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| Status |
Public on Oct 20, 2021 |
| Title |
MDMs, MAP_1 |
| Sample type |
SRA |
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| Source name |
bovine peripheral blood mononuclear macrophages, infected with Mycobacterium avium subsp. paratuberculosis
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| Organism |
Bos taurus |
| Characteristics |
cell type: Bovine peripheral blood mononuclear macrophages
infection: MAP
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the mRNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
A cDNA library constructed by technology from the pooled RNA was sequenced with Illumina Novaseq 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
And then we performed the paired-end sequencing on an illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Oct 10, 2021 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Yanhong Bao |
| E-mail(s) |
[email protected]
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| Phone |
18243526681
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| Organization name |
Jilin Agricultural University
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| Street address |
jilin changchun
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| City |
Changchun |
| State/province |
jilin |
| ZIP/Postal code |
130118 |
| Country |
China |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE185609 |
mRNA expression profile of bovine monocyte derived macrophages infected with Mycobacterium avium subsp. Paratuberculosis (MAP) |
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| Relations |
| BioSample |
SAMN22203061 |
| SRA |
SRX12565933 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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