title: JA917 (WZ33) Replicate 1


title: JA916 (WZ33) Replicate 2

status: Public on Dec 16 2009

type: genomic

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

description: These samples were hybridized to two color-reversal arrays

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Complexity-reduced representations, consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit

tag: tissue

value: Ductal Breast Carcinoma

tag: cell line

value: EBV Immortalized Fibroblast Reference


title: JA922 (WZ36) Replicate 2


title: JA943 (WZ43) Replicate 1


title: JA814 (WZ20) Replicate 2


title: JA915 (WZ32) Replicate 1


title: JA912 (WZ31) Replicate 2


title: JA913 (WZ31) Replicate 1


title: JA919 (WZ34) Replicate 1


title: JA815 (WZ20) Replicate 1


title: JA924 (WZ37) Replicate 2


title: JA811 (WZ18) Replicate 1


title: JA806 (WZ16) Replicate 2


title: JA813 (WZ19) Replicate 1


title: JA810 (WZ18) Replicate 2


title: JA812 (WZ19) Replicate 2


title: JA808 (WZ17) Replicate 2


title: JA796 (WZ11) Replicate 2


title: JA809 (WZ17) Replicate 1


title: JA914 (WZ32) Replicate 2


title: JA803 (WZ14) Replicate 1


title: EL694 (MicMa709) Replicate 2


title: JA798 (WZ12) Replicate 2


title: JA801 (WZ13) Replicate 1


title: JA802 (WZ14) Replicate 2


title: JA805 (WZ15) Replicate 1


title: JA797 (WZ11) Replicate 1


title: JA807 (WZ16) Replicate 1


title: EL689 (MicMa391) Replicate 1


title: EL690 (MicMa391) Replicate 2


title: JA804 (WZ15) Replicate 2


title: JA800 (WZ13) Replicate 2


title: EL693 (MicMa709) Replicate 1


title: EL691 (MicMa627) Replicate 1


title: EL687 (MicMa357) Replicate 1


title: EL685 (MicMa246) Replicate 1


title: JA799 (WZ12) Replicate 1


title: EL688 (MicMa357) Replicate 2


title: EL681 (MicMa232) Replicate 1


title: EL678 (MicMa146) Replicate 2


title: EL682 (MicMa232) Replicate 2


title: EL674 (MicMa101) Replicate 2


title: EL673 (MicMa101) Replicate 1


title: EL677 (MicMa146) Replicate 1


title: EL675 (MicMa122) Replicate 1


title: EL686 (MicMa246) Replicate 2


title: EL669 (MicMa089) Replicate 1


title: EL670 (MicMa089) Replicate 2


title: EL664 (MicMa052) Replicate 2


title: EL671 (MicMa098) Replicate 1


title: EL659 (MicMa570) Replicate 1


title: EL660 (MicMa570) Replicate 2


title: EL676 (MicMa122) Replicate 2


title: EL653 (MicMa150) Replicate 1


title: EL663 (MicMa052) Replicate 1


title: EL658 (MicMa539) Replicate 2


title: EL656 (MicMa285) Replicate 2


title: EL654 (MicMa150) Replicate 2


title: EL692 (MicMa627) Replicate 2


title: EL649 (MicMa330) Replicate 1


title: EL655 (MicMa285) Replicate 1


title: EL672 (MicMa098) Replicate 2


title: EL665 (MicMa083) Replicate 1


title: EL666 (MicMa083) Replicate 2


title: EL657 (MicMa539) Replicate 1


title: EL646 (MicMa269) Replicate 2


title: EL650 (MicMa330) Replicate 2


title: EL648 (MicMa281) Replicate 2


title: EL645 (MicMa269) Replicate 1


title: EL651 (MicMa359) Replicate 1


title: EL652 (MicMa359) Replicate 2


title: EL640 (MicMa130) Replicate 2


title: EL641 (MicMa144) Replicate 1


title: EL643 (MicMa210) Replicate 1


title: EL638 (MicMa107) Replicate 2


title: EL647 (MicMa281) Replicate 1


title: EL644 (MicMa210) Replicate 2


title: EL636 (MicMa087) Replicate 2


title: EL634 (MicMa077) Replicate 2


title: EL637 (MicMa107) Replicate 1


title: EL642 (MicMa144) Replicate 2


title: EL633 (MicMa077) Replicate 1


title: EL627 (MicMa066) Replicate 1


title: EL622 (MicMa010) Replicate 2


title: EL630 (MicMa069) Replicate 2


title: EL629 (MicMa069) Replicate 1


title: EL215 (MicMa171) Replicate 1


title: EL628 (MicMa066) Replicate 2


title: EL624 (MicMa016) Replicate 2


title: EL626 (MicMa064) Replicate 2


title: EL623 (MicMa016) Replicate 1


title: EL639 (MicMa130) Replicate 1


title: EL176 (MicMa221) Replicate 2


title: EL173 (MicMa220) Replicate 1


title: EL625 (MicMa064) Replicate 1


title: EL621 (MicMa010) Replicate 1


title: EL175 (MicMa221) Replicate 1


title: EL170 (MicMa218) Replicate 2


title: EL172 (MicMa187) Replicate 2


title: EL213 (MicMa167) Replicate 1


title: EL631 (MicMa075) Replicate 1


title: EL171 (MicMa187) Replicate 1


title: EL174 (MicMa220) Replicate 2


title: EL168 (MicMa209) Replicate 2


title: EL635 (MicMa087) Replicate 1


title: Pseudomonas-treatment 2

status: Public on Oct 07 2010

type: RNA

city: Potsdam

first: Jens

last: Schwachtje

address: Am Mühlenberg 1

department: Energy Metabolism

country: Germany

institute: Max-Planck-Institute for Molecular Plant Physiology

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ GeneChip Expression Analysis Technical Manual. The final concentration of cRNA was 60 ng/μl. Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4.

data_processing: Data (.cel files) were quality-checked and normalized using robust multi array averaging (rma) with ROBIN software (Lohse et al. 2010) and analyzed with MapMan software (Usadel et al. 2005).

