|
| Status |
Public on Jun 21, 2019 |
| Title |
ATAC-Seq_WT_R1 |
| Sample type |
SRA |
| |
|
| Source name |
flowers
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 4 weeks
genotype/variation: WT
background ecotype: Columbia-0
|
| Growth protocol |
Plants were grown in soil in a greenhouse under long day conditions for 4 weeks. Flowers were collected for nuclei extraction. Two replicates for each genotype were collected.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated as described in Liu, W et al, 2018. ATAC-seq was performed as described in Buenrostro, J.D., et al, 2013.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ATAC seq read adaptors were been removed with trim_galore
Reads were mapped using Bowtie2 (-X 2000 -m 1).
Chloroplast and mitochondrial DNA aligned reads were filtered out and duplicate reads were removed using Samtools
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig, narrowPeak
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
Jun 21, 2019 |
| Contact name |
magdalena ewelina potok |
| Organization name |
UCLA
|
| Department |
MCDB
|
| Lab |
Jacobsen lab
|
| Street address |
4045 Terasaki Life Sciences Building
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7239 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE123257 |
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ATAC-Seq] |
| GSE123263 |
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. |
|
| Relations |
| BioSample |
SAMN10517054 |
| SRA |
SRX5088430 |
