GSM4261636: STARRseq_input_DNA_2iL_rep2; Mus musculus; OTHER
Total RNA were extracted with RNeasy maxi prep kit (Qiagen, #75162) then polyA RNA were isolated with Dynabeads Oligo-dT25 (Invitrogen, #61002) and concentrated according to the RNeasy Mini kit (Qiagen, #74106) clean-up procedure. Input DNA were extracted with Plasmid Maxi Kit (Qiagen, #12165) All the polyA RNA were transcribed to STARR-seq cDNA in 25 reactions with reporter-RNA specific primer and the cDNA were amplified with reporter-specific primers for 15 cycles. Amplified cDNA was purified with 0.8x AMpureXP beads. Illumina sequencing indexes were added to the amplified cDNA according to PCR for 8 cycles with NEBNext Multiplex Oligos for Illumina (NEB, #E7335L and #E7500L) in 25 reactions. The indexed library was size-selected on 1% agarose gel to eliminate all small fragments.  For input library, every 100ng of input was amplified using input-specific primers (GATTTGATATTCACCTGGCCCGC & CTTATCATGTCTGCTCGA*A*G*C; where * indicates phosphonothioate bonds) and size-selected for a range of 1600-2200bp on 1% agarose gel. 10 reactions were performed in total. Indexes were added to purified input DNA following the same indexing procedure as for STARR-seq cDNA in 10 reactions and purified/size-selected again on 1% agarose gel.
GEO Accession
GSM4261636