title: Kidney - fetal versus Spleen [GenomeTiling_MRK313]


title: Thymus versus Uterus [GenomeTiling_MRK283]

status: Public on Mar 04 2004

type: RNA

city: Seattle

first: Stephen

middle: W

last: Edwards

state: WA

department: Research Genetics

country: USA

institute: Rosetta Inpharmatics (Merck & Co.)

description:
Samples were purchased from Clontech as mRNA.
Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end.  shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3'  shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3'  1.5  g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was  degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C.  The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick).
The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification.  Multiple polymerase chain reactions were run using 0.15  g of double stranded DNA and standard reaction conditions.  Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase)  DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3'  T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3'  followed by Qiaquick purification.
Further amplification was achieved using in vitro transcription reactions with X0.5  g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and  reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II).
The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray.
Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, http://genomebiology.com/2003/4/10/R66 , Roberts CJ et al., Science 2000, 287:873-880, and Schadt, Edwards, et al., unpublished.
Normalization of single channel data is described in Ying, et al., "Identification of Chromosomal Regions Containing Transcribed Sequences Using Microarrays and Computational Methods" , 2003 Proceedings of the American Statistical Association, Biopharmaceutical Section [CD-ROM], Alexandria, VA: American Statistical Association, 2003.
Briefly, an invariant set of probes was selected based on their intensity ranks.  Then, a LOESS regression model was fit for Cy5 vs. Cy3 intensities for all probes in the invariant set.  Finally, for all probes on the array the Cy5 intensities were normalized to the corresponding Cy3 intensities using prediction values from the regression model.
Note that the normalized intensity values given here were used for all analyses reported in the accompanying paper.  The ratio values reported here were not used for the analysis described in the manuscript and are not calculated from the normalized intensity values given below.

molecule: total RNA

organism: Homo sapiens

source_name: Thymus

source_name: Uterus


title: Spleen versus Kidney - fetal [GenomeTiling_MRK282]

source_name: Spleen

source_name: Kidney - fetal


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK282]

source_name: CL: Leukemia Chronic Myelogenous (K562)

source_name: T lymphocyte (Jurkat)


title: Uterus versus Thymus [GenomeTiling_MRK312]


title: Brain - thalamus versus Testis [GenomeTiling_MRK313]

source_name: Brain - thalamus

source_name: Testis


title: Uterus versus Thymus [GenomeTiling_MRK283]


title: Thymus versus Uterus [GenomeTiling_MRK312]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK283]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK279]


title: Testis versus Brain - thalamus [GenomeTiling_MRK282]


title: Uterus versus Thymus [GenomeTiling_MRK282]


title: Testis versus Brain - thalamus [GenomeTiling_MRK312]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK282]


title: Thymus versus Uterus [GenomeTiling_MRK282]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK283]


title: Testis versus Brain - thalamus [GenomeTiling_MRK283]


title: Testis versus Brain - thalamus [GenomeTiling_MRK279]


title: Uterus versus Thymus [GenomeTiling_MRK279]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK283]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK279]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK283]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK279]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK312]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK312]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK282]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK312]


title: Uterus versus Thymus [GenomeTiling_MRK281]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK279]


title: Brain - thalamus versus Testis [GenomeTiling_MRK279]


title: Thymus versus Uterus [GenomeTiling_MRK281]


title: Brain - thalamus versus Testis [GenomeTiling_MRK283]


title: Uterus versus Thymus [GenomeTiling_MRK278]


title: Brain - thalamus versus Testis [GenomeTiling_MRK312]


title: Uterus versus Thymus [GenomeTiling_MRK311]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK312]


title: Thymus versus Uterus [GenomeTiling_MRK311]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK281]


title: Testis versus Brain - thalamus [GenomeTiling_MRK281]


title: Thymus versus Uterus [GenomeTiling_MRK275]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK275]


title: Uterus versus Thymus [GenomeTiling_MRK275]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK281]


title: Brain - thalamus versus Testis [GenomeTiling_MRK282]


title: Thymus versus Uterus [GenomeTiling_MRK278]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK275]


title: Testis versus Brain - thalamus [GenomeTiling_MRK311]


title: Testis versus Brain - thalamus [GenomeTiling_MRK278]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK311]


title: Testis versus Brain - thalamus [GenomeTiling_MRK275]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK278]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK278]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK278]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK281]


title: Thymus versus Uterus [GenomeTiling_MRK273]


title: Brain - thalamus versus Testis [GenomeTiling_MRK278]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK275]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK281]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK311]


title: Brain - thalamus versus Testis [GenomeTiling_MRK281]


title: Uterus versus Thymus [GenomeTiling_MRK273]


title: Thymus versus Uterus [GenomeTiling_MRK277]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK311]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK273]


title: Testis versus Brain - thalamus [GenomeTiling_MRK273]


title: Uterus versus Thymus [GenomeTiling_MRK274]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK311]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK277]


title: Testis versus Brain - thalamus [GenomeTiling_MRK277]


title: Thymus versus Uterus [GenomeTiling_MRK310]


title: Uterus versus Thymus [GenomeTiling_MRK277]


title: Brain - thalamus versus Testis [GenomeTiling_MRK275]


title: Brain - thalamus versus Testis [GenomeTiling_MRK311]


title: Uterus versus Thymus [GenomeTiling_MRK310]


title: Testis versus Brain - thalamus [GenomeTiling_MRK310]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK274]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK273]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK275]


title: Testis versus Brain - thalamus [GenomeTiling_MRK274]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK274]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK278]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK274]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK277]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK274]


title: Brain - thalamus versus Testis [GenomeTiling_MRK274]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK310]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK273]


title: Brain - thalamus versus Testis [GenomeTiling_MRK273]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK310]


