title: 101777-50

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N4856


title: 101777-12

status: Public on May 21 2014

type: RNA

city: Amsterdam

first: Michiel

middle: Emanuel

last: Adriaens

address: Meibergdreef 15

department: Experimental Cardiology

country: Netherlands

institute: AMC

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N1212

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using neqc background correction and quantile normalisation with the beadarray package in R (2.15.3).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: heart, left ventricle

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with mirVana miRNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser and spectrophotometry. The Illumina TotalPrep-96 RNA Amplification Kit was used to generate cRNA starting from 200 ng total RNA.

tag: gender

value: male

tag: tissue

value: left ventricular myocardium

tag: age

tag: center


title: 101777-110

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H36


title: 101777-07

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
4043


title: 101777-104

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
643M

value: female


title: 101777-48

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3064


title: 101777-125

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N2658


title: 101777-165

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
503M


title: 101777-46

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H45


title: 101777-58

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H47


title: 101777-23

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
916M


title: 101777-02

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
LV4


title: 101777-139

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H14


title: 101777-10

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H61


title: 101777-35

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H85


title: 101777-55

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N2917


title: 101777-76

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H81


title: Limousin (Cy5) vs. Holstein-Friesian (Cy3) 2

status: Public on Feb 28 2014

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 2 of 4. Control - Limousine muscle tissue

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Bos taurus

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions (A&A BIOTECHNOLOGY)

value: bull

tag: breed

value: Limousine (LIM)

value: 15 months

value: muscle  m. semitendinosus

value: Holstein-Friesian (H-F)


title: Hereford (Cy5) vs. Limousin (Cy3) 3

description: Biological replicate 3 of 4. Control - Limousine muscle tissue

label_protocol: according to the manufacturer's protocol

value: Hereford (HER)


title: 101777-05

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
3160


title: Limousin (Cy5) vs. Holstein-Friesian (Cy3) 1

description: Biological replicate 1 of 4. Control - Limousine muscle tissue


title: Hereford (Cy5) vs. Limousin (Cy3) 1


title: Limousin (Cy5) vs. Holstein-Friesian (Cy3) 4

description: Biological replicate 4 of 4. Control - Limousine muscle tissue


title: 101777-112

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H10


title: 101777-74

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
669M


title: Hereford (Cy5) vs. Limousin (Cy3) 4


title: Limousin (Cy5) vs. Holstein-Friesian (Cy3) 3


title: 101777-17

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
5048


title: Hereford (Cy5) vs. Limousin (Cy3) 2


title: 101777-57

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
31


title: 101777-70

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H80


title: MDA_MVAC20

status: Public on Feb 10 2014

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

country: USA

institute: Md Anderson Cancer center

hyb_protocol: Standard Illumina whole genome DASL hybridization protocol

data_processing: Quantile normalization in the R language environment was used to normalize the data

label: whole genome DASL

label_protocol: Standard Illuminal whole genome DASL method

extract_protocol: Total RNA from FFPE was extracted by High Pure miRNA Isolation Kit (Roche). Quality control was performed by NanoDrop ND-1000.

tag: tissue type

value: muscle-invasive bladder cancer (MIBC)

tag: response to mvac (downstaged to p0 or t1 w/ nac)

value: yes

tag: subset type

value: luminal

tag: cstage

tag: pstage


title: MDA_MVAC23


title: MDA_MVAC22

value: no

value: basal


title: MDA_MVAC18


title: MDA_MVAC19


title: MDA_MVAC15


title: MDA_MVAC11


title: MDA_MVAC10


title: MDA_MVAC13


title: MDA_MVAC16


title: 101777-122

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H84


title: MDA_MVAC12


title: MDA_MVAC8


title: MDA_MVAC14


title: MDA_MVAC9


title: FVB_C3(1)-Tag-TEC.A3

status: Public on Mar 21 2014

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

organism: Mus musculus

source_name: Whole Mouse Reference RNA

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

tag: reference

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

extract_protocol: Total RNA isolated using Qiagen Rneasy Kit

tag: sample

value: C3 Tag cancer tumor endothelial cell line


title: MDA_MVAC7


title: FVB_C3(1)-Tag-TEC.A4.2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: 252550310117-2

status: Public on Apr 17 2014

description: Strain_MMTV-Cre_Lfng-flox/flox_3132_Egan

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Whole Mouse Reference RNA-2009

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-504

growth_protocol: described in He et al., 2004. BioTechniques, Vol. 37:464–468

extract_protocol: Qiagen Rneasy Kit

value: Whole Mouse Reference

source_name: Tumor RNA, Non-treated

tag: tumor

value: Mouse tumor derived RNA


title: FVB_C3(1)-Tag-NEC.p14

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

value: C3 Tag normal endothelial cell line


title: FVB_C3(1)-Tag-TEC.A5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132


title: MDA_MVAC6


title: MDA_MVAC17


title: MDA_MVAC3


title: FVB_C3(1)-Tag-NonEC

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

value: C3 Tag cancer cell line


title: FVB_C3(1)-Tag-TEC.A4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130


title: 252550310118-1

description: Strain_MMTV-Cre_Lfng-flox/flox_3751_Egan

treatment_protocol: described in He et al., 2004. BioTechniques, Vol. 37:464–468

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: FVB_C3(1)-Tag-NEC.p10.2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: 252550310117-3

description: Strain_MMTV-Cre_Lfng-flox/flox_3134_Egan

growth_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: FVB_C3(1)-Tag-NEC.p10


title: MDA_MVAC2


title: FVB_C3(1)-Tag_125653a_two-week-treatment_Non-responder

status: Public on Jan 01 2014

description: carbo/taxol treated

source_name: carboplatin/paclitaxel treated mouse tumor derived RNA

extract_protocol: total RNA

treatment_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

tag: strain

value: FVB

value: mammary adenocarcinoma

tag: promoter

value: C3(1) rat

tag: transgene

value: Simian virus 40 T antigen

tag: origin

value: Jeff Green NIH

tag: availability

value: Jackson Laboratories strain #013591


title: MDA_MVAC4

value: muscle-invasive bladder cancer (MIBC)


title: FVB_C3(1)-Tag-122387_two week-treatment_Responder

description: carbo/taxol treated

tag: tissue


title: FVB_C3(1)-Tag_125905_two-week-treatment_Non-responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag_117338-1_untreated

description: Non-treated

source_name: Non-treated mouse tumor derived RNA


title: FVB_C3(1)-Tag-120555_untreated

description: Non-treated


title: MDA_MVAC5


title: MDA_MVAC1


title: FVB_C3(1)-Tag-124051T1-three-week-treatment_Non-responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag_116410B_untreated

description: Non-treated


title: FVB_C3(1)-Tag_120157_untreated

description: Non-treated


title: FVB_C3(1)-Tag-121415_untreated

description: Non-treated


title: FVB_C3(1)-Tag_117517_untreated

description: Non-treated

extract_protocol: Total RNA


title: FVB_C3(1)-Tag_120865_two-week-treatment_Non-responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag_118657_three-week-treatment_Non-responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag_121491-three-week-treatment_Non-responder

description: carbo/taxol treated


title: T47D_3D_202-22

description:
RNA from a primary culture cell line
established breast cancer cells

source_name: Stratagene Human Universal Reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: cell type

value: established breast cancer cells


title: FVB_C3(1)-Tag_123051-three-week-treatment_Non-responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag-122738-three week-treatment_Responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag_123240-two-week-treatment_Non-responder

description: carbo/taxol treated


title: T47D_3D_202-24


title: FVB_C3(1)-Tag-124051T2-three-week-treatment_Responder

description: carbo/taxol treated


title: FVB_C3(1)-Tag-121450T2-three-week-treatment_Non-responder

description: carbo/taxol treated


title: T47D_3D_202-23


title: SUM149_3D_202-27


title: SUM159_3D_190d12


title: SUM159_3D_CH190c4


title: SUM159_3D_190d11


title: SKBR3_3D_202-20


title: MDA231_3D_190d9b


title: SKBR3_3D_202-19


title: BEC_3D_202-43

description:
RNA from a primary culture cell line
Blood vascular endothelial cells

value: Blood vascular endothelial cells


title: SUM149_3D_202-25


title: MDA231_3D_190d9


title: MDA231_3D_190d10


title: MCF7_3D_190d7


title: FVB_C3(1)-Tag_116409C_untreated

description: Non-treated


title: MCF7_3D_190d8


title: LEC_SUM149_Transwell_136C

description:
RNA from a primary culture cell line
lymphatic vascular endothelial cells (subjected to transwell culture with cancer cells)


title: LEC_SUM159_Transwell_136C

value: lymphatic vascular endothelial cells (subjected to transwell culture with cancer cells)


title: LEC_T47D_Transwell_136e9


title: LEC_SUM159_Transwell_136B


title: LEC_SUM149_Transwell_136A


title: LEC_T47D_Transwell_136D2


title: SKBR3_3D_202-21


title: LEC_SKBR3_Transwell_136e3


title: MCF7_3D_CH190c2


title: BEC_3D_190d1


title: LEC_SUM149_Transwell_136B


title: LEC_MDA231_Transwell_136g19


title: LEC_SUM159_Transwell_136A


title: LEC_MDA231_Transwell_136h9


title: LEC_SKBR3_Transwell_136D


title: LEC_T47D_Transwell_136D


title: SUM149_3D_202-26


title: LEC_MCF7_Transwell_136h3


title: LEC_SKBR3_Transwell_136D2


title: LEC_MCF7_Transwell_136g7


title: LEC_136D

description:
RNA from a primary culture cell line
lymphatic vascular endothelial cells

value: lymphatic vascular endothelial cells


title: LEC_MCF7_Transwell_136g5


title: LEC_MDA231_Transwell_136g17


title: BEC_T47D_Transwell_136D2

description:
RNA from a primary culture cell line
Blood vascular endothelial cells (subjected to transwell culture with cancer cells)


title: BEC_T47D_Transwell_136D

value: Blood vascular endothelial cells (subjected to transwell culture with cancer cells)


title: LEC_i


title: BEC_SUM159_Transwell_136A


title: BEC_T47D_Transwell_136e7


title: BEC_MDA231_Transwell_136g13


title: BEC_SKBR3_Transwell_136e1


title: BEC_MDA231_Transwell_136g15


title: LEC_136D3

description:
RNA from a primary culture cell line
Lymphatic vascular endothelial cells from Lonza,  Catalog CC-2810, 38 year old female


title: BEC_SUM159_Transwell_136B


title: BEC_i


title: BEC_SUM149_Transwell_136C


title: BEC_SUM149_Transwell_136B


title: BEC_SKBR3_Transwell_136D2


title: BEC_SUM149_Transwell_136A


title: Bone_Marrow_Biochain_hREF

description:
RNA from a single human donors
Bone Marrow RNA from Biochain, Catalog R1234024-10, 44 year old male


title: BEC_SUM159_Transwell_136C


title: BEC_MDA231_Transwell_136h7


title: BEC_136D3


title: HUVEC_CH236

description:
RNA from a primary culture cell line
Human umbilical vein endothelial cells from Lonza, Catalog, CC2519, pooled donors

source_name: HUVEC

value: HUVEC


title: BEC_SKBR3_Transwell_136D


title: BEC_MCF7_Transwell_136g1


title: Bone_Marrow_Clontech_hREF

description:
RNA from a single human donors
Bone Marrow RNA from Clontech, Catalog 636591, pooled from 56 Asian males/females


title: Ambion Lung vs. RefB2_AgiScan

description:
RNA from a single human donors
Lung RNA from Ambion, Catalog #AM7968, 65 year old caucasian male

source_name: Lung

value: Lung


title: BEC_3D_190d4

description:
RNA from a primary culture cell line
Blood vascular endothelial cells from Lonza, Catalog CC-2811, 38 year old female


title: BEC_MCF7_Transwell_136g3


title: BEC_136D2


title: Ambion Liver vs. RefB2_AgiScan

description:
RNA from a single human donors
Liver RNA from Ambion, Catalog #AM7960, 69 year old caucasian male

source_name: Liver

value: Liver


title: Ambion LN vs. RefB2_AgiScan

description:
RNA from a single human donors
Lymph Node RNA from Ambion, Catalog #AM7894, 76 year old caucasian female


title: 0 µM Cy3 x 25 µM Cy5_Repl1

status: Public on Dec 31 2013

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of an experiment that aimed at evaluating gene expression modulation in P. brasiliensis yeast cells exposed to thioridazine.

