title: HCC123 Cy3 - mAdbID:56960

description: mAdb experiment ID: 56960

source_name: HCC123 - Cy3


title: HCC116 Cy5 - mAdbID:56931

status: Public on Jan 26 2006

type: RNA

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

country: USA

institute: National Cancer institute/NIH

description: mAdb experiment ID: 56931

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

molecule: total RNA

organism: Homo sapiens

source_name: Pooled Normal Liver Sample - Cy3

label_protocol: Cy3 Sample Labeling Protocol - generic

extract_protocol:
CsCl Extraction Protocol
Extraction method: ultracentrifugation

tag: Tissue

value: liver

tag: Developmental stage

value: adult

tag: Cell type

value: Hepatocyte

source_name: HCC116 - Cy5

label_protocol: Cy5 Sample Labeling Protocol - generic

tag: Gender

value: female

tag: Age

tag: Disease state

value: Hepatocellular carcinoma

tag: Individual


title: HCC116 Cy3 - mAdbID:56932

description: mAdb experiment ID: 56932

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC116 - Cy3


title: HCC118 Cy5 - mAdbID:56947

description: mAdb experiment ID: 56947

source_name: HCC118 - Cy5


title: HCC117 Cy5 - mAdbID:56945

description: mAdb experiment ID: 56945

source_name: HCC117 - Cy5


title: HCC113 Cy3 - mAdbID:56926

description: mAdb experiment ID: 56926

source_name: HCC113 - Cy3


title: HCC125 Cy3 - mAdbID:56964

description: mAdb experiment ID: 56964

source_name: HCC125 - Cy3


title: Expression profiling of ovarain cancer cell lines

city: BOSTON

first: Kuan-Chun

last: Huang

state: MA

address: 221 Longwood Ave. BLI-431

department: OB-GYN

institute: Brigham and Women's Hospital

description: Expression profiling between drug sensitive ovarian cancer cell line and drug resistant ovarian cancer cell line.

data_processing: GEM tool

source_name: Drug-sensitive ovarian cancer cell line

tag: A drug sensitive ovarian cancer cell line.

source_name: Drug-resistant ovarian cancer cell line

tag: A multi-drug resistant ovarian cancer cell line.


title: HCC119 Cy3 - mAdbID:56950

description: mAdb experiment ID: 56950

source_name: HCC119 - Cy3


title: HCC117 Cy3 - mAdbID:56946

description: mAdb experiment ID: 56946

source_name: HCC117 - Cy3


title: HCC115 Cy3 - mAdbID:56930

description: mAdb experiment ID: 56930

source_name: HCC115 - Cy3

value: male


title: HCC114 Cy5 - mAdbID:56927

description: mAdb experiment ID: 56927

source_name: HCC114 - Cy5


title: HCC115 Cy5 - mAdbID:56929

description: mAdb experiment ID: 56929

source_name: HCC115 - Cy5


title: HCC119 Cy5 - mAdbID:56949

description: mAdb experiment ID: 56949

source_name: HCC119 - Cy5


title: 8r20 (6.4kv4 array)

status: Public on Jan 25 2006

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

country: Israel

institute: Weizmann Institute

description: S. cerevisiae cells,   Transfered at 8 hours of sporulation to YPD and monitored 20 minutes after the transfer

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience) and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.

organism: Saccharomyces cerevisiae

label_protocol: The cDNA of sporulation derived samples and reference (YPA growing cells) was synthesized from total RNA and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method. The RNA (20 µg) was annealed with 4 µg oligo dT12-18, and reverse-transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2h at 45°C in the presence of 2.5mM MgCl2,  0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. After hydrolysis of RNA in 0.2 M NaOH (30min, 65oC), Tris was removed from the reaction with a Microcon-30 concentrator.

growth_protocol: wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPA. Each YPA culture was monitored 20, 80 and 140 minutes after the transfer.

tag: Strain

value: SK1 wild type (NKY1551), diploid

source_name: S. cerevisiae grown in YPA at 30oC

extract_protocol: 5x10^8 cells were collected, pelleted and immediately frozen. Total RNA was obtained using RNeasy Midi Kit (Qiagen); same RNA was used as reference for the whole series


title: 8r1h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 8 hours of sporulation to YPD and monitored 80 minutes after the transfer

extract_protocol: 5x10^8 cells were collected, pelleted and immediately frozen. Total RNA was obtained using RNeasy Midi Kit (Qiagen)


title: 9r1h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 9 hours of sporulation to YPD and monitored 80 minutes after the transfer


title: 7r2h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 7 hours of sporulation to YPD and monitored 140 minutes after the transfer


title: 9r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 9 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: 5r1h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 5 hours of sporulation to YPD and monitored 80 minutes after the transfer


title: 5r2h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 5 hours of sporulation to YPD and monitored 140 minutes after the transfer


title: 6r2h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 6 hours of sporulation to YPD and monitored 140 minutes after the transfer


title: 7r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 7 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: HCC112 Cy5 - mAdbID:54496

description: mAdb experiment ID: 54496

source_name: Pooled Normal Liver Sample - Cy3

source_name: HCC112 - Cy5


title: HCC112 Cy3 - mAdbID:54497

description: mAdb experiment ID: 54497

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC112 - Cy3


title: HCC113 Cy5 - mAdbID:56925

description: mAdb experiment ID: 56925

source_name: HCC113 - Cy5


title: 4r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 4 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: 4r2h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 4 hours of sporulation to YPD and monitored 140 minutes after the transfer


title: 6r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 6 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: 4r1h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 4 hours of sporulation to YPD and monitored 80 minutes after the transfer


title: 2r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 2 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: 2r1h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 2 hours of sporulation to YPD and monitored 80 minutes after the transfer


title: 5r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 5 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: 2r2h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 2 hours of sporulation to YPD and monitored 140 minutes after the transfer


title: 3r20 (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 3 hours of sporulation to YPD and monitored 20 minutes after the transfer


title: 3r2h20m (6.4kv4 array)

description: S. cerevisiae cells,   Transfered at 3 hours of sporulation to YPD and monitored 140 minutes after the transfer


title: 8s (6.4kv4 array)

description: S. cerevisiae cells,  8 hours of Sporulation


title: 6s (6.4kv4 array)

description: S. cerevisiae cells,  6 hours of Sporulation


title: 9s (6.4kv4 array)

description: S. cerevisiae cells,  9 hours of Sporulation


title: 4s (6.4kv4 array)

description: S. cerevisiae cells,  4 hours of Sporulation


title: 5s (6.4kv4 array)

description: S. cerevisiae cells,  5 hours of Sporulation


title: 3s (6.4kv4 array)

description: S. cerevisiae cells,  3 hours of Sporulation


title: 7s (6.4kv4 array)

description: S. cerevisiae cells,  7 hours of Sporulation


title: 2s (6.4kv4 array)

description: S. cerevisiae cells,  2 hours of Sporulation


title: RTG_6R40_2 (6.4kv4 array)

description: sum1 deleted cells, Transfered at 6 hours of sporulation to YPD and harvested 40 minutes after the transfer

data_processing: : For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.

