At one site (#10), three different batches of MTRRM (see E-TABM-16), were labeled with two different kits (Enzo and Affymetrix) and hybridized to two different Affymetrix Arrays (RAE230A and RAE230_2).

Transcription profiling of rat mixed-tissue RNA samples using different labeling protocols

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples

Affymetrix GeneChip Rat Expression Array RAE230A [RAE230A]

Affymetrix GeneChip Rat Genome 230 2.0 [Rat230_2]

rawData

scan

processedDataMatrix

BATCH

SITE

At one site (#10), three different batches of MTRRM (see E-TABM-16), were labeled with two different kits (Enzo and Affymetrix) and hybridized to two different Affymetrix Arrays (RAE230A and RAE230_2).


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MTAB-341

P-MTAB-342

P-MTAB-343

Total RNA was quantitated by ultraviolet/visible wavelength spectrophotometry.  For each tissue, equal amounts of RNA were pooled from each of the 8 animals in the same shipment to create tissue shipment specific pools.  2 mg each of two mixtures (Mix1 and Mix2) were prepared for each shipment from the pooled same-tissue RNAs.   Mix1 consisted of 200 ug testis RNA,  600 ug liver RNA, 800 ug brain RNA, and 400 ug kidney RNA.  Mix2 consisted of 800 ug testis RNA,  400 ug liver RNA, 400 ug brain RNA, and 400 ug kidney RNA.  50 ug aliquots of each mixture were frozen at -70C.

P-MTAB-344

Microarray Suite v. 5.0.0.032 software (Affymetrix, Inc.) was used to calculate signal values using default settings (Parameters: Gamma 1L, 0.0045; Gamma 1H, 0.0045; Gamma 2L, 0.006; Gamma 2H, 0.006; Perturbation, 1.1; alpha1, 0.05; alpha2, 0.065; tau, 0.015). All data was global scaled to a target intensity of 500.

P-MTAB-345

P-MTAB-346

Rodents received certified rodent diet #5002C ad lib and drinking water purified by reverse osmosis.   The animals were acclimated for 6 days prior to euthanasia.   The animals were on a 12 hr light/dark cycle and euthanasia was performed consistently within 4-6  hr after the start of the light cycle.

Transcription profiling of rat mixed-tissue RNA samples using different labeling protocols

Submitter Supplied Information

Samples