|
| Status |
Public on Jun 21, 2019 |
| Title |
ChIPSeq_Flag_WT |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 13 DAG shoots
chip antibody: Flag (Sigma-Aldrich, F1804)
genotype/variation: wildtype
ecotype: Col-0
|
| Growth protocol |
About 5 g of 13 DAG T4 MBD9-3XFLAG and Col-0 seedlings grown on 1% MS were fixed in vivo and flash frozen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated nuclei were sonicate, cell lysates were cleared and histone-DNA complexes were isolated with antibody.
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 2500 |
| |
|
| Data processing |
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie57 using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized read coverage tracks were generated using the USeq package Sam2Useq application
ChIP-Seq peaks were called using callpeak function in MACS2 (v2.1.1.)
ChIP-seq data metaplots and k-means clustering were generated by NGSPLOT (v4.02.48)59
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using bioloobox bam2wig.pl application
|
| |
|
| 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 |
GPL17639 |
| Series (2) |
| GSE123261 |
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_MBD9] |
| GSE123263 |
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. |
|
| Relations |
| BioSample |
SAMN10517076 |
| SRA |
SRX5088559 |