source_name: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPD and harvested 40 minutes after the transfer

growth_protocol: sum1 deleted SK1 cells (JPY214) were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight.   The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At 6 hours of the sporulation process, cells were kept for RNA extraction. Part of the culture was centrifuged and resuspended in YPD, and was monitored 20 and 40 minutes after the transfer.

value: SK1 cells, in which sum1 is deleted (JPY214) , diploid


title: Sporulation_6h_2 (6.4kv4 array)

description: sum1 deleted cells, 6 hours of Sporulation

source_name: S. cerevisiae cells, 6 hours of Sporulation


title: RTG_9R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to glucose and harvested 40 minutes after the transfer

growth_protocol: wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in glucose solution (4%). Each glucose culture was monitored immediately after the transfer, after 20 and 40 minutes.


title: RTG_5.5R40 (6.4kv4 array)

description: SPS4p-NDT80 cells, Transfered at 5.5 hours of sporulation to YPD and harvested 40 minutes after the transfer

source_name: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPD and harvested 40 minutes after the transfer

growth_protocol: SK1 cells, in which NDT80 is expressed under the promoter of SPS4 (GF18), were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight.   The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At 5.5 hours of the sporulation process, cells were kept for RNA extraction. Part of the culture was centrifuged and resuspended in YPD, and was monitored immediately, 20 and 40 minutes after the transfer.

value: SK1 cells, in which NDT80 is expressed under the promoter of SPS4 (GF18), diploid


title: RTG_5.5R0 (6.4kv4 array)

description: SPS4p-NDT80 cells, Transfered at 5.5 hours of sporulation to YPD and harvested immediately after the transfer

source_name: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_5.5R20 (6.4kv4 array)

description: SPS4p-NDT80 cells, Transfered at 5.5 hours of sporulation to YPD and harvested 20 minutes after the transfer

source_name: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_9R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_9R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_8R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_7R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_8R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_4R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_8R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_5R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_3R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: Sporulation_5.5h (6.4kv4 array)

description: SPS4p-NDT80 cells, 5.5 hours of Sporulation

source_name: S. cerevisiae cells, 5 hours of Sporulation


title: RTG_6R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_3R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_5R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_3R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_4R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_6R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_6R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_7R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_7R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_4R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_5R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to glucose and harvested immediately after the transfer


title: RTG_2R40 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to glucose and harvested 40 minutes after the transfer


title: RTG_2R20 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to glucose and harvested 20 minutes after the transfer


title: RTG_2R0 (6.4kv4 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to glucose and harvested immediately after the transfer


title: Sporulation_6h (6.4kv4 array)

description: S. cerevisiae cells, 6 hours of Sporulation


title: Sporulation_5h (6.4kv4 array)

description: S. cerevisiae cells, 5 hours of Sporulation


title: Sporulation_9h (6.4kv4 array)

description: S. cerevisiae cells, 9 hours of Sporulation


title: Sporulation_7h (6.4kv4 array)

description: S. cerevisiae cells, 7 hours of Sporulation


title: Sporulation_8h (6.4kv4 array)

description: S. cerevisiae cells, 8 hours of Sporulation


title: RTG_9R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to YPD and harvested 20 minutes after the transfer

growth_protocol: Cells were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. Part of that culture was used as reference for all hybridizations preformed in this study. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPD. Each YPD culture was monitored immediately after the transfer, after 20 and 40 minutes.


title: Sporulation_4h (6.4kv4 array)

description: S. cerevisiae cells, 4 hours of Sporulation


title: RTG_8R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to YPA and harvested immediately after the transfer

growth_protocol: wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPA. Each YPA culture was monitored immediately after the transfer, after 20 and 40 minutes.


title: RTG_10R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 10 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_9R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_10R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 10 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_8R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_8R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_7R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: HCC121 Cy3 - mAdbID:56956

description: mAdb experiment ID: 56956

source_name: HCC121 - Cy3


title: RTG_10R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 10 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_8R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_10R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 10 hours of sporulation to YPD and harvested immediately after the transfer


title: Sporulation_3h (6.4kv4 array)

description: S. cerevisiae cells, 3 hours of Sporulation


title: RTG_10R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 10 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_9R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_7R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_9R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_8R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_10R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 10 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_6R20_2 (6.4kv4 array)

description: sum1 deleted cells, Transfered at 6 hours of sporulation to YPD and harvested 20 minutes after the transfer

source_name: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: Sporulation_2h (6.4kv4 array)

description: S. cerevisiae cells, 2 hours of Sporulation


title: RTG_8R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 8 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_7R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_7R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_7R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_7R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 7 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_6R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_6R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_6R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_6R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_6R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_5R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_5R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_5R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_5R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_5R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_6R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 6 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_4R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_3R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_4R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to YPD and harvested immediately after the transfer


title: RTG_2R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_3R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_3R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_3R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: RTG_2R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_4R20 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to YPA and harvested 20 minutes after the transfer


title: RTG_4R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_2R40 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to YPD and harvested 40 minutes after the transfer


title: RTG_4R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to YPA and harvested immediately after the transfer


title: Sporulation_8h (16k1.2 array)

description: S. cerevisiae cells, 8 hours of Sporulation


title: Sporulation_9h (16k1.2 array)

description: S. cerevisiae cells, 9 hours of Sporulation


title: RTG_3R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_2R0 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to YPA and harvested immediately after the transfer