title: Uterus versus Thymus [GenomeTiling_MRK272]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK310]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK277]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK277]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK273]


title: Thymus versus Uterus [GenomeTiling_MRK272]


title: Thymus versus Uterus [GenomeTiling_MRK276]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK272]


title: Testis versus Brain - thalamus [GenomeTiling_MRK276]


title: Brain - thalamus versus Testis [GenomeTiling_MRK310]


title: Uterus versus Thymus [GenomeTiling_MRK271]


title: Testis versus Brain - thalamus [GenomeTiling_MRK272]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK266]


title: Thymus versus Uterus [GenomeTiling_MRK266]


title: Uterus versus Thymus [GenomeTiling_MRK266]


title: Uterus versus Thymus [GenomeTiling_MRK276]


title: Thymus versus Uterus [GenomeTiling_MRK271]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK310]


title: Testis versus Brain - thalamus [GenomeTiling_MRK266]


title: Brain - thalamus versus Testis [GenomeTiling_MRK277]


title: Thymus versus Uterus [GenomeTiling_MRK274]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK272]


title: Testis versus Brain - thalamus [GenomeTiling_MRK271]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK276]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK271]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK276]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK272]


title: Brain - thalamus versus Testis [GenomeTiling_MRK276]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK272]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK271]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK276]


title: Brain - thalamus versus Testis [GenomeTiling_MRK272]


title: Brain - thalamus versus Testis [GenomeTiling_MRK266]


title: Brain - thalamus versus Testis [GenomeTiling_MRK271]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK266]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK271]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK271]


title: Uterus versus Thymus [GenomeTiling_MRK263]


title: Thymus versus Uterus [GenomeTiling_MRK267]


title: Uterus versus Thymus [GenomeTiling_MRK267]


title: Thymus versus Uterus [GenomeTiling_MRK264]


title: Thymus versus Uterus [GenomeTiling_MRK263]


title: Testis versus Brain - thalamus [GenomeTiling_MRK264]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK266]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK267]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK266]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK276]


title: Testis versus Brain - thalamus [GenomeTiling_MRK263]


title: Uterus versus Thymus [GenomeTiling_MRK270]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK264]


title: Uterus versus Thymus [GenomeTiling_MRK264]


title: Thymus versus Uterus [GenomeTiling_MRK270]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK263]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK270]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK267]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK263]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK264]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK267]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK264]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK267]


title: Brain - thalamus versus Testis [GenomeTiling_MRK267]


title: Testis versus Brain - thalamus [GenomeTiling_MRK267]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK270]


title: Brain - thalamus versus Testis [GenomeTiling_MRK264]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK270]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK263]


title: Brain - thalamus versus Testis [GenomeTiling_MRK263]


title: Thymus versus Uterus [GenomeTiling_MRK262]


title: Uterus versus Thymus [GenomeTiling_MRK262]


title: Testis versus Brain - thalamus [GenomeTiling_MRK265]


title: Uterus versus Thymus [GenomeTiling_MRK259]


title: Brain - thalamus versus Testis [GenomeTiling_MRK270]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK265]


title: Uterus versus Thymus [GenomeTiling_MRK265]


title: Testis versus Brain - thalamus [GenomeTiling_MRK259]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK265]


title: Uterus versus Thymus [GenomeTiling_MRK269]


title: Testis versus Brain - thalamus [GenomeTiling_MRK270]


title: Testis versus Brain - thalamus [GenomeTiling_MRK269]


title: Testis versus Brain - thalamus [GenomeTiling_MRK262]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK262]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK259]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK262]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK259]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK264]


title: Thymus versus Uterus [GenomeTiling_MRK259]


title: Thymus versus Uterus [GenomeTiling_MRK265]


title: Thymus versus Uterus [GenomeTiling_MRK269]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK265]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK265]


title: Brain - thalamus versus Testis [GenomeTiling_MRK265]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK262]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK259]


title: Uterus versus Thymus [GenomeTiling_MRK261]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK269]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK262]


title: Brain - thalamus versus Testis [GenomeTiling_MRK269]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK269]


title: Uterus versus Thymus [GenomeTiling_MRK258]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK269]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK263]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK269]


title: Uterus versus Thymus [GenomeTiling_MRK257]


title: Thymus versus Uterus [GenomeTiling_MRK258]


title: Uterus versus Thymus [GenomeTiling_MRK268]


title: Thymus versus Uterus [GenomeTiling_MRK261]


title: Brain - thalamus versus Testis [GenomeTiling_MRK262]


title: Testis versus Brain - thalamus [GenomeTiling_MRK257]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK258]


title: Testis versus Brain - thalamus [GenomeTiling_MRK258]


title: Testis versus Brain - thalamus [GenomeTiling_MRK261]


title: Thymus versus Uterus [GenomeTiling_MRK257]


title: Thymus versus Uterus [GenomeTiling_MRK268]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK261]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK257]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK259]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK268]


title: Testis versus Brain - thalamus [GenomeTiling_MRK268]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK258]


title: Brain - thalamus versus Testis [GenomeTiling_MRK259]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK257]


title: Brain - thalamus versus Testis [GenomeTiling_MRK258]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK257]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK268]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK258]


title: Brain - thalamus versus Testis [GenomeTiling_MRK268]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK268]


title: Testis versus Brain - thalamus [GenomeTiling_MRK256]


title: Brain - thalamus versus Testis [GenomeTiling_MRK257]


title: Thymus versus Uterus [GenomeTiling_MRK256]


title: Uterus versus Thymus [GenomeTiling_MRK255]


title: Uterus versus Thymus [GenomeTiling_MRK256]


title: Testis versus Brain - thalamus [GenomeTiling_MRK255]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK261]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK268]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK261]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK270]


title: Uterus versus Thymus [GenomeTiling_MRK260]


title: Thymus versus Uterus [GenomeTiling_MRK255]


title: Brain - thalamus versus Testis [GenomeTiling_MRK261]


title: Thymus versus Uterus [GenomeTiling_MRK260]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK258]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK257]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK256]


title: Thymus versus Uterus [GenomeTiling_MRK254]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK260]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK256]


title: Uterus versus Thymus [GenomeTiling_MRK254]


title: Testis versus Brain - thalamus [GenomeTiling_MRK260]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK255]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK256]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK255]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK254]


title: Brain - thalamus versus Testis [GenomeTiling_MRK256]


title: Testis versus Brain - thalamus [GenomeTiling_MRK254]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK254]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK255]


title: Brain - thalamus versus Testis [GenomeTiling_MRK254]


