|
| Status |
Public on Jan 06, 2023 |
| Title |
MC72_5_DMSO treated_Vehicle control |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Treated with 0.1% DMSO for 72 hours
cell type: Breast cancer cell line
cell line: MCF-7
genotype: Wild type
|
| Treatment protocol |
MCF-7 cells were seeded at a density of 0.2 million cells/ well using M1 medium in 6-well plates. After 48 hours of seeding, the cells were given phenol red-free DMEM supplemented with 10% heat-inactivated charcoal-stripped fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M2 medium) for 24 h. Then the cells were treated with M2 medium containing 10 μM enterolactone or 0.1% DMSO (vehicle control) for 72 h. The treatment medium was replenished every 24 h.
|
| Growth protocol |
MCF-7 cells were grown in a humidified chamber maintained at 37 °C and 5% CO2. The cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM), supplemented with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M1 medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNA extraction reagent prepared in-house as per Chomczynski and Sacchi, with modifications
mRNA enrichment was performed using KAPA mRNA capture kit. Libraries were prepared according to instructions accompanying the KAPA RNA Hyper prep kit (Roche, Switzerland). mRNA was fragmented and reverse transcribed using oligo-dT primers to synthesize cDNA. The double-stranded cDNAs were end-repaired, polyadenylated, and ligated with adapter sequences. Sequencing was performed using Nextseq2K Platform in 150 paired-end reads length format.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Quality control check - FastQC Version 0.11.5: It checks for read quality
Data Trimming Steps - Trimmomatic Version 0.36: Adapter trimming and filtering out low quality reads
Quality Control Check - FastQC Version 0.11.5: Re-assess the quality of filtered reads prior to successive mapping.
Read Alignment - STAR Aligner Version 2.7.6a: Mapping the reads against the reference genome.
Assembly: Ensemble Homo sapiens GRCh38 genome
Quantification of Reads - featureCounts v2.0.0: Quantification of mapped reads.
Annotation Reference File - Homo sapiens GRCh38 (gtf):
Supplementary files format and content: Raw_gene_counts_matrix
|
| |
|
| Submission date |
Oct 30, 2022 |
| Last update date |
Jan 06, 2023 |
| Contact name |
Anil Mukund Limaye |
| E-mail(s) |
amul@iitg.ac.in
|
| Phone |
+91-0361-2582218
|
| Organization name |
Indian Institute of Technology Guwahati
|
| Department |
Department of Biosciences and Bioengineering
|
| Street address |
IIT Guwahati
|
| City |
Guwahati |
| State/province |
Assam |
| ZIP/Postal code |
781039 |
| Country |
India |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE216876 |
Genome-wide effects of enterolactone on gene expression in MCF-7 cells |
|
| Relations |
| BioSample |
SAMN31526738 |
| SRA |
SRX18082304 |
