11


title: 10_BA11


title: B2_Beer_058_GEJAC

value: IIB

value: 79 yr

value: male


title: 183


title: 342738


title: B2_Beer_039_GEJAC

value: III

value: 67 yr

value: white American


title: B2_Beer_060_GEJAC

value: esophageal adenocarcinoma

value: 57 yr

value: female


title: B2_Beer_083_GEJAC

value: esophagectomy specimen

value: IV

value: 51 yr


title: 342737

value: Yes

value: Depleted Plasma


title: B2_Beer_049_GEJAC

value: 66 yr


title: B2_Beer_052_GEJAC

value: IIA

value: 60 yr


title: 179

value: White (not of Hispanic origin)

value: No


title: 177


title: 342673


title: 342810


title: 342671


title: 173


title: B2_Beer_037_GEJAC

value: 75 yr

value: male


title: 342667


title: 183_BA25

value: cortex, Brodmann area 25

value: MDD suicide case

value: M


title: 172


title: 175


title: 342661


title: B2_Beer_029_GEJAC

value: esophageal adenocarcinoma

value: 31 yr

value: white American


title: 169


title: 342658


title: B2_Beer_064_GEJAC

value: esophagectomy specimen

value: IV

value: 79 yr


title: 20_BA25

value: non-psychiatric sudden death


title: B2_Beer_026_GEJAC

value: III

value: 69 yr


title: 230_BA25


title: B2_Beer_027_GEJAC

value: 74 yr


title: B2_Beer_017_GEJAC

value: 71 yr

value: unknown


title: 168

value: White (not of Hispanic origin)

value: No

value: Depleted Plasma


title: 203_BA25

value: cortex, Brodmann area 25

value: MDD suicide case

value: F


title: 342657

value: Yes


title: 164


title: 342634


title: 163


title: 184_BA25

value: M


title: 342629


title: B2_Beer_020_GEJAC

value: esophageal adenocarcinoma

value: esophagectomy specimen

value: 58 yr

value: male

value: white American


title: 342599


title: 342584


title: B2_Beer_034_GEJAC

value: III

value: 46 yr


title: 162


title: 342571


title: 161


title: 158


title: 342583


title: 342569


title: 155

value: Asian or Pacific Islander


title: 157


title: 154


title: 153


title: 342568


title: 342563


title: 152


title: 148


title: 342561


title: 146


title: 342559


title: 143


title: 342554


title: 142


title: 342566


title: 342552


title: 179_BA25


title: 342551


title: 141


title: Bisulfite-converted gDNA from BL2 AID-/- cells

city: New Haven

first: Yang

last: Xi

address: 300 George St

department: Cancer Center

institute: Yale University

description:
The BL2 AID-/- cell line was created from the BL2 cell line by knock out.
This GEO Sample represents 2 biological replicates.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 BeadChip using standard Illumina protocol.

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

data_processing: GenomeStudio software 2011.

label: Cy5, Cy3

source_name: BL2 AID-/- cells

label_protocol: Standard Illumina protocol.

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

tag: cell line

value: BL2 AID-/-

tag: cell type

value: Burkitt lymphoma cell line


title: B2_Beer_014_GEJAC

value: 78 yr


title: 137

source_name: Depleted Plasma

value: White (not of Hispanic origin)

value: Depleted Plasma


title: 342543


title: 342548


title: Bisulfite-converted gDNA from BL2 cells

description: This GEO Sample represents 2 biological replicates.

source_name: BL2 cells


title: 140

value: No


title: 136


title: 342502


title: 134


title: B1_Beer_037_GEJAC

value: I

value: 69 yr

value: female


title: B2_Beer_001_GEJAC

value: esophageal adenocarcinoma


title: 342492

value: Yes


title: 105_BA11

value: cortex, Brodmann area 11

value: MDD suicide case

value: M


title: B1_Beer_052_GEJAC

value: esophagectomy specimen

value: III

value: 79 yr

value: male

value: white American


title: 342491


title: 221_BA25

value: cortex, Brodmann area 25

value: non-psychiatric sudden death

value: F


title: B1_Beer_032_GEJAC

value: IIB

value: 86 yr

value: unknown


title: 130

value: White (not of Hispanic origin)

value: No

value: Depleted Plasma


title: B2_Beer_013_GEJAC

value: esophageal adenocarcinoma

value: 74 yr

value: female


title: B1_Beer_038_GEJAC

value: esophagectomy specimen

value: 78 yr


title: B1_Beer_031_GEJAC

value: III

value: 80 yr


title: 131


title: 342490


title: 128


title: 342489

value: Yes


title: 125


title: B2_Beer_012_GEJAC

value: IIA

value: male

value: white American


title: 342477


title: 124


title: 342425


title: B1_Beer_030_GEJAC

value: 25 yr


title: B1_Beer_026_GEJAC

value: I

value: 62 yr


title: Paromomycin resistant Leishmania donovani (test 2)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Lab generated paromomycin resistant parasite adapted to 100 µM drug pressure (Test sample 2)

hyb_protocol: 600ng of labeled cRNA were hybridized on the array (AMADID: 27511) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned using the Agilent Microarray G2505C scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Leishmania donovani

source_name: Leishmania donovani promastigote

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using WT primer with a T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Leishmania donovani parasites isolated from Bone marrow aspirate of antimony sensitive kala azar patient and was allowed to grow as promastigote in vitro in Medium 199 and 10% FCS. This isolate was denoted as WT.

extract_protocol: Total parasite RNA was extracted using Trizol regent according to manufacturer's instructions.

treatment_protocol: The WT parasite was adapted stepwise to 100 µM paromomycin pressure till it attained growth equivalent to its wild type counterpart.

tag: strain

value: K133 PMM


title: 121

value: White (not of Hispanic origin)


title: 342424

value: No

value: Depleted Plasma


title: B1_Beer_027_GEJAC

value: esophageal adenocarcinoma

value: 76 yr


title: B2_Beer_003_GEJAC

value: esophagectomy specimen

value: 68 yr


title: B1_Beer_025_GEJAC

value: 52 yr

value: female


title: Paromomycin resistant Leishmania donovani (test 3)

description: Lab generated paromomycin resistant parasite adapted to 100 µM drug pressure (Test sample 3)


title: B1_Beer_024_GEJAC

value: III

value: 56 yr


title: B1_Beer_029_GEJAC

value: IIA

value: male


title: Paromomycin resistant Leishmania donovani (test 1)

description: Lab generated paromomycin resistant parasite adapted to 100 µM drug pressure (Test sample 1)


title: Paromomycin sensitive Leishmania donovani (Control 3)

description: Corresponding wild type paromomycin sensitive parasite (Control sample 3)

value: K133 WT


title: B2_Beer_011_GEJAC

value: IIB

value: 80 yr

value: white American


title: B1_Beer_023_GEJAC

value: I


title: 120

value: White (not of Hispanic origin)

value: No


title: B2_Beer_008_GEJAC

value: esophageal adenocarcinoma

value: 70 yr


title: 342423

value: Depleted Plasma


title: B1_Beer_020_GEJAC

value: esophagectomy specimen

value: 51 yr


title: Paromomycin sensitive Leishmania donovani (Control 2)

description: Corresponding wild type paromomycin sensitive parasite (Control sample 2)


title: Paromomycin sensitive Leishmania donovani (Control 1)

description: Corresponding wild type paromomycin sensitive parasite (Control sample 1)


