{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan Kubovčiak"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14686"],"description":["While familial and sporadic forms of myeloproliferative neoplasms (MPNs) have long been recognized, emerging evidence implicates germline variations, in predisposing individuals to JAK2 V617F-positive myeloproliferative neoplasms (MPN). Understanding the role of genetic variants, such as the JAK2 germline mutations, in MPN susceptibility, along with the contribution to disease pathogenesis, is crucial for elucidating the underlying mechanisms driving MPN development and progression. To study the biology of germline JAK2 R1063H mutation in more detail, we edited the endogenous Jak2 locus by CRISPR/Cas9 technology. We performed expression gene profiling of young (3 months) and old (12 months) HSC (defined as Lin-, Sca1+/ckithigh, CD150high/CD48low) and LK cells (defined as Lin-, Sca1-/ckithigh)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated using RNeasy Micro Kit (Qiagen) as described in the manufacturer’s protocol.","Sample Collection - Mice were sacrificed by cervical dislocation, femurs and tibias were isolated, and crunched using a pestle and mortar. Sorting of bone marrow hematopoietic stem cells and progenitors was performed by two subsequent steps. First, the Lin+ fraction of the BM cells was labeled using biotinylated lineage markers CD45/B220 (RA3-6B2), CD3 (145-2c11), Ter119 (TER-119), Gr1 (RB6-8C5), and CD11b (M1/70). These cells were then incubated with anti-biotin magnetic beads (Miltenyi Biotec) and were isolated using MACS separator. Second, the Lin- fraction of the BM was labeled with the c-Kit PE (2B8), Sca-1 APC (E13-161.7), CD48 FITC (HM48-1), CD150 Pe-Cy7 (TC15-12F12.2) antibodies and with streptavidin-eFluor450. Cell suspensions were stained with Hoechst 33258 to exclude dead cells and HSCs were sorted using Influx instrument (BD Biosciences).","Library Construction - Libraries were prepared with a SMARTer® Stranded Total RNA-Seq – Pico Input Mammalian library preparation kit v2 (Takara).","Sequencing - Libraries were sequenced in two runs (LK samples and HSC samples separately) on Illumina NextSeq500 instrument using High-output kit and 75 nt read length, single end."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Salmon 1.5.2 was used to quantify per gene expression from reads aligned to GRCm39 assembly (Ensembl annotation version 104). Quantified per-gene expression for each sample is provided as processed data.","Sequence Alignment - Data was processed with  nf-core/rnaseq pipeline version 3.5 using STAR 2.6.1d and Salmon 1.5.2 to quantify per gene expression against GRCm39 assembly (Ensembl annotation version 104)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Jan Kubovčiak","Lucie Lanikova"],"additional_accession":[]},"is_claimable":false,"name":"Expression profiling of hematopoietic stem cells/progenitors from young (3 months) and old (12 months) homozygous Jak2 R1063H mice and wild-type controls","description":"While familial and sporadic forms of myeloproliferative neoplasms (MPNs) have long been recognized, emerging evidence implicates germline variations, in predisposing individuals to JAK2 V617F-positive myeloproliferative neoplasms (MPN). Understanding the role of genetic variants, such as the JAK2 germline mutations, in MPN susceptibility, along with the contribution to disease pathogenesis, is crucial for elucidating the underlying mechanisms driving MPN development and progression. To study the biology of germline JAK2 R1063H mutation in more detail, we edited the endogenous Jak2 locus by CRISPR/Cas9 technology. We performed expression gene profiling of young (3 months) and old (12 months) HSC (defined as Lin-, Sca1+/ckithigh, CD150high/CD48low) and LK cells (defined as Lin-, Sca1-/ckithigh).","dates":{"release":"2025-08-22T00:00:00Z","modification":"2025-08-19T00:01:30.482Z","creation":"2024-12-11T00:52:53.73Z"},"accession":"E-MTAB-14686","cross_references":{"ENA":["ERP166990"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}