title: RNAseq of human fetal intestinal epithelium: MM-E
design: Cryopreserved epithelial cell layers (in RNAlater, Ambion) were lysed using QIAshredder (QIAGEN) columns and RNA was extracted using RNAqueous kit (ThermoFisher). RNA was quantified using Qubit RNA HS Assay (ThermoFisher), normalized, and converted to cDNA using SMARTer cDNA Synthesis Kit (Takara Bio) using 7 cycles of amplification. RNA and cDNA quality was determined by Bioanalyzer (Agilent). cDNA was fragmented, ligated with Illumina adapters using Nextera XT kit (Illumina), following manufacturers instructions, and sequenced on NovaSeq6000 sequencer using two lanes. Paired-end 100 by 100 bp reads were obtained, demultiplexed, quality filtered, removed of Illumina adapters using TrimGalore (github.com/FelixKrueger/TrimGalore), and aligned to the human genome (Hg38 release) using STAR47 with ENCODE recommended parameters. Features were assigned to transcripts using featureCounts48, normalized using DESEQ249.
library_name: Human fetal intestinal epithelium 1610