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| Status |
Public on Jun 13, 2017 |
| Title |
Basal_BptfKO_ATACseq_Rep3a |
| Sample type |
SRA |
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| Source name |
BptfKO Mammary Cells
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| Organism |
Mus musculus |
| Characteristics |
gender: Female
tissue: Mammary Gland
compartment: Basal
cell type: Basal Mammary Epithelial Cells
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| Treatment protocol |
Tamoxifen was given to mice (total 15mg/kg body) prioir to cell isolation; Eph4 cells were treated for 24 hours with Bptf inhibitor AU-1 (5uM) or DMSO
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| Growth protocol |
Eph4 Cells were grown in DMEM with 5% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei obtained from Eph4 cells or FACS-sorted mammary epithelial cells were incubated with reagents from Illumina Nextera kit (Illumina), following DNA purification with purified with DNA Clean-up & Concentration kit (Zymo) according the manufacturer's instruction
Nextera treated, purified DNA was amplified and barcoded using previously described protocol (Buenrostro e at, 2013), then pooled for sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Tn5 transposed purified DNA
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| Data processing |
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie with no mismatches allowed and multi-mappers excluded
MACS was used for peak-calling from the mapped BAM file. Parameters used for MACS included a tag size of 25bp and a strict p-value cutoff of 1.00e-5
Peaks were annotated using HOMER with the standard mm9 reference included with the software. Location of peaks was then grouped into intergenic, promoter and genic (containing 5’UTR, Exons, Introns, Transcription Termination Sites, 3’UTR, ncRNA, miRNA, snoRNA, and rRNA) regions. Pie Charts were made from the resulting HOMER output.
ROSE was preformed to identify putative enhancer regions using default conditions, which included a 2.5 Kb exclusion zone surrounding the TSS and a 12.5 Kb stitching distance.
The UCSC genome browser was used to analyze enhancers for overlap, using the table browser intersect function. Any overlap was enough to consider two regions “shared” and no overlap, between the enhancers defined the regions as ONLY being in one sample.
The comparison of differential enhancers was made into a venn diagram using Galaxy’s Cistrome server. Identification of genes closest to these differentially called enhancer regions, was preformed using Genomic Regions Enrichment of Annotations Tool (GREAT)
Homer was used to create histograms of MACS-called ATAC-seq peaks and MACS-called H3K27ac peaks using standard mm9 TSS annotations in Homer’s software package. Histograms of ATAC-seq peaks distribution around distal H3K27ac peaks were made by excluding H3K27ac peaks that associated with TSS/Promoter regions, as defined by HOMER.
Spearman correlation coefficients ranging from -1 to 1, where 1 indicates the strongest relationship between samples, were used to assess the integrity of the replicates.
DREME and TOMTOM were used to identify motifs in differential enhancer regions. Parameters used for DREME include a default E-value threshold of 0.05 and a search of both the given strand and the reverse complement strand of the queried sequence. TOMTOM was run with a default E-value of 0.05 a well.
Genome_build: mm9
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| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wesley D. Frey |
| E-mail(s) |
[email protected]
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| Organization name |
Cold Spring Harbor Laboratory
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| Street address |
One Bungtown Road
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| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE98001 |
Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells [ATAC-Seq] |
| GSE98004 |
Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells |
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| Relations |
| BioSample |
SAMN06768577 |
| SRA |
SRX2748797 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2585301_KO_BPTF_MYOEPITHELILA_ATACSEQ_REPC1.bigwig |
45.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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