title: GSM9282297: Digit tip regenerates, 14 dpa, wildtype; Mus musculus; RNA-Seq
library_construction_protocol: Regenerating mouse digit tips were harvested and trimmed to exclude all tissue proximal to the distal interphalangeal joint. Digits were flash frozen in a mortar immersed in liquid nitrogen, then pulverized with a pestle. Powderized samples were then transferred to a Dounce homogenizer with Trizol (Invitrogen, CA) for an additional stage of homogenization. RNA was extracted from the Trizol mixture according to the manufacturer's instructions, followed by clean up with an RNA Clean & Concentrator Kit (Zymo Research, CA). Generation of RNA libraries and sequencing was performed by Innomics Inc (San Jose, CA). RNA samples were first enriched for mRNA containing poly-A tails using oligo(dT) beads, followed by fragmentation. Fragmented mRNA molecules were reverse transcribed into first-strand cDNA using random primers. Second-strand cDNA was synthesized using dUTP instead of dTTP to facilitate strand-specific sequencing. The resulting cDNA was end-repaired and 3' adenylated, followed by the ligation of adaptors to the ends of the 3' adenylated cDNA fragments. PCR amplification was then performed to enrich the cDNA library, which underwent quality control assessments. Libraries were circularized and amplified to form DNA nanoballs (DNBs). DNBs were loaded onto the DNBSEQ-T7 sequencing platform according to the manufacturer's protocol. High-throughput sequencing was performed, generating paired-end reads of 150 bp in length. The raw sequencing reads were QCed and filtered with SOPAnuke(50) to remove low quality reads. Final sequencing quality was assessed using FastQC.
identifiers.namespace: GEO
identifiers.id: GSM9282297_r1