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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 30, 2018 |
| Title |
ATAC_8h |
| Sample type |
SRA |
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| Source name |
mouse mammary epithelial cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: NMuMG
chip antibody: NA
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| Treatment protocol |
TGFβ was added at a final concentration of 1-5 ng/ml to induce EMT in NMuMG cells.
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| Growth protocol |
NMuMG cells were maintained in Dubelcco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Invitrogen) supplemented with 10μg/ml of insulin (Sigma) at 37ºC in 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed as previously described (Herranz et al., 2008, PubmedID: 18519590). RNA extraction was performed with GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich). ATAC experiments were performed as previously described (Buenrostro et al., 2013, PubmedID: 24097267).
Libraries were prepared according to Illumina instructions.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ATAC experiment
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| Data processing |
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Cufflinks (PubMed ID 22383036) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq. ATACseq analysis: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq and ATACseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP_LB1_0h_11732_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_8h_11733_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_24h_11734_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_0h_11864.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_8h_11865.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_24h_11866.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_0h_11732_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_LB1_8h_11733_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_LB1_24h_11734_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_0h_11864.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_8h_11865.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_24h_11866.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: FPKM_0h-8h-24h.txt (FPKM values)
Supplementary_files_format_and_content: FPKMs_0CT1_0CT2_0shLB1_0shLB2-8CT1_8CT2_8shLB1_8shLB2-24CT1_24CT2_24shLB1_24shLB2.txt (FPKM values)
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| Submission date |
Mar 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
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| Phone |
+34 93 316 01 00
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| Organization name |
Center for Genomic Regulation (CRG)
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| Department |
Gene Regulation, Stem Cells and Cancer
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| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
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| Street address |
Dr. Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE96033 |
Genome-wide Mapping of Lamin B1 Reveals the Existence of Dynamic and Functional Euchromatin Lamin B1 Domains (eLADs) at the onset of the Epithelial to Mesenchymal Transition |
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| Relations |
| BioSample |
SAMN06555219 |
| SRA |
SRX2628289 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2527712_ATAC_8h_11865.bedgraph.gz |
8.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM2527712_ATAC_8h_11865_peaks.bed.gz |
148.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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