title: B1_Beer_019_GEJAC

value: IV

value: 66 yr


title: B2_Beer_016_GEJAC

value: 67 yr

value: female


title: 119


title: 342422


title: B1_Beer_021_GEJAC

value: 75 yr


title: B1_Beer_034_GEJAC

value: III

value: 81 yr

value: male


title: 117


title: B1_Beer_028_GEJAC

value: white American


title: B1_Beer_022_GEJAC

value: 77 yr


title: 342395


title: 115

value: White (not of Hispanic origin)

value: Yes


title: B1_Beer_018_GEJAC

value: esophageal adenocarcinoma

value: 79 yr


title: 342389

value: Depleted Plasma


title: 111


title: 113


title: 342358

value: No


title: 109

value: Other


title: B1_Beer_015_GEJAC

value: esophagectomy specimen

value: 56 yr


title: 342356


title: 342301


title: 106


title: 342354


title: B1_Beer_016_GEJAC

value: I


title: 342399


title: 108

value: Asian or Pacific Islander


title: 105


title: 116


title: 342298


title: 342292


title: 100


title: 342265


title: 96


title: 342263


title: 342300


title: 94


title: 91


title: 342257


title: 104


title: 90


title: 342260


title: B1_Beer_009_GEJAC

value: 74 yr


title: B1_Beer_014_GEJAC

value: 80 yr

value: female


title: 89


title: 99


title: B1_Beer_010_GEJAC

value: male


title: 88


title: 342191


title: B1_Beer_007_GEJAC

value: III

value: 84 yr

value: white American


title: 342264


title: B1_Beer_005_GEJAC


title: B1_Beer_011_GEJAC

value: IIA

value: 81 yr


title: 86

value: White (not of Hispanic origin)

value: Yes


title: B1_Beer_013_GEJAC

value: esophageal adenocarcinoma

value: IIB

value: 68 yr


title: B1_Beer_002_GEJAC

value: esophagectomy specimen


title: B1_Beer_053_GAS

source_name: normal gastric mucosa

value: normal gastric mucosa

value: 79 yr


title: B1_Beer_004_GEJAC

value: 88 yr


title: 342124

value: No

value: Depleted Plasma


title: B1_Beer_006_GEJAC

value: 71 yr

value: male


title: B1_Beer_008_GEJAC

value: IV

value: 69 yr


title: B1_Beer_003_GEJAC

value: IIA

value: 56 yr

value: white American


title: B1_Beer_001_GEJAC

value: III

value: 85 yr

value: female


title: B1_Beer_012_GEJAC

value: esophageal adenocarcinoma

value: 82 yr


title: 81

value: Black or African-American


title: 342123


title: 342203


title: 342121


title: B1_Beer_036_GAS

value: esophagectomy specimen

value: normal gastric mucosa

value: 74 yr


title: 84

value: White (not of Hispanic origin)

value: No

value: Depleted Plasma


title: 342101


title: 78

value: Yes


title: 342058


title: 79


title: B1_Beer_047_GAS

value: male


title: B1_Beer_051_ESO

source_name: normal esophageal squamous

value: normal esophageal squamous


title: 76


title: 341661


title: 75


title: 342122


title: 71


title: 341643


title: B1_Beer_046_GAS

value: 71 yr


title: B1_Beer_050_ESO

value: white American


title: B1_Beer_048_ESO

value: 68 yr

value: black American


title: B1_Beer_044_GAS

value: female


title: 341632


title: 67


title: 341631


title: 341629


title: 64


title: 341616


title: 341644


title: 61


title: B1_Beer_039_ESO

value: esophageal adenocarcinoma

value: 70 yr


title: B1_Beer_041_ESO

value: 53 yr


title: 341615


title: 68


title: B1_Beer_040_ESO

value: esophagectomy specimen


title: B1_Beer_045_ESO


title: 341610


title: 58


title: B1_Beer_035_ESO


title: 341599


title: 57


title: 62


title: 55


title: A2780_CP20_Exosome, Biological rep. 2

city: Houston

first: Gabriel

last: Lopez-Berestein

state: TX

address: 1901 East Rd

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

description:
Epithelial
miRNA

hyb_protocol: Following biotinylation, hybridization coctailed was prepared with 21.5ul labeled sample and incubated at 95C for minutes , then 45C for 5minutes.  Following sample loading, arrays were loaded into trays and incibated at 48C abd 60rpm for 16 to 18hours.

scan_protocol: The instructions for using the scanner can be found in Affymetrix Command Console User Guide.

data_processing: The data were analyzed with Expression Console. RMA + DABG analysis was performed for the normalization.

source_name: A2780-CP20 Exosome

label_protocol: Biotinylated polyA tailed RNA were prepared according to the standard Affymetrix protocol (FlashTag Biotin HSR RNA Labeling Kit, Affymetrix).

growth_protocol: All cells were maintained at 37°C with 5% CO2 and 95% air.

extract_protocol: Ovarian cancer cells were plated in cell culture medium containing 10% FBS and cultured for 24 h to 70% confluence. Media were replaced with 10% exosome-depleted FBS and cells were grown for 24hours more. Cells were collected by centrifugation and exosomes were isolated using supernatant with Total exosome isolation reagent (Invitrogen, Waltham, MA).

tag: tissue type

value: Ovarian cancer


title: 341593


title: A2780_PAR_Exosome, Biological rep. 2

description:
Epithelial
miRNA

source_name: A2780-PAR Exosome


title: HEYA8_Exosome, Biological rep. 2

description:
Epithelial
miRNA

source_name: HEYA8 Exosome


title: YCVI_G

city: Geneva 14

first: PIerre

last: Burkhard

address: 4 rue Gabrielle-Perret-Gentil

department: Department of Clinical Neurosciences

country: Switzerland

institute: HUG

description: Gene expression data from the periodontal ligament of 43 days old rat

hyb_protocol: 5.5 ug of biotinilated cDNA were hybridized for 16 hr at 45°C on GeneChips Rat Gene 2.0 ST Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned on a 7G affymetrix GeneChip Scanner.

data_processing: The data was processed with the Partek Genomics Suite and RMA normalized.

organism: Rattus norvegicus

source_name: Control / left molar

label_protocol: cRNA were prepared with the Ambion WT expression kit according to manufacturer specifications, with a total RNA starting amount of 200 ng. After cRNA reverse transcription, single-strand cDNA were fragmented and labeled with the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: 4 week old male Wistar rats

extract_protocol: total RNA was extracted using the Rneasy Mini Kit (Qiagen)

treatment_protocol: periodontal ligament tissue from the first right and left mandibular molars was isolated after tooth extraction

value: Wistar

value: 43 days old

value: periodontal ligament


title: YCVI_D

source_name: Control / right molar


title: SKOV3_TR_Exosome, Biological rep. 2

description:
Epithelial
miRNA

source_name: SKOV3-TR Exosome


title: HIO180_CELL, Biological rep. 2

description:
immortalized non-transformed human ovarian surface epithelial cell line
miRNA

source_name: HIO180 Cell

value: Normal ovarian


title: YCV_D


title: 54

value: White (not of Hispanic origin)

value: Yes

value: Depleted Plasma


title: HEYA8_MDR_Exosome, Biological rep. 2

description:
Epithelial
miRNA

source_name: HEYA8-MDR Exosome


title: YCII_G

description: Gene expression data from the periodontal ligament of 31 days old rat