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK254]


title: Brain - thalamus versus Testis [GenomeTiling_MRK255]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK256]


title: Spleen versus Kidney - fetal [GenomeTiling_MRK260]


title: Brain - thalamus versus Testis [GenomeTiling_MRK260]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK255]


title: T lymphocyte (Jurkat) versus CL: Leukemia Chronic Myelogenous (K562) [GenomeTiling_MRK260]


title: Kidney - fetal versus Spleen [GenomeTiling_MRK261]


title: 12417307

status: Public on Mar 03 2004

city: Guelph

first: John

last: Nash

state: ON

address: 110 Stone Road West

department: Laboratory for Foodborne Zoonoses

country: Canada

institute: Public Health Agency of Canada

description:
Competitive hybridization of V1 variant of genome sequenced C. jejuni strain 11168 versus V1 variant in which flhA gene has been disrupted.

Category: cDNA
Subcategory: Expression profile
Scanner: VIRTEK ChipReader
Image processing software: Array-Pro Analyser

organism: Campylobacter jejuni


title: 12417309

description:
Competitive hybridization of V1 variant versus V26 variant of genome sequenced C. jejuni strain 11168

Category: cDNA
Subcategory: Expression profile
Scanner: VIRTEK ChipReader
Image processing software: Array-Pro Analyser


title: 12258747


title: 12411946

description:
Competive hybridization of V1 variant of genome sequenced C. jejuni strain 11168 versus V1 variant in which fliA gene encoding sigma 28 has been disrupted

Category: cDNA
Subcategory: Expression profile
Scanner: VIRTEK ChipReader
Image processing software: Array-Pro Analyser


title: 12417306


title: 12411947


title: 12411915


title: 12411889


title: 12412139


title: PAMH Treated Neonatal Rat Ventricular Myocytes

status: Public on Mar 02 2004

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

description:
Neonatal rat ventricular myocytes cultured for 48 hours in the presence of one micromolar PAMH
Keywords = Rattus
Keywords = Ventricular Myocytes
Keywords = Cardiomyocytes
Keywords = Hypertrophy
Keywords = Phenylephrine
Keywords = PAMH
Keywords = 5-hydroxytryptamine
Keywords = Pyridine

organism: Rattus norvegicus

source_name: Neonatal Rat Ventricular Myocytes


title: 12412053


title: Unstimulated Neonatal Rat Ventricular Myocytes

description:
Neonatal rat ventricular myocytes cultured for 48 hours.
Keywords = Rattus
Keywords = Ventricular Myocytes
Keywords = Cardiomyocytes
Keywords = Hypertrophy
Keywords = Phenylephrine
Keywords = PAMH
Keywords = 5-hydroxytryptamine
Keywords = Pyridine


title: Phenylephrine Treated Neonatal Rat Ventricular Myocytes

description:
Neonatal rat ventricular myocytes cultured for 48 hours in the presence of twenty micromolar phenylephrine.
Keywords = Rattus
Keywords = Ventricular Myocytes
Keywords = Cardiomyocytes
Keywords = Hypertrophy
Keywords = Phenylephrine
Keywords = PAMH
Keywords = 5-hydroxytryptamine
Keywords = Pyridine


title: 12412349


title: 39C7di_convSTi_R6

status: Public on Mar 01 2004

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description:
Hver1.3.1
Cy3 3A-STACbi 7d (3)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-20

source_name: 3A-empty 7d (3)

source_name: 3A-STACbi 7d (3)


title: 39C7di_convDUi_R7

description:
Hver1.3.1
Cy3 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-DUSP1i 7d (4)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-5

source_name: 3A-empty 7d (4)

source_name: 3A-DUSP1i 7d (4)


title: 39C7di_convNRi_R7

description:
Hver1.3.1
Cy3 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-NR4A3i 7d (4)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-25


title: 39C7di_convNRi_R8

description:
Hver1.3.1
Cy3 3A-NR4A3i 7d (4)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-26


title: 39C7di_convSTi_R8

description:
Hver1.3.1
Cy3 3A-STACbi 7d (4)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-24

source_name: 3A-STACbi 7d (4)


title: 39C7di_convSTi_R7

description:
Hver1.3.1
Cy3 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-STACbi 7d (4)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-24


title: 39C7di_convPHi_R7

description:
Hver1.3.1
Cy3 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-PHLDA1i 7d (4)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-21

source_name: 3A-PHLDA1i 7d (4)


title: 39C2di_convB2i_R7

description:
Hver1.3.1
Cy3 3A-empty 2d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-BTG2i 2d (4)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 533-42

source_name: 3A-empty 2d (4)


title: 39C7di_convPHi_R8

description:
Hver1.3.1
Cy3 3A-PHLDA1i 7d (4)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-22


title: 39C7di_convDUi_R8

description:
Hver1.3.1
Cy3 3A-DUSP1i 7d (4)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-4


