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Sample GSM2527716 Query DataSets for GSM2527716
Status Public on Aug 30, 2018
Title RNA_8h_1
Sample type SRA
 
Source name mouse mammary epithelial cells
Organism Mus musculus
Characteristics cell line: NMuMG
chip antibody: NA
Treatment protocol TGFβ was added at a final concentration of 1-5 ng/ml to induce EMT in NMuMG cells.
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.
Extracted molecule total RNA
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNAseq experiment
FPKM_0h-8h-24h.txt
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)
 
Submission date Mar 09, 2017
Last update date May 15, 2019
Contact name Enrique Blanco
E-mail(s) enrique.blanco@crg.eu
Phone +34 93 316 01 00
Organization name Center for Genomic Regulation (CRG)
Department Gene Regulation, Stem Cells and Cancer
Lab Epigenetic Events in Cancer (L. Di Croce's lab)
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
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
Relations
BioSample SAMN06555215
SRA SRX2628293

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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