hyb_protocol: Labeled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 µl of 1X Hybridization buffer, containing 6X SSC, 5X Denhardt´s solution, 0,25 mg/ml salmon sperm DNA, 0,01 % SDS, 50 % formamide and 92,5 ng/ul poly (dT) 25u (Amersham). Arrays were hybridized overnight (42 °C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42 °C) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100 % laser power and 70 % PMT gain Cy5 channel was scanned at 100 % laser power and 80 % PMT gain

data_processing: Images were analyzed with the TIGR Spotfinder program (v.3.1.1). All spots with less than 50 % of the pixels with values lower than the median local background plus two SD have been flagged and excluded from further analyses. Raw data were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array

organism: Paracoccidioides brasiliensis

source_name: P. brasiliensis 0 µM thioridazine

label_protocol: The amplified RNA sample was further labeled by incorporation of Cy3-dCTP. Briefly, 10 µg of amplified RNA were mixed with 3 µL of 3 µg/µL random hexamer and the reaction volume was adjusted to 15.9 µL. The tube was then heated at 70 °C for 10 min and allowed to cool to room temperature for 5 min for primer annealing. Next, the reaction was mixed with 6 µL of 5x first strand buffer (Invitrogen), 3 µL of 0.1 M DTT, 0.6 µL of low-dNTP solution (25 mM dTTP, 25 mM dGTP, 25 mM dATP and 10mM dCTP), 3 µL of Cy3-labeled dCTP 1mM (Amersham), 0.5 µL de RNAsin® and 2.5 µL de Superscript™ II RT  (Invitrogen). The reaction was incubated at 42 °C for 2 h. The RNA was degraded by adding 1.5 µL of 0.5 M EDTA, 1.5 µL of 1 M NaOH and incubation at 70 °C for 20 min followed by adding 1.5 µL of 1 M HCl. The resulting labeled cDNA was purified using a Cyscribe™ GFX™ Purification Kit (Amersham) according to the manufacturer's instructions.

growth_protocol:
We used P. brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker
Fungal cells were cultivated in YPD medium (1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5) at 36 °C (yeast phase); liquid cultures were shaken at 120 rpm in a rotatory shaker.

extract_protocol:
Yeast cells were disrupted with glass beads and by grinding in liquid nitrogen, respectively, and immediately mixed with Trizol (Invitrogen) for RNA extraction following the supplier’s recommendations. After extraction, RNA samples were further purified with Qiagen RNAeasy columns, to ensure removal of most contaminating DNA. Next, RNA samples were treated with RNAse-free RQ1 DNAse (1 unit/µg of RNA), for 2 hours, at 37oC, as recommended by the supplier (Promega) and purified again in RNAeasy columns. Next, the RNA sample was amplified as described by Wang et al., 2000, with minor modifications. Briefly, 3-5 µg of total RNA (concentrated in 6 µL of RNAse-free water) was mixed with 1 µL of 0.5 µg/µL oligo-dT (15)-T7 and heated to 70 °C for 10 min. The tube was briefly chilled on ice and mixed with 4 µL of 5x first-strand buffer, 2 µL of 0.1 M dithiothreitol,  2 µL of 10 mM dNTP, 1 µL of RNAsin® (Promega, Madison, WI), 3 µL of T5 template switch primer (Clontech, Palo Alto, CA) and 2 µL of Superscript™ II Reverse Transcriptase  (Invitrogen). Reaction was then incubated at 42°C for 2 h. Next, the resulting cDNA was mixed with 64.3 µL of DNAse-free water, 10 µL of Advantage PCR buffer (Clontech), 2 µL of 10 mM dNTP mix, 0.7 µL of RNAse H (Invitrogen) and 2 µL of Advantage cDNA polymerase (Clontech). The reaction tube was subjected to the following thermocycling conditions: 37 oC – 10 min; 94 oC – 3 min; 65 oC – 5 min e 75oC – 30 min. At the end of the cycle, the reaction was terminated by incubation with 5 µL of 1 M NaOH: 2 mM EDTA at 65 °C for 10 min. Double-stranded cDNA (ds-cDNA) sample was purified with phenol-chloroform-isoamyl alcohol (25:24:1), precipitated with ethanol in the presence of 1 µL of 5 mg/mL linear acrylamide and resuspended in 10 µL of RNAse-free water.
To in vitro transcription, 10 µL of the ds-cDNA was mixed with 7.5 µL of 25 mM rNTP, 5 µL of 5x reaction buffer and 2.5 µL of enzyme mix (RNAse inhibitor and T7 phage polymerase) (Ribomax™ Large Scale RNA Production System T-7, Promega) and the reaction was incubated at 37 oC for 6 h. The amplified RNA was purified with Trizol-chloroform and resuspended in 6 µL of RNAse-free water.
In the second round of amplification, the resulting RNA was reverse transcribed in cDNA using 3 µL of 3 µg/µL random hexamer, 4 µL of 5x first strand buffer, 2 µL of 0.1 M dithiothreitol, 2 µL of 10 mM dNTP, 1 µL de RNAsin® and 2 µL Superscript™ II Reverse Transcriptase. The reaction tube was incubated at 42 oC for 2 h. Second-strand cDNA synthesis was initiated in the same conditions used in the first round. In vitro transcription of amplified RNA was carried out as for the first round.

tag: treatment

value: 0 µM thioridazine

source_name: P. brasiliensis 25 µM thioridazine

label_protocol: The amplified RNA sample was further labeled by incorporation of Cy5-dCTP. Briefly, 10 µg of amplified RNA were mixed with 3 µL of 3 µg/µL random hexamer and the reaction volume was adjusted to 15.9 µL. The tube was then heated at 70 °C for 10 min and allowed to cool to room temperature for 5 min for primer annealing. Next, the reaction was mixed with 6 µL of 5x first strand buffer (Invitrogen), 3 µL of 0.1 M DTT, 0.6 µL of low-dNTP solution (25 mM dTTP, 25 mM dGTP, 25 mM dATP and 10mM dCTP), 3 µL of Cy5-labeled dCTP 1mM (Amersham), 0.5 µL de RNAsin® and 2.5 µL de Superscript™ II RT  (Invitrogen). The reaction was incubated at 42 °C for 2 h. The RNA was degraded by adding 1.5 µL of 0.5 M EDTA, 1.5 µL of 1 M NaOH and incubation at 70 °C for 20 min followed by adding 1.5 µL of 1 M HCl. The resulting labeled cDNA was purified using a Cyscribe™ GFX™ Purification Kit (Amersham) according to the manufacturer's instructions.

growth_protocol:
We used P. brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker.
Fungal cells cells were grown in YPD supplemented with thioridazine at 36°C for 168 hours at 120 rpm in a rotatory shaker. Following the TR exposure period, yeast cells were harvested by filtration and immediately frozen in liquid nitrogen.

treatment_protocol: 168 hours incubation at 36 °C in YPD supplemented with thioridazine (25 µM), at 120 rpm in a rotatory shaker.

value: 25 µM thioridazine


title: 0 µM Cy3 x 25 µM Cy5_Repl2

growth_protocol:
We used P. brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker.
Fungal cells were cultivated in YPD medium (1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5) at 36 °C (yeast phase); liquid cultures were shaken at 120 rpm in a rotatory shaker.


title: 0 µM Cy3 x 20 µM Cy5_Repl2

source_name: P. brasiliensis 20 µM thioridazine

treatment_protocol: 168 hours incubation at 36 °C in YPD supplemented with thioridazine (20 µM), at 120 rpm in a rotatory shaker.

value: 20 µM thioridazine


title: Ambion Brain, pooled vs. RefB2_AgiScan

description:
RNA from a pool of human donors
Brain RNA from Ambion, Catalog# AM6050, pooled male and female donors

source_name: Brain

value: Brain


title: 0 µM Cy3 x 20 µM Cy5_Repl1


title: SUM149_3

description:
251510210377-2-44K
established breast cancer cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: Homo sapiens

growth_protocol: Total RNA isolated by stratagene

extract_protocol: Total RNA isolated by stratagene

value: Human Reference B

source_name: SUM149, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence

tag: exptid

tag: printid

tag: tumor cell line


title: MCF7_2

description:
251510210382-2-44K
established breast cancer cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

source_name: MCF7, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: SKBR3_2

description:
251510210373-3-44K
established breast cancer cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: SKBR3, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: MDA231_1

description:
251510210382-3-44K
established breast cancer cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

source_name: MDA231, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: T47D_E_2

description:
251510210598-2-44K
established breast cancer cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141

source_name: T47D, parental cell lines were grown in mammary glands of nude mice, tumors were extracted and sublines were grown in steroid-depleted media supplemented with 1nM estradiol-17β supplemented media (E)


title: 0 µM Cy5 x 25 µM Cy3_Repl1

growth_protocol:
We used P. brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker
Fungal cells cells were grown in YPD supplemented with thioridazine at 36°C for 168 hours at 120 rpm in a rotatory shaker. Following the TR exposure period, yeast cells were harvested by filtration and immediately frozen in liquid nitrogen.


title: 0 µM Cy5 x 25 µM Cy3_Repl2


title: 0 µM Cy5 x 20 µM Cy3_Repl1


title: 0 µM Cy5 x 20 µM Cy3_Repl2


title: 0 µM Cy3 x 15 µM Cy5_Repl2

source_name: P. brasiliensis 15 µM thioridazine

treatment_protocol: 168 hours incubation at 36 °C in YPD supplemented with thioridazine (15 µM), at 120 rpm in a rotatory shaker.

