|
| Status |
Public on Oct 13, 2023 |
| Title |
WT [atac] |
| Sample type |
SRA |
| |
|
| Source name |
cadiac nuclei
|
| Organism |
Mus musculus |
| Characteristics |
cell type: purified nuclei from heart
strain: C57BL/6
genotype: Wildtype
|
| Treatment protocol |
WT and NFYa cKO embryos at E15.5 were used for Multiome RNA + ATAC sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hearts at E15.5 were dissected and flash-frozen in liquid nitrogen. Genotyping was performed to ensure proper pooling of hearts with the same genotype. Four hearts with the same genotype were pooled for each sample. Cardiac nuclei isolation was performed as previously described.
Total cardiac nuclei were used to generate joint snRNA and snATAC libraries using Single Cell Multiome ATAC + Gene Expression (10×Genomics) according to the manufacturer’s protocol. Sequencing was performed on an Illumina Nextseq 500 system operated by the Next Generation Sequencing Core of Children’s Research Institute at UT Southwestern using the 150bp high output sequencing kit (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
KO+WT_atac_fragments.tsv.gz
KO+WT_atac_fragments.tsv.gz.tbi
|
| Data processing |
The Cell Ranger Single-Cell Software Suit was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
Briefly, cellranger-ARC aggr was run for combined WT and NFYa KO samples and generated a single feature-barcode matrix containing all the data that were normalized between samples. “Gene Expression” and “Peaks” files from cellranger-ARC output were used to construct Seurat objects in R. A shared peak set derived from the integration of peaks identified for each sample was used to analyze the snATAC dataset. The combined Seurat object was QC’d using the same metrics: 100 < nCount_ATAC < 100,000; 1000 < nCount_RNA < 100,000; and percent mitochondrial reads < 20
Assembly: mm10
Supplementary files format and content: count matrix
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
Oct 13, 2023 |
| Contact name |
Miao Cui |
| E-mail(s) |
miaocui713@gmail.com
|
| Phone |
6263768016
|
| Organization name |
UTSW
|
| Street address |
UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE232961 |
Transcription factor NFYa controls cardiomyocyte metabolism and proliferation during fetal heart development [Multiome] |
| GSE232963 |
Transcription factor NFYa controls cardiomyocyte metabolism and proliferation during fetal heart development |
|
| Relations |
| BioSample |
SAMN35220720 |
| SRA |
SRX20452978 |
