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| Status |
Public on Jul 24, 2019 |
| Title |
BT2_RNA-seq |
| Sample type |
SRA |
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| Source name |
BT_REPC
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| Organism |
Bos taurus |
| Characteristics |
breed: Hostein
treatmnet: 24h post-Butyrate treatment
cell type: Rumen Epithelial Primary Cells (REPC)
replicate: Replicate2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 6 rumen epithelial cell samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Qiagen, Valencia, CA, USA). RNA integrity was verified using Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). High-quality RNA (RNA integrity number [RIN]: 9.0) was processed using an Illumina TruSeq RNA sample prep kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA).
After quality control (QC) procedures, individual RNA-seq libraries were pooled based on their respective sample-specific 6-bp (base pairs) adaptors and pair-end sequenced at 150 bp/sequence read (PE150) using an Illumina HiSeq 2500 sequencer (Illumina, Inc. San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Lib_Bulk_BT2
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| Data processing |
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We then mapped the clean reads to the cattle reference genome UMD3.1.1 using STAR (version 020201)
We used Ensembl genes as the gene annotation file, including 24,616 genes, and the gene expression levels were then determined by FPKM values for accounting for differences in sequence depth and gene length. The FPKM of genes were quantified using Cufflinks
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: txt
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| Submission date |
Apr 05, 2019 |
| Last update date |
Jul 24, 2019 |
| Contact name |
George E. Liu |
| E-mail(s) |
george.liu@usda.gov
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| Phone |
301-504-9843
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| Organization name |
USDA-ARS
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| Lab |
Animal Genomics and improvement Lab.
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| Street address |
10300 Baltimore Ave Bldg 306
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| City |
Beltsville |
| State/province |
Maryland (MD) |
| ZIP/Postal code |
20705 |
| Country |
USA |
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| Platform ID |
GPL19172 |
| Series (2) |
| GSE129416 |
Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 1] |
| GSE129423 |
Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation |
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| Relations |
| BioSample |
SAMN11352800 |
| SRA |
SRX5649064 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3712671_Bulk_BT2.gene.fpkm.txt.gz |
867.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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