value: male

value: 31 days old


title: 341591

value: No


title: 341590


title: 51


title: 48


title: 341589


title: HIO180_CELL, Biological rep. 1


title: 47


title: 341588


title: 341587


title: SKOV3_ip1_Exosome, Biological rep. 2

description:
Epithelial
miRNA

source_name: SKOV3-ip1 Exosome


title: 44


title: 341586


title: YCII_D


title: 341585


title: 52


title: 43


title: YUVII_D

source_name: Experimental / right molar


title: A2780_CP20_Exosome, Biological rep. 1

description:
Epithelial
miRNA


title: 42


title: YUV_G

source_name: Experimental / left molar


title: YUV_D


title: YUVII_G


title: 39


title: 341583


title: A2780_PAR_Exosome, Biological rep. 1

description:
Epithelial
miRNA


title: YCV_G


title: 38


title: A2780_PAR_CELL, Biological rep. 2

description:
Epithelial
miRNA

source_name: A2780-PAR Cell


title: 341581

source_name: Depleted Plasma


title: A2780_PAR_CELL, Biological rep. 1

description:
Epithelial
miRNA


title: 37


title: 341549


title: A2780_CP20_CELL, Biological rep. 2

description:
Epithelial
miRNA

source_name: A2780-CP20 Cell


title: A2780_CP20_CELL, Biological rep. 1

description:
Epithelial
miRNA


title: 341584


title: YUIV_D


title: YUIV_G


title: HEYA8_MDR_Exosome, Biological rep. 1

description:
Epithelial
miRNA


title: YCIII_D


title: YCIV_D


title: 36


title: YCIV_G


title: HEYA8_MDR_CELL, Biological rep. 2

description:
Epithelial
miRNA

source_name: HEYA8-MDR Cell


title: 341547


title: 34


title: HEYA8_MDR_CELL, Biological rep. 1

description:
Epithelial
miRNA


title: YCIII_G


title: 341527


title: HEYA8_Exosome, Biological rep. 1

description:
Epithelial
miRNA


title: 32


title: 341528


title: YCI_D


title: YUIII_D


title: YCI_G


title: 27


title: HEYA8_CELL, Biological rep. 1

description:
Epithelial
miRNA

source_name: HEYA8 Cell


title: 341509


title: 341493


title: 341492


title: 23

value: Asian or Pacific Islander


title: 22


title: 25

value: Black or African-American


title: 341479


title: SKOV3_TR_Exosome, Biological rep. 1

description:
Epithelial
miRNA


title: 341477


title: 19


title: SKOV3_TR_CELL, Biological rep. 1

description:
Epithelial
miRNA

source_name: SKOV3-TR Cell


title: HEYA8_CELL, Biological rep. 2

description:
Epithelial
miRNA


title: 29


title: SKOV3_TR_CELL, Biological rep. 2

description:
Epithelial
miRNA


title: 341424


title: YUI_D


title: 341425


title: YUIII_G


title: SKOV3_ip1_CELL, Biological rep. 2

description:
Epithelial
miRNA

source_name: SKOV3-ip1 Cell


title: 16


title: YUI_G


title: 341422


title: SKOV3_ip1_Exosome, Biological rep. 1

description:
Epithelial
miRNA


title: H10180_Exosome, Biological rep. 1

source_name: H10180 Exosome


title: 14

value: Other


title: 341410


title: 15


title: SKOV3_ip1_CELL, Biological rep. 1

description:
Epithelial
miRNA


title: 13


title: H10180_Exosome, Biological rep. 2


title: 8


title: 341366


title: 341317


title: 341402


title: 341316


title: 6


title: 7


title: 341315


title: 4


title: 341296


title: 341295


title: 20


title: 2


title: reoxygenation 8 hours I

city: Maastricht

first: Michiel

last: Adriaens

address: Universiteitssingel 60

department: Maastricht Centre for Systems Biology - MaCSBio

country: Netherlands

institute: Maastricht University

hyb_protocol: According to manufacturer’s protocol

scan_protocol: According to manufacturer’s protocol

data_processing: Data preprocessing and data analysis were done with R (http://www.R-project.org; version 2.15) using Bioconductor (http://www.bioconductor.org; version 2.11). Data were background-corrected using gcRMA(Wu et al. 2004) and normalized using GRSN rank-invariant normalization  (Pelz et al. 2008). Updated ENSEMBL based probe set annotation was used from Brain Array (http://brainarray.mbni.med.umich.edu/brainarray/).

label_protocol: According to manufacturer’s protocol

growth_protocol: MCF7 (human mammary adenocarcinoma) were cultured at 37°C, 5% CO2, 100% humidity in Dulbecco's Modified Eagle Medium:Nutrient Mixture F-12 (DMEM/F12 1:1; MCF7) and DMEM McCoy’s 5A medium (DU145). The culture medium was supplemented with 10% fetal calf serum (FCS), 200 mM L-glutamine and antibiotics.

extract_protocol: MCF7 cells were transferred to hypoxic culturing conditions for the indicated durations and immediately fixed to avoid reoxygenation. After 24 hours of hypoxia, cells were reoxygenated for 8 hours. Cells were disrupted by sonication. RNA for microarray application was isolated using RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol.

treatment_protocol: For hypoxic exposure, cells were transferred to a MACS VA500 microaerophilic workstation (Don Whitley Scientific, Shipley, UK) for the indicated duration. The atmosphere in the chamber consisted of <0.02% O2, 5% H2, 5% CO2, and 74% N2.

tag: oxygen state

value: normoxia

tag: timepoint

value: 32 hours

tag: oxygen concentration


title: reoxygenation 8 hours II


title: 08HBOV

first: Yasushi

last: Shibata

state: Washington

address: 1122 NE Boat Street

department: SAFS

institute: University of Washington

description: This sample is of isolated Oryzias latipes ovarian follicles at 8 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

hyb_protocol: Hybridization was performed by Roche Diagnostics K.K., Tokyo, Japan following their standard operating protocol.

scan_protocol: Scanning was performed by Roche Diagnostics K.K., Tokyo, Japan, following their standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization, and background correction as implemented in the DEVA software version 1.2 (Roche NimbleGen, Inc.).

organism: Oryzias latipes

source_name: Isolated ovarian follicles at 8 hr before spawning stage

label_protocol: Labeling was performed by Roche Diagnostics K.K., Tokyo. Labeled cDNA was synthesized by using NimbleGen One-Color DNA Labeling Kit (Roche NimbleGen Inc., Madison, WI) including Cy3 Random Nonamers and Klenow enzyme (3'->5' exo-) according to the manufacturer’s instructions.

growth_protocol: Medaka (Oryzias latipes) were maintained under the reporoductive condition (at 27°C, 14-hr light/10-hr dark). The ovaries were removed from females at each smpling time. The ovaries were dissected and the largest and second-largest ovarian follicles were isolated at each time point.

