Processed data and resources for TE-chimeric analysis

This dataset contains sorted and indexed BAM files derived from RNA-seq experiments on mouse embryonic stem cells (mESCs), including 2-cell-like (2C-like) states and Zscan4-positive subpopulations. These data were generated to support TE-chimeric transcript discovery using the TEDDY pipeline. RNA-seq reads were aligned to the **mm10 mouse genome** using STAR. The BAM files were processed using **GENCODE M7 annotation** and a corresponding **mm10 transposable element (TE) annotation file**, serving as the input for TEDDY. **Experimental details:** **MEF and ESC culture** Mouse embryonic fibroblasts (MEFs) were derived from ICR mouse embryos at E13.5 and cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1 mM L-glutamine, and standard additives. R1 ESCs were cultured on mitomycin C–treated MEF feeder layers in ESC medium (DMEM, 15% FBS, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, nonessential amino acids, and 1000 U/mL LIF), under 5% CO₂ at 37°C. **Generation of Zscan4/MERVL reporter lines** The R1 mESC line was engineered to stably express **Zscan4-EGFP** and **MERVL-tdTomato** reporters. The Zscan4-EGFP construct was built by inserting a 2570 bp Zscan4c promoter upstream sequence into a Fugw vector lacking the CMV promoter. The MERVL::tdTomato vector was obtained from Addgene (#40281, courtesy of Samuel Pfaff). Vectors were linearized, purified, and introduced into R1 mESCs using nucleofection. Stable colonies were selected and validated based on fluorescence and previously published criteria. These BAM files correspond to RNA-seq from sorted populations including Zscan4⁺, 2C-like, and control mESCs. Raw FASTQ data will be deposited to GEO upon manuscript acceptance. Additionally, we provide the TE annotations structured for compatibility with the TEDDY pipeline as .rds objects: mm10_TE_annotation.rds hg38_TE_annotation.rds These data can be loaded directly using readRDS() in R.