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Whole Arabidopsis seedlings, 18 days old

label_protocol: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II 96 Kit (Cat. No. 1819), starting with 1 μg of total RNA

growth_protocol: One or two Arabidopsis seedlings were grown in 1.5 ml Eppendorf tubes, from which the tip was cut off. The tubes contained sandy soil and were placed on peat substrate. Light conditions were 12 light/12 dark at 20°C and 18 °C, respectively.

extract_protocol: Twenty-five seedlings were pooled for each of three  replicates per treatment. RNA was extracted from seedlings with RNeasy Mini Kit from Quiagen according to the manufacturer´s protocol.

treatment_protocol: Six hours before harvesting 18-day old seedlings, 500 µl of P. sp. G62 (OD 0.5 in 10 mM MgSO4), or MgSO4 only for controls was applied to the medium.

value: whole seedling

tag: ecotype

tag: age

value: 18 days

tag: treatment group

value: pseudomonas treated


title: EL169 (MicMa218) Replicate 1


title: EL216 (MicMa171) Replicate 2


title: EL214 (MicMa167) Replicate 2


title: EL632 (MicMa075) Replicate 2


title: EL167 (MicMa209) Replicate 1


title: EL164 (MicMa190) Replicate 2


title: EL160 (MicMa163) Replicate 2


title: EL161 (MicMa165) Replicate 1


title: EL162 (MicMa165) Replicate 2


title: EL153 (MicMa137) Replicate 1


title: EL159 (MicMa163) Replicate 1


title: DE492 (WZ10) Replicate 1


title: DE494 (WZ25) Replicate 2


title: EL156 (MicMa139) Replicate 2


title: EL157 (MicMa140) Replicate 1


title: EL155 (MicMa139) Replicate 1


title: DE487 (WZ29) Replicate 2


title: EL154 (MicMa137) Replicate 2


title: DE496 (WZ30) Replicate 1


title: DE493 (WZ25) Replicate 1


title: DE485 (WZ28) Replicate 2


title: DE495 (WZ30) Replicate 2


title: DE488 (WZ29) Replicate 1


title: DE483 (WZ27) Replicate 2


title: DE489 (WZ6) Replicate 2


title: DE490 (WZ6) Replicate 1


title: DE486 (WZ28) Replicate 1


title: DE482 (WZ26) Replicate 1


title: DE481 (WZ26) Replicate 2


title: DE434 (WZ85) Replicate 1


title: DE491 (WZ10) Replicate 2


title: genotype: Cree - time: 3 days - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Cree grains after 3 days of germination replication 3

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: seed (genotype: Cree - time: 3 days)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Trizol RNA extraction followed by RNeasy purification

tag: germplasm name

value: hv cv. cree

tag: organism part

tag: development stage

tag: growth media

value: not specified

value: 3 days


title: DE423 (WZ75) Replicate 2


title: DE425 (WZ76) Replicate 2


title: DE430 (WZ83) Replicate 1


title: DE428 (WZ82) Replicate 1


title: DE433 (WZ85) Replicate 2


title: DE429 (WZ83) Replicate 2


title: DE421 (WZ73) Replicate 2


title: DE424 (WZ75) Replicate 1


title: DE432 (WZ84) Replicate 1


title: DE484 (WZ27) Replicate 1


title: DE427 (WZ82) Replicate 2


title: EL163 (MicMa190) Replicate 1


title: DE419 (WZ72) Replicate 2


title: DE420 (WZ72) Replicate 1


title: DE426 (WZ76) Replicate 1


title: DE406 (WZ70) Replicate 1


title: DE422 (WZ73) Replicate 1


title: EL158 (MicMa140) Replicate 2


title: DE408 (WZ71) Replicate 1


title: DE403 (WZ69) Replicate 2


title: DE405 (WZ70) Replicate 2


title: DE431 (WZ84) Replicate 2


title: DE401 (WZ68) Replicate 2


title: DE399 (WZ48) Replicate 2


title: DE397 (WZ66) Replicate 2


title: DE396 (WZ65) Replicate 1


title: DE400 (WZ48) Replicate 1


title: DE398 (WZ66) Replicate 1


title: DE394 (WZ64) Replicate 1


title: DE393 (WZ64) Replicate 2


title: DE372 (WZ59) Replicate 1


title: DE387 (WZ61) Replicate 2


title: DE395 (WZ65) Replicate 2


title: DE391 (WZ63) Replicate 2


title: DE388 (WZ61) Replicate 1


title: DE386 (WZ60) Replicate 1


title: DE367 (WZ54) Replicate 2


title: DE390 (WZ62) Replicate 1


title: DE385 (WZ60) Replicate 2


title: DE404 (WZ69) Replicate 1


title: DE366 (WZ52) Replicate 1


title: DE368 (WZ54) Replicate 1


title: DE389 (WZ62) Replicate 2


title: DE370 (WZ58) Replicate 1


title: DE365 (WZ52) Replicate 2


title: DE371 (WZ59) Replicate 2


title: DE392 (WZ63) Replicate 1


title: DE361 (WZ49) Replicate 2


title: DE364 (WZ51) Replicate 1


title: JA697 (WZ9) Replicate 2


title: DE359 (WZ41) Replicate 2


title: DE358 (WZ40) Replicate 1


title: DE362 (WZ49) Replicate 1


title: DE360 (WZ41) Replicate 1


title: DE357 (WZ40) Replicate 2


title: DE402 (WZ68) Replicate 1


title: JA689 (WZ5) Replicate 2


title: GIC-1

status: Public on Dec 01 2009

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

hyb_protocol: Labeled probes were used for the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the manufacturer’s instructions.

data_processing: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix) to generate CEL data. The CEL data were then analyzed with dChip software, which can normalize and process multiple datasets simultaneously.

organism: Mus musculus

source_name: mouse NSC

label_protocol: Five micrograms of total RNA were labeled with biotin by in vitro transcription (IVT) using the One-Cycle Target Labeling procedure for biotin labeling by in vitro transcription (Affymetrix), according to the manufacturer’s instruction.

growth_protocol: Neuroepithelial cells were prepared from embryonic day 14.5 mouse telencephalon and expanded in serum-free Dulbecco's Modified Eagle's medium (DMEM) /F12 medium containing bovine insulin (10 μg/ml), human transferrin (100 μg/ml), BSA (100 μg/ml), progesterone (60 ng/ml), putrescine (16 μg/ml), sodium selenite (40 ng/ml), N-acetylcysteine (60 μg/ml), forskolin (5 μM), PDGF (10 ng/ml), penicillin, streptomycin, and bFGF as floating spheres. Neural stem cells (NSCs) were transfected with pCMS-EGFP-HRasL61 and pBabe-neo by electroporation and cultured in 0.5 mg/ml neomycin. The GFP-positive stable NSCs (NSCL61s) were purified by flow cytometry.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (QIAGEN).

