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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 25, 2022 |
| Title |
Primary Mammary Epithelial Cells Infected with S. aureus 1 |
| Sample type |
SRA |
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| Source name |
Milk
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| Organism |
Capra hircus |
| Characteristics |
tissue: (Mammary Gland)
cell type: Primary cells
agent: S. aureus
age: Passage 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 HiSeq 2500 |
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| Description |
S1
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| Data processing |
The raw reads acquired from RNA seq were filtered by removing the adapter sequences and low quality reads. All the filtered reads were submitted to FastQC for quality control analysis. Each library was investigated for distribution of base quality score, sequence quality score, Average base content per read, GC distribution in the reads and for over-represented sequences.
On the basis FastQC report, we trimmed the reads wherever necessary and retained only high quality reads for down stream analysis. For filtering low quality reads Trimgalore was used. To identify lncRNAs, first we built the reference genome index through Bowtie and used TopHat to map all sequenced reads to the Capra hircus reference genome (ARS1).
To identify novel lncRNAs from PMECs with high confidence, an inflexible pipeline was used to filter transcripts with any coding capacity. First, the transcripts <200nts long or with single exon were filtered out. Next, four independent algorithms, CNCI, PLEK, CPAT and Pfam were applied to extract potential noncoding transcripts.
For DE analysis, reads were mapped to the lncRNA reference using CuffDiff. DE genes were screened based on p-value < 0.05 and absolute log2FC ≥ 1. The expression value of lncRNAs was calculated in terms of RPKM (reads per kilo base per million) and EDGE tests were used for identification of DE genes between different groups.
To regulate false discovery because of multiple testing, p-values were Bonferroni-corrected. Expression was considered significant only at a fold-change of ± 2 and a corrected p-value < 0.05.
Supplementary_files_format_and_content: RPKM,fold-change data
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| Submission date |
Feb 26, 2021 |
| Last update date |
Jan 25, 2022 |
| Contact name |
Basharat Ahmad Bhat |
| E-mail(s) |
bb284@snu.edu.in
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| Phone |
9469662374
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| Organization name |
Sher-e-Kashmir University of Agricultural Sciences and Technology
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| Department |
Animal Biotechnology
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| Street address |
Shuhama
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| City |
Gandarbal |
| State/province |
Kashmir |
| ZIP/Postal code |
190006 |
| Country |
India |
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| Platform ID |
GPL19149 |
| Series (1) |
| GSE167591 |
Transcriptional landscape of pathogen-responsive lncRNAs in primary mammary epithelial cells reveals insights in immune response and defense mechanism. |
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| Relations |
| BioSample |
SAMN18062964 |
| SRA |
SRX10175291 |
| 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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