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

value: ovary

value: follicles

tag: developmental stage

value: 8 hr before spawning


title: YUII_D

value: Wistar


title: hypoxia 8 hours III

value: hypoxia

value: 8 hours


title: hypoxia 24 hours I

value: 24 hours


title: 14HBOV

description: This sample is of isolated Oryzias latipes ovarian follicles at 14 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

source_name: Isolated ovarian follicles at 14 hr before spawning stage

value: 14 hr before spawning


title: 02HBOV

description: This sample is of isolated Oryzias latipes ovarian follicles at 5 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

source_name: Isolated ovarian follicles at 2 hr before spawning stage

value: 2 hr before spawning


title: 32HBOV

description: This sample is of isolated Oryzias latipes ovarian follicles at 32 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

source_name: Isolated ovarian follicles at 32 hr before spawning stage

value: 32 hr before spawning


title: 341245

value: Yes

value: Depleted Plasma


title: hypoxia 8 hours II


title: 341278


title: 23HBOV

description: This sample is of isolated Oryzias latipes ovarian follicles at 23 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

source_name: Isolated ovarian follicles at 23 hr before spawning stage

value: 23 hr before spawning


title: hypoxia 24 hours II


title: 341199


title: 341184


title: 47HBOV

description: This sample is of isolated Oryzias latipes ovarian follicles at 47 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

source_name: Isolated ovarian follicles at 47 hr before spawning stage

value: 47 hr before spawning


title: hypoxia 8 hours I


title: normoxia III

value: 0 hours


title: 341105


title: hypoxia 24 hours III


title: 35HBOV

description: This sample is of isolated Oryzias latipes ovarian follicles at 35 hour before spawning stage. Hundred ovarian follicles of this stage were collected and total RNAs were extructed.

source_name: Isolated ovarian follicles at 35 hr before spawning stage

value: 35 hr before spawning


title: normoxia II

value: normoxia


title: 341093


title: 340995

value: No


title: 340996


title: 340986


title: 340994


title: 341082


title: 341107


title: 340989


title: reoxygenation 8 hours III

value: 32 hours


title: 340985


title: mutant RAW cell (Mut#1)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Mus musculus

source_name: ENU-mutated macrophage-like cell line

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: RAW cells were cultured in RPMI-1640 with 10 % FCS.

extract_protocol: 18-28 ug of Total RNA could be extracted from two million parental or mutant RAW cells by using RNeasy Micro kit (Quiagen).

treatment_protocol: After treatmentof parental RAW cell with ENU (1 mg/ml), mutant RAW cell lines were developed by sorting the mutated cells which did not internalize fluorescence-conjugated peroxiredoxin protein and following limiting dilution.

tag: genotype/variation

value: Msr1 and Mafb deficient


title: mutant RAW cell (Mut#2)


title: 340981


title: 340984


title: mutant RAW cell (Mut#3)


title: 340980


title: Boosted_rep5

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

hyb_protocol: hybridization, washing and staining were performed using an Affymetrix GeneTitan system

scan_protocol: scanning was performed using an Affymetrix GeneTitan system

data_processing: Affymetrix CEL files were analyzed in R using the Bioconductor suite of packages. Raw probe signals were background-corrected using the maximum likelihood estimation of the normal-exponential mixture model and normalized using the variance stabilization normalization, followed by quantile normalization. For summarization, probe signals for each probe set of each sample were summarized into a single value using the summarization step of the Robust Multichip Average (RMA) approach

source_name: Boosted NP-specific plasma cells

label_protocol: total RNA was reverse transcribed into double-stranded cDNA in a two-step process, introducing a SPIA tag sequence. Bead-purified cDNA was amplified by a SPIA amplification reaction followed by an additional bead purification. 3 µg of SPIA cDNA were fragmented and terminally biotin-labeled according to the standard Affymetrix protocol

growth_protocol: Cells have been stimulated in vivo and no further in vitro treatment has been applied before extract preparation.

extract_protocol: After pelleting, the RNAprotect buffer was replaced by RLT Plus buffer (Qiagen) and the samples were homogenized by vortexing for 1 min. Genomic DNA contamination was removed using gDNA Eliminator spin columns (Qiagen). After addition of ethanol, the samples were applied to RNeasy MinElute spin columns (Qiagen) followed by several washing steps. Finally total RNA was eluted in 12 μl of nuclease-free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent).

treatment_protocol: The control group is constituted of NP-specific plasma cells sorted from mice primed with NP-dextran and boosted with PBS 60 days later. The boosted group is constituted of NP-specific plasma cells sorted from mice primed with NP-dextran/CpG and boosted with NP-dextran 60 days later

value: bone marrow


title: Boosted_rep4


title: Boosted_rep3


title: Boosted_rep2


title: Control_rep5

source_name: Control NP-specific plasma cells


title: Control_rep4


title: normoxia I


title: Boosted_rep1


title: Control_rep1


title: Control_rep3


title: RAW cell (parental)

source_name: macrophage-like cell line

value: parental


title: Control_rep2


title: supT1_infected_30h_rep2

status: Public on Oct 31 2016

city: Gent

first: Wim

last: Trypsteen

state: East-Flanders

address: Corneel Heymanslaan 10

department: Internal Medicine

country: Belgium

institute: UGent

hyb_protocol: 600 ng of each ofthe cRNA samples was fragmented at 60°C for 30 min in total volume of 25 µL with 10X Blocking Agent and 25X fragementation buffer. Afterwere hybridized to the microarray slides for 18 hours in a hybridization oven rotator (Agilent) at 65 °C. Next, microarray slides were washed three times with gene expression washing buffers 1 and 2 (Agilent) containing 0.005% Triton X-102 for 1 min at RT and 1 min 37°C respectively. At last, samples are dried immediately by brief centrifugation.

scan_protocol: SureScan Microarray Scanner (Agilent) using one color scan setting: AgilentG3_GX_1Color.

data_processing: Processing of the raw fluorescent microarray signals was performed with the Bioconductor R package limma (v3.20.9). Background correction and quantile normalization between arrays was applied for all 16 samples.

source_name: SupT1 (T cell line)

label_protocol: 100 ng total RNA was used per sample as input for the generation of fluorescent complementary RNA (cRNA). This involved cDNA synthesis and amplification with simultaneous incorporation of cyanine 3-labeled CTP by the T7 RNA polymerase. Subsequently, the cRNA was purified with the RNeasy kit (Qiagen) as instructed by the manufacturer’s protocol and RNA concentrations measured by NanoDrop ND-1000 (Thermo Scientific).

extract_protocol: Total RNA extraction by Trizol Reagent (Invitrogen) according to manufacturer's protocol.

treatment_protocol: (72 x 5x10^6) SupT1 cells were either mock infected or infected with 15 µg p24 equivalent of an HIV-based vector (NL4.3Δenv::eGFP, VSV.G pseudotyped) by spinoculation at 1500 g for 30 min at room temperature in presence of 5 µg/ml polybrene (Sigma). After spinoculation, cells were washed and refreshed with culture medium (R-10). Subsequently, every two hours post infection, a fraction (3 x 10^6) of mock infected and infected SupT1 cells were washed with PBS and collected together with supernatant, until the 30 hour time point was reached.