tag: strain

tag: genome/variation

tag: developmental stage

value: E14.5 embryo

value: brain

tag: cell type

value: neural stem cells

tag: tumorigenic subline

value: Glioma Initiating Cell-like cells


title: GIC-2

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix) to generate CEL data.


title: JA695 (WZ8) Replicate 2


title: non-GIC-2

tag: nontumorigenic subline

value: non-Glioma Initiating Cell-like cells


title: non-GIC-1


title: JA698 (WZ9) Replicate 1


title: JA685 (WZ3) Replicate 2


title: JA688 (WZ4) Replicate 1


title: DE363 (WZ51) Replicate 2


title: JA682 (WZ1) Replicate 1


title: CD4_uninfected sample control_rep1 pull 2 ATE 105

status: Public on Oct 01 2009

city: Lausanne

first: Margalida

last: Rotger

address: Bugnon 48

department: University of Lausanne

country: Switzerland

institute: Institute of Microbiology

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were processed using a variance-stabilizing transformation and a robust-spline normalization, as implemented in the lumi package of R

source_name: CD4 T cells purified from frozen PBMC from HIV infected individuals

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

extract_protocol: Total RNA was extracted from purified CD4+ T cells using mirVana miRNA isolation kit (Ambion) according to the manufacturer’s protocol for total RNA extraction. Quality control was performed with Agilent Bioanalyser.