title: RTG_4R40 (16k1.2 array)

description: S. cerevisiae cells, Transfered at 4 hours of sporulation to YPA and harvested 40 minutes after the transfer


title: RTG_3R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 3 hours of sporulation to YPD and harvested immediately after the transfer


title: Sporulation_2h (6.4k1v2 array)

description: S. cerevisiae cells, 2 hours of Sporulation


title: Sporulation_7h (16k1.2 array)

description: S. cerevisiae cells, 7 hours of Sporulation


title: RTG_2R0 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to YPD and harvested immediately after the transfer


title: Sporulation_6h (16k1.2 array)

description: S. cerevisiae cells, 6 hours of Sporulation


title: RTG_2R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 2 hours of sporulation to YPD and harvested 20 minutes after the transfer


title: Sporulation_4h (16k1.2 array)

description: S. cerevisiae cells, 4 hours of Sporulation


title: Sporulation_9h (6.4kv2 array)

source_name: S. cerevisiae cells, 9 hours of Sporulation


title: Sporulation_8h (6.4kv2 array)

source_name: S. cerevisiae cells, 8 hours of Sporulation


title: Sporulation_6h (6.4kv2 array)


title: Sporulation_10h (6.4kv2 array)

description: S. cerevisiae cells, 10 hours of Sporulation


title: sporesR30 (6.4kv3.48 array)

description: 3 days old spores were transfered YPD and monitored 30 minutes after the transfer

source_name: S. cerevisiae cells, 3 days old spores were transfered to YPD and harvested  40 minutes after the transfer

growth_protocol: Wild type SK1 cells (DS1) were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours and plated on sporulation plates (0.25% yeast extract, 1.5% Potassium acetate, 0.05% glucose supplemented with all amino acids).  3 days old asci were harvested and suspended in YPD at 30oC to initiate spore germination. RNA for microarray hybridization was extracted at the indicated times.

value: SK1 wild type (DS1), diploid

source_name: S. cerevisiae logarithmic growing haploid cells. Mata and Mat? cells were grown separately in YPD. RNA was extracted and pooled together.

value: SK1 wild type Mata and Mat? cells that were pooled after RNA extraction


title: Sporulation_5h (6.4kv2 array)

description: S. cerevisiae cells, 5 hours of Sporulation

source_name: S. cerevisiae grown in YPA at 30oC


title: Sporulation_3h (16k1.2 array)

description: S. cerevisiae cells, 3 hours of Sporulation


title: Sporulation_2h (16k1.2 array)

source_name: S. cerevisiae cells, 2 hours of Sporulation


title: Sporulation_5h (16k1.2 array)


title: spores (6.4kv3.48 array)

description: 3 days old spores

source_name: S. cerevisiae cells, 3 days old spores


title: sporesR15 (6.4kv3.48 array)

description: 3 days old spores were transfered YPD and monitored 15 minutes after the transfer

source_name: S. cerevisiae cells, 3 days old spores were transfered to YPD and harvested  20 minutes after the transfer


title: Sporulation_3h (6.4k1v2 array)

source_name: S. cerevisiae cells, 3 hours of Sporulation


title: Sph 1, chip MOE430B

status: Public on Jan 24 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis.
Stembase Experiment ID:			E205
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205
SCGP Sample ID:				S269
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_246
Short description:			Adult mouse muscle was enzymatically dissociated. Muscle derived stem cells proliferate unattached, in spheres, in the proliferation medium.
Analysis requested:			mouse genechips
RNA concentration:			0.336ug/uL
Sample volume:				14uL total

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

label: Biotin

organism: Mus musculus

source_name: derived stem cell, muscle

growth_protocol:
Growth medium:				DMEM/F12 (1:1)
Media supplements:			EFG, B27, FGF
Culture conditions:			7 days

extract_protocol: RNA prep method:				Trizol

tag: Strain:					C57BC/10J


title: Sph 3, chip MOE430B


title: Sporulation_4h (6.4kv2 array)

source_name: S. cerevisiae cells, 4 hours of Sporulation


title: Sph 2, chip MOE430B


title: D4-E1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S169
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_129
Short description:			Early passage, low chimerism, no germline transmission.
Estimated purity:				>90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul

source_name: C57 BL/6 ES cells (D4), Blastocyst

growth_protocol:
Growth medium:				DMEM with 15% fetal bovine serum
Media supplements:			LIF, sodium pyruvate, non-essential amino acids, beta-mercaptoethanol, glutamine
Culture conditions:			5% CO2, 37 C

extract_protocol:
RNA prep method:				RNeasy
Contaminating cell type:			Mouse primary embryonic fibroblasts (MEF)
Method for estimating purity:		ES cells grown on MEFs were trypsinized lightly to keep feeders attached. Cell suspension plated on fresh plate at 37 C for 1 hour

treatment_protocol: Assays to confirm viability:		Production of chimeras

tag: Strain:					C57 BL/6

tag: Gender:					Male

tag: Karyotype:				Normal


title: D4-E2, chip MOE430B


title: D4-A2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S167
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_127
Short description:			Late passage, high chimerism, germline, attached.
Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul

growth_protocol:
Growth medium:				Thromb-XTX-WES
Media supplements:			LIF, sodium pyruvate, non-essential amino acids, beta-mercaptoethanol, glutamine
Culture conditions:			5% CO2, 37 C


title: C2-E2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S166
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_126
Short description:			Early passage, low chimerism, no germline transmission., !Sample_description = Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul

source_name: C57 BL/6 ES cells (C2), Blastocyst


title: C2-A3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S164
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_124
Short description:			Late passage, high chimerism, germline, attached.
Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul

extract_protocol:
RNA prep method:				RNeasy
Contaminating cell type:			Mouse primary embryonic fibroblasts (MEF)
Method for estimating purity:		ES cells grown on MEFs were trypsinized lightly to keep feeders attached. Cell suspension plated on fresh plate at 37 C for 1 hour.


