GSM9114472: iPSc_to_AFE with DOE[DE to AFE]24; Homo sapiens; RNA-Seq
Total RNA was extracted using RLT Lysis buffer and RNAeasy mini kit (Qiagen) from cells harvested at day 7 (AFE stage), day 11 (3PPE stage), and day 13 (TEP stage) of the differentiation protocol. RNA extraction was performed prior to transcriptomic analyses. For 3′ Digital Gene Expression (DGE) bulk RNA sequencing, library preparation was performed according to the authors' implementation of a previously published protocol (Kilens et al., Nat. Commun. 2018). A total of 10 ng of total RNA was used as input. Polyadenylated transcripts were tagged using adapters specific to poly(A) tails, well-specific barcodes, and unique molecular identifiers (UMIs) during template-switching reverse transcription. cDNAs were pooled and PCR-amplified using the Advantage 2 PCR Enzyme System (Clontech, 639206), then tagmented using the Nextera DNA kit (FC-121-1031) to enrich 3′ ends. Purification and size selection were performed using the Zymo purification kit (D4004-1-L), QIAquick Gel Extraction Kit, and Agencourt AMPure XP magnetic beads. Sequencing was carried out on an Illumina NovaSeq 6000 platform.
GEO
GSM9114472_r1