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| Status |
Public on Aug 26, 2020 |
| Title |
MG52D |
| Sample type |
SRA |
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| Source name |
CD49fmid/P-cadherinhigh
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| Organism |
Bos taurus |
| Characteristics |
breed: Piedmontese
animal id: MG52
cell type: Primary mammary epithelial cells
cell fraction: CD49fmid/P-cadherinhigh
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| Treatment protocol |
Cells were directly sorted with a FACSAria III
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| Growth protocol |
Cell were isolated from bovine udders
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted in tubes containing 0,1% volume of FBS, centrifuged and lised with Trizol. RNA was then extracted and quantified.
Truseq mRNA non stranded (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
52D_CCGTCC_L001
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| Data processing |
Basecalling was performed with software bcl2fastq v1.8
Sequenced reads were mapped to bosTau8 whole genome using STAR v2.5
Aligned reads were counted at the gene level with Rsubread's featureCounts (with options useMetaFeatures = T, GTF.featureType = 'exon', countMultiMappingReads = F, countChimericFragments=F, allowMultiOverlap = F, strandSpecific = 0, isPairedEnd = Y) using ENSEMBL annotation v85.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were obtained using R package edgeR's rpkm function.
Genome_build: bosTau8 UMD3.1, genome-build-accession NCBI:GCA_000003055.3
Supplementary_files_format_and_content: RPKM normalized counts
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| Submission date |
Apr 10, 2020 |
| Last update date |
Aug 26, 2020 |
| Contact name |
Eugenio Martignani |
| E-mail(s) |
[email protected]
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| Phone |
+390116709173
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| Organization name |
University of Torino
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| Department |
Veterinary Science
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| Street address |
Largo Braccini 2
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| City |
Grugliasco |
| State/province |
TO |
| ZIP/Postal code |
10095 |
| Country |
Italy |
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| Platform ID |
GPL19172 |
| Series (1) |
| GSE148447 |
Whole transcriptome sequencing of bovine mammary epithelial subpopulations |
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| Relations |
| BioSample |
SAMN14573292 |
| SRA |
SRX8094366 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4471626_MG52D_RPKM.xlsx |
343.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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