PRJNA764826
Bulk bone sequencing data for chromosome 8 CYP11B1
Bulk bone RNA was isolated as described elsewhere. All the prepared libraries were analyzed in a single batch. TruSeq RNA Library prep kit V2 (Illumina, USA) was used to capture poly(A) RNA from 1000ng total RNA. Subsequently cDNA was prepared to which single indexed adapters were ligated. Material was then cloned for 13 cycles with PCR. Paired-end sequencing of 2x50 bp was performed using the Illumina HiSeq2000 (Illumina, USA) platform to obtain at least 6.000.000 reads per library. They were aligned to reference genotype (GRCh37.p13, gencode release 19) using STAR 2-pass methodology. Picard tools were used to add readgroups to bam files, reorder contigs according to the reference file and remove PCR duplicates. In the next step, GATK was used to split cigar reads, realign reads around indels, and recalibrate quality scores of the resulting reads. Picard was again used to extract QC metrics . In the end, raw transcription level expression values were extracted using featureCounts. For this submission specifically, chromosomal region 8 spanning 143,000,000 - 144,000,000 bp of the (GRCh37/hg19) assembly was extracted (CYP11B1 region).