|
| Status |
Public on Dec 13, 2021 |
| Title |
Uwt12018 RNA |
| Sample type |
SRA |
| |
|
| Source name |
endometrial epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
genotype: Control wild-type
|
| Treatment protocol |
Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).
|
| Growth protocol |
Mice were housed at the Van Andel Research Institute Animal Facility and the Michigan State University Grand Rapids Research Center in accordance with protocols approved by the Van Andel Research Institute and Michigan State University, under AUF# 01/16-099-00.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Lexogen SIRV-set2 RNAs were spiked into RNA prior to library preparation at a concentration of 1% by mass. RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 100 ng of total RNA material.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA library. Second flow cell. Cells from pooled mice. Retrieved from GEO accession GSE129784.
|
| Data processing |
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting. Lexogen SIRVome was independently aligned and quantified for qualitative assessment of library concordancy.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file. Raw gene counts were combined with control cell data retrieved from GEO accession GSE129784.
Low count genes were filtered (at least 1 count per sample on average) prior to normalization factor calculation, dispersion estimation, negative binomial generalized linear model fitting, and Wald hypothesis testing in DESeq2 for differential gene expression analysis. For linear modeling, the design matrix was constructed from a single “condition” variable with the inclusion of an intercept term, in the form: ~ condition. Calculated differential gene expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including per-sample gene counts (STAR output) and non-thresholded DESeq2 differential gene expression analysis.
|
| |
|
| Submission date |
Feb 22, 2021 |
| Last update date |
Dec 13, 2021 |
| Contact name |
Ronald L. Chandler |
| E-mail(s) |
rlc@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Obstetrics, Gynecology and Reproductive Biology
|
| Street address |
3100-4 400 Monroe NW
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE167275 |
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis [RNA-seq] |
| GSE184499 |
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis |
|
| Relations |
| Alternative to |
GSM3722008 |
| BioSample |
SAMN18029168 |
| SRA |
SRX10151553 |
