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| Status |
Public on Jun 25, 2021 |
| Title |
ATAC-Seq miR Control_1 |
| Sample type |
SRA |
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| Source name |
cultured fetal lung fibroblast
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblast
cell culture: WI-38
treatment: control miR
treatment duration: 4 days
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| Treatment protocol |
Cells were transfected with 50 nM control miRNA, pre-miR-340-5p, or siLBR and cultured for an additional four days, changing media every 48h (DMEM with 20% FBS). Cells exposed to 10 Gy of IR were cultured for an additional 10 days.
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| Growth protocol |
WI-38 fibroblasts were plated in a six-well plate at a density of 1 x 10^5 cells for 24h in DMEM + 20% FBS.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Using 50,000 intact cells as input. Cells were washed and lysed to generate a crude nuclei preparation.
Library for ATAC-seq was prepared according to a published protocol (Buenrostro et al., 2013). Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR amplified and subsequently purified using Qiagen MinElute PCR Purification Kit (Qiagen, Maryland, USA). Final library quality and quantity were analyzed and measured by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), respectively. The final libraries were sequenced using 150 bp paired-end reads on Illumina HiSeq Sequencer (Illumnia Inc., San Diego, CA).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
miR Control_1
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| Data processing |
The reads were aligned to the hg38 human genome using Bowtie2 version 2.1.0
Data were filtered to remove mitochondrial and non-unique reads
Peaks were called using MACS2 in the BAMPE mode and annotated with ChipSeeker package from Bioconductor
Differential peaks were identified using the EdgeR GLM algorithm in DiffBind and annotated by CHIPpeakAnno package from Bioconductor
Significant Peaks are used to do further Functional Analysis by ChipSeeker on GeneOntology/Reactom Pathway/Kegg Pathway
Genome_build: human genome hg38
Supplementary_files_format_and_content: .xls text file
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| Submission date |
Jan 25, 2021 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
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| Department |
Laboratory of Genetics and Genomics
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| Lab |
Computational Biology & Genomics Core
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| Street address |
251 Bayview Blvd
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE165465 |
Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis (ATAC-Seq) |
| GSE165469 |
Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis |
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| Relations |
| BioSample |
SAMN17530738 |
| SRA |
SRX9933105 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5034259_Ctr_miR_1.peaks.xls.gz |
4.0 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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