value: T cell line SupT1

tag: infection

value: HIV infected (NL4.3Δenv::eGFP, VSV.G pseudotyped)

tag: time

value: 30 h post infection


title: supT1_infected_18h_rep2

value: 18 h post infection


title: supT1_infected_2h_rep1

value: 2 h post infection


title: supT1_uninfected_18h_rep2

value: uninfected


title: supT1_uninfected_6h_rep2

value: 6 h post infection


title: supT1_infected_18h_rep1


title: supT1_infected_6h_rep2


title: supT1_uninfected_30h_rep2


title: supT1_infected_30h_rep1


title: supT1_uninfected_18h_rep1


title: supT1_uninfected_2h_rep1


title: supT1_uninfected_30h_rep1


title: Rb1_+/+_L3

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

country: Canada

institute: Western University

description:
Wild-type control matched to LL mutant
E1694

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics

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

data_processing: CEL files were converted to expression values using Partek Genomics suite

source_name: Arrested MEF RNA

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: MEFs grown in DMEM supplimented with 10% FBS until passage 4

extract_protocol: Total RNA was extracted according to Trizol manufacturer protocol, then re-precipitated with sodium acetate and 100% ethanol

treatment_protocol: Cytostasis achieved with 0.1% FBS for 72 hours

tag: genotype

tag: growth condition

value: serum starved

value: Mouse embryonic fibroblasts


title: supT1_uninfected_6h_rep1


title: supT1_infected_2h_rep2


title: supT1_uninfected_2h_rep2


title: Rb1_L/L_2

description:
Mutant
E1696

value: Rb1 L/L mutant


title: Rb1_+/+_L2

description:
Wild-type control matched to LL mutant
E1693


title: Rb1_L/L_3

description:
Mutant
E1697


title: Rb1_+/+_S3

description:
Wild-type control matched to SS mutant
E0982


title: Rb1_+/+_L1

description:
Wild-type control matched to LL mutant
E1692


title: AT3G5Cs 18

city: Canoas

first: Lindolfo

last: da Silva Meirelles

state: RS

address: Av. Farroupilha 8001

department: PPGBioSaúde

country: Brazil

institute: Lutheran University of Brazil

description: freshly isolated adipose tissue 3G5+/CD31- cells, donor 18

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the “Gene Expression Hybridization Kit” (Agilent, 5188-5242). After posthybridization washes (“Wash Buffers 1 and 2 Kit”, Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies).

data_processing: Images were analyzed with the software “Agilent Feature Extraction 11.5” and parameter values were extracted. To compare data from the two microarray design IDs, one tab-delimited text file corresponding to each design was selected to define probes common to both using Microsoft Excel’s VLOOKUP function after filtering out probes corresponding to controls. Since both designs contain a nonmatching number of repeated probes, the resulting probe list had duplicate probes removed by checking the option “unique records only” in Excel’s advanced filter. The resulting unique probe list, which contained 18,561 probes, was used as a reference to remove probes (and their associated parameter values) which were not shared by both designs using Excel’s VLOOKUP function after organizing probe names in ascending order. Excel’s advanced filter was used to remove non-unique probes, and data files were used for downstream analyses. Analyses were performed using using BRB-ArrayTools (version 4.3.1) developed by Dr. Richard Simon and the BRB-ArrayTools Development Team, available at http://linus.nci.nih.gov/BRB-ArrayTools.html. Data files were imported to BRB-ArrayTools using its general format importer tool. The unique ID was defined as the probe name, the intensity value was set as the processed signal of the green channel (gProcessedSignal column), the column gIsFeatNonUnifOL was set as a flag and the column gNumPix was set as the spot size descriptor. Expression data were converted to log2 values and subjected to quantile normalization. Whenever samples were grouped, log2 expression values for each probe were averaged within each group.

source_name: AT3G5Cs from donor 18

label_protocol: Cy3-labelled cRNA was generated using the “Quick Amp Labeling Kit, one-color” (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (“One Color RNA Spike-In Kit”, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

growth_protocol: Human subcutaneous adipose tissue was enzymatically disaggregated. Adipose tissue-derived 3G5+CD31- cells (AT3G5Cs) were isolated from the stromal-vascular fraction by fluorescence-activated cell sorting.

extract_protocol: Total RNA was extracted using TRIzol (Life Technologies) following the manufacturer's instructions. RNA was further cleaned up using was cleaned up using the RNeasy mini kit (QIAGEN)  prior to Cy3 labelling.

treatment_protocol: RNAs from AT3G5Cs were extracted for microarray analyses.

tag: donor id

value: Adipose tissue


title: Rb1_+/+_S2

description:
Wild-type control matched to SS mutant
E0981


title: Rb1_L/L_1

description:
Mutant
E1695


title: Rb1_S/S_2

description:
Mutant
E0984

value: Rb1 S/S mutant


title: WP3-4°C/25°C-rep5

status: Public on Oct 01 2016

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

description:
4C-cy5+25C-cy3.gpr
WP3 cDNA at 4°C was labled with Cy5 and WP3 cDNA at 25°C was labled with Cy3

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
For every microarray slide, there are 16416 spots, which were divided into 48 blocks. For every block, there are 18 columns and 19 rows.
16416=48*18*19.
There are 3 spots for a single gene on a single microarray slide, thus we get 3 ratios of the expression level of this gene in 2 samples (rep1, rep2 and rep3).
As dye-swaps were performed (label cDNA with different fluorecent dye), we can get another 3 ratios of the expression level of this gene in 2 samples (rep4, rep5 and rep6).
Taken together, for each experiment, we can get 6 ratios of the expression level of one single gene (rep1, rep2 and rep3 from one microarray slides and rep4, rep5 and rep6 from another microarray slides).
The raw data of these two microarray slides are recorded in 4C-cy3+25C-Cy5.gpr and 4C-cy5+25C-Cy3.gpr, respectively.

S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) at 4°C and 25°C, respectively.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: protocol

value: WP3 cells were cultured at 4°C in 2216E medium

value: WP3 cells were cultured at 25°C in 2216E medium


title: WP3-4°C/25°C-rep3

description:
4C-cy3+25C-cy5.gpr
WP3 cDNA at 4°C was labled with Cy3 and WP3 cDNA at 25°C was labled with Cy5


title: WP3-4°C/25°C-rep2


title: NSF5_a18-4-1

status: Public on Mar 07 2016

type: SRA

city: Raleigh

first: Vincent

middle: L

last: Chiang

state: NC

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

library_source: transcriptomic

data_processing:
Six to twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for Illumina GAIIx or HiSeq 2000 sequencing
68 to 100 bp average read lengths were obtained.  After removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: Populus trichocarpa gene model name (version 3)
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts

organism: Populus trichocarpa

source_name: Stem differentiating xylem

growth_protocol: P. trichocarpa Wild type and transgenic trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 6 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation. Due to limited greenhouse space, different batch of transgenic trees with respective wild type were planted in soil and harvest at different time, there are total six batch trees were labeled with NSF1 to NSF6

extract_protocol:
Stem defferentiating xylem were scraped from the surface of the debark stem using a single-edge razor into liquid nitrogen immediately. collected tissues were ground into powder and stored in liquid nitrogen. Total RNA of SDX sample were extracted by uing Qiagen RNeasy Mini Kit (Invitrogen/Life Technologies, Grand Island, NY) with DNase I treatment option as suggested by kit manunal.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Agrobacterium mediated transformation of binary vector to knockdown or overexpression target genes driven by xylem specific promoter of 4-coumarate:CoA ligase gene[EU603323]

tag: gene perturbation type

value: knockdown of HCT6

tag: batch of trees

value: Stem differentiating xylem


title: WP3-4°C/25°C-rep4


title: WP3-4°C/25°C-rep6


title: supT1_infected_6h_rep1

tag: cell line


title: AT3G5Cs 17

description: freshly isolated adipose tissue 3G5+/CD31- cells, donor 17

source_name: AT3G5Cs from donor 17

tag: tissue

tag: cell type

value: Adipose tissue-derived 3G5+CD31- cells (AT3G5Cs)


title: Human primary keratinocytes, vehicle treated, bio rep 2

status: Public on May 01 2016

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

description: Gene expression data from vehicle treated-cultured human epidermal primary keratinocytes for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Affymetrix Expression Console software 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: Cultured human primary epidermal keratinocytes, vehicle treated, 24 hours

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

growth_protocol: Normal human keratinocytes (NHK) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

