|
| Status |
Public on Jul 31, 2017 |
| Title |
AZF1 ChIP from Col - bioRep 1 |
| Sample type |
SRA |
| |
|
| Source name |
30 hrs old plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col
transgene: gAZF1-Myc in Col
ip antibody: anti-Myc
antibody source: Sigma
antibody lot: C3965
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Plants were grown in long day (16 hr light/ 8 hr dark, light intensity: ~110 μMol/m2s1) on standard growth plates (1/2 Murashige and Skoog (MS) medium)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assay is performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA was end repaired, A-tailed, and ligated to universal PE adapters using reagents from enzymatics. Libraries were amplified using custom-designed dual-indexed oligos.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Col.AZF1.merge.bw
Col.AZF1.minus.input.bw
|
| Data processing |
reads were aligned to the genome using bowtie2
reads were extended to 200 bp using bedtools
coverage was calculated using bedtools
coverage was normalized to 10 million reads mapped per million reads sequenced (10RPM) using a custom script
mean coverage from replicates was calculated using wiggleTools
in some tracks (input-corrected) mean input noise was subtracted from the mean ChIP signal using wiggleTool (diff command)
Genome_build: TAIR10 release 31 (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/arabidopsis_thaliana/dna/)
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for single replicates
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
Supplementary_files_format_and_content: peaks were called using MACS version 2.1.1.20160309 using default parameters for AZF, BPC, and FIE, and the broad peaks option for H3K27me3; peak lists were filtered for Q-value < 1e-10
|
| |
|
| Submission date |
Jul 17, 2016 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE84483 |
ChIP-seq for Polycomb and associated transcription factors in Arabidopsis |
|
| Relations |
| BioSample |
SAMN05412829 |
| SRA |
SRX1957726 |
