biostudies-arrayexpressZuzana Sumbalova KoledovaMus musculusFastQC 0.11.9; MultiQC 1.18; Cutadapt 4.4; HISAT2 2.2.1; SAMtools 1.13; UMI-tools 1.1.6; IGV 2.9https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16579Bulk RNA-seq of thoracic and inguinal nipple skin from lactating S100a4-Cre;DTA (\"S100a4\") and control DTA (\"DTA\") female mice, lactation day 1. 5 independent samples/genotype.biostudies-arrayexpressLibrary Construction - 500 ng of total RNA was used as input for library preparation using QuantSeq 3′ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt (Lexogen) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen). Library quantity and size distribution was checked using QuantiFluor dsDNA System (Promega) and High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies).Nucleic Acid Extraction - RNA isolation from frozen tissue was performed using 1.4mm Ceramic Bead Media (Revity), QIAzol Lysis Reagent (Qiagen) and NucleoSpin RNA kit (Macherey-Nagel). First, ceramic beads were added to the tissue in 800 μl of Qiazol followed by tissue disruption in homogenizer Bead Ruptor 4 (Omni International). Subsequently, the aqueous phase containing RNA was separated using 80 μl of BCP (Molecular Research Center). The aqueous phase was pipetted out, mixed with 70% EtOH in a ratio of 1:1 and applied to the column from NucleoSpin RNA kit. The rest of the isolation was performed according to manufacturer’s protocol of NucleoSpin RNA kit. RNA concentration was determined by Nanodrop 2000c (Thermo Scientific) and RNA integrity was checked on the Fragment Analyzer using RNA Kit 15 nt (Agilent Technologies).Sequencing - Library pool was sequenced using AVITI 2x75 Sequencing Kit Cloudbreak FS High Output (Element Biosciences) at AVITI System (Element Biosciences), resulting in an average of 11 million reads per sample.Sample Collection - Thoracic and inguinal nipples were dissected from the skin of L1 lactating dams as a patch of a approx. 2 mm in diameter and transferred to QIAzol Lysis Reagent (Qiagen). All samples were stored in -80 °C until collection of the complete experimental sample set.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - The reference genome of Mus musculus version GRCm39 was downloaded from Genome Reference Consortium (https://www.ncbi.nlm.nih.gov/grc/mouse). Read quality was checked using FastQC version 0.11.9 and MultiQC version 1.18. Low-quality base pairs, polyadenine tails and adapter contamination were removed using Cutadapt version 4.4. Clean reads were aligned to the genome sequence using HISAT2 2.2.1 and SAMtools 1.13. Aligned reads were deduplicated using UMI-tools version 1.1.6. Alignment was inspected visually in the IGV browser version 2.9.Data Transformation - Gene counts were normalized using median of rations method with DESeq2 R package.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsElement AVITIRNA-seq of coding RNAMus musculusViacheslav ZemlianskiDenisa Jaroš BelisováEma GrofováZuzana Sumbalova KoledovafalseDepletion of S100A4+ stromal cells results in abnormal nipple development and nursing failureBulk RNA-seq of thoracic and inguinal nipple skin from lactating S100a4-Cre;DTA (\"S100a4\") and control DTA (\"DTA\") female mice, lactation day 1. 5 independent samples/genotype.2026-07-01T00:00:00Z2026-07-01T01:04:19.721Z2026-01-27T14:40:10.918ZE-MTAB-16579ERP188213EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184