title: 242_437374_P16_H112811

tag: bmi


title: 239_437377_P16_H112811

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: ethnicity

value: White

tag: hormone replacement therapy

value: No

tag: tissue

value: Depleted Plasma


title: 244_436977_P16_H112811


title: UMichTumor19_copy_number

type: genomic

city: Boston

first: Tony

middle: Edward

last: Godfrey

state: Massachusetts

address: 700 Albany Street

department: Surgery

institute: Boston University

description: Michigan 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: M

tag: diagnosis

value: Cancer

tag: tumor histology

value: Adeno

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

value: III

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: UMichTumor18_copy_number

description: Michigan patient tumor

value: I


title: 238_437389_P16_H112811

tag: age

tag: bmi


title: 257_440417_P21_H112911

tag: ethnicity

tag: hormone replacement therapy

value: Yes


title: UMichTumor25_copy_number

description: Michigan patient tumor

tag: tissue

tag: gender

value: IIA


title: UMichTumor16_copy_number

description: Michigan patient tumor

value: F

tag: diagnosis

tag: tumor histology


title: 233_437398_P16_H112811

value: Non-white


title: 227_437588_P13_H112311


title: 235_437392_P16_H112811


title: UMichTumor14_copy_number

description: Michigan patient tumor

tag: t-stage

tag: n-stage


title: 226_436707_P13_H112311


title: UMichTumor13_copy_number

description: Michigan patient tumor

tag: m-stage

tag: overall stage

value: IIB


title: UMichTumor15_copy_number

description: Michigan patient tumor

tag: neoadjuvant therapy

tag: perioperative death


title: 232_437597_P13_H112311


title: 223R_437479_P17_H010512


title: UMichTumor11_copy_number

description: Michigan patient tumor

tag: vital status

tag: OS time


title: UMichTumor12_copy_number

description: Michigan patient tumor

tag: recurrence status

tag: dfs time


title: 221R_437515_P17_H010512

tag: age

tag: bmi


title: 220_439129_P19_H112211

tag: ethnicity

tag: hormone replacement therapy


title: UMichTumor10_copy_number

description: Michigan patient tumor

tag: tissue

tag: gender


title: UMichTumor8_copy_number

description: Michigan patient tumor

tag: diagnosis

tag: tumor histology


title: UMichTumor9_copy_number

description: Michigan patient tumor

tag: t-stage

tag: n-stage


title: 218_439122_P19_H112211


title: 212_439104_P19_H112211


title: 214_439110_P19_H112211


title: UMichTumor7_copy_number

description: Michigan patient tumor

tag: m-stage

tag: overall stage


title: UMichTumor6_copy_number

description: Michigan patient tumor

value: IV

tag: neoadjuvant therapy

tag: perioperative death


title: UMichTumor5_copy_number

description: Michigan patient tumor

tag: vital status

tag: OS time


title: UMichTumor17_copy_number

description: Michigan patient tumor

tag: recurrence status

tag: dfs time


title: 208_438928_P19_H112211

tag: age

tag: bmi


title: 206_438925_P19_H112211

tag: ethnicity

tag: hormone replacement therapy


title: UMichTumor3_copy_number

description: Michigan patient tumor

tag: tissue

tag: gender


title: 203_438909_P19_H112211


title: UMichTumor4_copy_number

description: Michigan patient tumor

tag: diagnosis

tag: tumor histology


title: UMichTumor2_copy_number

description: Michigan patient tumor

tag: t-stage

tag: n-stage


title: UMichTumor1_copy_number

description: Michigan patient tumor

tag: m-stage

tag: overall stage


title: 198_438850_P24_H112111


title: 187_438820_P24_H112111


title: 184_438832_P24_H112111


title: 190_439289_P24_H112111


title: 195_439253_P24_H112111


title: 192_439295_P24_H112111


title: 182_439439_P19_H111811


title: 179_439436_P19_H111811


title: 177_439430_P19_H111811


title: 176_439425_P19_H111811


title: 168_439404_P19_H111811


title: 171_439407_P19_H111811


title: 210_438934_P19_H112211


title: 160_438129_P20_H111711


title: 161_438250_P19_H111811


title: 158_438135_P20_H111711


title: 163_438303_P19_H111811


title: 166_439589_P19_H111811


title: 153_438144_P20_H111711


title: 199_438841_P24_H112111


title: 193R_437527_P17_H010512


title: 152_438150_P20_H111711


title: 148_434715_P20_H111711


title: 139_438122_P20_H111711


title: 144_434712_P20_H111711


title: 173_439413_P19_H111811


title: 133_438854_P23_H111611


title: 131_438860_P23_H111611


title: GMTMM-iCMs from TTFs (FBS)

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: GMTMM-iCMs from TTFs (FBS)

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.

molecule: total RNA

organism: Mus musculus

source_name: iCMs

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: The cells were cultured under serum-containing (FBS), serum-free (SF), or FGF2, FGF10, and VEGF (FFV) containing medium to generated induced cardiomyocytes (iCMs).

extract_protocol: RNA samples were extracted from cells using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012).

value: cardiomyocyte-like cells (iCMs)


title: 130_438857_P23_H111611


title: 150_437287_P20_H111711


title: 127_438872_P23_H111611


title: MT-iCMs (FFV)

description: MT-iCMs (FFV)


title: GMTMM-iCMs from TTFs (FFV)

description: GMTMM-iCMs from TTFs (FFV)


title: 126_438869_P23_H111611


title: 146_434709_P20_H111711


title: 123_440228_P23_H111611


title: iCM_4wk_FFV


title: heart (E12)

description: heart (E12)

source_name: heart

value: heart


title: 122_440231_P23_H111611

value: White


title: fibroblasts (TTFs)

description: fibroblasts (TTFs)

source_name: fibroblast

value: fibroblast


title: VD49V

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

description:
depigmented
illumina total RNA amplification kit from Ambion was used as per manufacturer protocol, for cDNA synthesis and RNA amplification

hyb_protocol: hybridization performed as per manufacturer's instructions (illumina)

scan_protocol: scanning performed as per manufacturer's instructions (illumina)

data_processing: Data was processed using bead studio module with average normalization after background subtration

label: biotin

source_name: Lesional Skin

label_protocol: labelling was performed as per instructions by manufacturer's using the Illumina total prep RNA labelling kit from Ambion

extract_protocol: Total RNA was isolated from cells using trizol method, isopropanol precipitated RNA was column purified using Qiagen RNA purification kit

treatment_protocol: 1.50 micro gram of each sample was hybridised to illumina's Sentrix Human-6 Expression BeadChips, Ver.3 ( cat no BD-101-0603) at 58 degree C overnight 18 h according to Illumina Whole-Genome Expression Direct Hybridization protocol, revision A

value: Lesional Vitiligo Skin


title: 141_434320_P20_H111711

value: Depleted Plasma


title: heart (P1)

description: heart (P1)


title: 120_440216_P23_H111611


title: fibroblasts (MEFs)

description: fibroblasts (MEFs)


title: 118_440014_P23_H111611


title: iCM_4wk_SF


title: VD49N

source_name: Normal Skin

value: Normal Vitiligo Skin


title: 115_440562_P21_H111511


title: iCM_4wk_FBS


title: VD44V

description:
pigmented
illumina total RNA amplification kit from Ambion was used as per manufacturer protocol, for cDNA synthesis and RNA amplification


title: iCM_2wk_FFV


title: 114_440568_P21_H111511


title: VD44N


title: 109_440478_P21_H111511


title: iCM_2wk_SF


title: VD40V


title: 107_439118_P21_H111511


title: VD40N


title: 104_440620_P21_H111511

value: No


title: 101_440605_P21_H111511


title: 98_440602_P21_H111511


title: 96_440690_P21_H111511


title: 100_440608_P21_H111511


title: VD38V


title: meningioma sample Jed70_MN

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description: GSE77259_GSM2046770; Gene expression data from primary brain tumor

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings.

source_name: meningioma, fibroblastic histology

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

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked using the Agilent Bioanalyzer.