value: 15 µM thioridazine


title: BEC_MCF7_Transwell_136h1


title: 0 µM Cy5 x 15 µM Cy3_Repl1


title: SUM159_2

description:
251510210442-1-44K
established breast cancer cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138

source_name: SUM159, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: 0 µM Cy3 x 15 µM Cy5_Repl1


title: 0 µM Cy5 x 15 µM Cy3_Repl2


title: WHIM4

status: Public on Dec 22 2013

description: Breast 251976012475 244Kv5

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142

value: Whole human total RNA

value: Xenograft


title: WHIM8 (E)

description: Breast 251976012965 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145


title: WHIM26(A4923)weak

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140


title: WHIM5 (C343)

description: Breast 251976012476 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143


title: WHIM20 (A1184)

description: Breast 251976012216 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

source_name: 9830-000060B NEW PROTOCOL V98


title: WHIM9 (E1114)

description: Breast 251976012966 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146


title: WHIM17 (C1226)

description: Breast 251976012214 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: 9830-000060B NEW PROTOCOL V95


title: WHIM3 (A94)

description: Breast 251976012474 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141


title: WHIM14 (B1164)

description: Breast 251976012212 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

source_name: 9830-000060B NEW PROTOCOL V93


title: WHIM18(A1542)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: 9830-000060B NEW PROTOCOL V96


title: WHIM11 (D1234)

description: Breast 251976012968 244Kv5

source_name: 9830-000060B NEW PROTOCOL V90


title: WashU-9403-244Kv5

source_name: 9830-000060B NEW PROTOCOL V88

value: Tumor

tag: age at diagnosis

tag: menopause status

tag: histopathology

tag: breast cancer subtype (pam50)

value: LumB

tag: er status

tag: hormone treated

tag: her2 status

tag: tumor grade

tag: tumor stage (t)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (months)


title: WashU-9028-244Kv5

tag: reference

tag: tissue

value: LumA


title: WHIM12 (C1375)

description: Breast 251976012969 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: 9830-000060B NEW PROTOCOL V91

tag: sample


title: WHIM21(C4936)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135

source_name: 9830-000060B NEW PROTOCOL V99


title: WashU-8690-244k

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

source_name: 9830-000060B NEW PROTOCOL V86


title: WHIM2 (E)

description: Breast 251976012473 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

source_name: 9830-000060B NEW PROTOCOL V97


title: WashU-9024-244Kv5


title: WHIM16 (B1158)

description: Breast 251976012213 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: 9830-000060B NEW PROTOCOL V94


title: WHIM13 (B1357)

description: Breast 251976012211 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

source_name: 9830-000060B NEW PROTOCOL V92


title: WHIM25(A4926)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139


title: WHIM23(A1585)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: WHIM10 (D665)

description: Breast 251976012967 244Kv5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

