biostudies-arrayexpressThorsten KlampflHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15481To investigate direct genomic targets of CDK6 and STAT5B in Anaplastic Large Cell Lymphoma (ALCL), ChIP-sequencing (ChIP-seq) was performed in both human and murine ALCL cell lines. We performed ChIP targeting STAT5B in five human ALCL cell lines (SU-DHL-1, DEL, SUP-M2, Karpas-299, SR-786) and ChIP targeting CDK6 in one murine ALCL cell line derived from a NPM-ALK(Tg/+) mouse.biostudies-arrayexpressSequencing - Sequencing was performed on a NovaSeq X sequencer (Illumina) in a 100 bp single-read format.Library Construction - Input DNA or DNA enriched through IP was subjected to sequencing library preparation using the NEBNext Ultra II chemistry (New England Biolabs)Nucleic Acid Extraction - Cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) in PBS under rotation at room temperature for 30 minutes. Cells were then washed and incubated with 1% formaldehyde in PBS for 10 minutes at room temperature under rotation. The formaldehyde crosslinking was quenched by adding 0.125 M glycine and rotating for 5 minutes. For immunoprecipitation, the following antibodies were used: Anti-STAT5B (5 µg; [EPR16671], Abcam, ab178941), Anti-CDK6 (5 µg; rabbit polyclonal, PA5-27978; Invitrogen, USA).Sample Collection - A total of 1.5 × 10e7 cells per sample were collected from cell culture and washed twice with ice-cold PBS containing 1 mM PMSF.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Blacklisted regions were removed with bedtools subtract. Multimappers and reads with low mapping quality were removed using samtools (version 1.14). We used MACS3 to perform peak calling with default parameters. For each ChIP-seq file we used the corresponding Input file as the control. The resulting narrowPeak files are provided here.Sequence Alignment - Raw data fastq files from different flowcell lanes were concatenated per sample. The concatenated fastq files were then quality controlled using the FASTQC software (version 0.12.1). Trimmomatic (version 0.39) was used to perform adapter trimming and quality-based filtering of reads. After another quality control using FASTQC, the filtered reads of mouse samples were mapped against the GRCm38 primary assembly (Gencode M25), the filtered reads of human samples against the GRCh38 primary assembly (Gencode v26) using bwa-mem (version 0.7.15). Alignment QC was done using Qualimap (version 2.2.2a).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XChIP-seqHomo sapiensKaroline KollmannThorsten KlampflJonatan KendlerfalseChIP-seq of STAT5B in human ALCL cell lines and CDK6 in a murine ALCL cell lineTo investigate direct genomic targets of CDK6 and STAT5B in Anaplastic Large Cell Lymphoma (ALCL), ChIP-sequencing (ChIP-seq) was performed in both human and murine ALCL cell lines. We performed ChIP targeting STAT5B in five human ALCL cell lines (SU-DHL-1, DEL, SUP-M2, Karpas-299, SR-786) and ChIP targeting CDK6 in one murine ALCL cell line derived from a NPM-ALK(Tg/+) mouse.2026-07-24T00:00:00Z2026-07-24T11:08:16.7Z2025-08-13T14:08:23.487ZE-MTAB-15481ERP178729EFO_0002944EFO_0004170EFO_0002692EFO_0004917EFO_0005518EFO_0003816EFO_0004184