normalization data transformation protocol
Primary analysis was carried out by Functional Genomics Core Facility in UNC-CH using Affymetrix Expression Console software. probe group file: MoGene-1_0-st-v1.r4.pgf meta-probeset file: MoGene-1_0-st-v1.r4.mps ID_REF = VALUE = RMA normalized signal intensity
array scanning protocol
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G by Functional Genomics Core Facility in UNC-CH using standard protocol.
Hybridization to Affymetrix MoGene-1_0-st-v1 array was carried out by Functional Genomics Core Facility in UNC-CH using standard protocol.
Biotin labeling was carried out by Functional Genomics Core Facility in UNC-CH using GeneChip WT Sense Target Labeling and Control Reagents and standard protocol.
E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).
sample treatment protocol
Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.
nucleic acid extraction protocol
Total RNA was extracted from the control and Kdm2b knockdown mESCs using RNeasy mini kit (QIAGEN) following manufacture's instructions.