source_name: 9830-000060B NEW PROTOCOL V89


title: WashU-8702-244Kv5


title: WHIM22(B4929)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136


title: WHIM24(C1498)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138


title: WashU-9023-244k

source_name: 9830-000060B NEW PROTOCOL V87

value: Basal


title: WHIM6-155140-244K

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144


title: WashU-8688-244Kv5


title: WashU-8701-244k


title: WashU-6067-244k

source_name: 9830-000060B NEW PROTOCOL V85


title: WashU-4771-244k

source_name: 9830-000060B NEW PROTOCOL V84


title: WashU-4766-244k

source_name: Human Reference

source_name: 9830-000060B NEW PROTOCOL V83


title: WashU-4770-244k


title: WashU-4769-244k


title: WashU-4763-244k


title: WashU-8677-244Kv5


title: WashU-4164-244k

source_name: 9830-000060B NEW PROTOCOL V79


title: WashU-4757-244Kv5


title: WashU-4631-244k


title: WashU-4627-244k


title: WashU-4653-244k

source_name: 9830-000060B NEW PROTOCOL V81


title: WashU-4756-244k

source_name: 9830-000060B NEW PROTOCOL V82


title: WashU-4160-244k


title: WashU-2859-244k


title: WashU-4774-244k


title: WashU-4365-244k

source_name: 9830-000060B NEW PROTOCOL V80


title: WashU-4750-244Kv5


title: WashU-3606-244Kv5

source_name: 9830-000060B NEW PROTOCOL V78


title: WashU-4686-244k


title: WashU-3615-244k


title: WashU-3604-244k


title: WashU-4363-244k


title: WashU-4772-244k


title: WashU-2858-244Kv5

source_name: 9830-000060B NEW PROTOCOL V77


title: WashU-4362-244k


title: WashU-2850-244Kv5


title: WashU-2851-244k

source_name: 9830-000060B NEW PROTOCOL V76


title: WashU-2855-244Kv5


title: WashU-2232-244k


title: WashU-2706-244Kv5B

value: Tumor sample


title: WashU-2396-244k


title: WashU-2231-244Kv5

source_name: 9830-000060B NEW PROTOCOL V74


title: WashU-15692-244k


title: WashU-19635-244k


title: WashU-2853-244k


title: WashU-19639-244k

value: Normal


title: WashU-2706-244Kv5

source_name: 9830-000060B NEW PROTOCOL V75


title: WashU-15726-244Kv5

source_name: 9830-000060B NEW PROTOCOL V73


title: WashU-15718-244k

source_name: 9830-000060B NEW PROTOCOL V72


title: WashU-14598-244k


title: WashU-15571-244k

source_name: 9830-000060B NEW PROTOCOL V70


title: WashU-15567-244Kv5


title: WashU-15563-244k

source_name: 9830-000060B NEW PROTOCOL V69


title: WashU-15584-244k


title: WashU-15574-244k


title: WashU-15575-244k

source_name: 9830-000060B NEW PROTOCOL V71


title: WashU-15565-244k


title: WashU-14541-244k


title: WashU-14542-244k

source_name: 9830-000060B NEW PROTOCOL V68


title: WashU-15573-244Kv5

source_name: Human Reference


title: WashU-14263-244Kv5


title: WashU-13642-244k


title: WashU-13644-244k


title: WashU-15724-244k


title: WashU-13768-244k


title: WashU-14540-244Kv5


title: WashU-14552-244k


title: WashU-14539-244Kv5

source_name: 9830-000060B NEW PROTOCOL V67


title: UNC98-0107B-244k-DGE


title: WashU-13785-244k

source_name: 9830-000060B NEW PROTOCOL V66


title: WashU-14531-244k


title: WashU-13640-244k

source_name: 9830-000060B NEW PROTOCOL V64


title: WashU-11728-244Kv5


title: WashU-10746-244Kv5

source_name: 9830-000060B NEW PROTOCOL V63


title: UNC-020464B-244k-DGE


title: WashU-13641-244k


title: UNC-990182B-244Kv5

source_name: 9830-000060B NEW PROTOCOL V62


title: UNC-030363B-244K2008

description: 251976010309-244k V5


title: WashU-11732-244Kv5


title: UNC-990216B-244Kv5


title: UNC-990158B-244Kv5


title: UNC-990141B-244K2008

description: 251976010307-244k V5


title: UNC-99-0363B-244Kv5

source_name: 9830-000060B NEW PROTOCOL V61


title: UNC-020157B-244K2008

description: 251976010297-244k V5

source_name: 9830-000060B NEW PROTOCOL V57


title: UNC-010456B-244Kv5

source_name: 9830-000060B NEW PROTOCOL V56


title: UNC-010353B-244k-DGE


title: WashU-13643-244k

source_name: 9830-000060B NEW PROTOCOL V65


title: BR94-0187B  NEW PROTOCOL V5

description: Agilent 251976010170 244K


title: BR000344B-244Kv5


title: UNC-040547B-244K2008

description: 251976010305-244k V5

source_name: 9830-000060B NEW PROTOCOL V60


title: UNC-000552B-244K2008

description: 251976010295-244k V5

source_name: 9830-000060B NEW PROTOCOL V54


title: PB277T-244k-DGE

source_name: 9830-000060B NEW PROTOCOL V53


title: UNC-010348B-244Kv5

value: Breast Tumor


title: UNC-040574B-244K2008

description: 251976010306-244k V5


title: UNC-000164B-244Kv5


title: BR01-0246B-244K

source_name: 9830-000060B NEW PROTOCOL V52


title: BR00-0284B NEW PROTOCOL V5

description: Agilent 251976010169 244K

source_name: 9830-000060B NEW PROTOCOL V51


title: BR-000587T  NEW PROTOCOL V5

description: Agilent 251976010132 244K


title: BR-970137B  NEW PROTOCOL V5

description: Agilent 251976010133 244K

source_name: 9830-000060B NEW PROTOCOL V50


title: BR96-0014B-244K


title: BC41T-244k-DGE


title: BR-990207B  NEW PROTOCOL V5

description: Agilent 251976010134 244K


title: BR-990348B  NEW PROTOCOL V5

description: Agilent 251976010135 244K


title: A17-3LivMet1-244K


title: A1-Primary T-2 244Kv5

description: Breast 251976012126 244Kv5


title: A7-1 LiverMet 244Kv5

description: Breast 251976012132 244Kv5


title: A7-1LivMet-244Kv5


title: A7-3 LungMet 244Kv5

description: Breast 251976012145 244Kv5


title: A1-AxLN-Met 244Kv5

description: Breast 251976012127 244Kv5


title: A17-9ChestMet-244K

source_name: 9830-000060B NEW PROTOCOL V47


title: A1-AdrenalG Met 244Kv5

description: Breast 251976012124 244Kv5

source_name: Human Reference


title: 990339B-244K


title: 9830-030077B-244Kv5


title: 9830-040550B-244Kv5


title: 9830-030363A-244Kv5

value: Normal breast sample


title: A5-SkinMet-244Kv5


title: 9830-020310B-244Kv5-2


title: A1-10-AdrenalG Met 244Kv5

description: Breast 251976012130 244Kv5

source_name: 9830-000060B NEW PROTOCOL V45


title: 9830-020310A-244Kv5


title: 9830-020185A-244Kv5


title: 9830-040550A-244Kv5

source_name: 9830-000060B NEW PROTOCOL V43


title: 9830-020039A-244Kv5


title: 9830-020039A-244Kv5-2

source_name: 9830-000060B NEW PROTOCOL V37


title: 9830-010255A-244Kv5


title: 9830-010193B-244Kv5


title: 9830-020185B-244Kv5


title: 9830-010214B-244Kv5


title: 9830-010384B-244K2008

description: 251976010290-244k V5

source_name: 9830-000060B NEW PROTOCOL V35


title: 9830-010038B-244K2008

description: 251976010289-244k V5

source_name: 9830-000060B NEW PROTOCOL V31


title: BR000387B-244Kv5


title: 9830-000248A-244Kv5


title: 9830-020018B-244Kv5

source_name: 9830-000060B NEW PROTOCOL V36


title: 9830-010255B-244Kv5


title: 9830-000471B-244Kv5

value: Breast Tumor, tamoxifen-treated patient


title: 982049B

description: Test 251976011586 244Kv5


title: 9830-010193A-244Kv5

source_name: 9830-000060B NEW PROTOCOL V32


title: 9819-01-0372B-244Kv5

source_name: 9830-000060B NEW PROTOCOL V27


title: 9819-01-0142B-244Kv5


title: 980019A

description: Test 251976011604 244Kv5

source_name: 9830-000060B NEW PROTOCOL V26


title: 9830-000030A-244Kv5


title: 9830-010214A-244Kv5


title: 971051A

description: Test 251976011603 244Kv5


title: 980019B

description: Test 251976011607 244Kv5


title: A7-3 LungMet-2 244Kv5

description: Breast 251976012146 244Kv5

source_name: 9830-000060B NEW PROTOCOL V49


title: 982048B-244K


title: 940326B-244K


title: A7-11-KidneyMet 244Kv5

description: Breast 251976012148 244Kv5

source_name: 9830-000060B NEW PROTOCOL V48


title: 950094B-244K

source_name: 9830-000060B NEW PROTOCOL V21


title: 941025B

description: Agilent 251976011254 244Kv5

source_name: 9830-000060B NEW PROTOCOL V19


title: 950061B-244K


title: 941025B-244Knew


title: 950061B

description: Agilent 251976011247 244Kv5

source_name: 9830-000060B NEW PROTOCOL V20


title: 9830-030446A-244Kv5

source_name: 9830-000060B NEW PROTOCOL V42


title: 940182B

description: Agilent 251976011244 244Kv5

source_name: 9830-000060B NEW PROTOCOL V18


title: 072471B-244K

source_name: Human Reference

source_name: 9830-000060B NEW PROTOCOL V17


title: 072288A-244K


title: 072288B-244K


title: 071750B-244K

source_name: 9830-000060B NEW PROTOCOL V16


title: 100% 971083B

description: Test 251976011599 244Kv5


title: A1-Primary T 244Kv5

description: Breast 251976012123 244Kv5

source_name: 9830-000060B NEW PROTOCOL V46


title: 941025B-244K


title: 071340B-244K

source_name: 9830-000060B NEW PROTOCOL V15


title: 070804B-244K

source_name: 9830-000060B NEW PROTOCOL V14


title: 071054A-244k


title: 9830-030363B-244Kv5


title: 071054B-244K


title: 070427B-244K


title: 070726B-244K


title: 071458B-244K


title: 9830-020039B-244Kv5-2


title: 070804A-244K


title: 9830-020416B-244k-DGE


title: 060952B-244K


title: 060545A-244K


title: 070726A-244K

source_name: 9830-000060B NEW PROTOCOL V13


title: Histone H1 ChIP-seq replicate 2

status: Public on Dec 01 2013

type: SRA

city: La Jolla

first: Graham

last: McVicker

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

library_source: genomic

data_processing:
HMGD1 SOLiD output files were converted to fastq using custom script
Mapped HMGD1 reads to the Drosophila genome using BWA v0.6.1
Estimated the mean HMGD1 fragment length of each replicate by computing the offset that gave the highest covariation of read depth between the forward and reverse strands
Estimated HMGD1 nucleosome midpoint locations as the read start plus the offset (or minus the offset for those that mapped to the reverse strand.
Aligned the MNase-seq and H1 paired-end reads to the genome using the standard SOLiD pipeline and discarded those where only one side of pair mapped
Estimated the distribution of H1 and MNase-seq fragment sizes from separation of read pairs, and discarded read pairs outside of the central 95% of distribution (101-191bp)
Estimated H1 and MNase-seq nucleosome midpoints as the midpoint between read pairs
Genome_build: dm3
Supplementary_files_format_and_content: wig files containing counts of mapped fragment midpoints at each genomic position

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: late embryonic stage cells

growth_protocol: D. Melanogaster S2-DRSC cells (obtained from the Drosophila Genomics Resource Center) were cultured in Schneider's Drosophila medium (Invitrogen) supplemented with 10% FCS (Hyclone).

extract_protocol:
MNase digested nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Applied Biosystems protocol for SOLiD fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on a SoLid flow cell for cluster generation.

tag: cell type

value: late embryonic cells

tag: passages

tag: strain

tag: antibody

value: Histone H1 (Active motif-39575)


title: 060117B-244K


title: 060545B-244K

source_name: 9830-000060B NEW PROTOCOL V11


title: 061398B-244K


title: 050362B-244K


title: 071567B-244K


title: 050364B-244K


title: 050093B-244K

source_name: 9830-000060B NEW PROTOCOL V8


title: FVB_MMTV_Myc_128818_untreated_GMurrow

status: Public on Nov 04 2013

description: Mammary Tumor

source_name: Whole Mouse Reference RNA

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

value: MMTV Myc


title: 050259B-244K

source_name: 9830-000060B NEW PROTOCOL V9


title: FVB_MMTV_Myc_128990_untreated_GMurrow

description: Mammary Tumor


title: 060708A-244K


title: 950105B-244K


title: C57Bl6_Mammary_Norm_131546_GMurrow

description: Normal Mammary

value: Normal Mammary


title: 100% 950184B

description: Test 251976011597 244Kv5


title: C57Bl6_Mammary_Norm_134742_GMurrow

description: Normal Mammary


title: FVB_MMTV_Myc_128492_untreated_GMurrow

description: Mammary Tumor


title: 050113B-244K


title: 050088B-244K


title: 061398A-244K

source_name: 9830-000060B NEW PROTOCOL V12


title: FVB_C3(1)-Tag_116966_untreated_GMurrow

description: Mammary Tumor

value: C3 Tag


title: C57Bl6_Mammary_Norm_131547_GMurrow

description: Normal Mammary


title: FVB_MMTV_Myc_128620_untreated_GMurrow

description: Mammary Tumor


title: FVB_MMTV_Myc_128491_untreated_GMurrow

description: Mammary Tumor


title: 050005B-244K

value: Whole human total RNA

source_name: 9830-000060B NEW PROTOCOL V7


title: Balbc_p53null_T11-CL-X1_128333_Perou

description: Mammary Tumor


title: Balbc_p53het_IR_C1201-4_spontaneous_GMurrow

description: Mammary Tumor

value: p53het, Irradiated


title: 020510B-244Kv5

source_name: 9830-000060B NEW PROTOCOL V6

tag: age at diagnosis

tag: menopause status


title: 040593B-244K


title: Mixed_Rb_7.Oct22.07_UHNC

description: Mammary Tumor

value: Rbnull


title: Histone H1 ChIP-seq replicate 1


title: 020300A-244K


title: 030459B-244Kv5

tag: histopathology

tag: breast cancer subtype (pam50)


