|
| Status |
Public on Oct 05, 2022 |
| Title |
T47D_WT_clone1_mimic_miR_301b_3p |
| Sample type |
SRA |
| |
|
| Source name |
T-47D
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T-47D
cell type: mammary gland ductal carcinoma
esr1 genotype: WT
treatment: hsa-mir-301b-3p mimic
|
| Treatment protocol |
T-47D cells were grown in 100mm plates in hormone-deprived media for four days then plated into 12-well plates at approximately 50% confluence and allowed to adhere for 24 hours. Cells were then transfected with a miRNA mimic or inhibitor for a given miRNA or with a mimic or inhibitor negative control at a 10nM final concentration.
|
| Growth protocol |
Cells were cultured in RPMI1640 Media (ThermoFisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (ThermoFisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24 hours post-transfection, cells were collected, washed with PBS, then treated with RLT Plus lysis buffer supplemented with 1% BME. RNA was extracted using a Quick-RNA RNA Miniprep kit (Zymo Research).
Poly-A selected RNA-seq libraries were generated using a KAPA Stranded mRNA-Seq kit (KAPA Biosystems) and 500ng RNA per sample as starting material.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the human genome using HISAT2.
Sam files were then converted to bam files and sorted via Samtools.
Read counts for each gene were determined from alignments to hg19 UCSC knownGene gene models using featuresCounts from the SubRead package.
Normalization and differential expression analysis were performed using DeSeq2.
Assembly: hg19
Supplementary files format and content: Raw gene counts in a text file
|
| |
|
| Submission date |
Sep 30, 2022 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Jason Gertz |
| E-mail(s) |
jay.gertz@hci.utah.edu
|
| Organization name |
University of Utah
|
| Lab |
Gertz
|
| Street address |
1950 Cir of Hope Dr
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE214579 |
Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs (RNA-Seq) |
| GSE214580 |
Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs |
|
| Relations |
| BioSample |
SAMN31111531 |
| SRA |
SRX17767600 |