tag: grade


title: 93_437075_P16_H111411


title: 92R_437524_P17_H010512


title: 88_437969_P16_H111411


title: 89_437962_P16_H111411


title: 112_440553_P21_H111511


title: 85_437975_P16_H111411


title: 82_436983_P16_H111411


title: VD38N


title: VD39V


title: 79_437052_P16_H111411


title: VD39N


title: iCM_2wk_FBS


title: meningioma sample Jed49_MN

description: GSE77259_GSM2046765; Gene expression data from primary brain tumor

source_name: meningioma, atypical histology

value: II


title: VD37V


title: 78_437076_P16_H111411


title: VD37N


title: 76_437054_P16_H111411


title: VD33V


title: VD33N


title: 74_437065_P16_H111411


title: 71_437786_P16_H111011


title: 70_437783_P16_H111011


title: 67_437795_P16_H111011


title: 66_437955_P16_H111011


title: 84_437984_P16_H111411


title: 63_437904_P16_H111011


title: 62_437902_P16_H111011


title: follicular variant PTC sample TM-301-12R-THY

description: GSE54958_GSM1327271; Gene expression data from follicular variant PTC

source_name: follicular variant PTC histology

value: III


title: 137_438445_P23_H111611


title: 53_436954_P16_H110111


title: 60R_437530_P17_H010512


title: VD32V


title: VD22N


title: PTC sample TM-279-08R-THY

description: GSE54958_GSM1327247; Gene expression data from PTC

source_name: PTC histology

value: M


title: PTC brain metastasis sample, Jed51_MTT

description:
Sample name: BT-51R
Gene expression data from brain metastasis from PTC


title: VD32N


title: follicular variant PTC sample TM-989-11R-THY

description:
Sample name: TM-989-11R
Gene expression data from FVPTC
same raw data as GSM1327273


title: VD24V


title: PTC brain metastasis sample, Jed51_MTT (tech repl)

description:
Sample name: BT-51R (tech repl)
Gene expression data from brain metastasis from PTC


title: 58_437996_P16_H111011


title: 55_437999_P16_H111011

value: Yes


title: PTC sample TM-892-11R-THY

description:
Sample name: TM-892-11R
Gene expression data from PTC
same raw data as GSM1327253


title: VD23V


title: 52_436952_P16_H111011


title: PTC sample TM-602-11R-THY

description:
Sample name: TM-602-11R
Gene expression data from PTC
same raw data as GSM1327248


title: VD24N


title: VD23N


title: PTC sample TM-824-12R-THY

description:
Sample name: TM-824-12R
Gene expression data from PTC
same raw data as GSM1327250


title: 49_438005_P17_H110911


title: PTC sample TM-187-11R-THY

description:
Sample name: TM-187-11R
Gene expression data from PTC
same raw data as GSM1327245


title: 47_437713_P17_H110911


title: 45_437718_P17_H110911


title: 39_439103_P21_H110811


title: VD22V


title: 38_439106_P21_H110811


title: 41_437654_P17_H110911


title: 36_439250_P21_H110811


title: 34_438369_P21_H110811


title: VD20V


title: VD20N


title: 29_439301_P21_H110811


title: 27_439670_P21_H110811


title: 25_439664_P21_H110811


title: 19_437913_P16_H110711


title: 24_439667_P21_H110811


title: 18R_437536_P17_H010512


title: 16_437925_P16_H110711


title: 14_437079_P16_H110711


title: 11_437083_P16_H110711


title: 10_437082_P16_H110711


title: 8_437086_P16_H110711


title: 5_437103_P16_H110711


title: 4_437101_P16_H110711


title: VD19V


title: VD13N


title: VD13V


title: VD19N


title: VD18V


title: VD18N


title: C57, morphine 3

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

description:
Prefrontal cortex from morphine-treated C57 mouse.
C57_M3

hyb_protocol: Cy3-labeled miRNA samples were hybridized in a reaction volume of 45 µl containing 1x Hi-PRM hybridization buffer and 1x GE blocking agent following the manufacturer's instructions. The mixed samples were hybridized to Agilent Human miRNA Microarrays (G4112A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (scan area: 61 x 21.6 mm, scan resolution: 5 µm, Dye channel: Green, Green PMT: XDR Hi 100%, Lo 5%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters for miRNA array to obtain background subtracted and spatially detrended Processed Signal intensities. The feature extraction files were imported to Agilent's GeneSpring program for data analysis. The quantile normalization and log transformation were applied to get the normalized data across the 8 arrays.

source_name: prefrontal cortex, morphine treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 250 ng RNA using Agilent's miRNA Complete Labeling according to the manufacturer's instructions. T4 RNA ligase and Cy-3-pCp were used for labeling the miRNA samples. The labeled RNA samples were purified by Micro Bio-Spin 6 column.

growth_protocol: Not applicable; these are tissue samples.

extract_protocol: RNA was prepared using the miRNeasy kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The protocol includes homogenization of prefrontal cortex samples, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were treated with saline or morphine.

tag: strain/background

value: prefrontal cortex

tag: treatment

value: morphine


title: C57, morphine 2

description:
Prefrontal cortex from morphine-treated C57 mouse.
C57_M2


title: 2_437147_P16_H110711


title: 22_437910_P16_H110711


title: C57, morphine 1

description:
Prefrontal cortex from morphine-treated C57 mouse.
C57_M1


title: 599

value: White (not of Hispanic origin)


title: BM_ctrl_Neu_5

city: St. Louis

first: Xiaodi

last: Wu

state: Missouri

address: 4940 Parkview Pl

institute: Washington University/HHMI

hyb_protocol: Biotinylated cRNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix)

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner

data_processing: Expression values were analyzed after RMA background correction and quantile normalization using ArrayStar software (DNASTAR)

source_name: BM neutrophil, Zeb2-sufficient

label_protocol: Target preparation was performed using the Ovation PicoSL kit (NuGEN)

growth_protocol: Mice were bred and maintained in a specific pathogen–free animal facility according to institutional guidelines and under approved protocols

extract_protocol: Total RNA was isolated from cells using an RNAqueous-Micro Kit (Ambion)

treatment_protocol: Mice were either untreated or treated twice within 48 h, each time with 150 ug poly(I:C) by intraperitoneal injection; bone marrow was collected three weeks later by brief centrifugation of dissected bones

