DOI: 10.5061/dryad.mcvdnck9s
title: PGRMC2 is a pressure-volume regulator critical for myocardial responses to stress in mice

description: Progesterone receptors are classified into nuclear and membrane-bound
 receptor families.  In this study, we evaluate the role of
 progesterone receptor membrane-bound component-2 (PGRMC2) in the heart. We
 use a heart-specific knockout (KO) mouse model (MyH6•Pgrmc2flox/flox) in
 which the Pgrmc2 gene was specifically deleted in cardiomyocytes. Here we
 show that PGRMC2 serves as a mediator of steroid hormones for rapid
 calcium signaling in cardiomyocytes to maintain cardiac contraction and
 support stroke volume and cardiac output by regulating the cardiac
 pressure-volume relationship. The KO hearts from both male and female mice
 exhibit impairment in regulating the pressure-volume
 relationship.  Under hypoxic conditions, this dysregulation in
 the KO hearts is subsequently progressed to congestive left and right
 ventricular failure.
description: Total mRNA transcriptome sequencing of heart samples was studied
 using the NovaSeq X Plus platform (Illumina).
description: # PGRMC2 is a pressure-volume regulator critical for myocardial responses
 to stress in mice ## Descriptions Comparing mRNA sequencing from mouse
 heart tissues in three wild-type (WT) and three PGRMC2 knockout (KO)
 samples. Sample: • WT.1, WT.2, WT.3, KO.1, KO.2, KO.3. • WT stands for
 Wild-Type (control group). • KO stands for Knockout (PGRMC2). • The
 species being studied is Mus musculus (mouse) FASTQ Entry data
 description: 1st Line (Identifier) • LH00626 → The High-Throughput
 sequencing identification Tag number • 19 → Run number. • 22GHMLLT4 → Flow
 cell ID. • 5 → Lane number. • 1101 → Tile number on the flow cell. •
 12313:1056 → X and Y coordinates of the cluster on the tile. •
 1:N:0:ATGTGATT+AAGTAACG o 1 → Read number (1 for forward read, 2 for
 reverse read in paired-end sequencing). o N → Indicates if this read
 failed (Y) or passed (N) quality filters. o 0 → Index number (likely a
 sample barcode). o ATGTGATT+AAGTAACG → Dual index adapters used for
 multiplexing. 2nd Line (Nucleotide Sequence)
 TNTAGTTCTAGTGCGATTAGGAATCCTAATACTGAAATAATTAGGGCTGTGGTTTTTAAAAATCATGGTATTGTGAGGACTGGAATGCTGGTTGGTGGAATATTATATGAGATGACAAATCCTGCAAAGATGCTTCCGAATGCAGATCGGA • This is the actual DNA sequence obtained from sequencing. • The "N" in the sequence indicates an ambiguous nucleotide (i.e., the sequencer was unsure of that nucleotide at that position). 3rd Line (Separator) • This is a mandatory placeholder separating the sequence from the quality scores. 4th Line (Quality Scores) • Each character corresponds to a Phred quality score for the respective nucleotide in the sequence. • Higher ASCII character values indicate higher sequencing accuracy. • I corresponds to a high-quality score, while # or - suggests lower confidence at those positions. What Does This Mean? • This is a single raw sequencing read from an Illumina sequencer. • The identifier tells us about the sequencing run, flow cell, lane, tile, and position. • The sequence contains the raw nucleotides, with N indicating uncertainty. • The quality scores give confidence levels for each base. ## Code/Software FASTQ file format entry was used for next-generation sequencing (NGS) data of total mRNA sequencing data. Whole transcriptome sequencing of six mouse samples yielded Illumina X Plus paired-end (PE) 100 bp reads. These reads were QC analyzed using FastQC, trimmed with Trimmomatic, and aligned to the mouse mm10 reference genome using a splice-aware short-read aligner (HISAT2). Gene quantification was performed using Salmon and featureCounts, followed by differential expression analysis with DESeq2.