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| Status |
Public on Jun 21, 2024 |
| Title |
recombinant CDV-infected ferret organ homogenate (passage 1) |
| Sample type |
SRA |
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| Source name |
lymph node / spleen / lung homogenate
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| Organisms |
Mustela putorius furo; canine distemper virus |
| Characteristics |
tissue: lymph node / spleen / lung homogenate
genotype: recombinant CDV r5804
treatment: passage 1
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| Growth protocol |
ferrets were intranasally infected with recombinant P0 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cell-associated infectious virus released from infected cells by freeze-thawing. 100 µl virus stock aliquots were processed with Trizol reagent using the Zymo Direct-zol RNA kit (Zymo Research Europe GmbH, Freiburg, Germany). To extract RNA from tissues, 100 mg pieces were homogenized in 350 µl RLT buffer and processed according to the instructions of the RNeasy Mini kit manual (Qiagen, Hilden, Germany).
500 µg of purified RNA were processed with the Illumina TrueSeq StrandedTotal RNA kit (Illumina, San Diego, USA), including depletion of ribosomal RNA via Ribo-Zero Gold rRNA Removal kit (Illumina, San Diego, USA) following the manufacturer’s protocols. Libraries generated with single indexed adapters were then validated and sequenced as 2x150 base pairs paired-end reads.
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| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Assembly: GCA_000215625.1
Adapter sequences were removed from raw fastq files using SeqPurge v0.1-1000-gb4d1b1c. Quality trimming was disabled (-qcut 0 -ncut 0) and adapter recognition sequences (read 1: GATCG GAAGA GCACA CGTCT GAACT CCAGT CACNN NNNNA TCTCG TATGC CGTCT TCTGC TTG; read2: AGATC GGAAG AGCGT CGTGT AGGGA AAGAG TGTAG ATCTC GGTGG TCGCC GTATC ATT) were provided.
Quality trimming and filtering was performed using Atropos version 1.1.17 with minimum base quality cutoffs of 30 at both sides of the read (-q 30,30) and discarding reads with Ns and a length below 30 bp after trimming (-max-n 0 -m 30).
Mapping was performed with BWA mem v 0.7.12-r1039 using default parameters unless stated otherwise. Host sequences in ferret- and cell culture-derived samples were removed by mapping quality-controlled reads against either the ferret (Mustela putorius furo) or the African green monkey genome (Chlorocebus sabeus), respectively, specifying the minimum seed length (-k 31). Unmapped reads were extracted using samtools v1.7, and bamToFastq v2.17.0, and subsequently mapped to the CDV reference genome.
Host-free alignments were deduplicated using picard-tools MarkDuplicates (http://broadinstitute.github.io/picard) and left aligned using GATK LeftAlignIndels v4.0.
Assembly: CDV5804_NGS_ref.fasta
Supplementary files format and content: base count tables (wig format) of bam alignments to CDV5804_NGS_ref.fasta reference sequence
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| Submission date |
Jun 21, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Christian Karl Pfaller |
| E-mail(s) |
pfaller.christian@mayo.edu
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| Organization name |
Mayo Clinic
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| Department |
Molecular Medicine
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| Street address |
200 First Street SW
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platform ID |
GPL34630 |
| Series (1) |
| GSE270448 |
Genetic diversity accelerates canine distemper virus adaptation to ferrets |
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| Relations |
| BioSample |
SAMN41856097 |
| SRA |
SRX24941396 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8343110_r5804_P1.wig.gz |
93.8 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
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