tag: cell type

value: neutrophil

tag: genotype

tag: genetic background


title: BM_CKO_Neu_4

source_name: BM neutrophil, Zeb2-deficient


title: BM_ctrl_Neu_4


title: 598

tag: age

tag: bmi


title: 593

tag: ethnicity

tag: hormone replacement therapy


title: C57, saline 3

description:
Prefrontal cortex from saline-treated C57 mouse.
C57_S3

source_name: prefrontal cortex, saline treatment

tag: tissue

value: saline


title: C57, morphine 4

description:
Prefrontal cortex from morphine-treated C57 mouse.
C57_M4


title: C57, saline 4

description:
Prefrontal cortex from saline-treated C57 mouse.
C57_S4


title: 591


title: UPittRef15_copy_number

description: Pittsburgh patient normal

source_name: White blood cells

value: White blood cells

tag: gender

tag: diagnosis

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: C57, saline 1

description:
Prefrontal cortex from saline-treated C57 mouse.
C57_S1

tag: strain/background

tag: treatment


title: 590


title: UPittRef14_copy_number

description: Pittsburgh patient normal

tag: tumor histology

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage


title: 588

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi


title: BM_ctrl_Mo_5

source_name: BM Ly-6C(hi) monocyte, Zeb2-sufficient

tag: cell type

value: Ly-6C(hi) monocyte

tag: genotype

tag: genetic background


title: BM_CKO_Neu_3


title: 587

source_name: Depleted Plasma

tag: tissue


title: BM_ctrl_Mo_4


title: UPittRef12_copy_number

description: Pittsburgh patient normal

tag: gender

tag: diagnosis

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status


title: BM_CKO_Mo_4

source_name: BM Ly-6C(hi) monocyte, Zeb2-deficient

tag: treatment


title: BM_CKO_Mo_3


title: BM_ctrl_Neu_3


title: 584


title: C57, saline 2

description:
Prefrontal cortex from saline-treated C57 mouse.
C57_S2

tag: strain/background


title: UPittRef11_copy_number

description: Pittsburgh patient normal

tag: tumor histology

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: dfs time


title: 583

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi


title: UPittRef9_copy_number

description: Pittsburgh patient normal

tag: tissue

tag: gender

tag: diagnosis

tag: neoadjuvant therapy


title: 582

value: Asian or Pacific Islander


title: UPittRef10_copy_number

description: Pittsburgh patient normal

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status


title: 577


title: BM_ctrl_Neu_2

tag: cell type

tag: genotype

tag: treatment

tag: genetic background


title: UPittRef13_copy_number

description: Pittsburgh patient normal

tag: tumor histology

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: dfs time


title: UPittRef7_copy_number

description: Pittsburgh patient normal

tag: tissue

tag: gender


title: UPittRef6_copy_number

description: Pittsburgh patient normal

tag: diagnosis

tag: neoadjuvant therapy


title: BM_CKO_Neu_1


title: 572

tag: age

tag: ethnicity

value: Black or African-American

tag: hormone replacement therapy

tag: bmi


title: BM_ctrl_Mo_2

tag: cell type

tag: genotype


title: BM_CKO_Mo_2

tag: treatment

tag: genetic background


title: 570


title: 569


title: UPittRef4_copy_number

description: Pittsburgh patient normal

tag: tumor histology

tag: t-stage

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status


title: UPittRef3_copy_number

description: Pittsburgh patient normal

tag: tissue

tag: gender

tag: n-stage

tag: m-stage

tag: overall stage

tag: dfs time


title: UPittRef8_copy_number

description: Pittsburgh patient normal

tag: diagnosis

tag: neoadjuvant therapy


title: 566

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi


title: BM_ctrl_Neu_1

tag: cell type

tag: genotype

tag: treatment

tag: genetic background


title: UPittRef2_copy_number

description: Pittsburgh patient normal

tag: tumor histology

tag: t-stage

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status


title: 563

tag: tissue


title: BM_ctrl_Mo_1


title: BM_ctrl_Mo_3


title: 575


title: 560


title: BM_CKO_Mo_1


title: Spleen_ctrl_CD172a_DC_4

source_name: Spleen CD172a(+) classical dendritic cells, Zeb2-sufficient

treatment_protocol: Spleens were minced and digested in Iscove's modified Dulbecco's medium + 10% fetal bovine serum supplemented with 250 ug/ml collagenase B (Roche) and 30 U/ml DNase I (Sigma-Aldrich) for 30 min to 1 h at 37 °C with stirring

value: CD172a(+) classical dendritic cell


title: BM_CKO_Neu_2


title: UPittTumor116_copy_number

description: Pittsburgh patient tumor

source_name: Esophagus tumor tissue

value: Esophagus tumor tissue

tag: gender

value: Female

tag: diagnosis

value: Cancer

value: Adeno

tag: n-stage

tag: m-stage

tag: overall stage

value: IIA

value: FALSE

value: Dead

tag: dfs time


title: Spleen_CKO_CD172a_DC_4

source_name: Spleen CD172a(+) classical dendritic cells, Zeb2-deficient

tag: cell type


title: UPittRef5_copy_number

description: Pittsburgh patient normal

tag: neoadjuvant therapy


title: Spleen_CKO_CD172a_DC_3

tag: genotype


title: 559

tag: age

tag: ethnicity

tag: hormone replacement therapy

value: Yes

tag: bmi

value: Depleted Plasma


title: 574

value: No


title: UPittTumor114_copy_number

description: Pittsburgh patient tumor

tag: tumor histology

tag: t-stage

tag: perioperative death

tag: vital status

value: Alive


title: UPittTumor113_copy_number

description: Pittsburgh patient tumor

tag: tissue

tag: gender

value: Male

value: III

tag: OS time

tag: recurrence status


title: UPittRef1_copy_number

description: Pittsburgh patient normal

value: White blood cells

tag: diagnosis

tag: n-stage

tag: m-stage

tag: overall stage


title: 553

value: White (not of Hispanic origin)


title: 551


title: UPittTumor111_copy_number

description: Pittsburgh patient tumor

tag: neoadjuvant therapy

tag: dfs time


title: UPittTumor112_copy_number

description: Pittsburgh patient tumor

value: I


title: 550

tag: age

tag: ethnicity


title: UPittTumor110_copy_number

description: Pittsburgh patient tumor

value: TRUE


title: 548

tag: hormone replacement therapy

tag: bmi


title: 546


title: UPittTumor109_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: tumor histology

tag: t-stage


title: UPittTumor115_copy_number

description: Pittsburgh patient tumor

value: Female

tag: perioperative death

tag: vital status


title: UPittTumor108_copy_number

description: Pittsburgh patient tumor

tag: tissue

tag: gender

value: Cancer


title: 555


title: Spleen_CKO_CD172a_DC_2

tag: cell type

value: CD172a(+) classical dendritic cell

tag: genotype

tag: genetic background


title: 545


title: 557


title: 544


title: Spleen_ctrl_CD24_DC_2

source_name: Spleen CD24(+) classical dendritic cells, Zeb2-sufficient

value: CD24(+) classical dendritic cell


title: UPittTumor107_copy_number

description: Pittsburgh patient tumor

tag: diagnosis

value: Adeno

tag: n-stage

tag: m-stage

value: IIB

value: FALSE

tag: OS time

tag: recurrence status


title: UPittTumor106_copy_number

description: Pittsburgh patient tumor

tag: overall stage

tag: neoadjuvant therapy

value: Dead

value: Yes

tag: dfs time


title: 541

tag: age

tag: ethnicity

tag: hormone replacement therapy

value: No

tag: bmi

value: Depleted Plasma


title: Spleen_ctrl_CD24_DC_3


title: Spleen_CKO_CD172a_DC_1


title: UPittTumor105_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Male

tag: tumor histology

tag: t-stage

value: IIA

tag: perioperative death

tag: vital status

value: Alive


title: Spleen_ctrl_CD172a_DC_2

tag: cell type

tag: genotype

tag: genetic background


title: Tg26-Lymphoma_6_rep2

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: Hybridization for Tg26-Lymphoma_6 ; batchB ; Lymphoma ; Lymph Node

hyb_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST Array were employed for all hybridizations. All experiments were performed at the Microarray Core facility of the Institute of Human Virology, University of Maryland, Baltimoreof, MD, according to the manufacturer’s instructions..

data_processing: Affymetrix microarray data were normalized at probe-level by using the Frozen Robust Multiarray Analysis (fRMA) method (packages: frma_1.20.0 and MoGene.1.0.st.v1frmavecs_1.1.0).

source_name: Hybridization for  Tg26-Lymphoma_6

growth_protocol: In this experiments heterozygous mice were used since homozygotes rarely survive to weaning. The colony developing leukemia/lymphoma was generated by cross-breeding heterozygous mice with skin lesions. Mice were euthanized at 5-12 months of age. All mice used were on the FVB/N background (Harlan). All animal studies were conducted at the Animal Care Facility of the Institute of Human Virology, University of Maryland, Baltimore, MD, and were approved by and conducted in accordance with Animal Care and Use Committee oversight.

extract_protocol: Total cellular RNA was prepared from spleen and lymph nodes from 3 groups of animals: FVB/N controls (n=3), Tg26 asymptomatic (n=6), and Tg26 with lymphoma (n=6) was isolated and subjected to a cleanup protocol with RNeasy mini kits (Qiagen), according to the manufacturer’s specifications. The quality of total RNA was assessed using an Agilent Bioanalyzer 2100.

treatment_protocol: Tg26 carries a pNL4-3 HIV-1 provirus lacking part of the gag-pol region, rendering the virus non-infectious. About 15% of the TG26 mice develop lymphoma)

tag: batch

tag: disease status

value: Lymph Node

tag: background strain

value: FVBN


title: Spleen_ctrl_CD172a_DC_3


title: UPittTumor104_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: gender

tag: diagnosis

tag: n-stage

tag: m-stage

tag: overall stage

value: III

tag: neoadjuvant therapy

tag: OS time

tag: recurrence status


title: 540

tag: age

tag: ethnicity

value: White (not of Hispanic origin)

tag: hormone replacement therapy

tag: bmi

tag: tissue


title: Spleen_ctrl_CD24_DC_1

tag: cell type

tag: genotype

tag: genetic background


title: Tg26-Lymphoma_4_rep2

description: Hybridization for Tg26-Lymphoma_4 ; batchB ; Lymphoma ; Lymph Node

scan_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST Array were employed for all hybridizations. All experiments were performed at the Microarray Core facility of the Institute of Human Virology, University of Maryland, Baltimoreof, MD, according to the manufacturer’s instructions..

