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Sample GSM4081328 Query DataSets for GSM4081328
Status Public on Sep 16, 2019
Title JGE190320_EGFP_3HR_R3
Sample type SRA
 
Source name Transgenic Sindbis virus
Organism Sindbis virus
Characteristics library preparation kit: KAPA HyperPlus (24 rxn) with SEQCAP Kit A & B
cell line: BHK21
culturing: transfected with pCMV-SSG cultured in MEM-alpha supplemented media.
barcode: TTAGGC
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using MagMax RNA isolation kits
Amplicons of target region were PCR'd and used for libraries constructed with KAPA HyperPrep kit or Illumina TruSeq RNA library kit v2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description barcoded amplicon
Data processing EGFP Data was trimmed to contain only paired reads with 100% matching sequences above a set length threshold
Trimmed reads were aligned to FASTA sequences (see supplement, JGE_EGFP.FASTA) using a Smith-Waterman alignment algorithm weighted m3, x1, o5, e1
Reads aligning to any part of the full length Sindbis genome were omitted, apart from those flanking the EGFP transgene
For EGFP alignments, individual base frequences per position were tabulated and mutations, insertions, and deletions were quantified per position and per read.
For NB alignments, data was aligned using a Smith-Waterman alignment algorith weighted m1, x5, o5, e5
Aligned NB reads was tabulated with score cut-offs at 25, 50, and 100. Individual base frequencies per position were tabulated.
Genome_build: Custom (see JGE_EGFP.FASTA)
Genome_build: Custom (see JGE_NB.FASTA)
Supplementary_files_format_and_content: Processed EGFP files (.csv) contain aggregate error frequencies at each position in the alignment (posstats) and error statistics for each individual read (readstats). Processed NB file (.xlsx) contain position and read length quantification.
 
Submission date Sep 16, 2019
Last update date Sep 17, 2019
Contact name Justin Gregory English
E-mail(s) jgenglis@email.unc.edu
Organization name UNC Chapel Hill
Department Pharmacology
Lab Roth
Street address 120 Mason Farm Rd., 2113 Genetic Medicine Bldg
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL25880
Series (1)
GSE123269 VEGAS: A Platform for Continuous Directed Evolution in Mammalian Cells (RNAseq)
Relations
BioSample SAMN12768341
SRA SRX6854843

Supplementary file Size Download File type/resource
GSM4081328_H03R3_fr_best_EGFP_FR_posstats.csv.gz 21.4 Kb (ftp)(http) CSV
GSM4081328_H03R3_fr_best_EGFP_FR_readstats.csv.gz 787.5 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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