|
| Status |
Public on Jun 16, 2019 |
| Title |
Curcumin_treated_2 |
| Sample type |
SRA |
| |
|
| Source name |
Theileria infected bovine leucocytes
|
| Organisms |
Theileria annulata; Bos taurus |
| Characteristics |
cell type: Theileria infected bovine leucocytes
|
| Treatment protocol |
Theileria annulata infected bovine leucocytes collected from field were treated with 20 µM of curcumin for 24 hrs. RNA isolated from untreates and treated samples.
|
| Growth protocol |
Cells cultured in RPMI media- 1640 supplemented with 10% fetal bovine serum, 2 mM L- glutamine, 25 mM HEPES, 0.1% PenStrep at 37o C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA isolation from the untreated and curcumin treated bovine leucocytes was performed using Trizol reagent as per standard protocol. The purity and concentration of total RNA extracted was checked using Nanodrop spectrophotometer by using 1 µl of total RNA against nuclease free water as blank to determine the absorbance ratio 260/280 nm. The quality check of the isolated RNA was performed in Agilent 2100 Bioanalyzer. RNA with RNA integrity number (RIN) greater than 7 was used for sequencing.
Sequencing libraries were constructed following NEBNext® Ultra™ Directional RNA Library Prep Kit protocol and were then processed by Illumina HiSeq Paired- end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Gene expression of curcumin treated cells after 24hr
|
| Data processing |
Adaters were removed using Cutadapt, raw read data was run through quality control metrics using FastQC.
Sequence reads were aligned to the Bos taurus genome (UMD3.1 build, Ensembl.org), Theileria annulata genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/225/GCF_000003225.3_ASM322v1/GCF_00 0003225.3_ASM322v1_genomic.fna.gz) using HISAT2.
Cufflinks was used to estimate and calculate transcript abundance. It results in normalized read count in the form of FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Cuffdiff was used to calculate the differentially expressed transcripts and categorize them into UP, Down and Neutrally regulated based on the log2fold change values.
|
| |
|
| Submission date |
Aug 28, 2018 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Anand Srivastava |
| E-mail(s) |
anand@niab.org.in
|
| Phone |
8790572126
|
| Organization name |
National Institute of Animal Biotechnology (NIAB)
|
| Street address |
Survey No 37/4, Gowalidoodi Area , Gopanpally
|
| City |
Hyderabad |
| State/province |
India |
| ZIP/Postal code |
500032 |
| Country |
India |
| |
|
| Platform ID |
GPL25502 |
| Series (1) |
| GSE119138 |
Transcriptome profile of Theileria infected bovine leucocytes under curcumin treatment |
|
| Relations |
| BioSample |
SAMN09927952 |
| SRA |
SRX4617962 |
