{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Carl MANN"],"organism":["Homo sapiens"],"software":["bowtie2, samtools, sambamba","sambamba, Deeptools"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17105"],"description":["Map H3-K27-acetyl marks associated with potential enhancers, promoters, and transcriptionally active chromatin in primary human fibroblasts from fetal lung (WI38), adult lung, adult abdomen, and adult breast under conditions of proliferation, X-irradiation, and treatment with 20 pg/ml IL1-alpha for 24 hours."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - PCR amplification of Cut & Tag fragmented DNA using Illmina multiplex oligonucleotide primers.","Sample Treatment - For irradiation, 40 Gy of 120 kV X-rays, then additional incubation for 10 days. For irradation + IL1-alpha, 40 Gy of 120 kV X-rays, then additional incubation for 9 days followed by incubation with 20 pg/ml IL1-apha for 1 day. For etoposide-induced senescence, treatment with 100 microM etoposide for 2 days followed by incubation for 8 days without etoposide.","Sequencing - Illumina NextSeq sequencing of multiplexed libraries","Growth Protocol - DMEM (4.5g/l glucose) + 10% FBS + stabilized glutamate + pyruvate + pen/strep in an incubator with 5% CO2 + 5% O2","Sample Collection - Trypsinized cells and used 50,000 for Cut & Tag with the nuclear permeabilization protocol described by the Henikoff lab.","Nucleic Acid Extraction - Phenol-chloroform extraction after the Cut & Tag reaction followed by ethanol precipitation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Fastq.gz files were aligned to the GRCh38 genome using bowtie2 with the following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant -k 1 -X 1000 -I 25. The resulting sam files were converted to bam files with samtools view. Duplicates were removed with sambamba markdup -r and reads mapping to the mitochondrial genome were removed.","Data Transformation - Bam files were sorted and indexed with sambamba and then converted to bigwig files with deeptools bamCoverage using CPM normalization and excluding the Encode hg38 blacklist regions."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Carl MANN"],"additional_accession":[]},"is_claimable":false,"name":"H3-K27Ac Cut & Tag of primary human fibroblasts","description":"Map H3-K27-acetyl marks associated with potential enhancers, promoters, and transcriptionally active chromatin in primary human fibroblasts from fetal lung (WI38), adult lung, adult abdomen, and adult breast under conditions of proliferation, X-irradiation, and treatment with 20 pg/ml IL1-alpha for 24 hours.","dates":{"release":"2026-07-09T00:00:00Z","modification":"2026-07-09T17:25:56.338Z","creation":"2026-05-20T18:20:19.005Z"},"accession":"E-MTAB-17105","cross_references":{"ENA":["ERP193648"],"Biostudies":["E-MTAB-17100","E-MTAB-14625","E-MTAB-16030","E-MTAB-14201"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}