biostudies-arrayexpressCarl MANNHomo sapiensBowtie2, samtools, sambamba, deepToolsCutadapt, Bowtie2, samtools, sambamba, deepToolshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14265Identification of open chromatin regions distinguishing primary human fibroblasts from abdomen, breast, and lung during proliferation or after 40 Gy X-irradiation, or after IL1-alpha or 1L1-beta treatments.biostudies-arrayexpressSequencing - Paired-End 42 nucleotides in an Illumina NextSeq 500 sequencer.Sample Treatment - For X-ray induced senescence, confluent cells in a 10 cm plate were irradiated with 40 Gy of 120 kV X-rays 20 or 40 Gy X-rays at 120 kV generated by a Faxitron 43855-D irradiator. The next day, cells were trypsinized and split into 3 x 10 cm dishes and incubated for 10 days before performing ATAC-seq. For some experiments, cells were irradiated with 40 Gy X-rays as above and incubated for 9 days. They were then treated with 20 pg/ml of recombinant IL1-alpha or IL1_beta for 24 hours before performing ATAC-seq. Finally, for some experiments, proliferating sub_confluent fibroblasts were treated with 20 pg/ml of recombinant IL1_alpha for 24 hours before performing ATAC_seq.Library Construction - ATAC-seq was performed with the Omni-ATAC protocol as described in Nature Protocols 2022 (DOI: 10.1038/s41596-022-00692-9). Assembled Tn5 transposase was prepared as described (DOI: 10.1101/gr.177881.114). For some experiments, assembled Tn5 was bought from Active Motif or Diagenode.Nucleic Acid Extraction - After the ATAC-seq tagmentation, the reaction was stopped by the addition of SDS to 0.1% final concentration and the addition of 10 midrograms of Proteinase K. The solution was incubated at 55°C for 15 mins, and DNA was then purified unsing the Macherey-Nagel PCR clean-up kit. The purified DNA was then amplified using Nextera-type PCR primers to add Illumina indexes for high_throughput sequencing.Sample Collection - Cell monolayers were trypsinized, neutralized with medium, washed with PBS, and centrifuged. Washed cell pellets were resuspended in Macherey-Nagel Nucleospin RNA Plus Lysis Buffer.Growth Protocol - Cells were grown in DMEM + 10% fetal bovine serum + sodium pyruvate + Gluta-Max + penicillin/streptomycin in a 5% 02 + 5% CO2 incubator at 37°C.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSequence Alignment - After trimming to remove Illumina adapter sequences, the fastq sequences were aligned to the hg38 human genome sequence using Bowtie2 using the following paramters: --very-sensitive --no-mixed --no-discordant --phred33 -I 25 -p 20Data Transformation - Paired-end fastq sequences were aligned to the hg38 human genome sequence with Bowtie2. After removing bam sequences, the reads were converted to the bigwig format with CPM normalization using deepTools bamlCoverage.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500Faxitron 43855-D irradiatorATAC-seqHomo sapiensReem HAMEDCarl MANNfalseATAC-seq of primary human fibroblastsIdentification of open chromatin regions distinguishing primary human fibroblasts from abdomen, breast, and lung during proliferation or after 40 Gy X-irradiation, or after IL1-alpha or 1L1-beta treatments.2026-01-01T00:00:00Z2026-01-02T02:02:42.431Z2024-07-22T10:12:27.795ZE-MTAB-14265ERP162181E-MTAB-14201EFO_0002944EFO_0007045EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969