title: 39C2di_convB2i_R8

description:
Hver1.3.1
Cy3 3A-BTG2i 2d (4)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 2d (4)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 43 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 533-41


title: 39C7di_convSTi_R5

description:
Hver1.3.1
Cy3 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-STACbi 7d (3)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-40


title: 39C7di_convPHi_R6

description:
Hver1.3.1
Cy3 3A-PHLDA1i 7d (3)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-39

source_name: 3A-PHLDA1i 7d (3)


title: 39C7di_convDUi_R6

description:
Hver1.3.1
Cy3 3A-DUSP1i 7d (3)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-37

source_name: 3A-DUSP1i 7d (3)


title: 39C7di_convPHi_R5

description:
Hver1.3.1
Cy3 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-PHLDA1i 7d (3)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-38


title: 39C2di_convB2i_R5

description:
Hver1.3.1
Cy3 3A-empty 2d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-BTG2i 2d (3)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-10

source_name: 3A-empty 2d (3)


title: 39C7di_convDUi_R5

description:
Hver1.3.1
Cy3 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-DUSP1i 7d (3)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-36


title: 39C2di_convB2i_R6

description:
Hver1.3.1
Cy3 3A-BTG2i 2d (3)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 2d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-11


title: 39C7di_convDUi_R4

description:
Hver1.2.1
Cy3 3A-DUSP1i 7d (2)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 248-30

source_name: 3A-empty 7d (2)

source_name: 3A-DUSP1i 7d (2)


title: 39C7di_convPHi_R3

description:
Hver1.2.1
Cy3 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-PHLDA1i 7d (2)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 248-35

source_name: 3A-PHLDA1i 7d (2)


title: 39C7di_convDUi_R3

description:
Hver1.3.1
Cy3 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-DUSP1i 7d (2)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-18


title: 39C7di_convSTi_R4

description:
Hver1.3.1
Cy3 3A-STACbi 7d (2)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-9

source_name: 3A-STACbi 7d (2)


title: 39C7di_convNRi_R5

description:
Hver1.3.1
Cy3 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-NR4A3i 7d (3)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-34


title: 39C7di_convNRi_R4

description:
Hver1.3.1
Cy3 3A-NR4A3i 7d (2)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-19


title: 39C7di_convPHi_R4

description:
Hver1.2.1
Cy3 3A-PHLDA1i 7d (2)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 248-36


title: 39C7di_convNRi_R6

description:
Hver1.3.1
Cy3 3A-NR4A3i 7d (3)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (3)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 41 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 510-35


title: 39C7di_convSTi_R3

description:
Hver1.3.1
Cy3 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-STACbi 7d (2)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-8


title: 39C7di_convNRi_R3

description:
Hver1.2.1
Cy3 3A-empty 7d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-NR4A3i 7d (2)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 248-31


title: 39C7di_convSTi_R1

description:
Hver1.3.1
Cy3 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-STACbi 7d (1)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-13

source_name: 3A-empty 7d (1)

source_name: 3A-STACbi 7d (1)


title: 39C7di_convNRi_R2

description:
Hver1.2.1
Cy3 3A-NR4A3i 7d (1)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (1)-
HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 267-40


title: 39C7di_convPHi_R2

description:
Hver1.3.1
Cy3 3A-PHLDA1i 7d (1)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-7

source_name: 3A-PHLDA1i 7d (1)


title: 39C2di_convB2i_R1

description:
Hver1.2.1
Cy3 3A-empty 2d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-BTG2i 2d (1)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 248-27

source_name: 3A-empty 2d (1)


title: 39C7di_convPHi_R1

description:
Hver1.3.1
Cy3 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-PHLDA1i 7d (1)-HMF3A cells retrovirally infected with pSUPER-PHLDA1i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-15


title: 39C7di_convDUi_R1

description:
Hver1.2.1
Cy3 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-DUSP1i 7d (1)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 265-11

source_name: 3A-DUSP1i 7d (1)


title: 39C2di_convB2i_R4

description:
Hver1.3.1
Cy3 3A-BTG2i 2d (2)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 2d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-16

source_name: 3A-empty 2d (2)


title: 39C7di_convSTi_R2

description:
Hver1.3.1
Cy3 3A-STACbi 7d (1)-HMF3A cells retrovirally infected with pSUPER-STACbi were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-12


title: 39C7di_convNRi_R1

description:
Hver1.2.1
Cy3 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-NR4A3i 7d (1)-HMF3A cells retrovirally infected with pSUPER-NR4A3i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 265-2


title: 39C2di_convB2i_R3

description:
Hver1.3.1
Cy3 3A-empty 2d (2)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-BTG2i 2d (2)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 542-17


title: 39C2di_convB2i_R2

description:
Hver1.2.1
Cy3 3A-BTG2i 2d (1)-HMF3A cells retrovirally infected with pSUPER-BTG2i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 2d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 248-28


title: 39C7di_convDUi_R2

description:
Hver1.2.1
Cy3 3A-DUSP1i 7d (1)-HMF3A cells retrovirally infected with pSUPER-DUSP1i were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-empty 7d (1)-HMF3A cells retrovirally infected with pSUPER-empty were cultured at 33C. Cells at passage 37 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 265-3


title: Pu_33CvGSE33C_R2

description:
Hver1.2.1
Cy3 3A-GSEp53 33C (3)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-Puro 33C (3)-HMF3A cells retrovirally infected with empty PLCPX were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 267-28


title: GSE_33Cv39C7d_R3

description:
Hver1.2.1
Cy3 3A-GSEp53 33C (2)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-GSEp53 39C 7d (2)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 267-25


title: Pu_33CvGSE33C_R1

description:
Hver1.2.1
Cy3 3A-Puro 33C (3)-HMF3A cells retrovirally infected with empty PLCPX were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-GSEp53 33C (3)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 267-27