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

treatment_protocol: At passge 2, when NHKs were confluent in culture, 200 μM of formaldehyde were treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

tag: cell

value: human epidermal keratinocytes

tag: treatment

value: vehicle for 24 hours


title: Rb1_S/S_1

description:
Mutant
E0983


title: Rb1_+/+_S1

description:
Wild-type control matched to SS mutant
E0980


title: Rb1_S/S_3

description:
Mutant
E0985


title: WP3-4°C/25°C-rep1


title: Human primary keratinocytes, vehicle treated, bio rep 1


title: HCLE_LB control 2

status: Public on Dec 31 2015

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: LB control 2

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

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

data_processing:
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.
GCOS 1.4 signal intensity. Presence/Absence flags for all 6 samples, and Increase/Decrease/No Change flags for all 15 pairwise comparisons were also provided (available in the 'complete_processed_data.txt).

source_name: HCLE_LB control

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:
HCLE (Gipson lab): Human corneal limbal epithelial (HCLE) cells (Gipson et al., 2003 PMID:12766048) were cultured at 37°C (5% CO2) in keratinocyte serum free medium (KSFM) containing penicillin, streptomycin, 0.2 ng/ml embryonic growth factor (EGF), and 25 ug/ml bovine pituitary extract.
Serratia marcescens PIC3611: Overnight bacterial cultures were prepared by inoculating a single colony of bacteria into 5 ml LB broth (0.5% yeast extract, 1% tryptone, 0.5% NaCl) with shaking incubation for 18-20 h at 30 C.   Bacterial cultures were normalized by dilution to O.D.600 = 2.0 with LB broth, and bacteria were removed by centrifugation for 2 min at 16,000 x g. Supernatant was filtered  (0.22 um PVDF filter) prior to use.

extract_protocol: Cells were then treated with Sigma RNA later and RNA was extracted using a Sigma GenElute Mammalian total RNA miniprep kit followed by a Zymo RNA clean up kit according to manufacturer’s protocols

treatment_protocol: HCLE cells  in KSFM were seeded into 12 well dishes at a density of 1.2 x 10^4 cells per well. After 24h in culture,  KSFM was removed from the confluent cells and replaced with fresh medium containing 500 uL filtered bacterial supernatant or with 500 uL LB medium.  After 5h medium was removed and the cells washed once with PBS.

value: immortalized human corneal-limbal epithelial (HCLE) cells

tag: culture medium

value: KSFM+LB


title: HCLE_LB control 1

description: LB control 1


title: H10_1_MS

status: Public on Feb 15 2016

city: Tartu

first: Triin

last: Laisk-Podar

address: Puusepa 8

department: Obstetrics and Gynecology

country: Estonia

institute: University of Tartu

description:
Endometrium from patients without endometriosis
SAMPLE 13

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The raw data were subject to quality control using the standard protocols suggested for the bioconductor R package minfi. Probes containing SNP sites, probes with the detection p-value > 0.01 in more than one sample and probes with the beadcount <3 in at least 5% of the samples  were removed using bioconductor champ package. The remaining probes were normalized for adjusting type1 and type2 probes using Beta-Mixture Quantile (BMIQ) normalization method.

label: Cy3, Cy5

source_name: Endometrium

label_protocol: According to Illumina protocol

extract_protocol: Genomic DNA was isolated using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions

tag: patient id

tag: condition

value: without endometriosis

tag: menstrual phase

value: Mid secretory

value: endometrium


title: H7_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 9


title: H22_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 16


title: H13_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 8


title: H14_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 1


title: H9_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 12


title: H20_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 7


title: H16_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 14


title: H11_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 6


title: H21_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 10


title: H12_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 4


title: H15_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 2


title: H6_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 3


title: H19_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 17


title: H17_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 15


title: H18_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 11


title: NHEK51

status: Public on Aug 27 2015

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: Gene expression data from NHEKs

hyb_protocol: Each sample was hybridized to Human Genome Array U133 Plus 2.0 according to Affymetrix GeneChip Analysis Technical Manual.

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

data_processing: Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control hybridization process and in summarizing probe cell intensity data. After hybridization, quality was checked with AGCC and Expression ConsoleTM 1.1. The data were normalized to remove variation between samples caused by non-biological reasons. Normalization of the array was performed using GCRMA. Data were subjected to statistical analysis with Chipster (CSC-IT Center for Science, Ltd, Espoo, Finland). R package Limma was used for performing the statistical analysis between the groups.

source_name: Normal human epidermal keratinocyte 51

label_protocol: Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol for GeneChip® expression analysis technical manual with specific protocols for using the GeneChip hybridization, wash and stain kit.

growth_protocol: NHEKs and cSCC cell lines were cultured and incubated at 37C.

extract_protocol: Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water ( Qiagen Rneasy kit, Qiagen GmbH, Hilden, Germany)

treatment_protocol: NHEK and cSCC cell lines were serum starved for 24 hours and the cell lysates were harvested.

value: keratinocyte


title: normal_N5

status: Public on Oct 01 2015

city: Wuhan

first: Juncheng

last: Wei

address: Jiefang Dadao 1095

department: Department of Obstetrics and Gynecology

institute: Huazhong University of Science and Technology

description: Gene expression data from normal breast tissues

hyb_protocol: The biotin-labeled cRNA (15µg) was mixed with 6µl of 59 fragmentation buffer and adjusted to a final volume of 30 µl. The fragmented cRNA was hybridized at 45℃ for 16 h onto a human genome U133 Plus 2.0 array in a 300µl hybridization reaction containing 0.05 nM control oligonucleotide, 1× eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/ml herring sperm DNA, 0.5 mg/ml BSA, and 1× hybridization buffer. After hybridization, the arrays were washed with 2× SSC with 0.05% SDS at room temperature for 2 min, 1× SSC at room temperature for 2 min, and three times with 0.2× SSC at 50℃ for 1 min.

scan_protocol: The arrays with hybridization probes were scanned with the Affymetrix® GeneChip Scanner 3000.

data_processing: The scanned images data were analyzed using GeneChip Expression Analysis Software and Microsoft Access.

source_name: Normal breast tissues

label_protocol: The resulting dsDNA was extracted as previously described,and was now ready for biotinylation. The second in vitro transcription (IVT) reaction was performed to produce biotin-labeled cRNA from the dsDNA.

growth_protocol: Normal breast tissues and invasive primary breast carcinoma tissues were obtained from patients undergoing surgery.

extract_protocol: Total RNA from the captured LECs was isolated using RNAqueous_-Micro Kit (Ambion, USA), according to manufacturer’s instructions for LCM-derived small samples. Owing to the small starting amounts of total RNA (10–100 ng), two rounds of cDNA synthesis and in vitro transcription (IVT) amplification were performed in order to produce sufficient amounts of labeled antisense RNA (aRNA) targets for microarray analysis.

treatment_protocol: After the fresh tissues were cut into several pieces (approximately 1.0 ×1.0 × 0.5 cm3) and fixed immediately in RNALater solution in the operating room, the fixed samples were preserved at -80℃.

value: breast

value: lymphatic endothelium

tag: diagnosis

value: normal


title: NHEK42

description: Gene expression data from NHEKs

source_name: Normal human epidermal keratinocyte 42


title: NHEK65

description: Gene expression data from NHEKs

source_name: Normal human epidermal keratinocyte 65


title: NHEKPC

description: Gene expression data from NHEKs

source_name: Normal human epidermal keratinocyte PC


title: H8_1_MS

description:
Endometrium from patients without endometriosis
SAMPLE 5


title: Elder with Sepsis 3

status: Public on Jun 10 2015

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

institute: University of São Paulo

description: Biological replicate 3 of 6: Elderly with sepsis  vs. common reference

