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| Status |
Public on Sep 16, 2019 |
| Title |
JGE190320_EGFP_12HR_R1 |
| Sample type |
SRA |
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| Source name |
Transgenic Sindbis virus
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| 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: CAGATC
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
barcoded amplicon
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| 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.
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| Submission date |
Sep 16, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Justin Gregory English |
| E-mail(s) |
jgenglis@email.unc.edu
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| Organization name |
UNC Chapel Hill
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| Department |
Pharmacology
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| Lab |
Roth
|
| Street address |
120 Mason Farm Rd., 2113 Genetic Medicine Bldg
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL25880 |
| Series (1) |
| GSE123269 |
VEGAS: A Platform for Continuous Directed Evolution in Mammalian Cells (RNAseq) |
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| Relations |
| BioSample |
SAMN12768337 |
| SRA |
SRX6854847 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4081332_H12R1_fr_best_EGFP_FR_posstats.csv.gz |
25.9 Kb |
(ftp)(http) |
CSV |
| GSM4081332_H12R1_fr_best_EGFP_FR_readstats.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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