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Sample GSM2865495 Query DataSets for GSM2865495
Status Public on Feb 13, 2019
Title Stage 1 sample 3 from Kashmiri cattle
Sample type SRA
Source name milk epithelial cells
Organism Bos indicus
Characteristics stage of lactation: 1st stage (March)
lactation number: 3rd time lactating
tissue: milk epithelial cells
breed: Kashmiri cattle
Treatment protocol Cells were stored at -80°C
Growth protocol Milk epithelial cells were extracted from milk
Extracted molecule total RNA
Extraction protocol RNA was extracted by TriZol method. RNA was quantified by spectrophotometer (ThermoFisher, USA) and the quality and integrity was assessed by Bioanalyzer (Agilent, USA). The RIN values ranged from 6.5 -9.3.
Library construction by Illumina Truseq stranded mRNA sample preparation kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
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 Capra hircus whole genome using bowtie v2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Assembly: UMD3.1 (GCA_000003055.3) – Cow
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Stage
Submission date Nov 27, 2017
Last update date May 15, 2019
Contact name Basharat Ahmad Bhat
Phone 9469662374
Organization name Sher-e-Kashmir University of Agricultural Sciences and Technology
Department Animal Biotechnology
Street address Shuhama
City Gandarbal
State/province Kashmir
ZIP/Postal code 190006
Country India
Platform ID GPL19746
Series (1)
GSE107366 Transcriptional profiling of milk epithelial cells of Kashmiri and Jersey cattle
BioSample SAMN08100435
SRA SRX3424128

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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