title: GSM4142878: Sample_5_VavPBcl2_SHMT2_repl2_RNAseq; Mus musculus; RNA-Seq
library_construction_protocol: VavPBcl2 hematopoietic stem cells (HSCs) collected from fetal liver (E13.5) were infected with either empty vector or MSCV-SHMT2 vector and injected into two times irradiated wild type mice. The lymphomagesis was followed by blood count and blood smear analysis. The B cells (B220+) were isolated from spleen. RNA-seq: RNA of B cells collected from VavPBcl2;vector or VavPBcl2;SHMT2 tumors were extracted using TRIZOL standard protocol. ChIP-seq: 3×106 mouse B220+ cells collected from VavPBcl2;vector and VavPBcl2;SHMT2 tumors were fixed with 1% formaldehyde for 10 min at room temperature and lysed. Fragmentation of fixed chromatin was performed by sonication of isolated nuclei (Covaris E220, Covaris) to achieve the enrichment of short chromatin fragments (100 - 500 bp). One μg of antibody (H3K4me1, ab8895, abcam; H3K4me3, ab8580, abcam) was added to the chromatin lysate and incubated overnight at 4 °C. Enriched DNA was isolated by Dynabeads protein A (Thermo Fisher Scientific) and subsequent reverse cross-linking and purification. RNA-seq: RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies) ChIP-seq: ChIPseq libraries were prepared from 1-5 ng ChIP DNA following the instructions of Illumina TruSeq ChIP Library Preparation Kit (IP-202-1012).
attributes.tag: GEO Accession
attributes.value: GSM4142878