value: CD4 T cells

tag: source

value: frozen PBMC

tag: group

value: Healthy blood donors

tag: viral load set point


title: CD4_uninfected sample control_rep2 pull 1_ATE 078

scan_protocol: Standard Illumina hybridization protocol


title: CD4_uninfected sample control_rep1 pull 1 ATE 063


title: JA686 (WZ3) Replicate 1

tag: tissue

tag: cell line


title: JA690 (WZ5) Replicate 1


title: CD4_uninfected sample control_rep3 pull 3 ATE 057


title: CD4_uninfected sample control_rep3 pull 2_ATE 196


title: CD4_uninfected sample control_rep1 pull 3_ATE 048


title: CD4_uninfected sample control_rep2 pull 2_ATE 108


title: CD4_uninfected sample control_rep2 pull 3_ATE 051


title: CD4_Untreated  NT5629

value: HIV infected individuals


title: JA683 (WZ2) Replicate 2

value: Ductal Breast Carcinoma


title: JA684 (WZ2) Replicate 1

value: EBV Immortalized Fibroblast Reference


title: JA681 (WZ1) Replicate 2


title: DE407 (WZ71) Replicate 2


title: CD4_succesfully treated 5628


title: CD4_succesfully treated paired 5626


title: CD4_Untreated 5623


title: CD4_Untreated paired NT5626


title: CD4_Untreated  NT5620


title: JA687 (WZ4) Replicate 2


title: CD4_Untreated paired NT5565


title: CD4_succesfully treated 5619


title: CD4_succesfully treated paired 5565


title: DE369 (WZ58) Replicate 2


title: CD4_succesfully treated paired 5615


title: CD4_Untreated 5563


title: CD4_Untreated 5616


title: CD4_Untreated 5586


title: CD4_Untreated paired NT5564


title: CD4_Untreated paired NT5613


title: CD4_Untreated paired NT5615


title: CD4_succesfully treated paired 5613


title: CD4_Untreated paired NT5558


title: CD4_Untreated paired NT5560


title: CD4_succesfully treated paired 5560


title: CD4_succesfully treated paired 5562


title: CD4_succesfully treated 5622


title: CD4_Untreated 5569


title: JA694 (WZ7) Replicate 1


title: JA696 (WZ8) Replicate 1


title: CD4_succesfully treated paired 5564


title: JA693 (WZ7) Replicate 2


title: CD4_Untreated paired NT5562


title: CD4_succesfully treated paired 5550


title: CD4_Untreated 5556


title: CD4_Untreated  NT5557


title: CD4_Untreated 5555


title: CD4_Untreated paired NT5550


title: CD4_succesfully treated paired 5534


title: CD4_Untreated 5542


title: CD4_Untreated 5533


title: CD4_Untreated 5532


title: CD4_succesfully treated paired 5558


title: CD4_Untreated NT5545


title: CD4_Untreated 5539


title: CD4_succesfully treated paired 5530


title: CD4_Untreated 5544


title: CD4_Untreated paired NT5518


title: CD4_Untreated paired NT5543


title: CD4_Untreated paired NT5534


title: CD4_Untreated 5510


title: CD4_Untreated NT5528


title: CD4_succesfully treated paired 5543


title: CD4_Untreated  NT5513


title: CD4_succesfully treated 5520


title: CD4_Untreated paired NT5522


title: CD4_succesfully treated paired 5535


title: CD4_Untreated paired NT5535


title: CD4_succesfully treated paired 5508


title: CD4_Untreated 5517


title: CD4_Untreated 5507


title: CD4_succesfully treated paired 5518


title: CD4_Untreated 5504


title: CD4_Untreated NT5519


title: CD4_Untreated 5503


title: CD4_Untreated paired NT5508


title: CD4_Untreated paired NT5530


title: CD4_Untreated 5501


title: CD4_Untreated paired NT5491


title: CD4_succesfully treated paired 5502


title: CD4_Untreated paired NT5502


title: CD4_succesfully treated paired 5497


title: CD4_succesfully treated paired 5500


title: CD4_Untreated paired NT5497


title: CD4_succesfully treated 5483


title: CD4_succesfully treated paired 5491


title: CD4_succesfully treated paired 5470


title: CD4_Untreated paired NT5470


title: CD4_succesfully treated 5496


title: CD4_succesfully treated paired 5498


title: CD4_Untreated 5487


title: CD4_Untreated 5492


title: CD4_succesfully treated 5490


title: CD4_Untreated 5471


title: CD4_Untreated paired NT3999


title: CD4_Untreated  NT5478


title: CD4_Untreated 5475


title: CD4_Untreated paired NT5500


title: CD4_Untreated paired NT5474


title: CD4_Untreated 5493


title: CD4_succesfully treated 5499


title: CD4_succesfully treated 5136


title: CD4_succesfully treated paired 5474


title: CD4_succesfully treated 5140


title: CD4_Untreated NT5002


title: CD4_Untreated paired NT3640


title: CD4_succesfully treated paired 3698


title: CD4_Untreated paired NT5498


title: CD4_succesfully treated paired 3999


title: CD4_succesfully treated paired 3639


title: CD4_Untreated paired NT3639


title: CD4_succesfully treated paired 3640


title: CD4_succesfully treated 3152


title: CD4_Untreated paired NT3698


title: CD4_Untreated NT3641


title: CD4_succesfully treated 3477


title: CD4_Untreated NT3579


title: CD4_succesfully treated paired 3218


title: CD4_Untreated  NT3083


title: CD4_Untreated  NT3100


title: CD4_Untreated paired NT3216


title: CD4_succesfully treated 3307


title: CD4_Untreated NT3423


title: CD4_Untreated paired NT3218


title: CD4_succesfully treated 3149


title: CD4_Untreated  NT3200


title: CD4_succesfully treated paired 3226


title: CD4_succesfully treated 3085


title: CD4_Untreated paired NT3226


title: CD4_Untreated paired NT3195


title: CD4_succesfully treated paired 3216


title: CD4_succesfully treated paired 5522


title: CD4_succesfully treated paired 3195


title: CD4_succesfully treated 5704


title: CD4_Untreated 5688


title: CD4_succesfully treated 5703


title: CD4_succesfully treated 5699


title: CD4_Untreated 5684


title: CD4_Untreated 5687


title: CD4_Untreated 5696


title: CD4_Untreated 5677


title: CD4_Untreated 5665


title: CD4_Untreated NT5701


title: CD4_Untreated 5690


title: CD4_Untreated 5669


title: CD4_Untreated 5683


title: CD4_Untreated 5681


title: CD4_Untreated 5686


title: CD4_Untreated 5668


title: CD4_Untreated NT5663


title: CD4_Untreated paired NT5674


title: CD4_succesfully treated 5685


title: CD4_succesfully treated paired 5674


title: CD4_Untreated 5682


title: CD4_succesfully treated 5659


title: CD4_Untreated 5676


title: CD4_succesfully treated 5672


title: CD4_Untreated 5671


title: CD4_Untreated 5662


title: CD4_Untreated 5675


title: CD4_Untreated 5666


title: CD4_Untreated 5679


title: CD4_succesfully treated 5652


title: CD4_Untreated paired NT5650


title: CD4_succesfully treated paired 5649


title: CD4_Untreated paired NT5649


title: CD4_succesfully treated 5637


title: CD4_Untreated 5646


title: CD4_Untreated 5641


title: CD4_Untreated 5645


title: CD4_succesfully treated paired 5650


title: CD4_succesfully treated 5633


title: CD4_Untreated 3984


title: CD4_Untreated 3517


title: CD4_Untreated 3907


title: CD4_Untreated 5647


title: CD4_Untreated 3595


title: CD4_Untreated 3539


title: CD4_Untreated 3535


title: CD4_Untreated 5627


title: CD4_Untreated 5640


title: CD4_Untreated 3422


title: CD4_Untreated 3713


title: CD4_succesfully treated paired 5554


title: CD4_Untreated 3130


title: CD4_Untreated 3011


title: CD4_Untreated paired NT5554


title: CD4_Untreated 3013


title: CD4_Untreated 3336


title: CD4_Untreated 3131


title: CD4_Untreated 5076


title: CD4_Untreated 5521


title: CD4_Untreated NT5494


title: CD4_Untreated 5486


title: CD4_Untreated 5488


title: Irradiated rat testes, with testosterone supplementation, biological rep 5

status: Public on Sep 30 2009

city: Houston

first: Wei

last: Zhou

state: TX

address: 1515 Holcombe Blvd

department: Department of Experimental Radiation Oncology

institute: M.D.Anderson Cancer Center

description: gene expression data from irradiated rat testes

hyb_protocol: cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner and quantified with Affymetrix GCOS 1.2.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. After normalization, the expression levels within each chip were divided by the median value for all the probes whose expression was regarded as present on the array, and then log base 2 transformed.

organism: Rattus norvegicus

source_name: Irradiated rat testes, with testosterone supplementation (GnRH antagonist and testosterone)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

extract_protocol: Total RNA extraction by RNeasy Midi Kit (Qiagen, Valencia, CA)

treatment_protocol: 6 Gy irradiation to the lower abdomen of the rats

tag: treatment

value: testes

tag: genotype

value: LBNF1 rat

tag: age

value: 25~27 weeks old


title: Irradiated rat testes, with FSH supplementation, biological rep 3

source_name: Irradiated rat testes, with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and FSH)


title: CD4_Untreated 5609


title: Irradiated rat testes, with testosterone supplementation, biological rep 4

value: Irradiated rat testes, with testosterone supplementation (GnRH antagonist and testosterone)


title: Irradiated rat testes, with testosterone supplementation, biological rep 3


title: CD4_succesfully treated 3862


title: Irradiated rat testes, with FSH supplementation, biological rep 1

value: Irradiated rat testes, with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and FSH)


title: CD4_succesfully treated 3073


title: Irradiated rat testes, with testosterone supplementation, biological rep 2


title: CD4_Untreated  NT5505


title: CD4_Untreated 3993


title: CD4_Untreated paired NT5481


title: CD4_Untreated 3078


title: CD4_Untreated paired NT3478


title: CD4_Untreated paired NT5538


title: CD4_succesfully treated paired 5538


title: CD4_succesfully treated 5567


title: Irradiated rat testes, with FSH supplementation, biological rep 5


title: CD4_succesfully treated paired 5481


title: CD4_succesfully treated paired 3478


title: Irradiated rat testes, with FSH supplementation, biological rep 2


title: CD4_succesfully treated 3937


title: CD4_Untreated 3724


title: Irradiated rat testes, with FSH supplementation, biological rep 4


title: CD4_succesfully treated 3487


title: Keap 1 replicate 2

status: Public on Aug 30 2009

city: Dunee

first: simon

middle: matthew

last: plummer

state: Angus

address: 2 James Lindsay Place

department: CXR

country: United Kingdom

institute: CXR Biosciences ltd

description: technical replicate 1

hyb_protocol: Arrays hybridised, washed and scanned on an Agilent Microarray Scanner according to the Agilent 2 colour protocol (G4140-90050)