title: GSE_33Cv39C7d_R4

description:
Hver1.2.1
Cy3 3A-GSEp53 39C 7d (2)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-GSEp53 33C (2)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 267-26


title: GSE_33Cv39C7d_R2

description:
Hver1.2.1
Cy3 3A-GSEp53 39C 7d (1)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 30 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-GSEp53 33C (1)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 30 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 250-26


title: Pu_33Cv39C7d_R3

description:
Hver1.2.1
Cy3 3A-Puro 33C (2)-HMF3A cells retrovirally infected with  empty PLCPX were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-Puro 39C 7d (2)-HMF3A-Puro cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 267-23


title: Pu_33Cv39C7d_R2

description:
Hver1.2.1
Cy3 3A-Puro 39C 7d (1)-HMF3A-Puro cells were cultured at 33C. Cells at passage 30 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-Puro 33C (1)-HMF3A cells retrovirally infected with empty PLCPX were cultured at 33C.  Cells were at passage 30 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 250-28


title: Pu_33Cv39C7d_R1

description:
Hver1.2.1
Cy3 3A-Puro 33C (1)-HMF3A cells retrovirally infected with empty PLCPX were cultured at 33C.  Cells were at passage 30 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-Puro 39C 7d (1)-HMF3A-Puro cells were cultured at 33C. Cells at passage 30 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 250-27


title: GSE_33Cv39C2d_R4

description:
Hver1.2.1
Cy3 3A-GSEp53 39C 2d (2)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 33 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-GSEp53 33C (3)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 267-34


title: Pu_33Cv39C2d_R3

description:
Hver1.2.1
Cy3 3A-Puro 33C (3)-HMF3A cells retrovirally infected with empty PLCPX were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-Puro 39C 2d (2)-HMF3A-Puro cells were cultured at 33C. Cells at passage 33 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 267-29


title: Pu_33Cv39C2d_R4

description:
Hver1.2.1
Cy3 3A-Puro 39C 2d (2)-HMF3A-Puro cells were cultured at 33C. Cells at passage 33 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-Puro 33C (3)-HMF3A cells retrovirally infected with empty PLCPX were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 267-30


title: GSE_33Cv39C7d_R1

description:
Hver1.2.1
Cy3 3A-GSEp53 33C (1)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 30 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-GSEp53 39C 7d (1)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 30 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 250-25


title: Pu_33Cv39C7d_R4

description:
Hver1.2.1
Cy3 3A-Puro 39C 7d (2)-HMF3A-Puro cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-Puro 33C (2)-HMF3A cells retrovirally infected with  empty PLCPX were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 267-24


title: GSE_33Cv39C2d_R3

description:
Hver1.2.1
Cy3 3A-GSEp53 33C (3)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 33 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-GSEp53 39C 2d (2)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 33 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 267-33


title: GSE_33Cv39C2d_R2

description:
Hver1.2.1
Cy3 3A-GSEp53 39C 2d (1)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-GSEp53 33C (2)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 265-7


title: GSE_33Cv39C2d_R1

description:
Hver1.2.1
Cy3 3A-GSEp53 33C (2)-HMF3A cells retrovirally infected with Genetic Supressor Element (GSE)56 for p53 were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-GSEp53 39C 2d (1)-HMF3A-GSEp53 cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 265-6


title: CL: Leukemia Chronic Myelogenous (K562) versus T lymphocyte (Jurkat) [GenomeTiling_MRK260]

description:
Samples were purchased from Clontech as mRNA.
Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end.  shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3'  shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3'  1.5  g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was  degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C.  The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick).
The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification.  Multiple polymerase chain reactions were run using 0.15  g of double stranded DNA and standard reaction conditions.  Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase)  DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3'  T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3'  followed by Qiaquick purification.
Further amplification was achieved using in vitro transcription reactions with X0.5  g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and  reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II).
The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray.
Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, http://genomebiology.com/2003/4/10/R66 , Roberts CJ et al., Science 2000, 287:873-880, and Schadt, Edwards, et al., unpublished.
Normalization of single channel data is described in Ying, et al., "Identification of Chromosomal Regions Containing Transcribed Sequences Using Microarrays and Computational Methods" , 2003 Proceedings of the American Statistical Association, Biopharmaceutical Section [CD-ROM], Alexandria, VA: American Statistical Association, 2003.
Briefly, an invariant set of probes was selected based on their intensity ranks.  Then, a LOESS regression model was fit for Cy5 vs. Cy3 intensities for all probes in the invariant set.  Finally, for all probes on the array the Cy5 intensities were normalized to the corresponding Cy3 intensities using prediction values from the regression model.
Note that the normalized intensity values given here were used for all analyses reported in the accompanying paper.  The ratio values reported here were not used for the analysis described in the manuscript and are not calculated from the normalized intensity values given below.

source_name: CL: Leukemia Chronic Myelogenous (K562)

source_name: T lymphocyte (Jurkat)


title: Pu_33Cv39C2d_R2

description:
Hver1.2.1
Cy3 3A-Puro 39C 2d (1)-HMF3A-Puro cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 3A-Puro 33C (2)-HMF3A cells retrovirally infected with  empty PLCPX were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 265-5


title: PRIM_FIB3_SEN_R4

description:
Hver1.2.1
Cy3 F1068 p15-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 15 the cells were no longer increasing in number, they displayed morphology associated with senescence and were lysed. Cells were fed the day before lysis.
Cy5 F1068 p7-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 7 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 71-57


title: PRIM_FIB3_SEN_R3

description:
Hver1.2.1
Cy3 F1068 p7-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 7 the cells were lysed. Cells were fed the day before lysis.
Cy5 F1068 p15-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 15 the cells were no longer increasing in number, they displayed morphology associated with senescence and were lysed. Cells were fed the day before lysis.

