title: Illumina HiSeq 2000 paired end sequencing; RNA-seq of TCF4 silencing in A431 cells
design: RNA-seq of TCF4 silencing in A431 cells
library_construction_protocol: A431 cells with different treatment (TCF4 siRNAs, and processing times) were harvested for RNA-seq. The TCF4 siRNA oligo (Sense: 5'- CUCAUCGUCUCCUAAUUAUTT -3', Antisense: 5'- AUGAUUCCAUGCAUGUCCCTT -3') is used to transient transfected into A431 cells, while the siRNA oligo (Sense: 5'- UUCUCCGAACGUGUCACGUTT -3', Antisense: 5'- ACGUGACACGUUCGGAGAATT -3') is used as blank group by lipo2000 (Thermo Fisher, USA). And non-treated A431 cells are used as negative control. Total RNA was isolated from the samples with RNeasy Mini kit (QIAGEN, Gemany) in accordance to the manufacturers protocol. RNA was quantified using the NanoPhotometer spectrophotometer (Implen Inc., CA, USA). We then measured RNA concentration using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA), and assessed RNA integrity using the RNA Nano 6000 Assay Kit in Bioanalyzer 2100 (Agilent Technologies, CA, USA). All the samples had a high RNA Integrity Number (RIN) score (>9.4). A total of 1ug of RNA per sample was submitted to the Genefund Co. Ltd (Shanghai, China) for library generation and sequencing. The sequencing library is generated by the kit of the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®(#E7760,New England Biolabs)
attributes.tag: Experimental Factor: genotype
attributes.value: scrambled siRNA