|
| Status |
Public on Oct 30, 2024 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
Breast; Mammary gland
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast; Mammary gland
cell line: MDA MB-231
cell type: Triple negative breast epithelial cell
genotype: Wild type
treatment: Control
|
| Treatment protocol |
MDA MB-231 cells were seeded and treated with 50 mM NaCl for 24 hours at the end of incubation period, RNA was harvested and subjected to RNA Sequencing
|
| Growth protocol |
MDA MB-231 cells were maintained in DMEM with 10% FBS and 1% Penicillin-Streptomycin , under humidified condition at 5 % CO2 and 37 degree.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MDA MB-231 cells were seeded and incubated for 12 hours before treatement in 10% FBS containing DMEM with 1% penicilln and streptomycin, Next day, Cells were treated with 50mM NaCl (0.2 micron sterile filtered) for 24 hours. At the end of incubation period , cells were stored in RNA Later and subjected to RNA Sequencing
Library preparation was performed using NEB Next®UltraTM II RNA Library Prep Kit for Illumina® following manufacturer’s instructions. Further quality and quantity were assessed using Agilent 4150 Tape Station system and Qubit 4 Fluorometer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control and preprocessing of raw reads obtained from sequencing in FASTQ format was performed open-source package fastp (v0.23.4).
Processed reads were aligned to Human genome version 38 using Hisat2 tool (v2.2.1) to generate BAM files.
Read counts were generated using the Feature Counts tool (v2.0.6).
Differential expression was calculated using the Bioconductor package edgeR R (v4.3) package.
Assembly: hg38
Supplementary files format and content: tab delimited text files containing read counts of each samples
|
| |
|
| Submission date |
Apr 26, 2024 |
| Last update date |
Oct 30, 2024 |
| Contact name |
Aditya Kumar |
| E-mail(s) |
[email protected]
|
| Organization name |
Tezpur University
|
| Department |
Molecular Biology and Biotechnology
|
| Lab |
Nucleix Lab
|
| Street address |
R107, Dept Of Molecular Biology & Biotechnology
|
| City |
Tezpur |
| State/province |
Assam |
| ZIP/Postal code |
784028 |
| Country |
India |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE265934 |
Global transcriptomic alterations in MDA-MB-231 cells following high salt treatment |
|
| Relations |
| BioSample |
SAMN41098288 |
| SRA |
SRX24382720 |
