biostudies-arrayexpressThorsten KlampflMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15404This experiment was performed to elucidate the effects of CDK6 on CALR-mutant Myeloproliferative Neoplasms. VavCre CALRdel52 knockin mice were crossed with full-body Cdk6-/- mice to obtain Cdk6-/- CALRdel52 mice. Bone marrow from mice of the four genotypes Cdk6+/+ CALR+/+ (wild-type), Cdk6+/+ CALRdel52 (CALR-mutant), Cdk6-/- CALR+/+ (Cdk6 knockout) and Cdk6-/- CALRdel52 (CALR-mutant with Cdk6 knockout) was isolated and stained for flow cytometry. To obtain megakaryocyte progenitors (MkPs) from the bone marrow, Lineage (CD11b, Gr-1, Ter119, CD3, CD19), c-Kit, sca-1, CD150 and CD41 surface markers were used. From the gating strategy: Lineage- c-Kit+ sca-1- CD150+ CD41+, MkPs were sorted into round-bottom collection tubes via fluorescence activated cell sorting (FACS). These cells were then used for RNA-isolation and subsequent RNA-Sequencing. The samples were harvested in two batches (Sample dates: \"February\" and \"April\").biostudies-arrayexpressNucleic Acid Extraction - RNA isolation was performed using RNA-Solv® reagent and manufacturer protocolSample Collection - Megakaryocyte progenitors were isolated from mouse bone marrow by means of flow cytometry. The isolated bone marrow was stained for surface markers and the following population was sorted: Lineage (CD11b, Gr-1, Ter119, CD3, CD19) negative, c-Kit positive, Sca-1 negative, CD150 positive and CD41 positive.Library Construction - Libraries were constructed using the Smartseq3 method (Michael Hagemann-Jensen, et al.; Nat Biotechnol. 2020 Jun;38(6):708-714)Sequencing - Libraries were sequenced using 50bp paired-end mode.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads overlapping exons were then counted with the FeatureCounts program of the Subread package (version 2.0.1) and summarised as total counts per gene. Raw counts form all samples were combined into a single count table.Sequence Alignment - Raw sequencing reads were processed using Trimmomatic (version 0.39) to trim adapters and umi-tools (version 1.1.1) to remove unique molecular identifier sequences. Quality control of raw and trimmed reads was done with Fastqc (version 0.11.9). The processed reads were aligned against the primary assembly of the GRCm38 mouse reference genome (Gencode vM25) using STAR (version 2.7.6a). The gene model used was the Gencode vM25 primariy assembly annotation. Alignment QC was done using Qualimap (version 2.2.2a).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusKaroline KollmannThorsten KlampflfalseRNA-Seq of murine megakaryocyte progenitors (MkPs) from Cdk6 knockout and Cdk6 wild-type CALR-mutant miceThis experiment was performed to elucidate the effects of CDK6 on CALR-mutant Myeloproliferative Neoplasms. VavCre CALRdel52 knockin mice were crossed with full-body Cdk6-/- mice to obtain Cdk6-/- CALRdel52 mice. Bone marrow from mice of the four genotypes Cdk6+/+ CALR+/+ (wild-type), Cdk6+/+ CALRdel52 (CALR-mutant), Cdk6-/- CALR+/+ (Cdk6 knockout) and Cdk6-/- CALRdel52 (CALR-mutant with Cdk6 knockout) was isolated and stained for flow cytometry. To obtain megakaryocyte progenitors (MkPs) from the bone marrow, Lineage (CD11b, Gr-1, Ter119, CD3, CD19), c-Kit, sca-1, CD150 and CD41 surface markers were used. From the gating strategy: Lineage- c-Kit+ sca-1- CD150+ CD41+, MkPs were sorted into round-bottom collection tubes via fluorescence activated cell sorting (FACS). These cells were then used for RNA-isolation and subsequent RNA-Sequencing. The samples were harvested in two batches (Sample dates: \"February\" and \"April\").2026-08-03T00:00:00Z2026-08-03T15:42:17.73Z2025-07-28T11:00:18.654ZE-MTAB-15404ERP177322EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184