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.
We further processed the agilent FE files using the Luminator system that makes an error weighted mean of data from the 4 replicates for each of the treatments to generate a 'signature' list.
Luminator-generated list of significantly altered genes files (error weighted mean of replicates made using Luminator) are available on Series record.

label_protocol: 2000 ng total RNA was labeled prior to microarray hybridisation using the Low Input RNA Fluorescent Linear Amplification Kit (Agilent# 5184-3523)

growth_protocol: HACAT cells will be maintained in a CO2 incubator at 37 ºC in Dulbecco’s modified Eagle Medium (DMEM) containing 10% fetal calf serum (FCS) and 2 mM L-glutamine

extract_protocol: 350 ul RLT buffer (Qiagen) cell  lysates were disrupted using a Qiashredder (Qiagen) and RNA purified using RNeasy mini columns according to the protocol on page 31 of the Qiagen manual entitled ‘RNeasy Mini Handbook’.

treatment_protocol: For Keap 1 or scrambled treatments siRNA oligos dissolved in 250 µl of OptiMEM reagent (Invitrogen); the second solution consists of 5 µl of Lipofectamine 2000 in 250 µl of OptiMEM reagent. For reference control treatment cells mock transfected with Optimem and  Lipofectamine

value: KEAP1 siRNA

value: HACAT

source_name: reference control

tag: reference

value: control


title: patient 10, non-del(7q) fibroid

status: Public on Aug 17 2009

city: Rochester

first: Jennelle

last: Hodge

state: MN

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

institute: Mayo Clinic

description: Matched del(7q) and non-del(7q) tumors identified by FISH or karyotyping from each of eleven women.

hyb_protocol: Following purification and fragmentation to reduce secondary structure, hybridization in a Model 640 hybridization chamber to GeneChip Human Genome U133 Plus 2.0 oligonucleotide expression microarrays (Affymetrix) occurred overnight at 45oC.  Arrays were washed using a Model 450 Fluidics station with GeneChip Operating Software (Affymetrix).

scan_protocol: Microarrays were scanned using the GeneChip Model 3000 7G

data_processing: Probe set expression values were calculated by GeneChip software using the MAS 5.0 algorithm

source_name: female non-del(7q) fibroid

label_protocol: Biotinylated according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix GeneChip Expression Analysis Technical Manual revision 4).

extract_protocol: Followed Affymetrix GeneChip Expression Analysis Technical Manual revision 4

value: non-del(7q) fibroid based on interphase FISH


title: Scrambled replicate 2

description: technical replicate 1

source_name: Scram 2

value: Scrambled siRNA


title: patient 11, non-del(7q) fibroid


title: patient 11, myometrium

source_name: female myometrium

value: myometrium


title: patient 10, del(7q) fibroid

source_name: female with del(7q) fibroid

value: del(7q) fibroid = 12% del(7q) nuclei by interphase FISH


title: Scrambled replicate 1

description: biological replicate 1

source_name: Scram 1


title: patient 11, del(7q) fibroid

value: del(7q) fibroid = 71% del(7q) nuclei by interphase FISH


title: Keap 1 replicate 1

description: biological replicate 1


title: Scrambled replicate 4

description: technical replicate 2

source_name: Scram 4


title: patient 9, non-del(7q) fibroid


title: patient 7, myometrium


title: patient 8, del(7q) fibroid

value: del(7q) fibroid = 34% del(7q) nuclei based on interphase FISH


title: patient 8, non-del(7q) fibroid


title: patient 6, non-del(7q) fibroid


title: patient 9, del(7q) fibroid

value: del(7q) fibroid = 37% del(7q) nuclei by interphase FISH


title: patient 8, myometrium


title: CD4_Untreated 3929

value: CD4 T cells

value: frozen PBMC

value: HIV infected individuals


title: patient 10, myometrium


title: patient 9, myometrium


title: patient 6, myometrium


title: Keap 1 replicate 3

description: biological replicate 2


title: Scrambled replicate 3

description: biological replicate 2

source_name: Scram 3


title: patient 5, non-del(7q) fibroid


title: patient 7, non-del(7q) fibroid

value: non-del(7q) fibroid based on intephase FISH


title: Keap 1 replicate 4

description: technical replicate 2


title: patient 7, del(7q) fibroid

value: del(7q) fibroid = 52% del(7q) nuclei by interphase FISH


title: patient 6, del(7q) fibroid

value: del(7q) fibroid = 62% del(7q) nuclei by inteprhase FISH


title: patient 5, del(7q) fibroid

value: del(7q) fibroid = 25% del(7q) nuclei by interphase FISH


title: patient 4, myometrium


title: patient 4, non-del(7q) fibroid


title: patient 5, myometrium


title: patient 3, myometrium


title: patient 3, del(7q) fibroid

value: del(7q) fibroid = 80% del(7q) nuclei by interphase FISH


title: patient 2, del(7q) fibroid

value: del(7q) fibroid = 50% del(7q) nuclei by interphase FISH


title: patient 1, myometrium


title: patient 3, non-del(7q) fibroid


title: patient 1, non-del(7q) fibroid


title: patient 2, non-del(7q) fibroid


title: Global gene expression of NASH patients, Normal control A486

status: Public on Aug 06 2009

city: Buffalo

first: Susan

last: Baker

address: 3435 Main street, 422 BRB

department: Pediatrics

institute: SUNY at Buffalo

description: These samples were derived from liver grafts of normal subjects with normal body mass index.  The ages of these normal controls were matched with our NASH patients.  No liver diseases were diagnosed with these normal controls.  Although the biochemistry data provided by Admet were limited, the healthy status of these livers was ascertained by the lower transcription levels of marker genes for inflammation and fibrosis.

hyb_protocol: 1, Fragmentation of cRNA. 2, Denature cRNA at 90C for 5 min. 3, Hybridization was performed at 37 C, for 18-24 hours. 4, Detection with Cy5-streptavidin conjugate.

scan_protocol: Microarray scanning and data acquisition were done at the gene expression facility, Roswell Park Cancer Institute, following their routine standard procedure.

data_processing: Data were median-normalized for comparison. Medium normalization were done by our collaborators at Roswell Park cancer institute and verified using MS Excel2003.

