biostudies-arrayexpressAlexander SchulzHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16566This study investigates the transcriptional consequences of Laminin-α5 (LAMA5) loss in human urine-derived stem cells (USCs) to understand the molecular etiology of idiopathic short stature. The experiment consists of two components: 1. Differentiation Profiling: CRISPR/Cas9-mediated LAMA5 knockout (KO) USCs and wild-type (WT) controls were profiled in three conditions: undifferentiated state, osteogenic differentiation, and chondrogenic differentiation. This analysis aims to interpret how cell-matrix interactions regulate lineage-specific transcriptional programs and spheroid architecture. 2. Pharmacological Rescue: To assess the functional role of canonical WNT signaling in LAMA5-mediated regulation, LAMA5 knockout USCs were undergoing chondrogenic differentiation were treated with the WNT agonist Lithium Chloride (LiCl) or left untreated. Data analysis identifies a LAMA5-dependent gene regulatory network enriched for limb morphogenesis factors (including WNT7A, PITX1, and FLI1) and demonstrates partial restoration of this network upon β-catenin stabilization via LiCl. Study Design / Samples Total Samples: 24 Organism: Homo sapiens Cell Type: Urine-derived stem cells (USCs) Detailed Sample List: Condition 1 (Genotype x Lineage): Comparison of WT vs. LAMA5 KO across three differentiation stages (n=18). 3x Wild-type (WT) - Undifferentiated 3x Wild-type (WT) - Osteogenic 3x Wild-type (WT) - Chondrogenic 3x LAMA5 KO - Undifferentiated 3x LAMA5 KO - Osteogenic 3x LAMA5 KO - Chondrogenic Condition 2 (Rescue Treatment): Effect of LiCl treatment on LAMA5 KO cells (n=6). 3x LAMA5 KO (Clone 2) - Untreated (Control) 3x LAMA5 KO (Clone 2) - Treated with LiClbiostudies-arrayexpressGrowth Protocol - Urine-derived stem cells (USCs) were expanded in proliferation medium at 37°C in a humidified 5% CO2 atmosphere. For differentiation experiments, cells were cultured in specific Osteogenic or Chondrogenic differentiation media.Sequencing - Depletion Sample libraries were sequenced on an Illumina [NovaSeq X Plus] platform to generate paired-end reads.Sample Collection - Cells were harvested directly from in-vitro culture plates. Culture medium was aspirated, and cells were washed with PBS. Cells were lysed immediately using lysis buffer for RNA extraction.Nucleic Acid Extraction - Total RNA was extracted from cells using [Qiagen RNeasy Mini Kit] following the manufacturer's instructions. RNA quality and concentration were assessed using a Fragment Analyzer [Agilent].Sequencing - Poly-A Enrichment Sample libraries were sequenced on an Illumina [NovaSeq 6000] platform to generate paired-end reads.Library Construction - Sequencing libraries were prepared using two distinct protocols depending on the sample batch. For Poly-A enrichment samples: Libraries were prepared using the Illumina Stranded mRNA Prep kit, utilizing Oligo(dT) beads for mRNA capture. For Depletion samples: Libraries were prepared using the Twist RNA Library Prep with Depletion kit, utilizing enzymatic depletion for rRNA and Globin removal. Both protocols generated strand-specific (first-strand) paired-end libraries.Sample Treatment - Samples designated for differentiation were treated with either Osteogenic or Chondrogenic induction media. For the subset of KO2 samples testing Lithium Chloride, cells were treated with LiCl or left untreated (vehicle control) prior to harvest.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads from each sequencing lane were aligned individually to the hg38 reference genome with Ensembl (release 106) gene annotations using STAR (version 2.7.10a). For each sample, resulting alignments were combined using the MergeSamFiles command from Picard (version 2.25.4, http://broadinstitute.github.io/picard/).Data Transformation - Gene quantification in form of a count matrix was generated using featureCounts (version 2.0.1) and Ensembl gene annotations corresponding to those of the alignment reference. Alignment and quantification levels were used for quality assessment.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensAlexander SchulzfalseTranscriptomic profiling of LAMA5-deficient human stem cell–derived chondrogenesis reveals a human-specific ECM–WNT signaling axisThis study investigates the transcriptional consequences of Laminin-α5 (LAMA5) loss in human urine-derived stem cells (USCs) to understand the molecular etiology of idiopathic short stature. The experiment consists of two components: 1. Differentiation Profiling: CRISPR/Cas9-mediated LAMA5 knockout (KO) USCs and wild-type (WT) controls were profiled in three conditions: undifferentiated state, osteogenic differentiation, and chondrogenic differentiation. This analysis aims to interpret how cell-matrix interactions regulate lineage-specific transcriptional programs and spheroid architecture. 2. Pharmacological Rescue: To assess the functional role of canonical WNT signaling in LAMA5-mediated regulation, LAMA5 knockout USCs were undergoing chondrogenic differentiation were treated with the WNT agonist Lithium Chloride (LiCl) or left untreated. Data analysis identifies a LAMA5-dependent gene regulatory network enriched for limb morphogenesis factors (including WNT7A, PITX1, and FLI1) and demonstrates partial restoration of this network upon β-catenin stabilization via LiCl. Study Design / Samples Total Samples: 24 Organism: Homo sapiens Cell Type: Urine-derived stem cells (USCs) Detailed Sample List: Condition 1 (Genotype x Lineage): Comparison of WT vs. LAMA5 KO across three differentiation stages (n=18). 3x Wild-type (WT) - Undifferentiated 3x Wild-type (WT) - Osteogenic 3x Wild-type (WT) - Chondrogenic 3x LAMA5 KO - Undifferentiated 3x LAMA5 KO - Osteogenic 3x LAMA5 KO - Chondrogenic Condition 2 (Rescue Treatment): Effect of LiCl treatment on LAMA5 KO cells (n=6). 3x LAMA5 KO (Clone 2) - Untreated (Control) 3x LAMA5 KO (Clone 2) - Treated with LiCl2026-01-31T00:00:00Z2026-05-30T17:00:19.101Z2026-01-23T15:42:48.824ZE-MTAB-16566ERP188096EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969