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| Status |
Public on Mar 10, 2019 |
| Title |
con3 |
| Sample type |
SRA |
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| Source name |
bovine vaginal control
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| Organism |
Bos taurus |
| Characteristics |
cell type: bovine vaginal ephithelial cell
treated: untreated group
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from untreated and SQ0048strain-treated BVECs was extracted using Trizol reagent (Invitrogen/Thermo Fisher Scientific, Carlsbad, CA, USA) following the manufacturer's instructions. The quantity and purity of total RNA were analyzed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, Santa Clara, CA, USA), yielding RIN scores >7.0. The cDNA libraries were constructed with RNA isolated from BVECs using a TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, CA, USA).
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 4000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ARS-UCD1.2 (GCA_002263795.2) whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: ARS-UCD1.2 (GCA_002263795.2)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all Sample
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| Submission date |
Mar 04, 2019 |
| Last update date |
Mar 10, 2019 |
| Contact name |
chunyu Niu |
| E-mail(s) |
1251674572@qq.com
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| Organization name |
Inner Mongolia Agricultural University
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| Street address |
college of inner mongolia agricultural university ,306 street zhao wu da ,huhhot ,inner mongolia,china
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| City |
Hohhot |
| ZIP/Postal code |
010010 |
| Country |
China |
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| Platform ID |
GPL23295 |
| Series (1) |
| GSE127808 |
New Insights from Transcriptome Profiling of Bovine Vaginal Epithelial Cell Response to Isolated Lactobacillus |
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| Relations |
| BioSample |
SAMN11051303 |
| SRA |
SRX5463287 |
| 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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