source_name: Hybridization for  Tg26-Lymphoma_4

tag: batch

tag: disease status

tag: background strain


title: UPittTumor103_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

value: Cancer

tag: tumor histology

tag: t-stage

tag: n-stage

tag: perioperative death

tag: vital status

tag: dfs time


title: 537

tag: age

tag: ethnicity

value: Asian or Pacific Islander

tag: hormone replacement therapy


title: 539

tag: bmi

tag: tissue


title: Spleen_ctrl_CD172a_DC_1

tag: cell type

value: CD172a(+) classical dendritic cell

tag: genotype

tag: genetic background


title: 533


title: Tg26-Lymphoma_5_rep2

description: Hybridization for Tg26-Lymphoma_5 ; batchB ; Lymphoma ; Lymph Node

source_name: Hybridization for  Tg26-Lymphoma_5

label_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST Array were employed for all hybridizations. All experiments were performed at the Microarray Core facility of the Institute of Human Virology, University of Maryland, Baltimoreof, MD, according to the manufacturer’s instructions.

tag: batch

tag: disease status

tag: background strain


title: Tg26-Asymptomatic_5_rep2

description: Hybridization for Tg26-Asymptomatic_5 ; batchB ; NoTumor ; Spleen

source_name: Hybridization for  Tg26-Asymptomatic_5

value: Spleen


title: UPittTumor102_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: tumor histology

value: Adeno

tag: m-stage

tag: overall stage

value: IIB

tag: neoadjuvant therapy

value: Chemo

value: FALSE

tag: OS time

tag: recurrence status


title: UPittTumor101_copy_number

description: Pittsburgh patient tumor

tag: t-stage

tag: n-stage

value: No

tag: perioperative death

tag: vital status

value: Dead

value: Yes

tag: dfs time


title: UPittTumor100_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Male


title: Tg26-Asymptomatic_4_rep2

description: Hybridization for Tg26-Asymptomatic_4 ; batchB ; NoTumor ; Spleen

source_name: Hybridization for  Tg26-Asymptomatic_4

tag: batch


title: 531

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi

value: Depleted Plasma


title: Tg26-Lymphoma_6_rep1

description: Hybridization for Tg26-Lymphoma_6 ; batchB ; Lymphoma ; Spleen

tag: disease status

tag: background strain

value: FVBN


title: UPittTumor99_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: gender

tag: diagnosis

tag: tumor histology

tag: m-stage

tag: overall stage

value: I


title: 530

value: White (not of Hispanic origin)


title: PTC sample TM-1039-11R-THY

description:
Sample name: TM-1039-11R
Gene expression data from PTC
same raw data as GSM1327240

source_name: PTC histology

tag: grade

value: IV

value: F


title: Tg26-Lymphoma_3_rep2

description: Hybridization for Tg26-Lymphoma_3 ; batchA ; Lymphoma ; Lymph Node

source_name: Hybridization for  Tg26-Lymphoma_3

value: Lymph Node


title: Tg26-Asymptomatic_6_rep2

description: Hybridization for Tg26-Asymptomatic_6 ; batchB ; NoTumor ; Spleen

source_name: Hybridization for  Tg26-Asymptomatic_6

value: Spleen


title: Tg26-Lymphoma_2_rep2

description: Hybridization for Tg26-Lymphoma_2 ; batchA ; Lymphoma ; Lymph Node

source_name: Hybridization for  Tg26-Lymphoma_2


title: 529


title: UPittTumor98_copy_number

description: Pittsburgh patient tumor

value: Cancer

value: Adeno

tag: t-stage

tag: n-stage

tag: neoadjuvant therapy

tag: perioperative death

value: Alive

tag: OS time

tag: recurrence status


title: 526

tag: age

tag: ethnicity

tag: tissue


title: UPittTumor97_copy_number

description: Pittsburgh patient tumor

value: III

value: FALSE

tag: vital status

tag: dfs time


title: 524

tag: hormone replacement therapy

value: No

tag: bmi


title: 525


title: UPittTumor96_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: tumor histology

value: Dead


title: Tg26-Asymptomatic_2_rep2

description: Hybridization for Tg26-Asymptomatic_2 ; batchA ; NoTumor ; Lymph Node

source_name: Hybridization for  Tg26-Asymptomatic_2

tag: batch

tag: disease status

tag: background strain


title: UPittTumor95_copy_number

description: Pittsburgh patient tumor

value: Male

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

value: Yes


title: 522

tag: age

tag: ethnicity

value: Depleted Plasma


title: Tg26-Asymptomatic_3_rep2

description: Hybridization for Tg26-Asymptomatic_3 ; batchA ; NoTumor ; Lymph Node

source_name: Hybridization for  Tg26-Asymptomatic_3

tag: tissue

value: FVBN


title: 520

source_name: Depleted Plasma

value: Black or African-American


title: UPittTumor94_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: UPittTumor93_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: tumor histology


title: FVBN_3_rep2

description: Hybridization for FVBN_3 ; batchA ; CTRL ; Lymph Node

source_name: Hybridization for  FVBN_3

tag: batch

tag: disease status

tag: background strain


title: 519

tag: hormone replacement therapy

tag: bmi


title: 518

value: Other


title: 513

value: White (not of Hispanic origin)


title: 512


title: UPittTumor89_copy_number

description: Pittsburgh patient tumor

value: Female

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

value: I

tag: neoadjuvant therapy


title: 509

tag: age

tag: ethnicity

tag: tissue


title: UPittTumor90_copy_number

description: Pittsburgh patient tumor

value: Cancer

value: IIA

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: Tg26-Asymptomatic_3_rep1

description: Hybridization for Tg26-Asymptomatic_3 ; batchA ; NoTumor ; Spleen

tag: batch

tag: disease status

value: Spleen


title: FVBN_2_rep2

description: Hybridization for FVBN_2 ; batchA ; CTRL ; Lymph Node

source_name: Hybridization for  FVBN_2

value: Lymph Node

tag: background strain


title: 508

tag: hormone replacement therapy

tag: bmi


title: UPittTumor88_copy_number

description: Pittsburgh patient tumor

source_name: Esophagus tumor tissue

tag: gender

tag: diagnosis

tag: tumor histology

value: Adeno

tag: t-stage

tag: n-stage

value: III

value: FALSE


title: UPittTumor92_copy_number

description: Pittsburgh patient tumor

value: Male

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

value: No

value: Dead


title: Tg26-Lymphoma_2_rep1

description: Hybridization for Tg26-Lymphoma_2 ; batchA ; Lymphoma ; Spleen

tag: tissue

value: FVBN


title: 507

tag: age

tag: ethnicity

value: Depleted Plasma


title: Tg26-Lymphoma_3_rep1

description: Hybridization for Tg26-Lymphoma_3 ; batchA ; Lymphoma ; Spleen


title: UPittTumor91_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: perioperative death

tag: vital status

value: Alive

tag: OS time

tag: recurrence status

tag: dfs time


title: FVBN_3_rep1

description: Hybridization for FVBN_3 ; batchA ; CTRL ; Spleen

tag: batch

tag: disease status

tag: background strain


title: UPittTumor87_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: tumor histology

value: Yes


title: Tg26-Asymptomatic_2_rep1

description: Hybridization for Tg26-Asymptomatic_2 ; batchA ; NoTumor ; Spleen


title: Tg26-Lymphoma_5_rep1

description: Hybridization for Tg26-Lymphoma_5 ; batchB ; Lymphoma ; Spleen


title: Tg26-Lymphoma_1_rep2

description: Hybridization for Tg26-Lymphoma_1 ; batchA ; Lymphoma ; Lymph Node

source_name: Hybridization for  Tg26-Lymphoma_1


title: 505

value: White (not of Hispanic origin)

