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Sample GSM7146169 Query DataSets for GSM7146169
Status Public on Sep 08, 2023
Title Tspan8- Basal cells, biol rep 1 [P6_1]
Sample type SRA
 
Source name Mammary epithelial cells
Organism Mus musculus
Characteristics tissue: Mammary epithelial cells
cell type: Tspan8- myoepithelial (active basal, ABa)
strain: FVB/N mice
developmental stage: adult (9-10 weeks of age)
Sex: female
mouse pool: 1
Extracted molecule genomic DNA
Extraction protocol Chromatin was crosslinked with formaldehyde and in situ digested with DNase followed by proximity ligation and introduction of capture beads.
Proximity ligated DNA was decrosslinked, end repaired and sequencing adapters added before capture of successfully re-ligated material and sequencing, following the manufacturer's protocol, Doveltail Omni-CTM.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description P6_1
Data processing Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads pairs from each sample were aligned to the mouse genome with Bowtie2. Technical replicates were merged with samtools merge.
Bam files were processed with FixMateInformatrion and MarkDuplicates from Picard tools.
Read pairs were filtered for artefacts using R package diffHic v1.26.0 and then counted into 50 kB bin pairs.
Assembly: mm10
Supplementary files format and content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.
 
Submission date Apr 04, 2023
Last update date Sep 08, 2023
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL19057
Series (2)
GSE227750 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells
GSE228954 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_Omni-C]
Relations
BioSample SAMN34070214
SRA SRX19867663

Supplementary file Size Download File type/resource
GSM7146169_P6-1-OmniC.mtx.gz 83.5 Mb (ftp)(http) MTX
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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