|
| Status |
Public on Jun 20, 2024 |
| Title |
ESTpro::MUTE, control, MNase |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
genotype: ESTpro::MUTE
treatment: mock
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were extracted based on ChIP protocol or MNase-seq protocol (see methods part in the publication)
per manufacturer's instructions
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
control.bw
|
| Data processing |
cutadapt to trim the raw reads
picard to remove PCR duplicates
bowtie2 to align the reads to TAIR10 gemone assembly
MACS2 (ChIP-seq) or DANPOS (MNase-seq) to define bound regions
Assembly: TAIR10
Supplementary files format and content: bw files to visualize the enrichment of corresponding reads
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Dominique C. Bergmann |
| E-mail(s) |
dbergmann@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Street address |
371 Jane Stanford Way
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE269849 |
bHLH transcription factors cooperate with chromatin remodelers to regulate cell fate decisions during Arabidopsis stomatal development |
|
| Relations |
| BioSample |
SAMN38860193 |
| SRA |
SRX22907881 |
