title: GSM5252617: 13T organoids; Homo sapiens; RNA-Seq
library_construction_protocol: RNA was isolated according to the manufacturer's protocol using the RNeasy Mini Kit (QIAGEN) Quality and quantity of the RNA samples and the libraries were measured with Agilent's Bioanalyzer2100 and Invitrogen™ Qubit™ 3.0 Fluorometer. Quality control was done using FastQC, alignment has been done using STAR (https://github.com/alexdobin/STAR/releases/tag/STAR_2.4.2a  ) and reads have been mapped to the GRCh37 version of the human reference genome. Quality control on the bams was done using Picard. Read counts were generated with Htseq-count after which normalization is done using DESeq. RPKMs have been calculated with edgeR. For the library preparation the TruSeq Stranded mRNA Library Prep kit from Illumina was used. Sequencing was performed on the nextseq500 sequencer (also Illumina) with single-end 75bp reads.
attributes.tag: GEO Accession
attributes.value: GSM5252617