|
| Status |
Public on Oct 22, 2019 |
| Title |
MS-275 treated repeat3 |
| Sample type |
SRA |
| |
|
| Source name |
BRIN-BD11 (ECACC 10033003) pancreatic beta cell line
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: BRIN-BD11 (ECACC 10033003)
cell type: A stable glucose-responsive insulin-secreting pancreatic beta-cell line established through electrofusion of RINm5F cells with New England Deaconess Hospital rat pancreatic islet cells
passages: Passage 25
strain: NEDH Rat
hdac inhibitor: MS-275(Entinostat); Class1 HDAC inhibitor
|
| Treatment protocol |
BRIN-BD11 pancreatic beta cells were seeded in 6-multiwell plates at a density of 500,000 cells/well. MS-275 (5µM, dissolved in 0.1%DMSO) was added 24h post seeding after cells were adhered and cultured for 16h in complete medium prior to RNA extraction
|
| Growth protocol |
BRIN-BD11 pancreatic beta cells (ECACC cat.no: 10033003) were cultured at 37oC with 5% CO2 in RPMI medium 1640 GLUTAMAX supplemented with 10% heat inactivated Fetal Bovine Serum (FBS), 1mM Sodium pyruvate, 10µg/ml gentamycin, 100units/ml penicillin ,100µg/ml streptomycin and 50μM beta mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were pelleted by centrifugation and flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit. 150 ng total RNA was used for preparing libraries for RNA sequencing.
The RNA was fragmented and then converted to cDNA according to the kit protocol (NEB #E7770S). The cDNA was end repaired and further purified using AMPure XP beads (A63880 AMPure XP).The cleaned cDNA was adapter ligated, purified and subjected to 12 PCR cycles of amplification using primers provided in the kit (NEB #E7770S). The PCR products were purified using AMPure XP beads. The quantification and size distribution of the prepared library was accomplished using Qubit fluorimeter and Agilent Tape station D1000 Kit (Agilent Technologies) following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with default parameter using Trimmomatic 0.36v
The reads that passed quality filters was mapped to the Rattus_norvegicus Rnor_6.0 using STAR 0.27v
Reads mapping to genes Rattus_norvegicus.Rnor_6.0 gene list [GTF] were counted using feature count module of sub reads package and were normalized in DESeq2v3.5
Differentially expressed genes were selected based on log2-ratio change with p-value <0.05 (Student‘s t test, unpaired).
Genome_build: Rnor_6.0 (GCA_000001895.4)
Supplementary_files_format_and_content: aligned bam files,tab-delimited text files include raw count values for each Sample, Differentially expressed genes list file
|
| |
|
| Submission date |
Oct 21, 2019 |
| Last update date |
Oct 22, 2019 |
| Contact name |
PRASENJIT MITRA |
| E-mail(s) |
prasenjit.mitra01604@gmail.com
|
| Phone |
04066571526
|
| Organization name |
Dr.Reddy’s Institute of Life Sciences
|
| Street address |
University of Hyderabad Campus, Gachibowli
|
| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500032 |
| Country |
India |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE139147 |
BRIN-BD11 pancreatic beta cell mRNA profile upon treatment with Class1 HDAC inhibitor MS-275 |
|
| Relations |
| BioSample |
SAMN13067456 |
| SRA |
SRX7027447 |