label: Biotin

source_name: Total RNA purchased from ADMET Technologies (Durham, NC), extracted from healthy liver tissue.

label_protocol:
Complementary DNA was prepared from total RNA.
In vitro transcription was then performed with biotin labeled substrate to produce biotin labeled cRNA.

extract_protocol: Samples were stored in RNAlater at -80 freezer before total RNA extraction with Qiagen RNeasy kit.

tag: disease state

value: normal (control)

value: liver


title: Global gene expression of NASH patients, P37

description: The human studies have been approved by the Institutional Review Board (IRB) of the State University of New York at Buffalo and Women and Children’s Hospital of Buffalo. Liver biopsies were obtained, with prior informed consent, from parents of patients suspected of having NASH as part of regular medical care. Patients from 7 to 18 years of age signed an assent to the research. Diagnosis of NASH was based on hepatic fat infiltration, inflammation and fibrosis as revealed by liver biopsy. Only children and adolescents were included in this study to ensure that our patients were not sustained alcohol users. All NASH patients included in this study exhibited significant insulin resistance (IR). IR was calculated based on the “homeostasis model assessment (HOMA)” method.

source_name: Patient liver biopsy

value: non-alcoholic steatohepatitis (NASH)


title: patient 4, del(7q) fibroid

value: del(7q) fibroid = 78% del(7q) nuclei by interphase FISH


title: Global gene expression of NASH patients, P55

source_name: patient liver biopsy


title: Global gene expression of NASH patient, P59


title: WT vs rpoN rep2

status: Public on Jul 18 2009

city: Hanover

first: Ronald

middle: K

last: Taylor

state: NH

address: N. College Street HB7550

department: Microbiology

institute: Dartmouth Medical School

description: Slide 13-32.DAT

hyb_protocol: Hybridization was carried out in 25% formamide at 42C overnight.

scan_protocol: Arrays were scanned at 550 and 650 nm at 70-90% laser power using a GMS418 Scanner. Images were saved as a tif files and imported into Scanalyze (Michael Eisen v2.50, Stanford University).

data_processing: Data was uploaded into Gene Traffic software (Stratagene v3.2-12). Intensities were normalized using global intensity method. Spots were flagged if intensity was below 2X background. Ratios represent Alexa647/Alexa555 (channel 2/ channel 1).

organism: Vibrio cholerae

source_name: Wild type cells

label_protocol: RNA was reverse transcribed using aadUTP followed by coupling to Alexa647 or Alexa555.

growth_protocol: Bacteria were grown in LBreg at 37 degrees (non-inducing conditions) and synchronized 3 times to OD~0.5.

extract_protocol: Trizol (Invitrogen) extraction and RNAeasy purification column (Qiagen) were used.

tag: genotype/variation

value: wild type

source_name: rpoN mutant

value: rpoN mutant


title: WT vs rpoN rep1

description: Slide 13-31.DAT

tag: strain


title: patient 2, myometrium

value: myometrium


title: CD8+ T-cells_gene therapy treated ADA-SCID_patient3

status: Public on Jul 29 2009

city: Milan

first: Alessandro

last: Aiuti

address: via olgettina 58

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)

description: Gene expression data from CD8+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells

hyb_protocol: Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).

source_name: CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt3

label_protocol: The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.

growth_protocol: Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.

extract_protocol: RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.

treatment_protocol: Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.

value: peripheral blood

value: CD8+ T-cells

tag: treatment type

value: gene therapy treated patient


title: Global gene expression of NASH patients, normal control A643

description: These samples were derived from liver grafts of normal subjects with normal body mass index. The ages of these normal controls were matched with our NASH patients. No liver diseases were diagnosed with these normal controls. Although the biochemistry data provided by Admet were limited, the healthy status of these livers was ascertained by the lower transcription levels of marker genes for inflammation and fibrosis.


title: Global gene expression of NASH patients, P35


title: Global gene expression of NASH patients, P53

description: The human studies have been approved by the Institutional Review Board (IRB) of the State University of New York at Buffalo and Women and Children’s Hospital of Buffalo.  Liver biopsies were obtained, with prior informed consent, from parents of patients suspected of having NASH as part of regular medical care.  Patients from 7 to 18 years of age signed an assent to the research.  Diagnosis of NASH was based on hepatic fat infiltration, inflammation and fibrosis as revealed by liver biopsy.  Only children and adolescents were included in this study to ensure that our patients were not sustained alcohol users.  All NASH patients included in this study exhibited significant insulin resistance (IR).  IR was calculated based on the “homeostasis model assessment (HOMA)” method


title: CD4+ T-cells_gene therapy treated ADA-SCID_patient3

description: Gene expression data from CD4+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt3

value: CD4+ T-cells


title: CD4+ T-cells_gene therapy treated ADA-SCID_patient4

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt4


title: Global gene expression of NASH patients, P41


title: patient 1, del(7q) fibroid

value: del(7q) fibroid = 42.3% del(7q) nuclei by interphase FISH


title: CD8+ T-cells_gene therapy treated ADA-SCID_patient4

source_name: CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt4


title: CD4+ T-cells_gene therapy treated ADA-SCID_patient1

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt1


title: RAG H3K4me3 ID92002b

status: Public on Apr 27 2009

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

description: Chip-chip Rag2-/- pro-B cells H3K4me3

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: log2(Signal Cy5/Signal Cy3) - tukey.biweight(Signal Cy5/Signal Cy3)

source_name: H3K4me3 ChIP DNA from Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice.

value: 5 days in culture

value: pro-B cells

tag: antibody

tag: type

value: ChIP

source_name: Input DNA from Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: see chanel 1

extract_protocol: see chanel 1

treatment_protocol: see chanel 1

value: Input


title: BOEC, VT sample 1

status: Public on Jul 15 2009

city: Minneapolis

first: Robert

middle: P.

last: Hebbel

address: MMC 480, 420 Delaware St. SE

department: Medicine

institute: University of Minnesota

hyb_protocol: After we prepared biotin-labeled cRNA fragments, samples were turned over immediately to our Microarray Core Facility which used Gene Chip Hybridization Oven 640, Affymetrix FS4000 Fluidics Station for staining with a streptavidin-fluorochrome probe and washing,

scan_protocol: An Affymetrix High Resolution Scanner was used according to the manufacturer's standard manual

data_processing: For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays). Expression measures were summarized based on log transformed PM (perfect match) values using Median Polish algorithm. Then, we used locally weighted scatterplot smoothing (LOWESS) to do within-array normalization. RMA and LOWESS were performed in Genedata Expressionist Pro3.1® (Basel, Switzerland).

