|
| Status |
Public on May 07, 2007 |
| Title |
NHGRI_MDA-MB415_HB7-88 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MDA-MB415
|
| Organism |
Homo sapiens |
| Characteristics |
Human Breast cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns
|
| Label |
Cy5
|
| Label protocol |
15-25 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Fluoro dUTP (Cy3/Cy5), after NaOH RNA hydrolysis, the labeled cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104)
|
| |
|
| Channel 2 |
| Source name |
HMEC
|
| Organism |
Homo sapiens |
| Characteristics |
Human Mammary Epithelial cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns
|
| Label |
Cy3
|
| Label protocol |
15-25 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Fluoro dUTP (Cy3/Cy5), after NaOH RNA hydrolysis, the labeled cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104)
|
| |
|
| |
| Hybridization protocol |
The combined Cy3 and Cy5 labeled cDNAs in 30 ul DEPC H20 are denatured for 2 minutes. 15 ul 20X SSC, 5 ul 100% Formamide, 0.5 ul 10% SDS, and 4 ul DEPC H20 are added and the mixture hybridized on the array slide under a coverslip at 65 degre for 16 hours.
|
| Scan protocol |
Agilent Scanner
|
| Description |
Human Breast cell line
|
| Data processing |
IPLab/DeArray
|
| |
|
| Submission date |
Dec 13, 2006 |
| Last update date |
May 07, 2007 |
| Contact name |
Christopher Pan |
| E-mail(s) |
cpan@mail.nih.gov
|
| Organization name |
NIH
|
| Department |
NHGRI
|
| Street address |
Rm 5228, Bldg 50, South Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL4611 |
| Series (1) |
| GSE6567 |
Chromosome 8 BAC Array CGH and Expression Studies Identify Amplification and Overexpression of TRMT12 in Breast Cancer |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log-ratio (log2 of calRatio with low quality (rQuality < 0.5) removed. (float) |
| PenAt |
Pen Position. It is always numbered from left-to-right, and top-to-bottom. (serpentine, start from top-left)(Integer) |
| RowAt |
Within each sub-array (pen), row offset (start from 1 at top-most) to the spot of interest(Integer) |
| ColumnAt |
Within each sub-array (pen), column offset (start from 1 at left-most) to the spot of interest(Integer) |
| SR_top |
Bonding box location in Red channel image coordinates - (top, left, bottom, right) (SR -- Sample in Red channel, or Ch1)(Integer) |
| SR_left |
see above(Integer) |
| SR_bottom |
see above(Integer) |
| SR_right |
see above(Integer) |
| SR_T. Int. |
Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.(Integer) |
| SR_Mean |
Mean Signal Intensity - Average gray-levels within the target area, after trimming top and bottom 5% (background subtracted)(float) |
| SR_S.Dev |
Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity(float) |
| SR_SNR |
Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background std. Dev.(float) |
| SR_iQuality |
The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)(float) |
| SR_bkMean |
Mean background Intensity (float) |
| SR_bkDev |
Std. Dev. Of background intensity(float) |
| SG_top |
Bonding box location in Red channel image coordinates - (top, left, bottom, right) (SG -- Sample in Green channel, or Ch2)(Integer) |
| SG_left |
see above(Integer) |
| SG_bottom |
see above(Integer) |
| SG_right |
see above(Integer) |
| SG_T. Int. |
Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.(Integer) |
| SG_Mean |
Mean Signal Intensity - Average gray-levels within the target area, after trimming top and bottom 5% (background subtracted)(float) |
| SG_S.Dev |
Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity(float) |
| SG_SNR |
Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background variation.(float) |
| SG_iQuality |
The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)(float) |
| SG_bkMean |
Mean background Intensity (float) |
| SG_bkDev |
Std. Dev. Of background intensity(float) |
| unionArea |
Union Area - the detected target area. All calculations are based on this region(Integer) |
| propArea |
Proportional area relatively to the mask size.(float) |
| calRatio |
Calibrated Red-to-Green ratio, (or normalized Ch1/Ch2 ratio)(float) |
| rQuality |
Ratio measurement quality (including all intensity measurement quality, plus the signal-to-noise-ratio requirement).(float) |
| confLevel |
Confidence Level, typically set at 99%(float) |
| lowerLimit |
Lower Limit of confidence interval for cal. Ratio(float) |
| upperLimit |
Upper Limit of confidence interval for cal. Ratio(float) |
| M |
Magnitude parameter for channel compensation(float) |
| CV |
Coefficient of variation of the intensity(float) |
| Flag |
User flagged. 0 - deleted spot by user, 1 - good spot(Integer) |