Lot batch = 71-56


title: PRIM_FIB3_SEN_R2

description:
Hver1.2.1
Cy3 F1068 p15-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 15 the cells were no longer increasing in number, they displayed morphology associated with senescence and were lysed. Cells were fed the day before lysis.
Cy5 F1068 p8-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 8 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 250-32


title: Pu_33Cv39C2d_R1

description:
Hver1.2.1
Cy3 3A-Puro 33C (2)-HMF3A cells retrovirally infected with  empty PLCPX were cultured at 33C.  Cells were at passage 31 (since original isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 3A-Puro 39C 2d (1)-HMF3A-Puro cells were cultured at 33C. Cells at passage 31 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 265-4


title: PRIM_FIB3_SEN_R1

description:
Hver1.2.1
Cy3 F1068 p8-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 8 the cells were lysed. Cells were fed the day before lysis.
Cy5 F1068 p15-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 15 the cells were no longer increasing in number, they displayed morphology associated with senescence and were lysed. Cells were fed the day before lysis.

Lot batch = 250-33


title: 3A_33Cv39C2d_R4

description:
Hver1.2.1
Cy3 HMF3A 39C 2d (2)-HMF3A cells were cultured at 33C. Cells at passage 57 (since isolation from tissue) were trypsinised  and then plated at 60% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 HMF3A 33C (9)-HMF3A cells were cultured at 33C. Cells were at passage 58 (since isolation from tissue). Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 120-14


title: 3A_33CvQUIES_R6

description:
Hver1.2.1
Cy3 HMF3A starved (2)-HMF3A cells were cultured at 33C.  Cells at passage 30 were trypsinised and replated, the next day the cells were washed twice with PBS and incubated in DMEM with 0.25% FCS for 1 week upon which time they were confluent.  The cells were washed twice during the week and re-fed with 0.25% FCS DMEM.
Cy5 HMF3A 33C (10)-HMF3A cells were cultured at 33C.  Cells were at passage 30 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 248-26

source_name: HMF3A starved (2)


title: Dwt_33Cv39C7d_R4

description:
Hver1.2.1
Cy3 HMF3Dwt 39C (2)-HMF3Dwt cells were cultured at 33C. Cells at passage 26 (since isolation from tissue) were trypsinised and then plated at 20% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 HMF3Dwt 33C (2)-HMF3Dwt cells were cultured at 33C.  Cells were at passage 27 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 124-23

source_name: HMF3Dwt 33C (2)

source_name: HMF3Dwt 39C (2)


title: PRIM_FIB3_LATE_R4

description:
Hver1.2.1
Cy3 F1068 p13-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 13 a large proportion (around 70%) displayed morphology associated with senescence with few cells visably undergoing division and so were lysed. Cells were fed the day before lysis.
Cy5 F1068 p4-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 4 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 121-37


title: 3A_33CvQUIES_R5

description:
Hver1.2.1
Cy3 HMF3A 33C (10)-HMF3A cells were cultured at 33C.  Cells were at passage 30 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A starved (2)-HMF3A cells were cultured at 33C.  Cells at passage 30 were trypsinised and replated, the next day the cells were washed twice with PBS and incubated in DMEM with 0.25% FCS for 1 week upon which time they were confluent.  The cells were washed twice during the week and re-fed with 0.25% FCS DMEM.

Lot batch = 248-25


title: PRIM_FIB3_LATE_R2

description:
Hver1.2.1
Cy3 F1068 p12-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 12 a large proportion (around 70%) displayed morphology associated with senescence with few cells visably undergoing division and so were lysed. Cells were fed the day before lysis.
Cy5 F1068 p6-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 6 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 71-51


title: PRIM_FIB3_LATE_R3

description:
Hver1.2.1
Cy3 F1068 p4-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 4 the cells were lysed. Cells were fed the day before lysis.
Cy5 F1068 p13-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 13 a large proportion (around 70%) displayed morphology associated with senescence with few cells visably undergoing division and so were lysed. Cells were fed the day before lysis.

Lot batch = 121-36


title: 3A_33Cv39C2d_R1

description:
Hver1.2.1
Cy3 HMF3A 33C (8)-HMF3A cells were cultured at 33C.  Cells were at passage 59 (since isolation from tissue). Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A 39C 2d (1)-HMF3A cells were cultured at 33C. Cells at passage 58 (since isolation from tissue) were trypsinised  and then plated at 60% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 119-8


title: Dwt_33Cv39C7d_R2

description:
Hver1.2.1
Cy3 HMF3Dwt 39C (1)-HMF3Dwt cells were cultured at 33C. Cells at passage 19 (since isolation from tissue) were trypsinised and then plated at 20% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 HMF3Dwt 33C (1)-HMF3Dwt cells were cultured at 33C. Cells were at passage 20 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 121-31

source_name: HMF3Dwt 33C (1)

source_name: HMF3Dwt 39C (1)


title: 3A_33Cv39C2d_R3

description:
Hver1.2.1
Cy3 HMF3A 33C (9)-HMF3A cells were cultured at 33C. Cells were at passage 58 (since isolation from tissue). Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A 39C 2d (2)-HMF3A cells were cultured at 33C. Cells at passage 57 (since isolation from tissue) were trypsinised  and then plated at 60% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 120-13


title: PRIM_FIB3_LATE_R1

description:
Hver1.2.1
Cy3 F1068 p6-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 6 the cells were lysed. Cells were fed the day before lysis.
Cy5 F1068 p12-Primary fibroblasts from human mammary stroma, donor 1068 were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 14 days.  At passage 12 a large proportion (around 70%) displayed morphology associated with senescence with few cells visably undergoing division and so were lysed. Cells were fed the day before lysis.

