biostudies-arrayexpressChristopher MulhollandMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15573targeted associated bisulfite sequencing (TaBA-seq) on LINE1 elements in Midnolin (Midn) KO ESCs, and wild-type (wt) ESCs harboring a doxycycline-inducible Midnolin transgene in which Midnolin overexpression was induced for 3 daysbiostudies-arrayexpressSample Collection - Mouse ESCs were cultured in N2B27 2i LIF conditions supplemented with or without doxycycline (1 µg/ml) for 3 days, and then harvested by trypsinizationNucleic Acid Extraction - Genomic DNA was isolated from ES cells using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The EZ DNA Methylation-Gold Kit (Zymo Research) was used for bisulfite conversion according to the manufacturer’s instructions with 500 ng of genomic DNA used as input and the modification that bisulfite converted DNA was eluted in 2 x 20 µL Elution Buffer.Sequencing - Dual indexed TaBA-seq libraries were sequenced on an Illumina MiSeq in 2x300 bp output mode.Library Construction - The sequences of the LINE1 (an abundant transposon class within the mouse genome) specific primers were appended with Illumina TruSeq and Nextera compatible overhangs. The amplification of bisulfite converted DNA was performed in 25 μL PCR reaction volumes containing 0.4 μM each of forward and reverse primers, 2 mM Betaine (Sigma-Aldrich, B0300-1VL), 10 mM Tetramethylammonium chloride solution (Sigma-Aldrich T3411-500ML), 1x MyTaq Reaction Buffer, 0.5 units of MyTaq HS (Bioline, BIO-21112), and 1 μL of the eluted bisulfite converted DNA (∼12.5 ng). The following cycling parameters were used: 5 min for 95°C for initial denaturation and activation of the polymerase, 40 cycles (95°C for 20 s, 58°C for 30 s, 72°C for 25 s) and a final elongation at 72°C for 3 min. Agarose gel electrophoresis was used to determine the quality and yield of the PCR. For purifying amplicon DNA, PCR reactions were incubated with 1.8x volume of CleanPCR beads (CleanNA, CPCR-0005) for 10 min. Beads were immobilized on a DynaMag-96 Side Magnet (Thermo Fisher, 12331D) for 5 min, the supernatant was removed, and the beads washed 2x with 150 μL 70% ethanol. After air drying the beads for 5 min, DNA was eluted in 15 μL of 10 mM Tris-HCl pH 8.0. Amplicon DNA concentration was determined using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher, P7589) and then diluted to 0.7 ng/μL. Thereafter, indexing PCRs were performed in 25 μL PCR reaction volumes containing 0.08 μM (1 μL of a 2 μM stock) each of i5 and i7 Indexing Primers, 1x MyTaq Reaction Buffer, 0.5 units of MyTaq HS (Bioline, BIO-21112), and 1 μL of the purified PCR product (diluted to 0.5 ng/μl) from the previous step. The following cycling parameters were used for the indexing PCR: 5 min for 95°C for initial denaturation and activation of the polymerase, 15 cycles (95°C for 10 s, 55°C for 30 s, 72°C for 40 s) and a final elongation at 72°C for 5 min. Agarose gel electrophoresis was used to determine the quality and yield of the PCR. An aliquot from each indexing reaction (5 μL of each reaction) was then pooled and purified with CleanPCR magnetic beads as described above and eluted in 1 μL x Number of pooled reactions. Concentration of the final library was determined using PicoGreen and the quality and size distribution of the library was assessed with a Bioanalyzer.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw paired-end TaBA-seq reads were adapter- and quality-trimmed with Trim Galore(v0.4.4_dev; paired-end; wrapper to cutadapt v1.15) using adapter sequences -a CTGTCTCTTATA and -a2 AGATCGGAAGAGC. Trimmed read pairs were then aligned to the Mus musculus reference genome (mm10) using BSMAP (v2.90) with parameters -v 5 -p 10 -I 8 (Xi and Li, 2009).Data Transformation - CpG methylation ratios were extracted with BSMAP’s methratio.py against mm10 using -x CG, producing per-site methylation tables (*.txt). No additional duplicate removal was applied; only reads passing trimming and mapping were retained for downstream analyses.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina MiSeqmethylation profiling by high throughput sequencingMus musculusUbiquitin-independent regulation of UHRF1 abundance by midnolin in ground pluripotent stateJingwen Liu, Miriam Lob, Enes Ugur, Christopher B. Mulholland, Matthias Mann, Heinrich Leonhardt, Weihua Qin1Christopher MulhollandfalseLINE-1 DNA methylation levels in Midnolin KO and Midnolin overexpressing mouse embryonic stem cellstargeted associated bisulfite sequencing (TaBA-seq) on LINE1 elements in Midnolin (Midn) KO ESCs, and wild-type (wt) ESCs harboring a doxycycline-inducible Midnolin transgene in which Midnolin overexpression was induced for 3 days2026-03-01T00:00:00Z2026-05-30T15:20:31.956Z2025-09-12T11:24:00.299ZE-MTAB-15573ERP180009EFO_0002944EFO_0004170EFO_0002761EFO_0004917EFO_0005518EFO_0003816EFO_0004184