|
Status |
Public on Jun 21, 2019 |
Title |
ATAC-Seq_mbd9-3_R1 |
Sample type |
SRA |
|
|
Source name |
flowers
|
Organism |
Arabidopsis thaliana |
Characteristics |
developmental stage: 4 weeks genotype/variation: mbd9-3 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 |
SAMN10517052 |
SRA |
SRX5088432 |