source_name: BOEC, VT sample 1

label_protocol: We used the Invitrogen SuperScript Choice system to reverse transcribe and synthesize double-stranded cDNA. For in vitro transcription and biotin-labeling, we synthesized biotin-labeled cRNA using the Enzo Life Sciences BioArray High Yield RNA Transcript Labeling kit. Then fragmentation of cRNA was done by standard protocol, and fragmentation was verified by gel electrophoresis.

growth_protocol: We obtained citrated fresh peripheral blood (50-100 ml) from each donor. For donors outside the Minneapolis metropolitan area, blood was shipped by same-day express delivery in Saf-T-Pak cartons that had been pre-equilibrated to room temperature. Samples were processed immediately upon arrival at the University of Minnesota. Blood buffy coat mononuclear cells were prepared and cultured on rat collagen I, in presence of endothelial cell growth factors, as previous described in detail 15,16. All samples were handled identically

extract_protocol: We prepared BOEC lysates by adding 10 ml trizol (Gibco) to each T75 flask to solubilize the sample. As necessary, trizol lysates were stored in liquid nitrogen. We then isolated total RNA, and cleaned it using an RNeasy kit (Qiagen, CA).

treatment_protocol: BOEC were always harvested at passage 3, which comprised a nominal million-fold expansion since establishing culture and amounted to ~3x107 BOEC. They were always harvested 4 hours after the last change of culture medium, and always when they were at 85-90% confluent.

tag: cell type

value: blood outgrowth endothelial cell

tag: vt sample

tag: status

value: Protein C Deficiency

tag: Sex

value: F


title: BOEC, VT sample 2

source_name: BOEC, VT sample 2


title: BOEC, VT sample 3

source_name: BOEC, VT sample 3


title: Irradiated rat testes, with testosterone supplementation, biological rep 1

source_name: Irradiated rat testes, with testosterone supplementation (GnRH antagonist and testosterone)

value: testes

value: LBNF1 rat

value: 25~27 weeks old


title: 8B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

status: Public on Dec 10 2007

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: breast tumor biopsy

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner

scan_protocol: standard Affymetrix procedures

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets using protocol described in Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556

extract_protocol: Biopsies were snap-frozen after collection and stored in liquid nitrogen.  Frozen sections were taken prior to RNA extraction to confirm the presence of cancerous tissue within the specimens.  Only samples in which the malignant component comprised at least 20% of the section area were used in further analyses.  Immediately before RNA extraction the biopsies were pulverised using U2 micro-dismembranator U (Braun Biotech).  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).


title: 7A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 7A;pretreatment;female;breast tumor

tag: 7A;pretreatment;female;breast tumor


title: 69B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 9A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 9A;pretreatment;female;breast tumor

tag: 9A;pretreatment;female;breast tumor


title: 69A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 69A;pretreatment;female;breast tumor

tag: 69A;pretreatment;female;breast tumor


title: 9B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 8A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 8A;pretreatment;female;breast tumor

tag: 8A;pretreatment;female;breast tumor


title: Global gene expression of NASH patients, P40

source_name: Patient liver biopsy

value: non-alcoholic steatohepatitis (NASH)

tag: tissue

value: liver


title: 68A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 68A;pretreatment;female;breast tumor

tag: 68A;pretreatment;female;breast tumor


title: 68B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 65B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 64B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 65A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 65A;pretreatment;female;breast tumor

tag: 65A;pretreatment;female;breast tumor


title: 14763: Cerebellum-wild type-biological rep1

status: Public on Apr 07 2009

first: Maria

last: Chahrour

address: 1 Baylor Plaza, T836

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Gene expression data

hyb_protocol: Following fragmentation of 15.0 mg of the labeled cRNA, a hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array.  The array was hybridized 16 hours

scan_protocol: The array was stained using the EukGEws2v5 protocol on the Fluidics Station 450.  The stained array was scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1 and scale factor of 500. Subsequently, R based analysis using exonmap package and rma normalization

source_name: Cerebellum, wild type

label_protocol: Total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled

extract_protocol: Total RNA was extracted from the cerebellum of 6 weeks old male mice using TRIzol reagent, DNaseI treated, and purified using the RNeasy mini kit, all according to the manufacturers protocols

tag: genotype

value: wild type

tag: gender

value: male

tag: age

value: 6 weeks


title: 63A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 63A;pretreatment;female;breast tumor

tag: 63A;pretreatment;female;breast tumor


title: 14760: Cerebellum-Mecp2-null-biological rep2

description: Gene expression data

source_name: Cerebellum, Mecp2-null

tag: strain


title: 14761: Cerebellum-wild type-biological rep4

description: Gene expression data


title: 14765: Cerebellum-Mecp2-null-biological rep1

description: Gene expression data


title: 63B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 7B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 14439: Cerebellum-MECP2-transgenic-biological rep4

description: Gene expression data

source_name: Cerebellum, MECP2-transgenic

value: FVB


title: 60A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 60A;pretreatment;female;breast tumor

tag: 60A;pretreatment;female;breast tumor


title: 14639: Cerebellum-Mecp2-null-biological rep4

description: Gene expression data


title: 59B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 5A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 5A;pretreatment;female;breast tumor

tag: 5A;pretreatment;female;breast tumor


title: 59A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 59A;pretreatment;female;breast tumor

tag: 59A;pretreatment;female;breast tumor


title: 14641: Cerebellum-Mecp2-null-biological rep3

description: Gene expression data


title: 14433: Cerebellum-MECP2-transgenic-biological rep5

description: Gene expression data


title: 5B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 14728: Cerebellum-Mecp2-null-biological rep5

description: Gene expression data


title: 14438: Cerebellum-wild type-biological rep1

description: Gene expression data


title: 14401: Cerebellum-wild type-biological rep3

description: Gene expression data


title: 14398: Cerebellum-MECP2-transgenic-biological rep2

description: Gene expression data


title: 14732: Cerebellum-wild type-biological rep2

description: Gene expression data


title: 58A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 58A;pretreatment;female;breast tumor

