Amplified scRNA-seq Library Preparation

scRNA-seq libraries were prepared by amplifying the 3′ untranslated region (UTR) of the transcripts by using the modified CEL-Seq2 protocol (Hashimshony et al., 2016 (link)), which replaced the SuperScript II reverse transcriptase with Maxima H minus (EP0752; Thermo Fisher Scientific), the second strand synthesis reagent with the second strand synthesis module (E6111; New England BioLabs). A total of 384 cells in the same plate were pooled after reverse transcription. Each condition was analyzed in triplicate. Sequencing reads were obtained from HiSeq 1500 platform at the following cycles: 15 cycles of Read1 (Unique Molecular Identifier: 6 bp, cell barcode: 9 bp) and 36 cycles of Read2 (Illumina, San Diego, CA, United States), as shown in Supplementary Table S2.