|
| Status |
Public on Sep 08, 2023 |
| Title |
Tspan8+ Basal cells H3K27me3 bio rep 1 [P7_H3K27me3_1] |
| 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
chip antibody: H3K27me3 (Merck Cat#07-449)
mouse pool: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cells were captured on ConA beads and genomic DNA treated with pA-Tn5 followed by overnight antibody incubation.
Libraries were constructed as per Kaya-Okur et al. 2019.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
P7_H3K27me3_1
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Bowtie2 with duplicates removed with Picard tools MarkDuplicates command.
Bam files for technical replicates were merged using samtools post-mapping.
BigWig files were generated with BamCoverage from Deeptools with bamCoverage --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: *.bw: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 50 bp bin. Coverage was normalization by reads Per Kilobase per Million mapped reads (RPKM).
Library strategy: CUT&Tag
|
| |
|
| 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 |
| GSE228950 |
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_CUT&Tag] |
|
| Relations |
| BioSample |
SAMN34070176 |
| SRA |
SRX19867574 |
