|
| Status |
Public on Nov 19, 2024 |
| Title |
maize_seedlings_pool7_scATAC |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Zea mays |
| Characteristics |
tissue: seedling
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See doi.org/10.1016/j.xpro.2021.100737
10x Genomics scATAC-seq per manufactures instructions
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ files from demultiplexed BCLs were processed with chromap and a custom barcode whitelist (depending on the Novaseq chemistry).
Chromap output BAM files were used as input for soup_or_cell to genotype cell barcodes.
Barcodes corresponding to the same genotype were aggregated in total (Merged_Genotype) or by cell type.
Chromatin accessibility scores for accessible chromatin regions were scored as counts per million and then inverse normal transformed.
Cis chromatin accessibility QTL were identified using tensorQTL
Assembly: Zea mays AGPv5
Supplementary files format and content: All_contexts.pass_FDR.cis_caQTL.rds: R data.frame object containing the results of caQTL mapping. The original matrix has been filtered to retain only caQTL meeting significance thresholds.
Supplementary files format and content: normalized_chromatin_accessibility_and_covariate_matrices.tar.gz: A directory containing the bed formatted matrices of inverse normal transformed chromatin accessibility scores across all ACRs and genotypes. One matrix per cell type. This directory includes the same number of matrices, but for covariates.
Supplementary files format and content: All_pools.socObj.raw.rds: an R object containing a sparse matrix with 500bp genome tiles as rows and cell barcodes as columns. 1 corresponds to at least 1 Tn5 insertion within the genomic window.
|
| |
|
| Submission date |
Jul 30, 2024 |
| Last update date |
Nov 19, 2024 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL25410 |
| Series (2) |
| GSE273478 |
The genetic architecture of cell-type-specific cis-regulation [ATAC-seq] |
| GSE275410 |
The genetic architecture of single-cell chromatin accessibility in maize |
|
| Relations |
| BioSample |
SAMN42396861 |
| SRA |
SRX25268035 |
