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| Status |
Public on Aug 19, 2021 |
| Title |
ATAC_C2_replicate_1 |
| Sample type |
SRA |
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| Source name |
Immortalized mouse embryonic fibroblast line A
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| Organism |
Mus musculus |
| Characteristics |
cell type: c-myc-immortalized mouse embryonic fibroblasts
genotype: wild-type
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| Treatment protocol |
wild-type
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| Growth protocol |
MEF cells were grown in DMEM supplemented with 10% FCS, 100 mM nonessential amino acids, 2 mM L-glutamine.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as previously described (Buenrostro et al., 2015, PMID 25559105) with transposition on 50,000 whole cells rather than nuclei in order to minimize mitochondrial DNA contamination as recommended by Karabacak Cakviello et al., 2019 (PMID 30791920).
Buenrostro et al., 2015, PMID 25559105
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Alignment to mouse genome allowing an insert size of up to 2 kb (Bowtie 2.2.9 with the following parameters: '--reorder -p 8 -D 70 -R 3 -N 0 -L 20 -i S,1,0.50 -X 2000')
Filtering of reads to exclude reads mapping to mitochondria or common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of RPKM values per 50bp bin and conversion to bigWig format (DeepTools bamCoverage)
Peak calling was performed on each replicate using SEACR (Meers et al., 2019, PMID 31300027) with a threshold of 0.006 and “stringent” mode, and Intersect (Galaxy v1.0.0) was used to identify overlapping pieces of intervals.
Genome_build: mm10
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)
Supplementary_files_format_and_content: .bed file contains peak coordinates
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| Submission date |
Mar 24, 2021 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Daniel Holoch |
| E-mail(s) |
daniel.holoch@curie.fr
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| Phone |
0156246553
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| Organization name |
Institut Curie, Centre de Recherche
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| Department |
Genetics and Developmental Biology Unit
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| Lab |
Raphaël Margueron
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| Street address |
26 rue d'Ulm
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| City |
Paris |
| State/province |
Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE147568 |
A cis-acting mechanism mediates trancriptional memory at Polycomb target genes in mammals |
| GSE169534 |
A cis-acting mechanism mediates trancriptional memory at Polycomb target genes in mammals [ATAC-seq] |
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| Relations |
| BioSample |
SAMN18474051 |
| SRA |
SRX10436304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5208935_ATAC_C2_replicate_1.bw |
157.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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