Lot batch = 71-50


title: Dwt_33Cv39C7d_R1

description:
Hver1.2.1
Cy3 HMF3Dwt 33C (1)-HMF3Dwt cells were cultured at 33C. Cells were at passage 20 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3Dwt 39C (1)-HMF3Dwt cells were cultured at 33C. Cells at passage 19 (since isolation from tissue) were trypsinised and then plated at 20% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 87-32


title: Dwt_33Cv39C7d_R3

description:
Hver1.2.1
Cy3 HMF3Dwt 33C (2)-HMF3Dwt cells were cultured at 33C.  Cells were at passage 27 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3Dwt 39C (2)-HMF3Dwt cells were cultured at 33C. Cells at passage 26 (since isolation from tissue) were trypsinised and then plated at 20% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 124-23


title: 3A_33CvBT33C3d_R8

description:
Hver1.2.1
Cy3 HMF3A ->33C +TGF Ab (2)-HMF3A cells were cultured at 33C. Cells at passage 53 (since isolation from tissue) were trypsinisedand then plated at 60% confluence in media with neutralising anti-TGF-beta antibody (0.5 microg/ml, R&D) and 5% FCS instead of 10% FCS. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and every 3 days with fresh antibody added each time.
Cy5 HMF3A 33C (7)-HMF3A cells were cultured at 33C.  Cells were at passage 54 (since isolation from tissue) in 5% FCS instead of 10% FCS. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 81-17

source_name: HMF3A ->33C +TGF Ab (2)


title: 3A_33Cv39C2d_R2

description:
Hver1.2.1
Cy3 HMF3A 39C 2d (1)-HMF3A cells were cultured at 33C. Cells at passage 58 (since isolation from tissue) were trypsinised  and then plated at 60% confluence. The next day they were shifted up to 39C. After 2 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 HMF3A 33C (8)-HMF3A cells were cultured at 33C.  Cells were at passage 59 (since isolation from tissue). Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 119-9


title: 3A_33CvBT33C3d_R4

description:
Hver1.2.1
Cy3 HMF3A ->33C +TGF Ab (1)-HMF3A cells were cultured at 33C. Cells at passage 52 (since isolation from tissue) were trypsinised and then plated at 60% confluence in media with neutralising anti-TGF-beta antibody (0.5 microg/ml). The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and every 3 days with fresh antibody added each time.
Cy5 HMF3A 33C (6)-HMF3A cells were cultured at 33C.  Cells were at passage 53 (since isolation from tissue) when lysed.  Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 91-27

source_name: HMF3A ->33C +TGF Ab (1)


title: 3A_33CvBT33C3d_R7

description:
Hver1.2.1
Cy3 HMF3A 33C (7)-HMF3A cells were cultured at 33C.  Cells were at passage 54 (since isolation from tissue) in 5% FCS instead of 10% FCS. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Cy5 HMF3A ->33C +TGF Ab (2)-HMF3A cells were cultured at 33C. Cells at passage 53 (since isolation from tissue) were trypsinisedand then plated at 60% confluence in media with neutralising anti-TGF-beta antibody (0.5 microg/ml, R&D) and 5% FCS instead of 10% FCS. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and every 3 days with fresh antibody added each time.

Lot batch = 56-3


title: 3A_33CvBT33C3d_R5

description:
Hver1.2.1
Cy3 HMF3A 33C (7)-HMF3A cells were cultured at 33C.  Cells were at passage 54 (since isolation from tissue) in 5% FCS instead of 10% FCS. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A ->33C 3d (2)-HMF3A cells were cultured at 33C. Cells at passage 53 (since isolation from tissue) were trypsinised and then plated at 60% confluence with 5% FCS instead of 10%. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.

Lot batch = 56-2


title: 3A_33CvBT33C3d_R6

description:
Hver1.2.1
Cy3 HMF3A ->33C 3d (2)-HMF3A cells were cultured at 33C. Cells at passage 53 (since isolation from tissue) were trypsinised and then plated at 60% confluence with 5% FCS instead of 10%. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.
Cy5 HMF3A 33C (7)-HMF3A cells were cultured at 33C.  Cells were at passage 54 (since isolation from tissue) in 5% FCS instead of 10% FCS. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 81-18


title: PRIM_FIB2_SEN_R2

description:
Hver1.2.1
Cy3 HMF3 p15-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 15 the cells were no longer increasing in number and were lysed. Cells were fed the day before lysis.
Cy5 HMF3 p9-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 9 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 57-52

source_name: HMF3 p9

source_name: HMF3 p15


title: 3A_33CvBT33C3d_R2

description:
Hver1.2.1
Cy3 HMF3A ->33C 3d (1)-HMF3A cells were cultured at 33C. Cells at passage 52 (since isolation from tissue) were trypsinised and then plated at 60% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.
Cy5 HMF3A 33C (6)-HMF3A cells were cultured at 33C.  Cells were at passage 53 (since isolation from tissue) when lysed.  Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 91-26


title: 3A_33CvBT33C3d_R3

description:
Hver1.2.1
Cy3 HMF3A 33C (6)-HMF3A cells were cultured at 33C.  Cells were at passage 53 (since isolation from tissue) when lysed.  Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A ->33C +TGF Ab (1)-HMF3A cells were cultured at 33C. Cells at passage 52 (since isolation from tissue) were trypsinised and then plated at 60% confluence in media with neutralising anti-TGF-beta antibody (0.5 microg/ml). The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and every 3 days with fresh antibody added each time.

