GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE89450 Query DataSets for GSE89450
Status Public on Feb 01, 2017
Title Identification of quiescent and spatially-restricted mammary stem cells that are hormone responsive
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: The aim of this study is to explore histone modification in four basal cell populations defined by Lgr5 and Tspan8 expression taken from adult mouse mammary glands using chromatin immunoprecipitation sequencing (ChIP-seq).
Methods: The ChIP DNA samples were prepared and indexed for Ilumina sequencing using the TruSeq DNA sample Prep Kit (Ilumina) as per manufacturer's instruction. The library was quantified using the Agilent Tapestation and the Qubit's RNA assay kit for Qubit 2.0 Fluorometer (Life Technologies). The indexed libraries were then prepared for paired-end 75bp sequencing on a NextSeq500 instrument using the 150 cycle kit v2 chemistry (Ilumina) as per manufacturer's instructions. Reads were aligned to the mouse genome (mm10) using the subread algorithm by Liao et al. (2013) and counted into bins associated with Entrez gene identifiers (27080 genes in total) using featureCounts in two different ways. Genebody counts summarised the number of reads overlapping anywhere between the first and last base of a given gene while promoter counts summarized the number of reads overlapping a region 3000 bases upstream to 2000 bases downstream of the TSS of each gene. For downstream analysis, genebody counts were used for the H3K27me3 marks and promoter counts were used for the H3K4me3 marks.
Overall design Enrichment of H3K4me3 and H3K27me3 epigentic marks are shown in the four mammary basal cell populations defined by the expression of Lgr5 and Tspan8.
Contributor(s) Fu NY, Rios AC, Pal B, Law CW, Jamieson P, Liu R, Vaillant F, Jackling F, Liu KH, Smyth GK, Lindeman GJ, Ritchie ME, Visvader JE
Citation(s) 28192422
Submission date Nov 02, 2016
Last update date May 15, 2019
Contact name Casey Ah-Cann
Organization name The Walter and Eliza Hall Institute of Medical Research
Street address 1G Royal Parade, Parkville
City Melbourne
State/province Victoria
ZIP/Postal code 3052
Country Australia
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (24)
GSM2372373 Input control in Lgr5+Tspan8hi rep1
GSM2372374 Input control in Lgr5+Tspan8hi rep2
GSM2372375 Input control in Lgr5+Tspan8- rep1
BioProject PRJNA354314
SRA SRP093653

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE89450_RAW.tar 1.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap