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| Status |
Public on Jul 03, 2023 |
| Title |
sc11 |
| Sample type |
SRA |
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| Source name |
tumour tissue
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| Organism |
Equus caballus |
| Characteristics |
tissue: tumour tissue
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| Treatment protocol |
The collected material was transferred into tubes with RNAlater and stored at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from tissue using using TRIzol reagent (Invitrogen, Carlsbad, California) in combination with a Direct-zol RNA kit (Zymo Research)
The RNA-seq was performed using Swift Rapid RNA Library Kit (Biosciences) with deplete rRNA (Ribo-off rRNA Depletion Kit (Vazyme)), according to the protocol. The libraries were ligated with different indexes, pooled in one pool and sequenced in the 150 pair-end cycles on Illumina NovaSeq.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-quality set to 20 and a minimum read length of 36 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The mapping procedure was utilized using Tophat2 software (Trapnell et al., 2009), followed by counting of the reads to the gtf annotation file of Equus Caballus 3.0 assemble release v. 97 with the use of htseq-count software (Anders et al., 2015).
The differential expression analysis was performed with the use of Deseq2 software with the log transformation method (Love et al., 2014)
Assembly: EquCab3.0
Supplementary files format and content: Files containing gene counts for every gene and every sample created with htseq-count software
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| Submission date |
Mar 09, 2023 |
| Last update date |
Jul 03, 2023 |
| Contact name |
Ewelina Semik-Gurgul |
| E-mail(s) |
ewelina.semik@iz.edu.pl
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| Organization name |
National Research Institute of Animal Production
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| Department |
Department of Animal Molecular Biology
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| Lab |
Laboratory of Genomics
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| Street address |
Krakowska 1
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| City |
Balice |
| ZIP/Postal code |
32083 |
| Country |
Poland |
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| Platform ID |
GPL26749 |
| Series (1) |
| GSE226986 |
Transcriptome sequencing of equine sarcoids and skin samples |
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| Relations |
| BioSample |
SAMN33697555 |
| SRA |
SRX19610648 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7089456_sc11count.txt.gz |
115.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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