|
| Status |
Public on Jul 25, 2022 |
| Title |
RBMS3_ACTD_3hr_REP1 |
| Sample type |
SRA |
| |
|
| Source name |
RBMS3_ACTD_3hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: HMLE
cell type: Immortalized mammary epithelial cells
genotype/variation: RbMS3 expression
treament: treated with ACTD at 180 minutes
|
| Treatment protocol |
the HMLE/LacZ and HMLE/RBMS3 cells were treated with 10 µg/mL of Actinomycin D for 4 different time points (0, 90, 180 and 360 mins).
|
| Growth protocol |
HMLE cells were cultured in 1:1 Dulbecco's Modified Eagle's Medium (DMEM)/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex), 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (EGF) (PromoCell), 0.5 µg/ml hydrocortisone (Sigma) and 10 µg/ml insulin (Sigma)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy Plus mini kit (Qiagen)
Library preparation using Lexogen's QuantSeq 3'mRNA-seq method. 75bp single reads with dual indexing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RBMS3_ACTD_3hr_REP1_S46_L002
|
| Data processing |
FASTQ files trimmed using Trim Galore (v0.6.6) with default parameters, except: --three_prime_clip_R1 12
Trimmed FASTQ files were quantified using Salmon (v1.4.0) with default parameters, except: --validateMappings -l A
Transcripts were mapped to genes using biomaRT (v2.48.1) and tximport (v1.20.0)
Normalized gene counts were computed using DESeq2 (v1.32.0) counts(normalized=TRUE)
Differential expression was computed using DESeq2 (v1.32.0) DESeq()
Genome_build: Gencode v36
Supplementary_files_format_and_content: tab-delimited quant.sf text files generated by Salmon for each sample
Supplementary_files_format_and_content: comma-delimited text file of normalized gene counts for all samples
|
| |
|
| Submission date |
Jul 30, 2021 |
| Last update date |
Jul 25, 2022 |
| Contact name |
Guojun Wu |
| Organization name |
Karmanos Cancer Institute
|
| Department |
Oncology
|
| Street address |
4100 John R
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE181237 |
RNA binding protein RBMS3 is a common effector of EMT program that promotes Triple-Negative Breast Cancer Progression by Regulation of PRRX1 mRNA Stability |
|
| Relations |
| BioSample |
SAMN20507179 |
| SRA |
SRX11613678 |
