|
| Status |
Public on Sep 18, 2019 |
| Title |
Zheng_3_S39 |
| Sample type |
SRA |
| |
|
| Source name |
normal skin tissue
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
disease stage: Normal
gender/animal/site: female/R4296/R4
route if infection: control (mock)
|
| Treatment protocol |
The rabbits were infected by pre-scarification protocol on the back skin, followed by either cutaneous or intravenous inoculation of virus innocullum.
|
| Growth protocol |
Eight adult (4 males and 4 females) outbred New Zealand white rabbits.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated using TriPure Reagent (Millipore-Sigma, Part No. 11667165001) and DNase-treated on column using RNeasy Mini Kit (Qiagen, Part No. 74104).
TruSeq Stranded Total RNA Kit (Illumina; RS-122-2201)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Skin sample from Control rabbit.
limma_DEG_Ectopic-Control_all_genes.txt
limma_DEG_Vein-Control_all_genes.txt
|
| Data processing |
Samples were pooled and sequenced on one HiSeq run using Illumina TruSeq Stranded Total RNA Kit RS-122-2201.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Supplementary_files_format_and_content: Tab-delimited text files are limma-voom normalized differential expression output.
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Sep 18, 2019 |
| Contact name |
Thomas Joshua Meyer |
| E-mail(s) |
thomas.meyer@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
CCBR
|
| Street address |
41 Center Drive, Building 41, Room B620
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL25392 |
| Series (1) |
| GSE124211 |
Transcriptome of CRPV-induced wart tissues |
|
| Relations |
| BioSample |
SAMN10621041 |
| SRA |
SRX5171261 |