title: FVB_NJ_NORMAL_CA03_603A_lactating

description: Mammary Normal Lactating

value: Mammary Normal Lactating


title: FVB_Wap_Myc_117252_PEROU

description: Mammary Tumor

value: Wap Myc


title: 050113A-244k


title: 050088A-244K


title: FVB_Wap_Myc_117250_PEROU

description: Mammary Tumor


title: 000587A

description: Test 251976011601 244Kv5

source_name: 9830-000060B NEW PROTOCOL V5


title: FVB_Wap_Myc_CA05_868A_CHURCHILL

description: Mammary Tumor


title: FVB_Wap_Myc_117254_PEROU

description: Mammary Tumor


title: FVB_NJ_NORMAL_CA02_451A_Lactating

description: Mammary Normal Lactating


title: FVB_MMTV_Wnt1_CA03_613A_CHURCHILL

description: Mammary Tumor

value: MMTV Wnt1


title: FVB_Wap_Myc_117166_bRep_PEROU

description: Mammary Tumor


title: FVB_MMTV_Wnt1_28T.4T_COWIN

description: Mammary Tumor


title: FVB_MMTV_Wnt1_9T.8T_COWIN

description: Mammary Tumor


title: FVB_Wap_Myc_CA04_812A_CHURCHILL

description: Mammary Tumor


title: 010349A

description: Test 251976011602 244Kv5


title: STAT1-/-_Schreiber_TAC80

description: Mammary Tumor


title: FVB_Wap_Myc_116885_untreated_GMurrow

description: Mammary Tumor


title: FVB_MMTV_Neu_641971_PEROU

description: Mammary Tumor

value: MMTV Neu


title: FVB_Wap_Myc_117318_bRep_PEROU

description: Mammary Tumor


title: FVB_MMTV_Wnt1_119265-2_cn_Usary

description: Mammary Tumor


title: FVB_MMTV_PyMT_393T_SHAW

description: Mammary Tumor

value: MMTV PyMT


title: NA_MMTV_HRAS_43_VARMUS

description: Mammary Tumor

value: MMTV HRAS


title: STAT1-/-_Schreiber_4524

description: Mammary Tumor


title: STAT1-/-_Schreiber_TAC59

description: Mammary Tumor


title: 050521B-244K

source_name: 9830-000060B NEW PROTOCOL V10

value: Tumor sample


title: FVB_MMTV_PyMT_311T_SHAW

description: Mammary Tumor


title: NA_MMTV_HRAS_44_VARMUS

description: Mammary Tumor


title: FVB_MMTV_Wnt1_531_USARY

description: Mammary Tumor


title: FVB_MMTV_PyMT_257T_SHAW

description: Mammary Tumor


title: FVB_MMTV_Wnt1_22T.8T_COWIN

description: Mammary Tumor


title: NA_MMTV_HRAS_29_VARMUS

description: Mammary Tumor


title: FVB_MMTV_PyMT_423T_SHAW

description: Mammary Tumor


title: STAT1-/-_Schreiber_TAC77

description: Mammary Tumor


title: FVB_MMTV_PyMT_574_PEROU

description: Mammary Tumor


title: FVB_NR_MMTV_FGF3_468_VARMUS

description: Mammary Tumor

value: MMTV FGF3


title: FVB_MMTV_PyMT_209T_SHAW

description: Mammary Tumor


title: FVB_MMTV_PyMT_103572-1_untreated_GMurrow

description: Mammary Tumor


title: STAT1-/-_Schreiber_11253

description: Mammary Tumor


title: FVB_MMTV_Aib1_T8_MBROWN

description: Mammary Tumor

value: MMTV Aib1


title: FVB_NR_MMTV_FGF3_467_VARMUS

description: Mammary Tumor


title: STAT1-/-_Schreiber_9444

description: Mammary Tumor


title: NA_MMTV_HRAS_4863_LI

description: Mammary Tumor


title: MMTV-Cre_R26-Pik3caH107R_9529_4R-Egan

description: Mammary Tumor

value: Pik3ca with H1047R mutation


title: PIK3CA _Egan_A0255

description: Mammary Tumor

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

source_name: MMTV-Cre_R26-Pik3caH1047R_A0255 _Egan


title: FVB_NR_MMTV_FGF3_466_VARMUS

description: Mammary Tumor


title: FVB_MMTV_PyMT_103571_untreated_GMurrow

description: Mammary Tumor


title: FVB_MMTV_Aib1_T36_MBROWN

description: Mammary Tumor


title: PIK3CA _Egan_9529

description: Mammary Tumor

source_name: MMTV-Cre_R26-Pik3caH1047R_9529 _Egan


title: NA_MMTV_HRAS_4861_LI

description: Mammary Tumor


title: FVB_MMTV_Neu_116843-2_untreated_GMurrow

description: Mammary Tumor


title: STAT1-/-_Schreiber_TAC78

description: Mammary Tumor


title: NA_MMTV_HRAS_4633_LI

description: Mammary Tumor


title: NA_MMTV_HRAS_4492_LI

description: Mammary Tumor


title: MMTV-Cre_R26-Pik3caH107R_9529_5L-Egan

description: Mammary Tumor


title: FVB_C57Bl6_C3(1)_Tag_117122_HERSCH

description: Mammary Tumor


title: NA_MMTV_HRAS_4379-1_LI

description: Mammary Tumor


title: FVB_MMTV_Aib1_T34_MBROWN

description: Mammary Tumor


title: PIK3CA _Egan_3073

description: Mammary Tumor

source_name: MMTV-Cre_R26-Pik3caH1047R_3073 _Egan


title: MMTV-Cre_R26-Pik3caH107R_A0835_3L-Egan

description: Mammary Tumor


title: MMTV-Cre_R26-Pik3caH107R_7281A_2R-Egan

description: Mammary Tumor


title: FVB_MMTV_Aib1_J355_MBROWN

description: Mammary Tumor


title: FVB_C3(1)-Tag-120209_no_treatment_Perou

description: Mammary Tumor


title: FVB_MMTV_Aib1_J348_MBROWN

description: Mammary Tumor


title: FVB_NR_MMTV_FGF3_469_VARMUS

description: Mammary Tumor


title: PIK3CA _Egan_4714

description: Mammary Tumor

source_name: MMTV-Cre_R26-Pik3caH1047R_4714 _Egan


title: PIK3CA _Egan_3093

description: Mammary Tumor

source_name: MMTV-Cre_R26-Pik3caH1047R _3093 _Egan


title: FVB_NR_MMTV_FGF3_465_VARMUS

description: Mammary Tumor


title: PIK3CA _Egan_7048A

description: Mammary Tumor

source_name: MMTV-Cre_R26-Pik3caH1047R _7048A _Egan


title: FVB_MMTV_Aib1_J246_MBROWN

description: Mammary Tumor


title: FVB_C3(1)-Tag_117733_untreated_GMurrow

description: Mammary Tumor


title: FVB_MMTV_Aib1_J225_MBROWN

description: Mammary Tumor


title: FVB_MMTV_Aib1_H323_MBROWN

description: Mammary Tumor


title: C57Bl6_Mammary_Norm_439_2_FURTH

description: Normal Mammary


title: C57Bl6_Mammary_Norm_443_1_FURTH

description: Normal Mammary


title: FVB_C3(1)-Tag_117485_untreated_GMurrow

description: Mammary Tumor


title: BALBc_p18null_426_XIONG

description: Mammary Tumor


title: BALBc_p18null_411_bRep_XIONG

description: Mammary Tumor


title: BALBc_p18null_474_XIONG

description: Mammary Tumor


title: FVB_MMTV-PyMT_117704_Non-treated

description: Mammary Tumor


title: C57Bl6_Mammary_Norm_437_1_FURTH

description: Normal Mammary


title: BALBc_p18null_228_XIONG

description: Mammary Tumor


title: BALBc_p18null_854_XIONG

description: Mammary Tumor


title: MMTV-Cre_R26-Pik3caH107R_7286A_5L-Egan

description: Mammary Tumor


title: FVB_MMTV-PyMT_118021_Non-treated

description: Mammary Tumor


title: BALBc_p18null_250_XIONG

description: Mammary Tumor


title: FVB_MMTV-Wnt1_124607_Non-treated

description: Mammary Tumor


title: FVB_MMTV-Neu_121576_non-treated

description: Mammary Tumor


title: FVB_MMTV-Neu_123299 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_123299 Non-treated


title: BALBc_p18null_200_XIONG

description: Mammary Tumor


title: BALBc_p18null_205_XIONG

description: Mammary Tumor


title: FVB_MMTV-Neu_121304-2 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_121304-2 Non-treated


title: FVB_MMTV_Aib1_J59_MBROWN

description: Mammary Tumor


title: PIK3CA _Egan_A0853

description: Mammary Tumor

source_name: MMTV-Cre_R26-Pik3caH1047R _A0853 _Egan


title: FVB_MMTV-Wnt1_125799_Non-treated

description: Mammary Tumor


title: Normal Breast Sort 5 EpCAM-/CD49f+ R5

status: Public on Oct 29 2013

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-223

tag: references

source_name: Normal Breast Sort 5 EpCAM-/CD49f+ R5

value: Cell Line


title: Normal Breast Sort 3 CD24-/CD44+

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-229

source_name: Normal Breast Sort 3 CD24-/CD44+


title: Normal Breast Sort 5 EpCAM+/CD49f+ R8

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-221

source_name: Normal Breast Sort 5 EpCAM+/CD49f+ R8


title: Normal Breast Sort 2 CD24-/CD44+ R7-

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-225

source_name: Normal Breast Sort 2 CD24-/CD44+ R7-


title: Normal Breast Sort CD24-CD44+ 2/13/09

description: 4x44K 251510210249-1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-228

source_name: Normal Breast Sort CD24-CD44+ 2/13/09


title: Normal Breast Sort 5 EpCAM+/CD49f- R6

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-222

source_name: Normal Breast Sort 5 EpCAM+/CD49f- R6


title: Normal Breast Sort CD24+CD44+ 2/13/09

description: 4x44K 251510210249-2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-227

source_name: Normal Breast Sort CD24+CD44+ 2/13/09


title: BALBc_p18null_133657

description: Mammary Tumor

source_name: Whole Mouse Reference RNA


title: Normal Breast Sort 2 CD24-/CD44- R6-

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-226

source_name: Normal Breast Sort 2 CD24-/CD44- R6-

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: Normal Breast Sort EpCAM+/CD49f+ P5

description: 4x44K 251510210247-2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-218

source_name: Normal Breast Sort EpCAM+/CD49f+ P5


title: Normal Breast Sort 5 EpCAM-/CD49f- R7

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-224

source_name: Normal Breast Sort 5 EpCAM-/CD49f- R7


title: BALB/c_p53null_9263-3_transplant_135908

description: Mammary Tumor


title: Normal Breast Sort 4 EpCAM-/CD49f- R7

description: 4x44K 251510210264-1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-217

source_name: Normal Breast Sort 4 EpCAM-/CD49f- R7


title: Normal Breast Sort 4 EpCAM+/CD49f- R8

description: 4x44K 251510210264-2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-215

source_name: Normal Breast Sort 4 EpCAM+/CD49f- R8


title: Normal Breast Sort 4 EpCAM+/CD49f+ R9

description: 4x44K 251510210264-3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-214

source_name: Normal Breast Sort 4 EpCAM+/CD49f+ R9


title: Normal Breast Sort 3 EpCAM-/CD49f- R7

description: 4x44K 251510210263-1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-213

source_name: Normal Breast Sort 3 EpCAM-/CD49f- R7


title: Normal Breast Sort EpCAM-/CD49f+ P6

description: 4x44K 251510210247-1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-219

source_name: Normal Breast Sort EpCAM-/CD49f+ P6


title: BALB/c_p53null_2250_transplant_135434

description: Mammary Tumor

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: BALB/c_p53null_2304_transplant_137326

description: Mammary Tumor


title: BALB/c_p53null_2250_transplant_147753

description: Mammary Tumor


title: Normal Breast Sort 4 EpCAM-/CD49f+ R6

description: 4x44K 251510210264-4

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-216

source_name: Normal Breast Sort 4 EpCAM-/CD49f+ R6


title: Normal Breast Sort 2 EpCAM-/CD49f- P4

description: 4x44K 251510210248-1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-209

source_name: Normal Breast Sort 2 EpCAM-/CD49f- P4


title: Normal Breast Sort 3 EpCAM+/CD49f- R8

description: 4x44K 251510210263-2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-211

source_name: Normal Breast Sort 3 EpCAM+/CD49f- R8


title: FVB_MMTV-Neu_121575 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_121575 Non-treated


title: Normal Breast Sort 3 EpCAM+/CD49f+ R9

description: 4x44K 251510210263-3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-210

source_name: Normal Breast Sort 3 EpCAM+/CD49f+ R9


title: Normal Breast Sort EpCAM-/CD49f- P4

description: 4x44K 251510210247-3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-220

source_name: Normal Breast Sort EpCAM-/CD49f- P4


title: HCC38 sorted R4 Exp4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-206

source_name: HCC38 sorted R4 Exp4


title: Normal Breast Sort 3 EpCAM-/CD49f+ R6

description: 4x44K 251510210263-4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-212

source_name: Normal Breast Sort 3 EpCAM-/CD49f+ R6


title: HCC38 sorted R3 Exp4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-204

source_name: HCC38 sorted R3 Exp4


title: BALB/c_p53null_2247_transplant_134654

description: Mammary Tumor

source_name: Whole Mouse Reference RNA


title: BALB/c_p53null_2224_transplant_137310

description: Mammary Tumor


title: HCC38 sorted R4 Exp2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-200

source_name: HCC38 sorted R4 Exp2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: Normal Breast Sort 2 EpCAM+/CD49f+ P5

description: 4x44K 251510210248-2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-207

source_name: Normal Breast Sort 2 EpCAM+/CD49f+ P5


title: HCC38 sorted R4 Exp3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-205

source_name: HCC38 sorted R4 Exp3


title: HCC38 sorted R3 Exp1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-199

source_name: HCC38 sorted R3 Exp1


title: HCC1143 sorted R4 Exp3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-195

source_name: HCC1143 sorted R4 Exp3


title: HCC38 sorted R3 Exp3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-203

source_name: HCC38 sorted R3 Exp3


title: HCC1143 sorted R4 Exp6

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-198

source_name: HCC1143 sorted R4 Exp6


title: Normal Breast Sort 2 EpCAM-/CD49f+ P6

description: 4x44K 251510210248-3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-208

source_name: Normal Breast Sort 2 EpCAM-/CD49f+ P6


title: HCC1143 sorted R4 Exp5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-196

source_name: HCC1143 sorted R4 Exp5


title: HCC1143 sorted R4 Exp2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-194

source_name: HCC1143 sorted R4 Exp2


title: HCC38 sorted R4 Exp1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-202

source_name: HCC38 sorted R4 Exp1


title: HCC38 sorted R3 Exp2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-201

source_name: HCC38 sorted R3 Exp2


title: HCC1143 sorted R3 Exp2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-191

source_name: HCC1143 sorted R3 Exp2


title: HCC1143 sorted R3 Exp3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-192

source_name: HCC1143 sorted R3 Exp3


title: HCC1143 sorted R3 Exp6

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-197

source_name: HCC1143 sorted R3 Exp6


title: HCC1143 sorted R3 Exp5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-193

source_name: HCC1143 sorted R3 Exp5


title: BALB/c_p53null_2153_transplant_137324

description: Mammary Tumor

source_name: Whole Mouse Reference RNA

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: hESC H9

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-183

source_name: hESC H9

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: SUM149 sorted 5b/R6  HuMEC CD49f+/EpCAM+ --Exp1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-188


title: hESC H7 -- Repl1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-181

source_name: hESC H7 -- Repl1


title: hESC H9 Repl1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-184

source_name: hESC H9 Repl1


title: RFM4-Kuperwasser

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-179


title: UACC812 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-175

source_name: UACC812 cell line


title: ZR75-B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-176


title: MDA-MB134-IV

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-173


title: HCC1954 cell_line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-177

