GSM8187080: iMEPM, plusPDGF_AA, IgG IP; Mus musculus; OTHER
eCLIP was performed according to Van Nostrand et al 2016, 2017. 2 million cells were UV-crosslinked, lysed and subject to IP with IgG or an Srsf3 antibody. IP samples underwent dephosphorylation, on-bead RNA adapater ligation, isolation and proteinase K digestion. RNA was isolated with acid phenol/chloroform/isoamyl alcohol (pH 6.5) and reverse transcribed with Superscript III (Thermo Fisher Scientific).  ExoSAP-IT (Affymetrix) was used to remove excess primers. DNA adapters were 3' ligated, and samples were cleaned up with Dynabeads MyOne Silane (Thermo Fisher).  Libraries were PCR amplified using Q5 PCR mix (New England Biolabs) for 16-25 cycles and sequenced on an Illumina NOVASEQ 6000