title: D4-E3, chip MOE430B


title: DIF 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis.
Stembase Experiment ID:			E205
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205
SCGP Sample ID:				S270
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_247
Short description:			Cells from sphere were incubated in a differentiation medium. They differentiated into neurons after 7 days in culture.
Analysis requested:			mouse genechips
RNA concentration:			0.689 ug/uL
Sample volume:				15 uL total

growth_protocol:
Growth medium:				DMEM/F12 (1:1)
Media supplements:			FBS NGF
Culture conditions:			7 days

extract_protocol:
RNA prep method:				Trizol
Contaminating cell type:			Myoblast, fibroblast
Method for estimating purity:		Immunocytochemistry

tag: Defining markers:				beta III tubulin


title: C2-D3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S165
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_125
Short description:			Late passage, high chimerism, germline, detached.
Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6 cells
Sample volume:				11 ul

tag: Karyotype:				normal


title: DIF 1, chip MOE430B


title: DIF 3, chip MOE430B


title: C2-A2, chip MOE430B


title: C2-D1, chip MOE430B


title: D4-D1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S168
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_128
Short description:			Late passage, high chimerism, germline, detached.
Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul


title: D4-A1, chip MOE430B


title: D4-D3, chip MOE430B


title: D4-A3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S167
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_127
Short description:			Late passage, high chimerism, germline, attached.
Estimated purity:				~90%
RNA concentration:			11.0 ul
Num cells for RNA prep:			2.0 ug/ul
Sample volume:				~10X10e6


title: C2-E3, chip MOE430B


title: C2-A1, chip MOE430B


title: C2-E1, chip MOE430B


title: P19aD2 (2), chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S132
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_100
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6

source_name: P19 Mouse embryonal carcinoma, Embryonic

growth_protocol:
Growth medium:				Alpha medium
Media supplements:			2.5% fetal bovine serum, 7.5% calf serum
Culture conditions:			Suspension culture

extract_protocol:
RNA prep method:				RNeasy
Method for estimating purity:		Pure clonal cell culture

treatment_protocol: Assays to confirm viability:		Northern probed for Brachyery confirm early stages of differentiation were initiated. Cultures allowed to incubate further contained expected the differentiated cell types, skeletal muscle and neurons.

tag: Strain:					C3H/He

tag: Karyotype:				XY:40


title: C2-D2, chip MOE430B


title: P19aD2 (3), chip MOE430B


title: Sporulation_7h (6.4kv2 array)

description: S. cerevisiae cells, 7 hours of Sporulation


title: P19aD2 (1), chip MOE430B


title: P19mD2 (1), chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S131
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_99
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6

growth_protocol:
Growth medium:				Alpha medium
Media supplements:			2.5% fetal bovine serum, 7.5% calf serum
Culture conditions:			Monolayer culture


title: DIF 1, chip MOE430A


title: P19mD1 (3), chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S129
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_97
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6

treatment_protocol: Assays to confirm viability:		Northern probed for Brachyery confirm early stages of differentiation were initiated. Cultures allowed to incubate further contained the expected differentiated cell types, skeletal muscle and neurons.


title: Sph 2, chip MOE430A


title: Sph 3, chip MOE430A


title: DIF 2, chip MOE430A


title: D4-E2, chip MOE430A


title: P19mD1 (1), chip MOE430B


title: P19mD1 (2), chip MOE430B


title: DIF 3, chip MOE430A


title: D4-E3, chip MOE430A


title: P19aD1 (3), chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S130
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_98
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6


title: Sph 1, chip MOE430A


title: D4-A3, chip MOE430A


title: D4-A2, chip MOE430A


title: D4-E1, chip MOE430A


title: D4-D1, chip MOE430A


title: P19mD2 (2), chip MOE430B


title: P19aD1 (1), chip MOE430B


title: D4-A1, chip MOE430A


title: C2-E3, chip MOE430A


title: C2-E2, chip MOE430A


title: C2-E1, chip MOE430A


title: HIF1a RNAi RL3 12h Hypoxia

city: Stanford

first: Edwin

last: Rodriguez

state: CA

address: Beckman, B439

institute: UC Stanford

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57999.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: stratagene Universal Control RNA

tag: stratagene Universal Control RNA

source_name: HIF1a RNAi RL3 12h Hypoxia

tag: HIF1a RNAi RL3 12h Hypoxia


title: RPTEC 6hr, 20%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45604.gif; format: GIF

source_name: Strategene

tag: Strategene

source_name: RPTEC 6hr, 20%

tag: RPTEC 6hr, 20%


title: Coronary EC hypoxia, 2% 3 hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39327.gif; format: GIF

source_name: Coronary EC hypoxia, 2% 3 hr

tag: Coronary EC hypoxia, 2% 3 hr


title: P19mD2 (3), chip MOE430B


title: C2-D3, chip MOE430A


title: HIF1a RNAi 0 12h Hypoxia

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58002.gif; format: GIF

source_name: HIF1a RNAi 0 12h Hypoxia

tag: HIF1a RNAi 0 12h Hypoxia


title: RPTEC#2, hypoxia 24hr, 20%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47097.gif; format: GIF

source_name: Stratagene

tag: Stratagene

source_name: RPTEC#2, hypoxia 24hr, 20%O2

tag: RPTEC#2, hypoxia 24hr, 20%O2


title: D4-D3, chip MOE430A


title: Coronary EC hypoxia, 3 hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39326.gif; format: GIF

source_name: Coronary EC hypoxia, 3 hr

tag: Coronary EC hypoxia, 3 hr


title: RPTEC#2, hypoxia 24hr, 2%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47098.gif; format: GIF

source_name: RPTEC#2, hypoxia 24hr, 2%O2

tag: RPTEC#2, hypoxia 24hr, 2%O2


title: P19aD1 (2), chip MOE430B


title: RPTEC#2, hypoxia 12hr, 0%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47096.gif; format: GIF

source_name: RPTEC#2, hypoxia 12hr, 0%O2

tag: RPTEC#2, hypoxia 12hr, 0%O2


title: C2-D2, chip MOE430A

tag: Strain:					C57 BL/6

tag: Gender:					Male


title: C2-D1, chip MOE430A


title: HIF1a RNAi T4 12h Hypoxia

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57996.gif; format: GIF

source_name: HIF1a RNAi T4 12h Hypoxia

tag: HIF1a RNAi T4 12h Hypoxia


title: HIF1a RNAi 0 12h CTL

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57991.gif; format: GIF

source_name: HIF1a RNAi 0 12h CTL

tag: HIF1a RNAi 0 12h CTL


title: C2-A3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S164
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_124
Short description:			Late passage, high chimerism, germline, attached.
Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul

tag: Karyotype:				Normal


title: HIF1a RNAi GL3 12h CTL

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57989.gif; format: GIF

source_name: HIF1a RNAi GL3 12h CTL

tag: HIF1a RNAi GL3 12h CTL


title: Coronary EC hypoxia, 2% 1hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39324.gif; format: GIF

source_name: Coronary EC hypoxia, 2% 1hr

tag: Coronary EC hypoxia, 2% 1hr


title: Coronary EC hypoxia, T0

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39322.gif; format: GIF

source_name: Coronary EC hypoxia, T0

tag: Coronary EC hypoxia, T0


title: Coronary EC hypoxia, 1hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39323.gif; format: GIF

tag: Strategene

source_name: Coronary EC hypoxia, 1hr

tag: Coronary EC hypoxia, 1hr


title: HIF1a RNAi 3UTR 12h Hypoxia

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57992.gif; format: GIF

source_name: stratagene Universal Control RNA

tag: stratagene Universal Control RNA

source_name: HIF1a RNAi 3UTR 12h Hypoxia

tag: HIF1a RNAi 3UTR 12h Hypoxia


title: HIF1a RNAi T4 12h CTL

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57988.gif; format: GIF

source_name: HIF1a RNAi T4 12h CTL

tag: HIF1a RNAi T4 12h CTL


title: SM, CorA, 12hr 20%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42581.gif; format: GIF

tag: Stratagene

source_name: SM, CorA, 20%O2 12hr

tag: SM, CorA, 20%O2 12hr


title: Coronary EC hypoxia,  0% 24 hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39331.gif; format: GIF

source_name: Strategene

source_name: Coronary EC hypoxia,  0% 24 hr

tag: Coronary EC hypoxia,  0% 24 hr


title: HIF1a RNAi T3 12h CTL

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57987.gif; format: GIF

source_name: HIF1a RNAi T3 12h CTL

tag: HIF1a RNAi T3 12h CTL


title: HIF1a RNAi T3 12h Hypoxia

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57993.gif; format: GIF

source_name: HIF1a RNAi T3 12h Hypoxia

tag: HIF1a RNAi T3 12h Hypoxia


title: Coronary EC hypoxia, 0% 1hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39325.gif; format: GIF

source_name: Coronary EC hypoxia, 0% 1hr

tag: Coronary EC hypoxia, 0% 1hr


title: SM, CorA, 6hr 0%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42580.gif; format: GIF

source_name: Stratagene

source_name: SM, CorA, 0%O2 6hr

tag: SM, CorA, 0%O2 6hr


title: HIF1a RNAi RL3 12h CTL

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57990.gif; format: GIF

source_name: HIF1a RNAi RL3 12h CTL

tag: HIF1a RNAi RL3 12h CTL


title: Coronary EC hypoxia,  2% 24 hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39330.gif; format: GIF

source_name: Coronary EC hypoxia,  2% 24 hr

tag: Coronary EC hypoxia,  2% 24 hr


title: HIF1a RNAi UTR3 12h CTL

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57986.gif; format: GIF

source_name: HIF1a RNAi UTR3 12h CTL

tag: HIF1a RNAi UTR3 12h CTL


title: HMEC_hypoxia, 24hr, 0%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44505.gif; format: GIF

source_name: HMEC_hypoxia, 24hr, 0%

tag: HMEC_hypoxia, 24hr, 0%


title: C2-A1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Marina Gertsenstein (gertsenstein@mshri.on.ca; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID:			E124
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID:				S164
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_124
Short description:			Late passage, high chimerism, germline, attached.
Estimated purity:				~90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~10X10e6
Sample volume:				11.0 ul

source_name: C57 BL/6 ES cells (C2), Blastocyst

tag: Strain:					C57 BL/6

tag: Gender:					Male

tag: Karyotype:				Normal


title: C2-A2, chip MOE430A


title: HIF1a RNAi GL3 12h Hypoxia

description:
Simple annotation: Hypoxia, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57997.gif; format: GIF

tag: stratagene Universal Control RNA

source_name: HIF1a RNAi GL3 12h Hypoxia

tag: HIF1a RNAi GL3 12h Hypoxia


title: HMEC_hypoxia, 24hr, 20%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44503.gif; format: GIF

source_name: HMEC_hypoxia, 24hr, 20%

tag: HMEC_hypoxia, 24hr, 20%


title: HMEC_hypoxia, 24hr, 2%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44504.gif; format: GIF

tag: Stratagene

source_name: HMEC_hypoxia, 24hr, 2%

tag: HMEC_hypoxia, 24hr, 2%


title: P19aD2 (1), chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S132
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_100
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6

source_name: P19 Mouse embryonal carcinoma, Embryonic

tag: Strain:					C3H/He

tag: Karyotype:				XY:40


title: P19aD2 (2), chip MOE430A


title: HMEC_hypoxia, 12hr, 2%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44501.gif; format: GIF

source_name: HMEC_hypoxia, 12hr, 2%

tag: HMEC_hypoxia, 12hr, 2%


title: SM, CorA, 6hr 20%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42578.gif; format: GIF

source_name: SM, CorA, 20%O2 6hr

tag: SM, CorA, 20%O2 6hr


title: RPTEC#2, hypoxia 12hr, 2%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47095.gif; format: GIF

source_name: RPTEC#2, hypoxia 12hr, 2%O2

tag: RPTEC#2, hypoxia 12hr, 2%O2


title: P19mD2 (3), chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S131
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_99
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6


title: P19mD2 (2), chip MOE430A


title: RPTEC#2, hypoxia 6hr, 0%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47093.gif; format: GIF

source_name: RPTEC#2, hypoxia 6hr, 0%O2

tag: RPTEC#2, hypoxia 6hr, 0%O2


title: SM, CorA, 3hr 2%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42576.gif; format: GIF

source_name: SM, CorA, 2%O2 3hr

tag: SM, CorA, 2%O2 3hr


title: RPTEC#2, hypoxia 12hr, 20%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47094.gif; format: GIF