tag: hormone replacement therapy

tag: bmi


title: UPittTumor85_copy_number

description: Pittsburgh patient tumor

value: Female

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy


title: FVBN_2_rep1

description: Hybridization for FVBN_2 ; batchA ; CTRL ; Spleen

tag: tissue


title: U-2OS pmiR-199a-3p

first: Zhenfeng

last: Duan

address: 55 Fruit Street Jackson Building

institute: Massachusetts General Hospital

description: osteosarcoma cell line with pmiR-199a-3p

hyb_protocol: Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu)

scan_protocol: The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide

data_processing: Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-199a-3p treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 foldchange or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

label_protocol: To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis

growth_protocol: The U-2OS and KHOS osteosarcoma cell lines were seeded onto the 100mm cell culture plate

extract_protocol: Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions

treatment_protocol: Cell were transfected miRSelect pEP-miR-199a-3p or miRSelect pEP-miR-Null

tag: cell line

tag: cell type

value: osteosarcoma cell line

tag: miRNA


title: COLO-320DM rep1

city: Tokyo

first: Tetsuo

last: Mashima

address: 3-8-31, Ariake,Koto-ku

institute: JFCR

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: parental line COLO320

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The cell line was cultured in vitro in 10cm dishes until 80-90% confluency and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

value: Human Colon Cancer


title: 320-IWR  rep1

source_name: tankyrase inhibitor-resistant cell line 320IWR

value: COLO-320DM derived 320IWR


title: COLO-320DM rep2


title: KHOS pmiR-199a-3p

source_name: osteosarcoma cell line with pmiR-199a-3p

value: KHOS


title: 503

tag: age

tag: ethnicity


title: Tg26-Asymptomatic_1_rep2

description: Hybridization for Tg26-Asymptomatic_1 ; batchA ; NoTumor ; Lymph Node

source_name: Hybridization for  Tg26-Asymptomatic_1

tag: batch

tag: disease status

value: Lymph Node

tag: background strain


title: UPittTumor84_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

value: Cancer

tag: tumor histology

value: Adeno

value: III

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: 320-IWR  rep2


title: Tg26-Asymptomatic_1_rep1

description: Hybridization for Tg26-Asymptomatic_1 ; batchA ; NoTumor ; Spleen

tag: tissue

value: Spleen


title: Huh7-shKLHL23-rep3

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: silence KLHL23

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

label_protocol: Standard Affymetrix protocol

growth_protocol: Hep-3B and Huh7 were cultured in DMEM (Sigma-Aldrich Corporation, St. Louis, MO, USA) and contained 10% FBS and 100 mg/mL streptomycin-penicillin.

extract_protocol: Cells were washed trice with ice-cold PBS. Total RNA was extracted with TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) by following manufacturer's instructions.

treatment_protocol: The shRNA viruses for KLHL23 or control were obtained from National RNAi Core, Taiwan. In this study we used shRNA lentivirus at the multiplicity of infection (MOI) of 2 to transduce hepatoma cells. Cells were infected with shKLHL23, shEV or shLuc for 48 hrs before puromycin selection.

tag: cell line

value: Hepatoma


title: 502

tag: hormone replacement therapy

value: No

tag: bmi


title: UPittTumor83_copy_number

description: Pittsburgh patient tumor

value: Male

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

value: IIA

tag: neoadjuvant therapy

value: FALSE


title: 498

tag: age

tag: ethnicity

value: Yes

value: Depleted Plasma


title: UPittTumor86_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: gender

value: Female

tag: diagnosis

tag: tumor histology

value: Dead


title: 497

value: White (not of Hispanic origin)


title: UPittTumor82_copy_number

description: Pittsburgh patient tumor

value: I

tag: perioperative death

tag: vital status

value: Alive

tag: OS time


title: UPittTumor81_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Cancer

tag: recurrence status

tag: dfs time


title: 494

tag: hormone replacement therapy

tag: bmi


title: UPittTumor80_copy_number

description: Pittsburgh patient tumor

value: Adeno

tag: t-stage

tag: n-stage


title: 493


title: 492


title: FVBN_1_rep1

description: Hybridization for FVBN_1 ; batchA ; CTRL ; Spleen

source_name: Hybridization for  FVBN_1

tag: batch

tag: disease status

tag: background strain

value: FVBN


title: Huh7-shKLHL23-rep1

description: silence KLHL23

tag: cell line

tag: cell type


title: UPittTumor78_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy


title: Tg26-Asymptomatic_5_rep1

description: Hybridization for Tg26-Asymptomatic_5 ; batchB ; NoTumor ; Lymph Node

source_name: Hybridization for  Tg26-Asymptomatic_5

tag: tissue

value: Lymph Node


title: 490

tag: age

tag: ethnicity


title: Tg26-Asymptomatic_4_rep1

description: Hybridization for Tg26-Asymptomatic_4 ; batchB ; NoTumor ; Lymph Node

source_name: Hybridization for  Tg26-Asymptomatic_4


title: 489

tag: hormone replacement therapy


title: UPittTumor77_copy_number

description: Pittsburgh patient tumor

tag: tumor histology

value: III

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: Huh7-shLuc-rep1

description: Control

tag: cell line

value: Hepatoma


title: UPittTumor76_copy_number

description: Pittsburgh patient tumor

value: Male

tag: t-stage

tag: n-stage

value: No


title: Tg26-Asymptomatic_6_rep1

description: Hybridization for Tg26-Asymptomatic_6 ; batchB ; NoTumor ; Lymph Node

tag: batch

tag: disease status

tag: background strain


title: UPittTumor79_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

value: FALSE


title: 487

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi

tag: tissue


title: UPittTumor75_copy_number

description: Pittsburgh patient tumor

tag: tumor histology

value: IIA

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: Huh7-shLuc-rep3

description: Control

tag: cell line

tag: cell type


title: Tg26-Lymphoma_4_rep1

description: Hybridization for Tg26-Lymphoma_4 ; batchB ; Lymphoma ; Spleen

source_name: Hybridization for  Tg26-Lymphoma_4

tag: batch

tag: disease status

value: Spleen

tag: background strain


title: 485

value: Yes

value: Depleted Plasma


title: Hep-3B-shKLHL23-rep3

description: silence KLHL23


title: beta-catenin activated pancreas, biological rep2

city: Seville

first: David

last: Cano

state: Seville

address: Manuel siurot s/n

country: Spain

institute: Institute of Biomedicine of Sevilla

description: Gene expression data from E13.5  embryonic pancreas

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip® Command Console Software (AGCC) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: E13.5 embryonic pancreas

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Embyonic pancreata from control and Pdx-Cre bcatexon3  floxed embryos

extract_protocol: Extraction of total RNA was performed with the RNA Isolation Kit RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: E13.5 Embryos were manually selected under the dissecting scope. Pancreas were dissected, rinsed with PBS and processed for RNA extraction following the RNeasy Mini Kit - QIAGEN instructions

value: Embryonic pancreas

tag: genotype

value: Pdx-Cre beta catenin-exon3 floxed (active)

value: E13.5 embryonic day


title: Hep-3B-shLuc-rep3

description: Control


title: UPittTumor74_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: gender

tag: diagnosis

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

value: Alive


title: Hep-3B-shKLHL23-rep1

description: silence KLHL23


title: SK-MElL-28, siRNA for ZIC5

city: Hachioji-city

first: Reiko

last: Satow

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Science

description: cultured cells

hyb_protocol: cRNA were hybridized according to Affymetrix.

scan_protocol: GeneChips were scanned according to Affymetrix protocol.

data_processing: The data were analyzed by RMA algolism and quantile normalized using Expression Console.

