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Sample GSM1782572 Query DataSets for GSM1782572
Status Public on Sep 01, 2016
Title Lgr5_epcam+_2_paired-end
Sample type SRA
 
Source name hair follicle
Organism Mus musculus
Characteristics genotype: Lgr5CreER/KRasLSL-G12D/p53fl/fl/Rosa-YFP+/+
cell type: hair follicle
gender: female
strain: mixed
Extracted molecule genomic DNA
Extraction protocol Tumours were dissected, minced, digested and filtered to get single cell suspension. Specific cell populations were isolated by FACS using PE-conjugated anti-CD45, PE-conjugated anti CD31, PE-conjugated anti-CD140a and APC-Cy7-conjugated anti-Epcam. Sorted cells were collected into lysis buffer for RNA extraction and ATAC-Seq.
Illumina Nextera DNA Library Prep Kit
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Genomic DNA of region that accessible to Tn5 transposase
ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013
Data processing Library strategy: ATAC-seq
Libraries are sequenced by Illumina HiSeq 2000
Raw reads are alligned to mouse genome version mm10 though bowtie2
Peak calling were performed using HOMER on individual sequence data and pooled by mergeBed in Bedtools
Genome_build: mm10
Supplementary_files_format_and_content: The bed file with called peaks contains the union of all peaks called on individual files; text files contain read counts for genomic features. The *.count.gz file is the HTseq-count output using ATAC_peaks.bed.gz and individual bam file from sequencing alignment. The coordinates of the genomic features are contained within the file "ATAC_peaks.bed.gz".
 
Submission date Jul 02, 2015
Last update date May 15, 2019
Contact name C├ędric Blanpain
E-mail(s) cedric.blanpain@ulb.ac.be
Organization name ULB
Street address Route de Lennik 808
City Brussels
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL13112
Series (2)
GSE70474 Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [ATAC-seq]
GSE71621 Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition
Relations
BioSample SAMN03838206
SRA SRX1079542

Supplementary file Size Download File type/resource
GSM1782572_PE_HTseq_Lgr5_Epcam+_2.count.txt.gz 657.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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