|
| Status |
Public on Sep 08, 2023 |
| Title |
ML cells, biol rep 3 [ML_ATAC_3] |
| Sample type |
SRA |
| |
|
| Source name |
Mammary epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary epithelial cells
cell type: mature luminal
strain: FVB/N mice
developmental stage: adult (9-10 weeks of age)
Sex: female
mouse pool: 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposed genomic DNA was extracted and amplified for sequencing as per Buenrostro et al. 2015.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ML_ATAC_3
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Fastq files for technical replicates were merged and reads were aligned to the mouse genome mm10 by Bowtie2 with duplicates removed with Picard tools MarkDuplicates command and mitochondrial reads excluded.
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).
|
| |
|
| 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 |
| GSE228917 |
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [MEC_ATAC] |
|
| Relations |
| BioSample |
SAMN34068382 |
| SRA |
SRX19865129 |