tag: 58A;pretreatment;female;breast tumor


title: 14399: Cerebellum-wild type-biological rep2

description: Gene expression data


title: 14430: Cerebellum-wild type-biological rep5

description: Gene expression data


title: 14640: Cerebellum-wild type-biological rep3

description: Gene expression data


title: 14434: Cerebellum-wild type-biological rep4

description: Gene expression data


title: 57B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 14642: Cerebellum-wild type-biological rep5

description: Gene expression data


title: 55A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 55A;pretreatment;female;breast tumor

tag: 55A;pretreatment;female;breast tumor


title: 14431: Cerebellum-MECP2-transgenic-biological rep3

description: Gene expression data


title: 58B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 14432: Cerebellum-MECP2-transgenic-biological rep1

description: Gene expression data


title: 55B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 56A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 56A;pretreatment;female;breast tumor

tag: 56A;pretreatment;female;breast tumor


title: 51A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 51A;pretreatment;female;breast tumor

tag: 51A;pretreatment;female;breast tumor


title: 56B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 53A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 53A;pretreatment;female;breast tumor

tag: 53A;pretreatment;female;breast tumor


title: 51B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 50A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 50A;pretreatment;female;breast tumor

tag: 50A;pretreatment;female;breast tumor


title: 53B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 57A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 57A;pretreatment;female;breast tumor

tag: 57A;pretreatment;female;breast tumor


title: 52B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 64A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 64A;pretreatment;female;breast tumor

tag: 64A;pretreatment;female;breast tumor


title: 50B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 4B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 52A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 52A;pretreatment;female;breast tumor

tag: 52A;pretreatment;female;breast tumor


title: 60B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 49B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 47B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 49A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 49A;pretreatment;female;breast tumor

tag: 49A;pretreatment;female;breast tumor


title: 48B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 48A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 48A;pretreatment;female;breast tumor

tag: 48A;pretreatment;female;breast tumor


title: 46B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 47A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 47A;pretreatment;female;breast tumor

tag: 47A;pretreatment;female;breast tumor


title: 4A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 4A;pretreatment;female;breast tumor

tag: 4A;pretreatment;female;breast tumor


title: 46A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 46A;pretreatment;female;breast tumor

tag: 46A;pretreatment;female;breast tumor


title: 45B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 45A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 45A;pretreatment;female;breast tumor

tag: 45A;pretreatment;female;breast tumor


title: 44B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 39B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 41A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 41A;pretreatment;female;breast tumor

tag: 41A;pretreatment;female;breast tumor


title: 39A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 39A;pretreatment;female;breast tumor

tag: 39A;pretreatment;female;breast tumor


title: 40A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 40A;pretreatment;female;breast tumor

tag: 40A;pretreatment;female;breast tumor


title: 41B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 37A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 37A;pretreatment;female;breast tumor

tag: 37A;pretreatment;female;breast tumor


title: 40B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 38B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 36B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 42A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 42A;pretreatment;female;breast tumor

tag: 42A;pretreatment;female;breast tumor


title: 37B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 42B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 35A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 35A;pretreatment;female;breast tumor

tag: 35A;pretreatment;female;breast tumor


title: 36A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 36A;pretreatment;female;breast tumor

tag: 36A;pretreatment;female;breast tumor


title: 44A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 44A;pretreatment;female;breast tumor

tag: 44A;pretreatment;female;breast tumor


title: 35B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 34A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 34A;pretreatment;female;breast tumor

tag: 34A;pretreatment;female;breast tumor


title: 34B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 33B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 38A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 38A;pretreatment;female;breast tumor

tag: 38A;pretreatment;female;breast tumor


title: 31A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 31A;pretreatment;female;breast tumor

tag: 31A;pretreatment;female;breast tumor


title: 30B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 2B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 30A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 30A;pretreatment;female;breast tumor

tag: 30A;pretreatment;female;breast tumor


title: 29A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 29A;pretreatment;female;breast tumor

tag: 29A;pretreatment;female;breast tumor


title: 29B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 2A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 2A;pretreatment;female;breast tumor

tag: 2A;pretreatment;female;breast tumor


title: 31B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 33A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 33A;pretreatment;female;breast tumor

tag: 33A;pretreatment;female;breast tumor


title: 28A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 28A;pretreatment;female;breast tumor

tag: 28A;pretreatment;female;breast tumor


title: 20B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 24A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 24A;pretreatment;female;breast tumor

tag: 24A;pretreatment;female;breast tumor


title: 22B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 25A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 25A;pretreatment;female;breast tumor

tag: 25A;pretreatment;female;breast tumor


title: 20A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 20A;pretreatment;female;breast tumor

tag: 20A;pretreatment;female;breast tumor


title: 21B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 18A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 18A;pretreatment;female;breast tumor

tag: 18A;pretreatment;female;breast tumor


title: 28B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 19A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 19A;pretreatment;female;breast tumor

tag: 19A;pretreatment;female;breast tumor


title: 27A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 27A;pretreatment;female;breast tumor

tag: 27A;pretreatment;female;breast tumor


title: 23B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 27B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 24B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 23A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 23A;pretreatment;female;breast tumor

tag: 23A;pretreatment;female;breast tumor


title: 17B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 18B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 22A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 22A;pretreatment;female;breast tumor

tag: 22A;pretreatment;female;breast tumor


title: 19B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 25B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 21A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 21A;pretreatment;female;breast tumor

tag: 21A;pretreatment;female;breast tumor


title: 15A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 15A;pretreatment;female;breast tumor

tag: 15A;pretreatment;female;breast tumor


title: 15B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 16A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 16A;pretreatment;female;breast tumor

tag: 16A;pretreatment;female;breast tumor


title: 14A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 14A;pretreatment;female;breast tumor

tag: 14A;pretreatment;female;breast tumor


title: 13A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 13A;pretreatment;female;breast tumor

tag: 13A;pretreatment;female;breast tumor


title: 12B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 14B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 17A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 17A;pretreatment;female;breast tumor

tag: 17A;pretreatment;female;breast tumor


title: 16B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 12A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 12A;pretreatment;female;breast tumor

tag: 12A;pretreatment;female;breast tumor


title: 11B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 10A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 10A;pretreatment;female;breast tumor

tag: 10A;pretreatment;female;breast tumor


title: 11A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 11A;pretreatment;female;breast tumor

tag: 11A;pretreatment;female;breast tumor


title: 10B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy