|
| Status |
Public on Sep 08, 2023 |
| Title |
Tspan8+ Basal cells, biol rep 2 [P7_2] |
| Sample type |
SRA |
| |
|
| Source name |
Mammary epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary epithelial cells
cell type: Tspan8+ myoepithelial (quiescent basal, QBa)
strain: FVB/N mice
developmental stage: adult (9-10 weeks of age)
Sex: female
mouse pool: 2
|
| 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 |
P7_2
|
| 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 |
SAMN34070210 |
| SRA |
SRX19867667 |