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent  Microarray Hybridization Chamber. After hybridization, slides were washed sequentially.

scan_protocol: Slides were read on a SureScan Microarray Scanner (Agilent, USA).

data_processing: Images were processed using the Feature Extraction Software v12 (Agilent, USA) for quality control, determination of feature intensities and ratios, and for background correction. The flag 'IsWellAboveBG'  in the FE output was used to select probes whose intensity were within a 99% confidence interval of being well above the background levels. 16698 out of 58717 probes with valid 'Well Above Background' flag  in both Cy3 and Cy5 channels in at least 5 out of 6  replicates of at least one group (elderly sepsis, elderly healthy, adult  sepsis, adult healthy)  were further analyzed.

source_name: Elder with Sepsis 3

label_protocol: 200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

growth_protocol: Neutrophils were isolated from blood samples immediately after the collection using a Ficoll gradient and stored at −80°C.

extract_protocol: Total RNA was isolated using Trizol reagent (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s protocol.

tag: age

value: neutrophil granulocytes

source_name: common reference RNA pool

tag: sample type

value: cyanine-5 labeled reference RNA (Universal Human Reference RNA, Agilent, cat #740000)


title: Elder with Sepsis 1

description: Biological replicate 1 of 6: Elderly with sepsis  vs. common reference

source_name: Elder with Sepsis 1


title: Elder with Sepsis 4

description: Biological replicate 4 of 6: Elderly with sepsis  vs. common reference

source_name: Elder with Sepsis 4


title: Elder with Sepsis 5

description: Biological replicate 5 of 6: Elderly with sepsis  vs. common reference

source_name: Elder with Sepsis 5


title: Elder with Sepsis 2

description: Biological replicate 2 of 6: Elderly with sepsis  vs. common reference

source_name: Elder with Sepsis 2


title: Elder with Sepsis 6

description: Biological replicate 6 of 6: Elderly with sepsis  vs. common reference

source_name: Elder with Sepsis 6


title: Healthy Elder 5

description: Biological replicate 5 of 6: healthy Elderly  vs. common reference

source_name: Healthy Elder 5


title: Healthy Elder 3

description: Biological replicate 3 of 6: healthy Elderly  vs. common reference

source_name: Healthy Elder 3


title: Healthy Elder 6

description: Biological replicate 6 of 6: healthy Elderly  vs. common reference

source_name: Healthy Elder 6


title: Healthy Elder 4

description: Biological replicate 4 of 6: healthy Elderly  vs. common reference

source_name: Healthy Elder 4


title: Healthy Elder 2

description: Biological replicate 2 of 6: healthy Elderly  vs. common reference

source_name: Healthy Elder 2


title: Adult with Sepsis 5

description: Biological replicate 5 of 6: Adult with sepsis  vs. common reference

source_name: Adult with Sepsis 5


title: Adult with Sepsis 6

description: Biological replicate 6 of 6: Adult with sepsis  vs. common reference

source_name: Adult with Sepsis 6


title: Healthy Elder 1

description: Biological replicate 1 of 6: healthy Elderly  vs. common reference

source_name: Healthy Elder 1


title: Adult with Sepsis 4

description: Biological replicate 4 of 6: Adult with sepsis  vs. common reference

source_name: Adult with Sepsis 4


title: Adult with Sepsis 3

description: Biological replicate 3 of 6: Adult with sepsis  vs. common reference

source_name: Adult with Sepsis 3


title: Adult with Sepsis 1

description: Biological replicate 1 of 6: Adult with sepsis  vs. common reference

source_name: Adult with Sepsis 1


title: NHEK59

description: Gene expression data from NHEKs

source_name: Normal human epidermal keratinocyte 59


title: SLE 7 (LN)

status: Public on Jan 06 2016

city: Kuwait

first: Suad

last: AlFadhli

address: Jabriya

department: Medical laboratory Sciences

country: Kuwait

institute: Kuwait University

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Kuwait University Research  Core Facility.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara, USA), following manufacture's protocol.

data_processing:
Data analysis was carried out using GeneSpring 12.5GX (Agilent) software. Data quality was evaluated by Principle component analysis (PCA) and any outlier sample was identified and removed. Normalization was carried out using Robust Multi-array Average (RMA) method on core probsets and baseline to median summarization was performed. At exon level, only probesets characterized by detection above background signal (DABG) p value <0.05 in atleast 50% of the samples in either group were accepted for subsequent analysis. Alternate splicing events between patients and control subjects were characterized by “Splice index (SI) model” (Affymerix Inc., 2006, Gardina et al., 2006). It is represented as the log ratio of the gene normalized intensity (NI) between the two tested sample groups. NI in turn indicates the ratio of exon-level probe set expression to gene-level transcript cluster expression. To identify the significant alternatively spliced genes, splicing ANOVA with Benjamini and Hochberg false discovery rate (FDR) correction was employed on gene normalized intensities of the tested sample groups. True positives with a p ≤0.05, SI 0.05 and Fold change (FC)>1 were considered as alternatively spliced.
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: Lupus nephritis

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Blood samples were collected from patients and healthy subjects in EDTA treated tubes and placed on ice.

extract_protocol: RNA was extracted from 2 ml of whole blood using QIAamp® RNA Blood Mini kit (Qiagen, Germany) following the manufacture’s protocol. Extracted RNA was further purified using DNase (Qiagen) to remove potential genomic DNA contamination. RNA integrity was determined by Agilent Bioanalyzer 2100 (Agilent, CA, USA). Total RNA samples with a RNA integrity number (RIN) greater than 7 were used. RNA (100ng) from each sample was processed using Ambion expression kit (Life technologies, USA).

tag: subject status

value: Lupus nephritis patient

tag: gender

value: female

value: blood


title: Adult with Sepsis 2

description: Biological replicate 2 of 6: Adult with sepsis  vs. common reference

source_name: Adult with Sepsis 2

source_name: common reference RNA pool


title: SLE 5

source_name: Lupus

value: Lupus patient


title: HC 2

source_name: Healthy control

value: Healthy control


title: Healthy Adult 6

description: Biological replicate 6 of 6: healthy Adult  vs. common reference

source_name: Healthy Adult 6


title: Healthy Adult 3

description: Biological replicate 3 of 6: healthy Adult  vs. common reference

source_name: Healthy Adult 3


title: SLE 6 (LN)


title: Healthy Adult 2

description: Biological replicate 2 of 6: healthy Adult  vs. common reference

source_name: Healthy Adult 2


title: SLE 2


title: Healthy Adult 1

description: Biological replicate 1 of 6: healthy Adult  vs. common reference

source_name: Healthy Adult 1


title: SLE 3


title: SLE 1


title: Normal Lacrimal gland 17_17ANo

status: Public on Jun 06 2015

city: Portland

first: James

last: Rosenbaum

state: OR

address: 3181 SW Sam Jackson Park Road

department: Casey Eye Institute

institute: Oregon Health & Science University

description:
17ANo
Gene expression data from biopsies

hyb_protocol: Biotin-labeled cDNA targets were hybridized with a GeneChip Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) according to standard Affymetrix protocol. Following hybridization, arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays scanned using the GeneChip Scanner 3000 7G system (Affymetrix) and Affymetrix GeneChip Command Console (AGCC) v. 3.1.1

data_processing: Initial quality control analysis was performed using Affymetrix Expression Console v. 1.1 software. Affymetrix CEL files preprocessed by the Robust Multi-array Analysis algorithm for R for expression analysis.