source_name: SK-MEL-28 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

extract_protocol: Total RNA was isolated from cells using a ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI)

tag: transfection

value: siRNA for ZIC5


title: 483

tag: age

tag: ethnicity

value: White (not of Hispanic origin)

tag: hormone replacement therapy

tag: bmi

tag: tissue


title: beta-catenin activated pancreas, biological rep3


title: 481


title: wild type pancreas, biological rep2

value: wild type


title: wild type pancreas, biological rep3


title: 479


title: SK-MEL-28, negative control siRNA

description: cultured cells

tag: cell line

value: negative control siRNA


title: UPittTumor72_copy_number

description: Pittsburgh patient tumor

value: Cancer

tag: tumor histology

value: Adeno

value: IIB

tag: perioperative death

tag: vital status

value: Dead

tag: OS time

tag: recurrence status

tag: dfs time


title: UPittTumor71_copy_number

description: Pittsburgh patient tumor

tag: gender

value: Male

tag: diagnosis

tag: t-stage

tag: n-stage

value: I

value: No

value: TRUE


title: beta-catenin activated pancreas, biological rep1

value: Embryonic pancreas

tag: genotype


title: Hep-3B-shLuc-rep1

description: Control

tag: cell type

value: Hepatoma


title: A375, siRNA for ZIC5

description: cultured cells

source_name: A375 cells

tag: transfection


title: 478

tag: age

tag: ethnicity

tag: hormone replacement therapy

value: Depleted Plasma


title: Cal12 cells treated with control vehicle for 72 hours

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Gene expression of Cal12 cells treated with control vehicle

hyb_protocol: The cRNA was hybridized to an Affymetrix U133 2.0 Plus GeneChip arrays using the standard manufacturer's protocol.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files)

data_processing: Raw expression data were normalized and summarized using the Robust Multichip Analysis (RMA) method along with log2 transformation using the integrated BRB-Array Tools software developed by Dr. Richard Simon and the BRB-Array Tools development team.

source_name: Cal12 lung cancer cells

label_protocol: 1.0 to 2.5 μg of total RNA was used to generate biotin-labeled cRNA using the GeneChip Expression 3’-Amplification Reagents Kit (Affymetrix) per manufacturer’s protocol.

growth_protocol: Cells were cultured in  RPMI 1640 medium containing 10% fetal bovine serum and 2 mmol/L glutamine at 37°C in a humidified atmosphere of 95% air and 5% CO2

extract_protocol: Total RNA was isolated following treatments using the RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Dasatinib was prepared as 20mM stock solution in DMSO. Cells were then treated with 150 nM dasatinib or DMSO (control vehicle) for 72 hours after which total RNA was isolated.

tag: treatment

value: Control vehicle

tag: time of rna isolation after sirna transfection

value: 72 hours


title: UPittTumor70_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Esophagus tumor tissue

tag: tumor histology

tag: m-stage

tag: overall stage

value: III

tag: neoadjuvant therapy

tag: perioperative death

value: FALSE

value: Yes


title: 476

source_name: Depleted Plasma

value: White (not of Hispanic origin)

tag: bmi


title: UPittTumor69_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

value: Cancer

value: Adeno

tag: t-stage

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: UPittTumor73_copy_number

description: Pittsburgh patient tumor

tag: n-stage

value: Alive


title: 475

tag: age

tag: ethnicity

tag: hormone replacement therapy


title: 473

tag: tissue


title: 472


title: 470


title: UPittTumor67_copy_number

description: Pittsburgh patient tumor

value: Male

tag: tumor histology

tag: m-stage

value: IIA


title: UPittTumor66_copy_number

description: Pittsburgh patient tumor

tag: overall stage

value: IIB

tag: neoadjuvant therapy

value: No

value: Dead


title: UPittTumor65_copy_number

description: Pittsburgh patient tumor

tag: perioperative death


title: H661 cells treated with dasatinib for 72 hours

description: Gene expression of H661 cells treated with dasatinib

source_name: H661 lung cancer cells

tag: cell type

tag: treatment

value: 150 nM dasatinib

tag: time of rna isolation after sirna transfection


title: UPittTumor64_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: t-stage

tag: vital status


title: FVBN_1_rep2

description: Hybridization for FVBN_1 ; batchA ; CTRL ; Lymph Node

tag: batch

tag: disease status

value: Lymph Node

tag: background strain

value: FVBN


title: H1666 cells treated with dasatinib for 72 hours

description: Gene expression of H1666 cells treated with dasatinib

source_name: H1666 lung cancer cells

value: 72 hours


title: H661 cells treated with control vehicle for 72 hours

description: Gene expression of H661 cells treated with control vehicle

value: Control vehicle


title: Cal12 cells treated with dasatinib for 72 hours

description: Gene expression of Cal12 cells treated with dasatinib


title: Tg26-Lymphoma_1_rep1

description: Hybridization for Tg26-Lymphoma_1 ; batchA ; Lymphoma ; Spleen

value: Spleen


title: 465

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi

value: Depleted Plasma


title: UPittTumor63_copy_number

description: Pittsburgh patient tumor

source_name: Esophagus tumor tissue

tag: tissue

value: Esophagus tumor tissue

tag: tumor histology

tag: n-stage

tag: m-stage

tag: overall stage

value: III

value: FALSE

tag: OS time

tag: recurrence status

tag: dfs time


title: A549 cells treated with dasatinib for 72 hours

description: Gene expression of A549 cells treated with dasatinib

source_name: A549 lung cancer cells

tag: cell type

tag: treatment

tag: time of rna isolation after sirna transfection


title: 463

value: White (not of Hispanic origin)


title: A375, negative control siRNA

description: cultured cells

tag: cell line

tag: transfection

value: negative control siRNA


title: UPittTumor68_copy_number

description: Pittsburgh patient tumor

tag: gender

value: Female

tag: diagnosis

value: Cancer

value: Adeno

tag: t-stage

value: I

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status

value: Alive


title: 462

tag: age

tag: ethnicity

tag: hormone replacement therapy

value: Yes

tag: bmi

tag: tissue


title: wild type pancreas, biological rep1

value: Embryonic pancreas

tag: genotype

value: wild type

value: E13.5 embryonic day


title: A549 cells treated with control vehicle for 72 hours

description: Gene expression of A549 cells treated with control vehicle

tag: cell type

value: Control vehicle

value: 72 hours


title: H1666 cells treated with control vehicle for 72 hours

description: Gene expression of H1666 cells treated with control vehicle

tag: treatment


title: UPittTumor62_copy_number

description: Pittsburgh patient tumor

value: Male

tag: tumor histology

tag: n-stage

tag: m-stage

tag: overall stage

value: IIB

value: No

tag: OS time

tag: recurrence status

tag: dfs time


title: 469

value: Depleted Plasma


title: UPittTumor61_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: gender

tag: diagnosis

tag: t-stage

value: IV

tag: neoadjuvant therapy

tag: perioperative death

value: FALSE

value: Dead


title: 460

tag: age

tag: ethnicity

value: White (not of Hispanic origin)

tag: hormone replacement therapy

tag: bmi


title: UPittTumor60_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Cancer

value: Adenosquamous

value: III

tag: vital status


title: 458


title: UPittTumor59_copy_number

description: Pittsburgh patient tumor

tag: tumor histology

value: Adeno

tag: n-stage

value: Alive


title: UPittTumor58_copy_number

description: Pittsburgh patient tumor

tag: m-stage

tag: overall stage


title: UPittTumor54_copy_number

description: Pittsburgh patient tumor

value: Female

value: MX

tag: OS time

tag: recurrence status


title: UPittTumor57_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: dfs time


title: UPittTumor55_copy_number

description: Pittsburgh patient tumor

tag: diagnosis

tag: t-stage


title: UPittTumor56_copy_number

description: Pittsburgh patient tumor

tag: neoadjuvant therapy

tag: perioperative death


title: UPittTumor52_copy_number

description: Pittsburgh patient tumor

value: I


title: UPittTumor50_copy_number

description: Pittsburgh patient tumor


title: UPittTumor51_copy_number

description: Pittsburgh patient tumor

value: Male


title: 457

tag: age

tag: ethnicity


title: 446

tag: hormone replacement therapy

value: Yes

tag: bmi


title: 453

tag: tissue


title: 444

value: No


title: 437

value: Depleted Plasma


title: 451


title: 439


title: 449


title: 440


title: 442


title: UPittTumor53_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: tumor histology

tag: vital status


title: 431


title: 433


title: UPittTumor47_copy_number

description: Pittsburgh patient tumor

tag: n-stage

tag: m-stage

value: IIA


title: UPittTumor46_copy_number

description: Pittsburgh patient tumor

tag: overall stage

value: FALSE

tag: OS time


title: 438


title: UPittTumor48_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: recurrence status


