 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 30, 2020 |
| Title |
ArabRoot-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embyronic root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col-0
treatment: Fresh
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
16,000 nuclei per library were extracted via FANS
10x Genomics scATAC-seq v1
Paired-end, dual index
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
At_Col0_ACR_x_cell.binary.sparse.gz
|
| Data processing |
BWA alignment
5',3' coordinate adjustment
MACS2 peak calling
Tn5 integration site intersection with ACRs
binarization
Genome_build: B73 v4/TAIR10
Supplementary_files_format_and_content: binary triplet matrix format of ACRs (column 1), nuclei ID (column 2), and 1/0 binarized counts of Tn5 intregation sites
|
| |
|
| Submission date |
Sep 25, 2020 |
| Last update date |
May 27, 2021 |
| 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 |
GPL26208 |
| Series (1) |
| GSE155178 |
A cis-regulatory atlas of maize single cells |
|
| Relations |
| BioSample |
SAMN16263054 |
| SRA |
SRX9191285 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