source_name: RPTEC#2, hypoxia 12hr, 20%O2

tag: RPTEC#2, hypoxia 12hr, 20%O2


title: SM, CorA, 6hr 2%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42579.gif; format: GIF

source_name: Stratagene

source_name: SM, CorA, 2%O2 6hr

tag: SM, CorA, 2%O2 6hr


title: P19aD2 (3), chip MOE430A


title: SM, CorA, 1hr 0%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42574.gif; format: GIF

source_name: SM, CorA, 0%O2 1hr

tag: SM, CorA, 0%O2 1hr


title: Coronary EC hypoxia, 0% 3 hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39328.gif; format: GIF

source_name: Strategene

tag: Strategene

source_name: Coronary EC hypoxia, 0% 3 hr

tag: Coronary EC hypoxia, 0% 3 hr


title: HMEC_hypoxia, 12hr, 20%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44500.gif; format: GIF

source_name: HMEC_hypoxia, 12hr, 20%

tag: HMEC_hypoxia, 12hr, 20%


title: P19mD2 (1), chip MOE430A


title: SM, CorA, 3hr 0%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42577.gif; format: GIF

source_name: SM, CorA, 0%O2 3hr

tag: SM, CorA, 0%O2 3hr


title: SM, CorA, 3hr 20%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42575.gif; format: GIF

source_name: SM, CorA, 20%O2 3hr

tag: SM, CorA, 20%O2 3hr


title: HMEC_hypoxia, 6hr, 0%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44499.gif; format: GIF

tag: Stratagene

source_name: HMEC_hypoxia, 6hr, 0%

tag: HMEC_hypoxia, 6hr, 0%


title: P19aD1 (3), chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S130
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_98
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6

tag: Strain:					C3H/He


title: SM, CorA, 1hr 20%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42572.gif; format: GIF

source_name: SM, CorA, 20%O2 1hr

tag: SM, CorA, 20%O2 1hr


title: HMEC_hypoxia, 3hr, 0%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44496.gif; format: GIF

source_name: HMEC_hypoxia, 3hr, 0%

tag: HMEC_hypoxia, 3hr, 0%


title: SM, CorA, 1hr 2%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42573.gif; format: GIF

source_name: SM, CorA, 2%O2 1hr

tag: SM, CorA, 2%O2 1hr


title: HMEC_hypoxia, 6hr, 2%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44498.gif; format: GIF

source_name: HMEC_hypoxia, 6hr, 2%

tag: HMEC_hypoxia, 6hr, 2%


title: RPTEC#2, hypoxia 6hr, 20%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47091.gif; format: GIF

source_name: RPTEC#2, hypoxia 6hr, 20%O2

tag: RPTEC#2, hypoxia 6hr, 20%O2


title: HMEC_hypoxia, 6hr, 20%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44497.gif; format: GIF

source_name: HMEC_hypoxia, 6hr, 20%

tag: HMEC_hypoxia, 6hr, 20%


title: RPTEC 24hr,  0%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45620.gif; format: GIF

source_name: RPTEC 24hr,  0%

tag: RPTEC 24hr,  0%


title: RPTEC 24hr, 2%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45619.gif; format: GIF

source_name: RPTEC 24hr, 2%

tag: RPTEC 24hr, 2%


title: HMEC_hypoxia, 3hr, 2%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44495.gif; format: GIF

source_name: Stratagene

source_name: HMEC_hypoxia, 3hr, 2%

tag: HMEC_hypoxia, 3hr, 2%


title: P19aD1 (1), chip MOE430A

source_name: P19 Mouse embryonal carcinoma, Embryonic

tag: Karyotype:				XY:40


title: P19aD1 (2), chip MOE430A


title: RPTEC#2, hypoxia 6hr, 2%O2

description:
Simple annotation: Hypoxia, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47092.gif; format: GIF

source_name: RPTEC#2, hypoxia 6hr, 2%O2

tag: RPTEC#2, hypoxia 6hr, 2%O2


title: HMEC_hypoxia, 3hr, 20%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44494.gif; format: GIF

source_name: HMEC_hypoxia, 3hr, 20%

tag: HMEC_hypoxia, 3hr, 20%


title: HMEC_hypoxia, 1hr, 2%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44493.gif; format: GIF

source_name: HMEC_hypoxia, 1hr, 2%

tag: HMEC_hypoxia, 1hr, 2%


title: RPTEC 24hr, 20%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45618.gif; format: GIF

source_name: Strategene

tag: Strategene

source_name: RPTEC 24hr, 20%

tag: RPTEC 24hr, 20%


title: RPTEC 12hr, 0%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45617.gif; format: GIF

source_name: RPTEC 12hr,0%

tag: RPTEC 12hr,0%


title: P19mD1 (3), chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael McBurney (michael.mcburney@orcc.on.ca; 503 Smyth Road) for analysis.
Stembase Experiment ID:			E97
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97
SCGP Sample ID:				S129
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=97#SAMPLE_97
Short description:			Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			2x10e6 to 3x10e6

tag: Strain:					C3H/He


title: P19mD1 (1), chip MOE430A


title: HMEC_hypoxia, 1hr, 20%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44491.gif; format: GIF

tag: Stratagene

source_name: HMEC_hypoxia, 1hr, 20%

tag: HMEC_hypoxia, 1hr, 20%


title: SM, CorA, 24hr 0%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42594.gif; format: GIF

source_name: SM, CorA, 0%O2 24hr

tag: SM, CorA, 0%O2 24hr


title: Patient_1373_Cy3

status: Public on Jan 21 2006

city: Heidelberg

first: Olaf

last: Thuerigen

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center

description: aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).

data_processing: spot replicates were averaged. Spots not recognized by the image analysis software "GenePix Pro 5.0" (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well.

source_name: 2µg breast tissue total RNA from patient Patient_1373, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

tag: Grading

value: no data, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:4, bcl2_Score:0