title: UPittTumor45_copy_number

description: Pittsburgh patient tumor

tag: diagnosis

tag: dfs time


title: UPittTumor44_copy_number

description: Pittsburgh patient tumor

tag: t-stage

tag: neoadjuvant therapy

value: Dead


title: MCF-7 + 1 nM E2 + 100 nM 4-hydroxytamoxifen rep1

city: Toledo

first: Robert

middle: J

last: Trumbly

state: OH

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

description: Gene expression data from MCF-7 cells treated with 1 nM E2 + 100 nM 4-hydroxytamoxifen

hyb_protocol: The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

data_processing: Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.   The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

label_protocol: Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

growth_protocol: Cells were routinely cultured at 37°C and in 5% CO2 in DMEM supplemented with FBS (10%), penicillin (100unit/ml), streptomycin (100μg/ml) and L-glutamine (2mM). Hormone depleted cells were grown in low glucose phenol-red free media supplemented with 5% charcoal-stripped FBS (v/v) and L-glutamine (2mM) for 48 hours before the experiments

extract_protocol: Total RNA was prepared using the RNeasy Mini kit (Qiagen).

treatment_protocol: Cells were plated at 20% confluence in low glucose phenol red free medium supplemented with 5% charcoal stripped FBS and glutamine 48h prior to treatment. Cells were harvested 48 h after treatment with vehicle, E2 (1nM) or OH-Tam (100nM).

tag: cell line

tag: treatment


title: MCF-7 + 1 nM E2 + 100 nM 4-hydroxytamoxifen rep2

source_name: MCF-7 cells treated with 1 nM E2 + 100 nM 4-hydroxytamoxifen


title: MCF-7 + 1 nM E2  rep2

description: Gene expression data from MCF-7 cells treated with 1 nM E2

source_name: MCF-7 cells treated with 1 nM E2

value: treated with 1 nM E2


title: MCF-7 + 1 nM E2  rep1


title: MCF-7 +  100 nM 4-hydroxytamoxifen rep2

description: Gene expression data from MCF-7 cells treated with 100 nM 4-hydroxytamoxifen

value: treated with 100 nM 4-hydroxytamoxifen


title: MCF-7 + vehicle rep1

description: Gene expression data from MCF-7 cells treated with vehicle

source_name: MCF-7 cells treated with vehicle

value: vehicle


title: MCF-7 +  100 nM 4-hydroxytamoxifen rep1

source_name: MCF-7 cells treated with 100 nM 4-hydroxytamoxifen


title: 430

tag: age

tag: ethnicity

value: White (not of Hispanic origin)

tag: hormone replacement therapy


title: 426

value: Other

tag: bmi

tag: tissue


title: 422


title: 419


title: UPittTumor39_copy_number

description: Pittsburgh patient tumor

value: Cancer

tag: tumor histology

value: Adeno

tag: n-stage

value: IV

tag: perioperative death

tag: vital status


title: 454


title: UPittTumor42_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: m-stage

tag: overall stage

value: I

value: Alive

tag: OS time


title: 415


title: UPittTumor43_copy_number

description: Pittsburgh patient tumor

value: Male

tag: diagnosis

tag: t-stage

tag: recurrence status

tag: dfs time


title: UPittTumor41_copy_number

description: Pittsburgh patient tumor

value: Female

value: Mx

value: III

tag: neoadjuvant therapy

value: No

value: Yes


title: 413

tag: age

tag: ethnicity

value: Depleted Plasma


title: 416

tag: hormone replacement therapy

tag: bmi


title: MCF-7 + vehicle rep2

tag: cell line

tag: treatment


title: UPittTumor49_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Esophagus tumor tissue

tag: tumor histology

tag: n-stage

value: IIB

tag: perioperative death

value: FALSE


title: UPittTumor38_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: m-stage

tag: overall stage

value: IIA

tag: vital status

value: Dead


title: 409

value: Black or African-American


title: 408

value: White (not of Hispanic origin)


title: UPittTumor36_copy_number

description: Pittsburgh patient tumor

tag: diagnosis

value: Cancer

value: Adeno

tag: t-stage

value: MX

tag: OS time

tag: recurrence status


title: UPittTumor40_copy_number

description: Pittsburgh patient tumor

tag: neoadjuvant therapy

value: Alive

tag: dfs time


title: UPittTumor37_copy_number

description: Pittsburgh patient tumor

value: Male


title: UPittTumor35_copy_number

description: Pittsburgh patient tumor


title: 405

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi


title: 407

tag: tissue


title: UPittTumor34_copy_number

description: Pittsburgh patient tumor

value: Female

tag: tumor histology

tag: n-stage


title: 423


title: 404


title: 393


title: 391


title: 396


title: 398


title: 400


title: UPittTumor33_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: perioperative death


title: 395


title: 390


title: UPittTumor29_copy_number

description: Pittsburgh patient tumor

tag: m-stage

tag: overall stage

value: III


title: UPittTumor32_copy_number

description: Pittsburgh patient tumor

tag: diagnosis

value: No

tag: vital status


title: UPittTumor27_copy_number

description: Pittsburgh patient tumor

tag: t-stage

tag: OS time


title: UPittTumor28_copy_number

description: Pittsburgh patient tumor

tag: neoadjuvant therapy

tag: recurrence status

value: Yes


title: UPittTumor31_copy_number

description: Pittsburgh patient tumor

tag: dfs time


title: UPittTumor26_copy_number

description: Pittsburgh patient tumor


title: UPittTumor30_copy_number

description: Pittsburgh patient tumor

value: I


title: UPittTumor25_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

value: IV


title: 392

tag: age

tag: ethnicity

value: Depleted Plasma


title: 387

tag: hormone replacement therapy

tag: bmi


title: UPittTumor24_copy_number

description: Pittsburgh patient tumor

tag: tissue

tag: tumor histology

value: TX

value: NX

value: FALSE


title: 386

value: Black or African-American


title: 385

value: White (not of Hispanic origin)


title: 380


title: 378


title: UPittTumor20_copy_number

description: Pittsburgh patient tumor

tag: gender

value: Cancer

value: Adeno

tag: n-stage

value: Dead


title: UPittTumor21_copy_number

description: Pittsburgh patient tumor

value: Male

tag: m-stage

value: MX

tag: perioperative death


title: UPittTumor22_copy_number

description: Pittsburgh patient tumor

tag: diagnosis

tag: overall stage


title: UPittTumor19_copy_number

description: Pittsburgh patient tumor

tag: t-stage

value: III

tag: vital status


title: UPittTumor23_copy_number

description: Pittsburgh patient tumor

tag: neoadjuvant therapy

value: No

tag: OS time


title: UPittTumor18_copy_number

description: Pittsburgh patient tumor

tag: recurrence status

value: Yes

tag: dfs time


title: 375

tag: age

tag: ethnicity


title: 377

tag: hormone replacement therapy

tag: bmi


title: 374

value: Other

tag: tissue


title: 343924


title: 343921


title: UPittTumor17_copy_number

description: Pittsburgh patient tumor

value: Esophagus tumor tissue

tag: gender

tag: tumor histology

value: I


title: 254706910110_b3 - Controle2_2 vs HA2_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Identification of xenobiotic direct sensing and of low chemical stress transduction networks in Arabidopsis thaliana.

hyb_protocol: HA2_2 Cy5 / Controle2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Growth chamber 22°C/20°C under a 16h light(6000 lux)/8h dark regime. Growth medium consisted of 0.8% (w/v) agar in Hoagland basal salt mix (H2395, Sigma-Aldrich) adjusted to pH 6.

treatment_protocol: Name:Hydroxyatrazine_1µM - abiotic stress - compound addition,hydroxyatrazine:quantity 1uM time 24hour . After 13 days of growth under optimal conditions, seedlings were transferred to fresh growth medium containing pesticides during 24 h (Control, Atrazine 1µM, Hydroxyatrazine 1µM or Desethylatrazine 1µM).