source_name: Lacrimal gland

label_protocol: Approximately 20 to 50 ng of RNA were amplified and  labeled with the SensationPlus FFPE Amplification and 3’ IVT Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: After deparaffinization, total RNA was extracted from tissue sections with the miRNeasy FFPE kit (Qiagen, Valencia, CA).

treatment_protocol: Biopsies were formalin-fixed and paraffin-embedded

value: Normal

value: Female

value: Lacrimal gland


title: Healthy Adult 4

description: Biological replicate 4 of 6: healthy Adult  vs. common reference

source_name: Healthy Adult 4


title: Normal Lacrimal gland 19_19ANo

description:
19ANo
Gene expression data from biopsies


title: Normal Lacrimal gland 15_15ANo

description:
15ANo
Gene expression data from biopsies


title: HC 3


title: Human primary keratinocytes, vehicle treated, biological replicate 1

status: Public on Oct 02 2014

description: Gene expression data from vehicle treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, vehicle treated, 24 hours

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

treatment_protocol: At passge 2, when NHKs were confluent in culture, cytokines were treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

value: human epidermal keratinocytes


title: Normal Lacrimal gland 20_20ANo

description:
20ANo
Gene expression data from biopsies

value: Male


title: HC 1


title: Normal Lacrimal gland 25_25ANo

description:
25ANo
Gene expression data from biopsies


title: Normal_MS 36A5

status: Public on Mar 18 2014

city: Boston

first: M. Simo

last: Arredouani

state: MA

address: 330 Brookline Ave.

department: Surgery

institute: Beth Israel Deaconess Medical Center

description: MS 36A5

hyb_protocol: cRNA (15 μg) was fragmented and hybridized to arrays according to the manufacturer's (Ambion® | Life Technologies) protocols.

scan_protocol: GeneArray Scanner G2500A (Hewlett-Packard)

data_processing: BioConductor R packages

source_name: benign tissue

label_protocol: Biotin-UTP was incorporated during the overnight in vitro transcription step according to the manufacturer's (Ambion® | Life Technologies) protocol.

growth_protocol: A biopsy punch was used to select the PCa tissues from the OCT prostate sample blocks.

extract_protocol: Total RNA was isolated using Trizol reagent. RNA was quantified by NanoDrop ND-1000 spectrophotometer, and quality was evaluated with Agilent RNA 6000 NanoChip and the 2100 Bioanalyzer, with 28S/18S ratios and RIN determined by 2100 Expert software.

treatment_protocol: Benign or PCa tissues were homogenized using a TissueLyser (Qiagen) at 28 Hz for 5 min.

tag: tissue type

value: Benign prostate tissue


title: Normal_MS 36D4

description: MS 36D4


title: Normal Lacrimal gland 22_22ANo

description:
22ANo
Gene expression data from biopsies


title: Human primary keratinocytes, vehicle treated, biological replicate 2


title: Normal Lacrimal gland 18_18ANo

description:
18ANo
Gene expression data from biopsies


title: Normal_MS 36C6

description: MS 36C6


title: Normal_MS 36A4

description: MS 36A4


title: Normal_MS 36D3

description: MS 36D3


title: LSG excised from healthy volunteer, clinical sample2

status: Public on Jun 23 2014

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description:
Gene expression data from labial salivary gland biopsy
HC_2

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with Factor Analysis for Robust Microarray Summarization (FARMS), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: labial salivary gland excised from healthy volunteer

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

extract_protocol: Total RNA was isolatedusing Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: The tissues were immersed in RNAlater (Ambion, Austin, USA) immediately after excision, then treated as per the manufacturer's protocols.

value: labial salivary gland


title: SLE 4


title: LSG excised from healthy volunteer, clinical sample3

description:
Gene expression data from labial salivary gland biopsy
HC_3


title: LSG excised from healthy volunteer, clinical sample1

description:
Gene expression data from labial salivary gland biopsy
HC_1


title: Normal_MS 36C7

description: MS 36C7


title: Normal_MS 36D5

description: MS 36D5


title: SLE 8 (LN)


title: lc_330

status: Public on Jan 22 2013

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina whole-genome DASL Assay System Manual.

data_processing: For each probe, replicate mesurements were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.

source_name: liver cirrhosis

extract_protocol: Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using TRIzol LS (Invitrogen).

value: liver biopsy specimen

tag: prediction

value: Good prognosis

tag: prediction confidence p-value

tag: prediction (p<0.05)

tag: presence of varices

tag: bilirubin ≥ 1.0mg/dl

tag: platelet < 100,000/mm3

tag: days to death

tag: death

tag: days to decomp

tag: decomp

tag: days to child

tag: child

tag: days to hcc

tag: hcc


title: lc_320

scan_protocol: Refer to the Illumina whole-genome DASL Assay System Manual.

tag: tissue

value: Poor prognosis

value: Intermediate prognosis


title: Normal prostate

status: Public on Mar 12 2013

city: Nankoku

first: Kenji

last: Tamura

state: Kochi

address: Kohasu, Oko-cho

department: Urology

institute: Kochi University

description: Normal prostatic epithelial cells that were microdissected from normal prostate tissue, procured by needle biopsy.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Analysis Technical Manual, 701021 Rev. 5)

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The scanned images were analyzed using the GeneChip operating software version 1.4 (Affymetrix 690036) with Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling was used as normalization method. The trimmed mean target intensity of each array was set to 500. Differentially expressed genes were extracted using DNA microarray viewer (Kurabo, osaka, Japan)

source_name: clinical normal prostatic epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 5).

extract_protocol: 100,00-200,000 tumor cells or normal cells were isolated selectively using the EZ cut system with a pulsed ultraviolet narrow beam-focus laser in accordance with the manufacturer’s protocols. RNA for microarray analysis was isolated with TRIzol reagent (Life Technologies, Rockville, MD, USA)  and purified with the RNeasy MiniElute kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: normal prostate (NP) epithelial cells


title: lc_315

label_protocol: Refer to the Illumina whole-genome DASL Assay System Manual


title: lc_329


title: lc_309


title: lc_310


title: lc_314


title: lc_313


title: lc_318


title: lc_305


title: lc_316


title: lc_322


title: lc_311


title: lc_319


title: lc_306


title: Healthy Adult 5

description: Biological replicate 5 of 6: healthy Adult  vs. common reference

source_name: Healthy Adult 5

tag: age

tag: cell type

value: neutrophil granulocytes

tag: sample type

value: cyanine-5 labeled reference RNA (Universal Human Reference RNA, Agilent, cat #740000)


title: lc_328

tag: prediction

tag: prediction confidence p-value


title: lc_303

tag: prediction (p<0.05)

tag: presence of varices


title: lc_324

tag: bilirubin ≥ 1.0mg/dl

tag: platelet < 100,000/mm3


title: lc_301

tag: days to death

tag: death


title: lc_307

tag: days to decomp

tag: decomp


title: lc_312

tag: days to child

tag: child


title: lc_317

tag: days to hcc

tag: hcc


title: lc_296

tag: tissue


title: lc_302


title: lc_308


title: lc_304


title: lc_294


title: lc_295


title: lc_297


title: lc_284


title: lc_291


title: lc_286


title: lc_290