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:not eligible, ypN:NA, cT_max:NA, bcl2_Score:NA


title: RPTEC 12hr, 2%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45608.gif; format: GIF

source_name: RPTEC 12hr, 2%

tag: RPTEC 12hr, 2%


title: Patient_1402_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1402, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:8, PR:9, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:5, bcl2_Score:2


title: P19mD1 (2), chip MOE430A


title: Patient_1396_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1396, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:3, ER:2, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:3, bcl2_Score:3


title: Patient_1396_Cy5


title: Patient_1400_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1400, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:5, bcl2_Score:0


title: Patient_1373_Cy5


title: SM, CorA, 12hr 0%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42591.gif; format: GIF

source_name: Stratagene

source_name: SM, CorA, 0%O2 12hr

tag: SM, CorA, 0%O2 12hr


title: SM, CorA, 24hr 20%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42592.gif; format: GIF

source_name: SM, CorA, 20%O2 24hr

tag: SM, CorA, 20%O2 24hr


title: RPTEC 6hr, 2%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45605.gif; format: GIF

source_name: RPTEC 6hr, 2%

tag: RPTEC 6hr, 2%


title: SM, CorA, 12hr 2%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42590.gif; format: GIF

source_name: SM, CorA, 2%O2 12hr

tag: SM, CorA, 2%O2 12hr


title: RPTEC 12hr, 20%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45607.gif; format: GIF

source_name: RPTEC 12hr, 20%

tag: RPTEC 12hr, 20%


title: Patient_1400_Cy5


title: HMEC_hypoxia, 1hr, 0%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44492.gif; format: GIF

source_name: HMEC_hypoxia, 1hr, 0%

tag: HMEC_hypoxia, 1hr, 0%


title: Patient_1405_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1405, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:6, PR:2, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:3


title: HMEC_hypoxia, 12hr, 0%

description:
Simple annotation: Hypoxia, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44502.gif; format: GIF

source_name: HMEC_hypoxia, 12hr, 0%

tag: HMEC_hypoxia, 12hr, 0%


title: RPTEC 6hr, 0%

description:
Simple annotation: Hypoxia, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45606.gif; format: GIF

source_name: Strategene

source_name: RPTEC 6hr, 0%

tag: RPTEC 6hr, 0%


title: Patient_1411_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1411, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:2, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:1


title: Patient_1410_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1410, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pNC, ypN:N0, cT_max:5.2, bcl2_Score:0

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).


title: Patient_1388_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1388, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:1, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:2.2, bcl2_Score:0


title: Patient_1405_Cy3


title: Patient_1378_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1378, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:5.5, bcl2_Score:0


title: Patient_1389_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1389, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:2


title: Patient_1388_Cy5


title: SM, CorA, 24hr 2%O2

description:
Simple annotation: Hypoxia, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42593.gif; format: GIF

source_name: Stratagene

source_name: SM, CorA, 2%O2 24hr

tag: SM, CorA, 2%O2 24hr


title: Patient_1395_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1395, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:6, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.7, bcl2_Score:1


title: Patient_1389_Cy3


title: Patient_1395_Cy3


title: Patient_1384_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1384, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G1, HER2:1, ER:6, PR:8, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.2, bcl2_Score:3


title: Patient_1397_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1397, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:3, ER:2, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:1


title: Patient_1410_Cy5


title: Patient_1390_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1390, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3.5, bcl2_Score:0


title: Patient_1413_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1413, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:2


title: Patient_1390_Cy5


title: Patient_1397_Cy3


title: Patient_1406_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1406, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:8, PR:8, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:3, bcl2_Score:2


title: Patient_1378_Cy5


title: Patient_1384_Cy5


title: Patient_1377_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1377, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N+, cT_max:3, bcl2_Score:0


title: Patient_1377_Cy3

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:not eligible, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_1408_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1408, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: no data, HER2:0, ER:6, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:3


title: Patient_1409_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1409, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:4, bcl2_Score:0


title: Coronary EC hypoxia,  24 hr

description:
Simple annotation: Endothelial cells, Anaerobic growth
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39329.gif; format: GIF

source_name: Strategene

tag: Strategene

source_name: Coronary EC hypoxia,  24 hr

tag: Coronary EC hypoxia,  24 hr


title: Patient_1394_Cy5

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).

source_name: 2µg breast tissue total RNA from patient Patient_1394, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:6, PR:6, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:7, bcl2_Score:0


title: Patient_1413_Cy3


title: Patient_1404_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1404, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.5, bcl2_Score:3


title: Patient_1408_Cy5


title: Patient_1385_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1385, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N+, cT_max:2.2, bcl2_Score:0


title: Patient_1409_Cy3


title: Patient_1394_Cy3


title: Patient_1404_Cy5


title: Patient_1374_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1374, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:2.5, bcl2_Score:0


title: Patient_1414_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1414, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:8, PR:4, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:4.4, bcl2_Score:0


title: Patient_1414_Cy3


title: Patient_1379_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1379, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:6, PR:9, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:ND, bcl2_Score:1


title: Patient_1379_Cy3


title: Patient_1383_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1383, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:6, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:2.1, bcl2_Score:3


title: Patient_1385_Cy5


title: Patient_1406_Cy5


title: Patient_1411_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1411, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:2, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:1


title: Patient_1386_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1386, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:8, PR:4, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3.3, bcl2_Score:1


title: Patient_1374_Cy5


title: Patient_1386_Cy5


title: Patient_1415_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1415, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_1380_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1380, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:4, PR:9, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:2.2, bcl2_Score:2


title: Patient_1402_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1402, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:8, PR:9, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:5, bcl2_Score:2


title: Patient_1383_Cy3


title: Patient_1380_Cy5


title: Patient_1415_Cy3


title: Patient_1382_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_1382, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.6, bcl2_Score:1


title: Patient_1382_Cy3


title: Patient_847_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_847, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:6, PR:6, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:2.6, bcl2_Score:0

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:no data, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_866_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_866, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:8, PR:2, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.5, bcl2_Score:1


title: Patient_847_Cy5


title: Patient_850_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_850, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:2


title: Patient_853_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_853, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pNC, ypN:N+, cT_max:4.5, bcl2_Score:0

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).