tag: sample type

value: Arabidopsis thaliana (columbia)  - age 16.5day

treatment_protocol: Name:Control - abiotic stress - compound addition,none:quantity 1uM time 24hour . After 13 days of growth under optimal conditions, seedlings were transferred to fresh growth medium containing pesticides during 24 h (Control, Atrazine 1µM, Hydroxyatrazine 1µM or Desethylatrazine 1µM).


title: 372

value: Depleted Plasma


title: UPittTumor16_copy_number

description: Pittsburgh patient tumor

tag: n-stage

tag: m-stage

tag: perioperative death

value: Alive


title: fibroblasts_pre-miR-Ctrl_rep3

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from fibroblasts transfected with control oligos with scrambled sequence.

hyb_protocol: The samples were hybridized to a Human Gene 2.1 ST Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.4 and the RMA method

source_name: fibroblasts transfected with pre-miR-Ctrl

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human dermal fibroblasts were isolated from adult human skin from routine abdominal reduction plastic surgery and cultured in DMEM medium (Gibco™) supplemented with 10% heat inactivated fetal bovine serum (Gibco™) and 1% penicillin streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: 48 hours after transfection, the total RNA was extracted with miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The fourth passage fibroblasts at 60-70% confluence were transfected with 20 nM miR-132 mimics or control oligos (Ambion) using Lipofectamine 2000 (Invitrogen).

value: skin


title: fibroblasts_pre-miR-Ctrl_rep1


title: ALDH+_ID8_T47D_Exp_7

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.

source_name: Aldefluor+ cells from T47D cell line treated with ID8, experiment 7

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

tag: fraction

value: Aldefluor+

tag: experiment

tag: collected cells (x10^6)

tag: collected rna (ng)


title: UPittTumor15_copy_number

first: Tony

last: Godfrey

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_protocol: As per manufacturer (Affymetrix)

tag: diagnosis

tag: t-stage

tag: overall stage

tag: neoadjuvant therapy

value: FALSE

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: ALDH-_ID8_T47D_Exp_7

source_name: Aldefluor- cells from T47D cell line treated with ID8, experiment 7

value: Aldefluor-


title: ALDH-_ID8_T47D_Exp_6

source_name: Aldefluor- cells from T47D cell line treated with ID8, experiment 6


title: fibroblasts_pre-miR-132_rep2

description: Gene expression data from fibroblasts with miR-132 overexpression.

source_name: fibroblasts transfected with pre-miR-132

tag: tissue


title: 254706910109_b4 - ATZ2_2 vs Controle2_2

hyb_protocol: Controle2_2 Cy5 / ATZ2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: sample type

treatment_protocol: Name:Atrazine_1µM - abiotic stress - compound addition,atrazine:quantity 1uM time 24hour . After 13 days of growth under optimal conditions, seedlings were transferred to fresh growth medium containing pesticides during 24 h (Control, Atrazine 1µM, Hydroxyatrazine 1µM or Desethylatrazine 1µM).


title: 254706910109_b2 - ATZ1_1 vs Controle1_1

hyb_protocol: Controle1_1 Cy5 / ATZ1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910111_b2 - DEA1_1 vs Controle1_1

hyb_protocol: Controle1_1 Cy5 / DEA1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Desethylatrazine_1µM - abiotic stress - compound addition,desethylatrazine:quantity 1uM time 24hour . After 13 days of growth under optimal conditions, seedlings were transferred to fresh growth medium containing pesticides during 24 h (Control, Atrazine 1µM, Hydroxyatrazine 1µM or Desethylatrazine 1µM).


title: 254706910110_b4 - HA2_2 vs Controle2_2

hyb_protocol: Controle2_2 Cy5 / HA2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910110_b1 - Controle1_1 vs HA1_1

hyb_protocol: HA1_1 Cy5 / Controle1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910111_b3 - Controle2_2 vs DEA2_2

hyb_protocol: DEA2_2 Cy5 / Controle2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910109_b1 - Controle1_1 vs ATZ1_1

hyb_protocol: ATZ1_1 Cy5 / Controle1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 343888

city: Seattle

first: Paul

last: Lampe

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

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.

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

tag: bmi


title: 254706910109_b3 - Controle2_2 vs ATZ2_2

hyb_protocol: ATZ2_2 Cy5 / Controle2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 371

tag: ethnicity

value: Asian or Pacific Islander


title: ALDH-_ID8_T47D_Exp_5

source_name: Aldefluor- cells from T47D cell line treated with ID8, experiment 5

tag: cell line

tag: treatment

tag: fraction

tag: experiment


title: 343887


title: ALDH+_ID8_T47D_Exp_6

source_name: Aldefluor+ cells from T47D cell line treated with ID8, experiment 6

tag: collected cells (x10^6)

tag: collected rna (ng)


title: 254706910111_b1 - Controle1_1 vs DEA1_1

hyb_protocol: DEA1_1 Cy5 / Controle1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ALDH+_ID8_T47D_Exp_5

source_name: Aldefluor+ cells from T47D cell line treated with ID8, experiment 5


title: fibroblasts_pre-miR-132_rep3


title: 254706910110_b2 - HA1_1 vs Controle1_1

hyb_protocol: Controle1_1 Cy5 / HA1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: UPittTumor13_copy_number

city: Boston

address: 700 Albany Street

description: Pittsburgh patient tumor

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.

tag: gender

tag: diagnosis

value: Cancer

tag: tumor histology

value: Adeno

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

tag: perioperative death


title: UPittTumor14_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Male

tag: vital status

value: Dead

tag: OS time

tag: recurrence status

tag: dfs time


title: 370

source_name: Depleted Plasma

tag: age

tag: ethnicity

tag: hormone replacement therapy

tag: bmi


title: 254706910111_b4 - DEA2_2 vs Controle2_2

hyb_protocol: Controle2_2 Cy5 / DEA2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: sample type


title: fibroblasts_pre-miR-Ctrl_rep2


title: 343885


title: ALDH-_DMSO_T47D_Exp_7

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

tag: cell line

tag: treatment

value: DMSO

tag: fraction

tag: experiment

tag: collected cells (x10^6)

tag: collected rna (ng)


title: fibroblasts_pre-miR-132_rep1


title: 343880

value: No


title: ALDH-_DMSO_T47D_Exp_6

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


title: 343817


title: 364

value: White (not of Hispanic origin)


title: UPittTumor12_copy_number

description: Pittsburgh patient tumor

source_name: Esophagus tumor tissue

value: Esophagus tumor tissue

tag: gender

tag: diagnosis

tag: tumor histology

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

value: III

tag: neoadjuvant therapy

tag: perioperative death

value: Yes


title: 343881

tag: age

tag: hormone replacement therapy

tag: bmi

tag: tissue

value: Depleted Plasma


title: 361

tag: ethnicity


title: UPittTumor11_copy_number

description: Pittsburgh patient tumor

value: IIB

value: TRUE

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: 357


title: 363


title: 343814


title: UPittTumor10_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

value: I


title: ALDH-_DMSO_T47D_Exp_5

source_name: Aldefluor- cells from T47D cell line treated with DMSO, experiment 5

tag: cell line

tag: treatment

tag: fraction

tag: experiment

tag: collected cells (x10^6)

tag: collected rna (ng)


title: 343816

tag: age


title: ALDH+_DMSO_T47D_Exp_5

source_name: Aldefluor+ cells from T47D cell line treated with DMSO, experiment 5

value: Aldefluor+


title: 343807

tag: hormone replacement therapy


title: 353

tag: bmi


title: 359

tag: tissue


title: 343806


title: UPittTumor6_copy_number

description: Pittsburgh patient tumor

tag: tumor histology

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

tag: perioperative death

value: FALSE


title: 343804


title: 355

tag: ethnicity


title: 352


title: UPittTumor5_copy_number

description: Pittsburgh patient tumor

tag: gender

tag: diagnosis

tag: vital status

value: Alive

tag: OS time

tag: recurrence status

tag: dfs time


title: UPittTumor9_copy_number

description: Pittsburgh patient tumor

value: Cancer


title: 350

tag: age

tag: hormone replacement therapy


title: UPittTumor7_copy_number

description: Pittsburgh patient tumor

tag: tissue

value: Adeno