adapter_barcode_ID
AD012
barcode_seq
CTTGTA
processing_pipeline
High-throughput RNA sequencing was performed on the Illumina HiSeq2000 platform (100 x 100 bp paired end read lengths) using TruSeq v3 cluster kits and TruSeq SBS chemistry (Illumina) at the Next Generation Sequencing Core / Functional Genomics Core (NGSC/FGC) at the Perelman School of Medicine at the University of Pennsylvania. DNA FASTQ read files were processed using FastQC v0.11.27 to review read lengths, quality scores, k-mer over-representation, adapter enrichment, and number of duplicate reads. Reads were trimmed using Trimmomatic v0.328 to remove adapter read-through, palindromic artifacts, low quality bases, and successive ambiguous base calls while also maintaining paired-end read ordering. The Illumina adapter-specific clipping strategy was performed using specific adapter lists for RNA libraries (please refer to supplemental files in associated publication). Clipping required an average quality of 20 over a sliding window of four nucleotides. Leading and trailing bases were required to have quality scores of three or higher, and only RNA reads with lengths of at least 50 bases were retained.
seq_center
FGC_NGSC
machine_ID
ST1160
run_ID
FGC0582
seq_chemistry
TruSeq v3 clustering, TruSeq SBS
fastq_encoding
illumina_1.9_sanger
software
CASAVA-1.8.2, RTA-1.17.21.3, HiSeqControlSoftware-2.0.10.0