title: Patient_851_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_851, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:9, PR:4, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:2


title: Patient_867_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_867, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:2.5, bcl2_Score:2


title: Patient_866_Cy5


title: Patient_849_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_849, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3.5, bcl2_Score:0


title: Patient_1398_Cy5

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:not eligible, ypN:NA, cT_max:NA, bcl2_Score:NA

source_name: 2µg breast tissue total RNA from patient Patient_1398, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:6, bcl2_Score:0


title: Patient_849_Cy5


title: Patient_1398_Cy3


title: Patient_850_Cy5


title: Patient_854_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_854, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G1, HER2:0, ER:4, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:2.5, bcl2_Score:3


title: Patient_853_Cy5


title: Patient_855_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_855, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:6, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:2.5, bcl2_Score:1


title: Patient_856_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_856, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:3.5, bcl2_Score:3


title: Patient_852_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_852, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: no data, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:2


title: Patient_861_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_861, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:4, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:0


title: Patient_856_Cy3


title: Patient_858_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_858, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:5, bcl2_Score:0


title: Patient_860_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_860, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:1, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:3, bcl2_Score:0


title: Patient_854_Cy5


title: Patient_858_Cy5


title: Patient_859_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_859, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:1, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:2


title: Patient_855_Cy3

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:no data, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_861_Cy5


title: Patient_860_Cy5


title: Patient_865_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_865, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:2, ER:9, PR:6, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:5, bcl2_Score:1


title: Patient_851_Cy3


title: Patient_859_Cy3


title: Patient_862_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_862, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:4, PR:12, Therapy_Status_Pathological:pPR, ypN:ND, cT_max:5, bcl2_Score:1


title: Patient_870_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_870, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:4, PR:8, Therapy_Status_Pathological:pNC, ypN:N+, cT_max:2.5, bcl2_Score:2


title: Patient_867_Cy3


title: Patient_864_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_864, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:3, ER:2, PR:9, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:4.6, bcl2_Score:0


title: Patient_863_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_863, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:0, Therapy_Status_Pathological:pNC, ypN:N+, cT_max:8, bcl2_Score:2

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).


title: Patient_869_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_869, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:5, bcl2_Score:3


title: Patient_864_Cy5


title: Patient_869_Cy5


title: Patient_862_Cy3


title: Patient_863_Cy5


title: Patient_865_Cy5


title: Patient_5_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_5, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G1, HER2:0, ER:6, PR:6, Therapy_Status_Pathological:pNC, ypN:N0, cT_max:4, bcl2_Score:2

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:NA, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_20_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_20, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:4, PR:6, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:0


title: Patient_19_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_19, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:6, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:2


title: Patient_46_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_46, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_5_Cy5


title: Patient_29_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_29, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:5, PR:6, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_28_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_28, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:8, PR:8, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:2.1, bcl2_Score:1


title: Patient_54_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_54, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:8, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:6, bcl2_Score:0


title: Patient_20_Cy3


title: Patient_2_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_2, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:7, bcl2_Score:0


title: Patient_63_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_63, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:2.1, bcl2_Score:0


title: Patient_46_Cy3


title: Patient_870_Cy3

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:no data, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_33_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_33, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:2.6, bcl2_Score:0


title: Patient_63_Cy3


title: Patient_71_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_71, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:6, PR:4, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:2


title: Patient_28_Cy5


title: Patient_33_Cy5


title: Patient_23_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_23, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:5, bcl2_Score:0


title: Patient_71_Cy3


title: Patient_23_Cy5


title: Patient_2_Cy5


title: Patient_54_Cy5


title: Patient_40_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_40, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3.3, bcl2_Score:3


title: Patient_19_Cy3


title: Patient_8_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_8, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:4, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_56_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_56, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:4, PR:0, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:6.5, bcl2_Score:0


title: Patient_8_Cy5

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).


title: Patient_18_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_18, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_9_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_9, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:4, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:2

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:NA, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_9_Cy5


title: Patient_48_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_48, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:0


title: Patient_27_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_27, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:0


title: Patient_70_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_70, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:6, Therapy_Status_Pathological:pNC, ypN:N+, cT_max:6, bcl2_Score:0


title: Patient_30_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_30, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:3, PR:6, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:3


title: Patient_59_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_59, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G1, HER2:0, ER:6, PR:6, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3, bcl2_Score:3


title: Patient_1_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_1, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:4, PR:8, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:2.3, bcl2_Score:0


title: Patient_36_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_36, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:0, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:10, bcl2_Score:0


title: Patient_29_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_29, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:5, PR:6, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_1_Cy5


title: Patient_32_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_32, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:1, ER:12, PR:12, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:10, bcl2_Score:0


title: Patient_18_Cy5


title: Patient_34_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_34, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G1, HER2:0, ER:6, PR:6, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:2.9, bcl2_Score:2


title: Patient_17_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_17, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:6, PR:8, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_50_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_50, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:9, PR:12, Therapy_Status_Pathological:pNC, ypN:N+, cT_max:2.6, bcl2_Score:2


title: Patient_73_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_73, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:12, PR:9, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:2.7, bcl2_Score:2


title: Patient_17_Cy5


title: Patient_50_Cy5


title: Patient_30_Cy3


title: Patient_73_Cy3


title: Patient_49_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_49, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:0, ER:8, PR:8, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:4, bcl2_Score:0


title: Patient_49_Cy5

source_name: 2µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000), amplified and labeled using TAcKLE Protocol (PMID: 15718295).


title: Patient_10_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_10, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:5, bcl2_Score:0


title: Patient_13_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_13, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:1, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.5, bcl2_Score:0


title: Patient_42_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_42, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:1, ER:6, PR:6, Therapy_Status_Pathological:pPR, ypN:N0, cT_max:3.2, bcl2_Score:3

value: NA, HER2:NA, ER:NA, PR:NA, Therapy_Status_Pathological:NA, ypN:NA, cT_max:NA, bcl2_Score:NA


title: Patient_41_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_41, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pPR, ypN:N+, cT_max:3, bcl2_Score:0


title: Patient_22_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_22, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G2, HER2:3, ER:9, PR:12, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:6, bcl2_Score:2


title: Patient_39_Cy3

source_name: 2µg breast tissue total RNA from patient Patient_39, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:3, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:5.5, bcl2_Score:1


title: Patient_22_Cy3


title: Patient_26_Cy5

source_name: 2µg breast tissue total RNA from patient Patient_26, amplified and labeled using TAcKLE Protocol (PMID: 15718295).

value: G3, HER2:0, ER:0, PR:0, Therapy_Status_Pathological:pCR, ypN:N0, cT_max:3.9, bcl2_Score:0


title: Patient_10_Cy3


title: Patient_13_Cy5