source_name: HCC1954 cell_line


title: UACC893 p47

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-178

source_name: UACC893 p47


title: MDA-MB-415

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-171


title: SUM190PT cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-174

source_name: SUM190PT cell line


title: MDA-MB-435

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-172


title: hESC H7

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-180

source_name: hESC H7


title: PB-p78

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-163


title: HMEC CB

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-182

source_name: HMEC CB


title: PB-p86

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-164


title: CAMA1 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-166

source_name: CAMA1 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: BT483 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-165

source_name: BT483 cell line


title: MDA-IBC3 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-170

source_name: MDA-IBC3 cell line


title: PB-p52

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-162


title: Mesench. Stem Cell #1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-155

source_name: Mesench. Stem Cell #1


title: Mesench. Stem Cell #3

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-160

source_name: Mesench. Stem Cell #3


title: PB-p48

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-161


title: MCF7 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-153

source_name: MCF7 cell line


title: HCC1937 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-152

source_name: HCC1937 cell line


title: Mani-HMLE-TWIST1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149


title: BT474 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-151

source_name: BT474 cell line


title: ZR75-1 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-157

source_name: ZR75-1 cell line


title: SUM102PT cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-156

source_name: SUM102PT cell line


title: HMEC BL* p2

description: 4x44K 251510210232-1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147

source_name: HMEC BL* p2


title: MDA-MB436 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146

source_name: MDA-MB436 cell line


title: HCC1395 cell line

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145

source_name: HCC1395 cell line


title: Mani-HMLE_HuMEC

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144


title: Mani-HMLE-SNAI1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: Mesench. Stem Cell #2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-159

source_name: Mesench. Stem Cell #2


title: HCC1187 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142

source_name: HCC1187 cell line


title: SKBR3 cell line p17

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

source_name: SKBR3 cell line p17


title: RFM3 p4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136

source_name: RFM3 p4


title: HCC38 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143

source_name: HCC38 cell line


title: SUM149 p12 HuMEC+5%FBS

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

source_name: SUM149 p12 HuMEC+5%FBS


title: RFM2 p4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135

source_name: RFM2 p4


title: SUM1315 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: SUM1315 cell line


title: SUM159 p12

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: MDA-MB468 parental cell line p13

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

source_name: MDA-MB468 parental cell line p13


title: RFM1 p4

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

source_name: RFM1 p4


title: HCC1143 p11

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139


title: C57 Ntg 160 days sample 4

status: Public on Oct 01 2013

city: Milan

first: giovanni

last: nardo

address: Via La Masa 19

country: Italy

institute: IRCCS-Mario Negri Institute

description: Gene expression data from murine motor neurons

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were analyzed with the PUMA bioconductor package (Pearson et al., 2009).

source_name: G93A non transgenic littermate 3258

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol:
8 um lumbar spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each animal 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: genotype/variation

value: non transgenic

tag: gender

value: female

tag: age

value: 160 day old


title: C57 Ntg 160 days sample 3

source_name: G93A non transgenic littermate 3261


title: HCC1428 cell line p12

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

value: Whole human total RNA

source_name: HCC1428 cell line p12


title: T47D p8

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

source_name: T47D p8


title: HCC1500 cell line p2

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: HCC1500 cell line p2


title: MB231 cell line p2 DMEM

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: MB231 cell line p2 DMEM

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: BT549 cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141

source_name: BT549 cell line


title: Hs578T p11

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

value: whole human total RNA

value: Cell Line Hs578T p11


title: C57 Ntg 160 days sample 1

source_name: G93A non transgenic littermate 3254


title: C57 Ntg 160 days sample 2

source_name: G93A non transgenic littermate 3256


title: 129Sv Ntg 121 days sample 2

source_name: G93A non transgenic littermate 3368

value: 121 day old


title: 129Sv Ntg 121 days sample 4

source_name: G93A non transgenic littermate 3357


title: C57.G93A 160 days sample 3

source_name: G93A mouse 3259

value: Transgenic


title: C57.G93A 160 days sample 4

source_name: G93A mouse 3252


title: C57.G93A 160 days sample 1

source_name: G93A mouse 3253


title: 129Sv Ntg 121 days sample 1

source_name: G93A non transgenic littermate 3387


title: 129Sv Ntg 121 days sample 3

source_name: G93A non transgenic littermate 3383


title: 129Sv.G93A 121 days sample 3

source_name: G93A mouse 3399


title: C57.G93A 160 days sample 2

source_name: G93A mouse 3260


title: 129Sv.G93A 121 days sample 2

source_name: G93A mouse 3376


title: C57 Ntg 152days sample 4

source_name: G93A non transgenic littermate 534

value: 152 day old


title: 129Sv.G93A 121 days sample 1

source_name: G93A mouse 3388


title: C57 Ntg 152 days sample 2

source_name: G93A non transgenic littermate 524


title: 129Sv.G93A 121 days sample 4

source_name: G93A mouse 3365


title: C57 Ntg 152days sample 3

source_name: G93A non transgenic littermate 520


title: C57 Ntg 152 days sample 1

source_name: G93A non transgenic littermate 543


title: C57.G93A 152 days sample 1

source_name: G93A mouse 544


title: C57.G93A 152 days sample 4

source_name: G93A mouse 545


title: C57.G93A 152 days sample 3

source_name: G93A mouse 532


title: 129Sv Ntg 111 days sample 4

source_name: G93A non transgenic littermate 1305

value: 111 day old


title: 129Sv Ntg 111 days sample 1

source_name: G93A non transgenic littermate 1331


title: 129Sv Ntg 111 days sample 3

source_name: G93A non transgenic littermate 1309


title: 129Sv Ntg 111 days sample 2

source_name: G93A non transgenic littermate 1328


title: C57.G93A 152 days sample 2

source_name: G93A mouse 523


title: 129Sv.G93A 111 days sample 4

source_name: G93A mouse 1330


title: C57 Ntg 133 days sample 3

source_name: G93A non transgenic littermate 2478

value: 133 day old


title: 129Sv Ntg 101 days sample 4

source_name: G93A non transgenic littermate 1357.2

value: 101 day old


title: 129Sv Ntg 101 days sample 3

source_name: G93A non transgenic littermate 1372


title: C57 Ntg 133 days sample 4

source_name: G93A non transgenic littermate 1481


title: C57.G93A 133 days sample 1

source_name: G93A mouse 1409


title: 129Sv.G93A 101 days sample 4

source_name: G93A mouse 1373


title: 129Sv.G93A 111 days sample 1

source_name: G93A mouse 1308


title: C57.G93A 133 days sample 4

source_name: G93A mouse 1483


title: 129Sv.G93A 101 days sample 1

source_name: G93A mouse 1358


title: 129Sv.G93A 101 days sample 2

source_name: G93A mouse 1391


title: 129Sv.G93A 111 days sample 2

source_name: G93A mouse 1306


title: C57 Ntg 133 days sample 1

source_name: G93A non transgenic littermate 1455


title: 129Sv.G93A 111 days sample 3

source_name: G93A mouse 1327


title: C57.G93A 56 days sample 3

source_name: G93A mouse 2461

value: 56 day old


title: C57 Ntg 56 days sample 2

source_name: G93A non transgenic littermate 2475


title: C57.G93A 56 days sample 4

source_name: G93A mouse 2496


title: C57.G93A 56 days sample 2

source_name: G93A mouse 2494


title: C57.G93A 56 days sample 1

source_name: G93A mouse 2493


title: 129Sv.G93A 101 days sample 3

source_name: G93A mouse 1395


title: C57.G93A 133 days sample 3

source_name: G93A mouse 1482


title: C57 Ntg 133 days sample 2

source_name: G93A non transgenic littermate 1408


title: 129Sv Ntg 101 days sample 2

source_name: G93A non transgenic littermate 1396


title: C57 Ntg 56 days sample 3

source_name: G93A non transgenic littermate 2472


title: 129Sv Ntg 56 days sample 3

source_name: G93A non transgenic littermate 2518


title: C57.G93A 133 days sample 2

source_name: G93A mouse 1454


title: C57 Ntg 56 days sample 1

source_name: G93A non transgenic littermate 2463


title: C57 Ntg 56 days sample 4

source_name: G93A non transgenic littermate 2471


title: 129Sv Ntg 101 days sample 1

source_name: G93A non transgenic littermate 1390.2


title: 129Sv.G93A 56 days sample 4

source_name: G93A mouse 2512


title: 129Sv.G93A 56 days sample 1

source_name: G93A mouse 2513


title: 129Sv Ntg 56 days sample 1

source_name: G93A non transgenic littermate 2505


title: FVCM3

status: Public on Sep 10 2013

city: New York

first: Ronald

middle: A

last: Li

state: NY

address: 1 Gustave Levy Pl

institute: Mount Sinai School of Medicine

description: replicate 3

data_processing: The data were normalized using the cubic spline algorithm available on the Illumina BeadStudio software package.

source_name: fetal ventricular cardiac tissue

label_protocol: Total RNA was labeled with biotinylated nucleotides using standard protocol from the Ambion TotalPrep -96 RNA Amplification kit (a variant of the Eberwine protocol)

extract_protocol: Whole RNA was extracted from cells using Trizol and 1:4 volume of chloroform. The aqueous phase was separated using heavy phase lock gel tubes and RNA was purified using the Qiagen RNeasy mini kit according to standard protocol. All samples were verified for high quality using Agilent Bioanalyzer.

tag: stage of cardiac development

value: fetal ventricular cardiac tissue

value: 18 weeks


title: 129Sv Ntg 56 days sample 2

source_name: G93A non transgenic littermate 2517


title: FVCM2

description: replicate 2

value: 20 weeks


title: 129Sv.G93A 56 days sample 2

source_name: G93A mouse 2520


title: 129Sv.G93A 56 days sample 3

source_name: G93A mouse 2503


title: NV-HMEC-SNAIL #1 vs. Empty Vector -Repl1

status: Public on Aug 19 2013

description: Breast Cancer Cell Line

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138

value: NV-HMEC Empty Vector

source_name: NV-HMEC-SNAIL #1 -Repl1

value: breast cancer


title: NV-HMEC-SNAIL #2 vs. Empty Vector

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

source_name: NV-HMEC-SNAIL #2


title: NV-HMEC-SNAIL #1 vs. Empty Vector

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137

source_name: NV-HMEC-SNAIL #1


title: NV-HMEC-SNAIL #2 vs. Empty Vector -Repl2

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142

source_name: NV-HMEC-SNAIL #2 -Repl2


title: NV-HMEC-SLUG #2 vs. Empty Vector -Repl2

description: Breast Cancer Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136

source_name: NV-HMEC-SLUG #2 -Repl2


title: NV-HMEC-SNAIL #2 vs. Empty Vector -Repl1

description: Breast Cancer Cell Line

source_name: NV-HMEC-SNAIL #2 -Repl1


title: NV-HMEC-SLUG #2 vs. Empty Vector

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

source_name: NV-HMEC-SLUG #2


title: Strain_HER2.rt.PIK3_plus_Dox_387_Arteaga

status: Public on Sep 03 2013

description: Mammary Tumor

source_name: Whole Mouse Reference RNA

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

tag: tumor

value: HER2 and PI3K H1047R overexpressing FVB mammary tumor


title: NV-HMEC-SLUG #1 vs. Empty Vector -Repl2

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

tag: reference

source_name: NV-HMEC-SLUG #1 -Repl2


title: NV-HMEC-SNAIL #1 vs. Empty Vector -Repl2

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139

source_name: NV-HMEC-SNAIL #1 -Repl2


title: NV-HMEC-SLUG #2 vs. Empty Vector -Repl1

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135

source_name: NV-HMEC-SLUG #2 -Repl1


title: Strain_HER2.rt.PIK3_plus_Dox_209_Arteaga

description: Mammary Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: Strain_HER2.rt.PIK3_plus_Dox_298_Arteaga

description: Mammary Tumor


title: Strain_rt.PIK3_plus_Dox_344_Arteaga

description: Mammary Tumor

value: PI3K H1047R overexpressing FVB mammary tumor


title: Strain_HER2.rt_plus_Dox_226_Arteaga

description: Mammary Tumor

value: HER2 overexpressing FVB mammary tumor


title: Strain_HER2.rt.PIK3_plus_Dox_250_Arteaga

description: Mammary Tumor


title: Strain_HER2.rt.PIK3_minus_Dox_269_Arteaga

description: Mammary Tumor


title: Strain_HER2.rt_plus_Dox_308_Arteaga

description: Mammary Tumor


title: Strain_rt.PIK3_plus_Dox_327_Arteaga

description: Mammary Tumor


title: Strain_HER2.rt.PIK3_minus_Dox_271_Arteaga

description: Mammary Tumor


title: Strain_HER2.rt.PIK3_plus_Dox_364_Arteaga

description: Mammary Tumor


title: Strain_HER2.rt.PIK3_plus_Dox_204_Arteaga

description: Mammary Tumor


title: 129Sv Ntg 56 days sample 4

source_name: G93A non transgenic littermate 2519

value: non transgenic

value: female


title: NV-HMEC-SLUG #1 vs. Empty Vector

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: NV-HMEC-SLUG #1


title: NV-HMEC-FLAG-SMARCD3 (6) vs. Empty Vector Repl1

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: NV-HMEC-FLAG-SMARCD3 (6)


title: Strain_HER2.rt.PIK3_plus_Dox_277_Arteaga

description: Mammary Tumor


title: NV-HMEC-SLUG #1 vs. Empty Vector -Repl1

description: Breast Cancer Cell Line

source_name: NV-HMEC-SLUG #1 -Repl1


title: NV-HMEC-FLAG-SMARCD3 (6) vs. Empty Vector

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: NV-HMEC-FLAG-SMARCD3 (1) vs. Empty Vector Repl1

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

source_name: NV-HMEC-FLAG-SMARCD3 (1)


title: Strain_rt.PIK3_plus_Dox_224_Arteaga

description: Mammary Tumor


title: Strain_HER2.PIK3_plus_Dox_202_Arteaga

description: Mammary Tumor


title: Strain_rt.PIK3_plus_Dox_305_Arteaga

description: Mammary Tumor


title: NV-HMEC-FLAG-SMARCD3 (1) vs. Empty Vector

description: Breast Cancer Cell Line

source_name: Human Reference


title: Strain_HER2.rt.PIK3_minus_Dox_272_Arteaga

description: Mammary Tumor


title: Strain_rt.PIK3_plus_Dox_228_Arteaga

description: Mammary Tumor


title: Strain_rt.PIK3_plus_Dox_365_Arteaga

description: Mammary Tumor


title: NV-HMEC-FLAG-SMARCD3 (3) vs. Empty Vector

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: NV-HMEC-FLAG-SMARCD3 (3)


title: NV-HMEC-FLAG-SMARCD3 (3) vs. Empty Vector Repl1

description: Breast Cancer Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: UNC-960028B-244Kv5

status: Public on Jun 25 2013

description: Tumor sample

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: Whole human total RNA

tag: tissue

value: Tumor

value: LumA

tag: er status

tag: hormone treated

tag: her2 status

tag: tumor grade

tag: tumor stage (t)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (months)


title: UNC-040011B-244K2008

description: Tumor sample

tag: age at diagnosis

tag: menopause status

tag: histopathology


title: UNC-030183B-244K2008

description: Tumor sample

tag: breast cancer subtype (pam50)

value: LumB


title: UNC-030065B-244K2008

description: Tumor sample

value: Basal


title: UNC-030370B-244K2008

description: Tumor sample

value: Normal


title: 9830-020310B-244Kv5

description: Tumor sample

value: Tumor sample


title: 9830-020025B-244Kv5

description: Tumor sample


title: 9830-030267B-244K2008

description: Tumor sample


title: UNC-030528B-244K2008

description: Tumor sample


title: WashU-15720-244Kv5

description: Tumor sample


title: 9830-030597B-244K2008

description: Tumor sample


title: UNC-010224B-244Kv5

description: Tumor sample


title: 9830-020039B-244Kv5

description: Tumor sample


title: 9830-020340B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-020340B NEW PROTOCOL V5


title: UNC-010509B-244K2008

description: Tumor sample


title: UNC-010208B-244K2008

description: Tumor sample


title: UNC-020320B-244K

description: Tumor sample


title: 9830-010461B-244Kv5

description: Tumor sample


title: 9830-030446B-244Kv5

description: Tumor sample


title: 9830-010214B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-010214B NEW PROTOCOL V5


title: 9830-020018B-244K2008

description: Tumor sample


title: 9830-010384B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-010384B NEW PROTOCOL V5


title: 9830-020416B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-020416B NEW PROTOCOL V5


title: UNC-020155B-244Kv5

description: Tumor sample


title: UNC-010304B-244Kv5

description: Tumor sample


title: 9830-010255B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-010255B NEW PROTOCOL V5


title: UNC-000279B-244K2008

description: Tumor sample


title: UNC-020578B-244k-DGE

description: Tumor sample


title: 9830-020185B-244K2008

description: Tumor sample


title: 9830-010130B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-010130B NEW PROTOCOL V5


title: 9830-010118B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-010118B NEW PROTOCOL V5


title: 9830-000517B-244Kv5

description: Tumor sample


title: 9830-000060B NEW PROTOCOL V5

description: Tumor sample

source_name: 9830-000060B NEW PROTOCOL V5


title: ML-5471-TG2

description: Xenograft

value: Xenograft


title: ML-4189-TG2

description: Xenograft


title: Baylor 4195 TG4

description: Xenograft

source_name: Baylor 4195 TG4


title: ML-5156-TG2

description: Xenograft


title: Baylor 4013 TG1

description: Xenograft

source_name: Baylor 4013 TG1


title: Baylor 3887 TG5

description: Xenograft

source_name: Baylor 3887 TG5


title: Baylor 4913 TG1

description: Xenograft

source_name: Baylor 4913 TG1


title: Baylor 3807 TG5

description: Xenograft

source_name: Baylor 3807 TG5


title: Baylor 3107 TG5

description: Xenograft

source_name: Baylor 3107 TG5


title: Baylor 3904 TG5

description: Xenograft

source_name: Baylor 3904 TG5


title: Baylor 4272 TG1

description: Xenograft

source_name: Human Reference

source_name: Baylor 4272 TG1


title: 9830-000094B-244K

description: Tumor sample


title: Baylor 4888 TG1

description: Xenograft

source_name: Baylor 4888 TG1


title: Baylor 3561 TG5

description: Xenograft

source_name: Baylor 3561 TG5


title: Baylor 4664 TG1

description: Xenograft

source_name: Baylor 4664 TG1


title: Baylor 3204 TG5

description: Xenograft

source_name: Baylor 3204 TG5


title: Baylor 3611 TG5

description: Xenograft

source_name: Baylor 3611 TG5


title: Baylor 3936 TG5

description: Xenograft

source_name: Baylor 3936 TG5


title: Baylor 4175 TG1

description: Xenograft

source_name: Baylor 4175 TG1


title: Baylor 2147 TG6

description: Xenograft

source_name: Baylor 2147 TG6


title: Strain_FL/FL_(HER3-/-_+PI3K)_11-110_Arteaga

status: Public on Jun 20 2013

description: Mammary Tumor

source_name: Whole Mouse Reference RNA

tag: tissue type

value: mammary tumor

tag: genotype/variation

value: ErbB3-/-; PIK3CA-H1047R


title: Baylor 3613A TG5

description: Xenograft

source_name: Baylor 3613A TG5


title: ML-5097-TG2

description: Xenograft


title: ML-5998-TG1

description: Xenograft


title: Baylor 2665A TG6

description: Xenograft

source_name: Baylor 2665A TG6


title: 9830-000424B-244Kv5

description: Tumor sample


title: Strain_FL/+_(HER3+/-_+PI3K)_11-109_Arteaga

description: Mammary Tumor

value: ErbB3+/-; PIK3CA-H1047R


title: Baylor 3963 TG5

description: Xenograft

source_name: Baylor 3963 TG5


title: Baylor 3143 TG5

description: Xenograft

source_name: Baylor 3143 TG5


title: Strain_FL/+_(HER3+/-_+PI3K)_11-107_Arteaga

description: Mammary Tumor

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups


title: Strain_FL/FL_(HER3-/-_+PI3K)_11-108_Arteaga

description: Mammary Tumor


title: Strain_FL/+_(HER3+/-_+PI3K)_11-089_Arteaga

description: Mammary Tumor


title: Strain_FL/FL_(HER3-/-_+PI3K)_11-090_Arteaga

description: Mammary Tumor


title: Strain_FL/+_(HER3+/-_+PI3K)_10-336_Arteaga

description: Mammary Tumor


title: Strain_FL/FL_(HER3-/-_+PI3K)_11-067_Arteaga

description: Mammary Tumor


title: Strain_FL/FL_(HER3-/-_+PI3K)_10-335_Arteaga

description: Mammary Tumor


title: Strain_FL/FL_(HER3-/-_+PI3K)_10-337_Arteaga

description: Mammary Tumor


title: 990543B-repeat-244k-customCGH

status: Public on Apr 22 2013

type: genomic

description: Mammary Tumor

hyb_protocol: Followed protocol described in Agilent Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling Manual, Manual Part Number G4410-90010, Version 6.2

source_name: Promega pooled genomic DNA

extract_protocol: Genomic DNA isolated by Promega

value: Pooled genomic DNA ordered from Promega, collected from multiple anonymous donors

extract_protocol: Genomic DNA isolated using Qiagen Dneasy Kit

tag: age

tag: er  (1=positive; 0=negative)

tag: node status (1=positive=1 or more nodes+; 0=negative)

tag: grade

tag: size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

tag: rfs event (0=no relapse, 1=relapsed at any site or died of disease)

tag: rfs months

tag: overall survival event (0=alive, 1=dod or doc)

tag: overall suvival months

tag: pam50 subtype plus claudin-low

tag: pam50 subtype


title: Strain_FL/+_(HER3+/-_+PI3K)_10-287_Arteaga

description: Mammary Tumor

tag: reference


title: 990357B-244k-customCGH

description: Mammary Tumor

label_protocol: Followed protocol described in Agilent Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling Manual, Manual Part Number G4410-90010, Version 6.2


title: 982118B-244k-customCGH

description: Mammary Tumor


title: 970055B-244k-customCGH

description: Mammary Tumor

value: Claudin


title: BC43T-repeat-244k-customCGH

description: Mammary Tumor


title: BC16T-244k-customCGH

description: Mammary Tumor


title: BC17T-244k-customCGH

description: Mammary Tumor


title: 982049B-repeat-244k-customCGH

description: Mammary Tumor


title: 971091B-244k-customCGH

description: Mammary Tumor


title: 971103B-244k-customCGH

description: Mammary Tumor


title: 971083B-244k-customCGH

description: Mammary Tumor


title: 960606B-244k-customCGH

description: Mammary Tumor


title: 990622B-244k-customCGH

description: Mammary Tumor


title: Strain_FL/+_(HER3+/-_+PI3K)_10-334_Arteaga

description: Mammary Tumor


title: 982048B-repeat-244k-customCGH

description: Mammary Tumor


title: 960047B-244k-customCGH

description: Mammary Tumor


title: 982079B-244k-customCGH

description: Mammary Tumor


title: 950185B-244k-customCGH

description: Mammary Tumor


title: 960096B-244k-customCGH

description: Mammary Tumor


title: 950094B-244k-customCGH

description: Mammary Tumor


title: 971069B-244k-customCGH

description: Mammary Tumor


title: 970105B-244k-customCGH

description: Mammary Tumor


title: 950105B-244k-customCGH

description: Mammary Tumor


title: 950165B-244k-customCGH

description: Mammary Tumor


title: 990276B1-244k-customCGH

description: Mammary Tumor


title: BR-000387B-244k-customCGH

description: Mammary Tumor


title: BR000284B-244k-customCGH

description: Mammary Tumor


title: 940326B-244k-customCGH

description: Mammary Tumor


title: BR950184B-244k-customCGH

description: Mammary Tumor


title: BR000344B-244k-customCGH

description: Mammary Tumor


title: A15-1 LNMet-244k-customCGH

description: Mammary Tumor

source_name: A15-1 LNMet-244k-customCGH


title: A6-1 LivMet-244k-customCGH

description: Mammary Tumor

source_name: A6-1 LivMet-244k-customCGH


title: 000552B-244k-customCGH

description: Mammary Tumor


title: 9830-020018B-244k-customCGH

description: Mammary Tumor


title: BC00097T-244k-customCGH

description: Mammary Tumor


title: BR-000587B-244k-customCGH

description: Mammary Tumor


title: BC00094T-244k-customCGH

description: Mammary Tumor


title: BR-010349B-244k-customCGH

description: Mammary Tumor


title: 010384-244k-customCGH

description: Mammary Tumor


title: 030477B-244k-customCGH

description: Mammary Tumor


title: BC00083-244k-customCGH

description: Mammary Tumor


title: A8-SpiCordMet-244k-customCGH

description: Mammary Tumor


title: 020575B-244k-customCGH

description: Mammary Tumor


title: BC00063T-244k-customCGH

description: Mammary Tumor


title: A12-5 LNMet-244k-customCGH

description: Mammary Tumor

source_name: A12-5 LNMet-244k-customCGH


title: 010509B-244k-customCGH

description: Mammary Tumor


title: A4-LLLmet-244k-customCGH

description: Mammary Tumor


title: BR990348B-244k-customCGH

description: Mammary Tumor


title: 030118B-244k-customCGH

description: Mammary Tumor


title: UNC000161B-244k-customCGH

description: Mammary Tumor


title: 030311B-244k-customCGH

description: Mammary Tumor


title: 9830-010255B-244k-customCGH

description: Mammary Tumor


title: 9830-030584B-244k-customCGH

description: Mammary Tumor


title: 9830-010214B-244k-customCGH

description: Mammary Tumor


title: BR-990207B-244k-customCGH

description: Mammary Tumor


title: 9830-020340B-244k-customCGH

description: Mammary Tumor


title: 9830-010130B-244k-customCGH

description: Mammary Tumor


title: 020416B-244k-customCGH-repeat

description: Mammary Tumor


title: 9830-010118B-244k-customCGH

description: Mammary Tumor


title: BR00-0572B-244k-customCGH-repeat

description: Mammary Tumor


title: BR000504B-244k-customCGH

description: Mammary Tumor


title: 9830-020310B-244k-customCGH-repeat

description: Mammary Tumor


title: A15-1LN-Met

description: Mammary Tumor

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Human Reference B

tag: tumor


title: 000248B-244k-customCGH-repeat

description: Mammary Tumor


title: 9830-000060B-244k-customCGH-repeat

description: Mammary Tumor


title: 000424B-244k-customCGH-repeat

description: Mammary Tumor


title: 9830-030399B-244k-customCGH

description: Mammary Tumor


title: Sum 149_C

description: Mammary Tumor

source_name: Sum 149_C

value: Immortalized Breast Tumor Cell Line, Sum149


title: 020461B-244k-customCGH

description: Mammary Tumor


title: A7-1 LivMet-244k-customCGH-repeat

description: Mammary Tumor

source_name: A7-1 LivMet-244k-customCGH-repeat


title: BC82T-244k-customCGH

description: Mammary Tumor


title: BR-990137B-244k-customCGH

description: Mammary Tumor


title: 000471B-244k-customCGH-repeat

description: Mammary Tumor


title: BC41T-244k-customCGH

description: Mammary Tumor


title: 030446B-244k-customCGH

description: Mammary Tumor


title: SUM149-244k-customCGH

description: Mammary Tumor

tag: pam50 subtype plus claudin-low:

tag: pam50 subtype:


title: Sum 102_C

description: Mammary Tumor

source_name: Sum 102_C

value: Immortalized Breast Tumor Cell Line, Sum102


title: 9830-000517B-244k-customCGH-repeat

description: Mammary Tumor


title: 020185B-244k-customCGH-repeat

description: Mammary Tumor


title: 030065B-244k-customCGH

description: Mammary Tumor


title: SUM102-244k-customCGH

description: Mammary Tumor


title: UNC020510B-244k-customCGH

description: Mammary Tumor


title: BC70T-244k-customCGH

description: Mammary Tumor


title: BC85T-244k-customCGH-repeat

description: Mammary Tumor


title: 990141B-244k-customCGH

description: Mammary Tumor


title: A9-LivMet-244k-customCGH

description: Mammary Tumor


title: UNC020242B-244k-customCGH

description: Mammary Tumor


title: BC24T-244k-customCGH

description: Mammary Tumor


title: UNC-040134B-244k-customCGH

description: Mammary Tumor


title: BC29T-244k-customCGH

description: Mammary Tumor


title: UNC99-0276B-44K

description: Mammary Tumor


title: UNC030459B-244k-customCGH

description: Mammary Tumor


title: UNC-010353B-244k-customCGH

description: Mammary Tumor


title: UNC010208B-244k-customCGH

description: Mammary Tumor


title: UNC040182B-244k-customCGH

description: Mammary Tumor


title: A1-17-244k-customCGH-repeat

description: Mammary Tumor


title: UNC-010456B-244k-customCGH

description: Mammary Tumor


title: UNC99-0363B-44K

status: Public on Feb 19 2013

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.

extract_protocol: Total RNA isolated by Stratagene.

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: ose (0=alive, 1=dod or doc)

tag: osm (os in months)

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)

tag: rfsm (rfs in months)

tag: sex_(1 = female, 0 = male)

value: Female

tag: race_(0 = non-black, 1 = black)

value: White

tag: age_(at breast cancer dx)

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

tag: nodal status (lymph node negative = 0, positive = 1)

tag: metastatic dx (negative = 0, positive = 1 present at diagnosis)

tag: stage at class level

value: II

tag: tissue type

value: Breast Tumor


title: 971083B-244Kv5

description: Mammary Tumor

tag: reference


title: UNC040114B-244k-customCGH

description: Mammary Tumor

tag: age

tag: er  (1=positive; 0=negative)

tag: node status (1=positive=1 or more nodes+; 0=negative)

tag: grade

tag: size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

tag: rfs event (0=no relapse, 1=relapsed at any site or died of disease)

tag: rfs months

tag: overall survival event (0=alive, 1=dod or doc)

tag: overall suvival months

tag: pam50 subtype plus claudin-low

value: LumB

tag: pam50 subtype


title: A5-244k-customCGH

description: Mammary Tumor

value: Basal


title: UNC99-0158B-44K

tag: ose (0=alive, 1=dod or doc)

tag: osm (os in months)

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)

tag: rfsm (rfs in months)

tag: sex_(1 = female, 0 = male)

tag: race_(0 = non-black, 1 = black)

value: Black

tag: age_(at breast cancer dx)

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

tag: her2 status (negative = 0, positive = 1 by ihc)


title: UNC-030408B-244k-customCGH

description: Mammary Tumor

tag: reference

tag: age

tag: er  (1=positive; 0=negative)

tag: node status (1=positive=1 or more nodes+; 0=negative)

tag: grade

tag: size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)


title: 982079B

description: Mammary Tumor

tag: tumor

value: LumA


title: UNC00-0164B-44K

tag: ose (0=alive, 1=dod or doc)

tag: nodal status (lymph node negative = 0, positive = 1)

tag: metastatic dx (negative = 0, positive = 1 present at diagnosis)

tag: stage at class level

tag: tissue type


title: 960047B-244Kv5

description: Mammary Tumor


title: 950105B

description: Mammary Tumor


title: 970105B-244Kv5

description: Mammary Tumor


title: BC86T-244k-customCGH

description: Mammary Tumor

tag: rfs event (0=no relapse, 1=relapsed at any site or died of disease)

tag: rfs months

tag: overall survival event (0=alive, 1=dod or doc)

tag: overall suvival months

tag: pam50 subtype plus claudin-low

tag: pam50 subtype


title: 971069B

description: Mammary Tumor

tag: reference


title: UNC99-0216B-44K

tag: osm (os in months)

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)

tag: sex_(1 = female, 0 = male)

tag: race_(0 = non-black, 1 = black)

tag: age_(at breast cancer dx)

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

tag: her2 status (negative = 0, positive = 1 by ihc)


title: UNC00-0552B-44K

source_name: Breast Tumor

tag: ose (0=alive, 1=dod or doc)

value: Other

tag: nodal status (lymph node negative = 0, positive = 1)

tag: metastatic dx (negative = 0, positive = 1 present at diagnosis)

tag: stage at class level

value: III


title: 990357B

description: Mammary Tumor

tag: tumor


title: BR00-0587B-UNC1X44K

source_name: Human Reference B

tag: rfsm (rfs in months)

tag: tissue type


title: 971091B

description: Mammary Tumor


title: UNC99-0456B-44K

hyb_protocol: Agilent quick amplification kit protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.87

source_name: Human reference

extract_protocol: Total RNA isolated using Qiagen RNeasy mini Kit


title: 982118B-244Kv5

description: Mammary Tumor


title: UNC99-0364B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.86

label_protocol: Agilent quick amplification kit protocol


title: 940326B

description: Mammary Tumor


title: 970055B-244Kv5

description: Mammary Tumor


title: 950094B

description: Mammary Tumor


title: UNC99-0281B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.82

value: IV


title: UNC98-2049B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.77


title: UNC99-0543B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.88


title: 960606B

description: Mammary Tumor

value: Normal