Lot batch = 85-6


title: PRIM_FIB2_SEN_R4

description:
Hver1.2.1
Cy3 HMF3 p15-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 15 the cells were no longer increasing in number and were lysed. Cells were fed the day before lysis.
Cy5 HMF3 p9-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 9 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 59-3


title: PRIM_FIB2_SEN_R1

description:
Hver1.2.1
Cy3 HMF3 p9-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 9 the cells were lysed. Cells were fed the day before lysis.
Cy5 HMF3 p15-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 15 the cells were no longer increasing in number and were lysed. Cells were fed the day before lysis.

Lot batch = 57-51


title: 3A_33CvBT33C7d_R4

description:
Hver1.2.1
Cy3 HMF3A ->33C 7d (2)-HMF3A cells were cultured at 33C. Cells at passage 42 were trypsinised and then plated at 60% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 7 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.
Cy5 HMF3A 33C (5)-HMF3A cells were cultured at 33C.  Cells were at passage 43 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 57-49


title: 3A_39CvQUIES_R3

description:
Hver1.2.1
Cy3 HMF3A 39C (3)-HMF3A cells were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 HMF3A starved (1)-HMF3A cells were cultured at 33C.  Cells at passage 39 were trypsinised and replated, the next day the cells were washed twice with PBS and incubated in DMEM with 0.25% FCS for 1 week upon which time they were confluent.  The cells were washed twice during the week and re-fed with 0.25% FCS DMEM.
Lot batch = 53-8

source_name: HMF3A starved (1)


title: PRIM_FIB1_SEN_R3

description:
Hver1.2.1
Cy3 HMF3 p8-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days.  At passage 8 the cells were lysed. Cells were fed the day before lysis.
Cy5 HMF3 p18-rimary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days.  At passage 18 the cells were no longer increasing in number and were lysed. Cells were fed the day before lysis.

Lot batch = 52-37

source_name: HMF3 p8

source_name: HMF3 p18


title: 3A_33CvBT33C3d_R1

description:
Hver1.2.1
Cy3 HMF3A 33C (6)-HMF3A cells were cultured at 33C.  Cells were at passage 53 (since isolation from tissue) when lysed.  Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A ->33C 3d (1)-HMF3A cells were cultured at 33C. Cells at passage 52 (since isolation from tissue) were trypsinised and then plated at 60% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 3 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.

Lot batch = 85-5


title: PRIM_FIB1_SEN_R4

description:
Hver1.2.1
Cy3 HMF3 p18-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days.  At passage 18 the cells were no longer increasing in number and were lysed. Cells were fed the day before lysis.
Cy5 HMF3 p8-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:641). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days.  At passage 8 the cells were lysed. Cells were fed the day before lysis.

Lot batch = 52-38


title: PRIM_FIB2_SEN_R3

description:
Hver1.2.1
Cy3 HMF3 p9-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 9 the cells were lysed. Cells were fed the day before lysis.
Cy5 HMF3 p15-Primary fibroblasts from human mammary stroma were isolated as described (O'Hare M.J et al. 2001, PNAS, 98:646). When the cells were first plated after isolation, they were said to be at passage 0.  The cells were fed twice weekly and re-plated at 25% confluence when they reached around 80% confluence, this usually occurred after 7 days. The cells were frozen down at passage 6. The cells were unfrozen and regrown as before. At passage 15 the cells were no longer increasing in number and were lysed. Cells were fed the day before lysis.

Lot batch = 59-2


title: 3A_39CvQUIES_R4

description:
Hver1.2.1
Cy3 HMF3A starved (1)-HMF3A cells were cultured at 33C.  Cells at passage 39 were trypsinised and replated, the next day the cells were washed twice with PBS and incubated in DMEM with 0.25% FCS for 1 week upon which time they were confluent.  The cells were washed twice during the week and re-fed with 0.25% FCS DMEM.
Cy5 HMF3A 39C (3)-HMF3A cells were cultured at 33C.  Cells were at passage 40 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 53-9


title: 3A_33CvBT33C7d_R1

description:
Hver1.2.1
Cy3 HMF3A 33C (4)-HMF3A cells were cultured at 33C.  Cells were at passage 42 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A ->33C 7d (1)-HMF3A cells were cultured at 33C. Cells at passage 41 were trypsinised and then plated at 60% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 7 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.

Lot batch = 52-39


title: 3A_33Cv39C7d_R10

description:
Hver1.2.1
Cy3 HMF3A 39C (3)-HMF3A cells were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.
Cy5 HMF3A 33C (3)-HMF3A cells were cultured at 33C.  Cells were at passage 40 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.

Lot batch = 53-3


title: 3A_39CvQUIES_R2

description:
Hver1.2.1
Cy3 HMF3A starved (1)-HMF3A cells were cultured at 33C.  Cells at passage 39 were trypsinised and replated, the next day the cells were washed twice with PBS and incubated in DMEM with 0.25% FCS for 1 week upon which time they were confluent.  The cells were washed twice during the week and re-fed with 0.25% FCS DMEM.
Cy5 HMF3A 39C (3)-HMF3A cells were cultured at 33C. Cells at passage 39 (since isolation from tissue) were trypsinised and then plated at 50% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were lysed.  Media was changed a day before lysis.

Lot batch = 52-28


title: 3A_33CvBT33C7d_R3

description:
Hver1.2.1
Cy3 HMF3A 33C (5)-HMF3A cells were cultured at 33C.  Cells were at passage 43 (since isolation from tissue) when lysed. Media was changed a day before lysis. Cells were lysed at around 80% confluence.
Cy5 HMF3A ->33C 7d (2)-HMF3A cells were cultured at 33C. Cells at passage 42 were trypsinised and then plated at 60% confluence. The next day they were shifted up to 39C. After 7 days at 39C the cells were shifted down to 33C. After 7 days at 33C the cells were lysed.  Media was changed a day before lysis and twice a week.

Lot batch = 57-50