|
| Status |
Public on Jun 05, 2020 |
| Title |
Ear_MNase_seq_rep2_heavy_digest |
| Sample type |
SRA |
| |
|
| Source name |
Ear primordia nuclei
|
| Organism |
Zea mays |
| Characteristics |
genotype: B73
developmental stage: Ear primordia 1-5 mm
developmental stage: pool ~ 170 hand-dissected inflorescence primordia
|
| Treatment protocol |
The ground tissue was cross linked to fix nucleosome bound DNA in fixation buffer (15 mM Pipes·NaOH at pH 6.8, 0.32 M sorbitol, 80 mM KCl, 20 mM NaCl, 0.5 mM EGTA, 2mM EDTA, 1 mM DTT, 0.15 mM spermine, and 0.5 mM spermidine) with 1% formaldehyde
|
| Growth protocol |
B73 seeds were grown in climate controlled growth facility at 27°C/23°C day/night for 4-5 weeks for tassel and 6-7 weeks for ear and primordia were hand dissected
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The nuclei were isolated with tissue disrupture and purified with a percol gradient. Nuclei were digested with different concentrations of micrococcal nuclease and DNA was extracted with in house protocol.
The libraires were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following manufacturer instructions.
50 bp paired-end reads were generated using the Illumina Illumina HiSeq 2500 platform
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
The bed files for this sample contain information of the iSeg peak calls differential nuclease sensitivity (DNS) (light - heavy digest) for ear at bc 2.0 and bc 3.0 threshold for replicate 2
|
| Data processing |
Paired-end reads were first trimmed for adapter sequences using Cutadapt
Cleaned reads were mapped to maize AGPB73_v3 using Bowtie2
BAM files were seperated based on size. small fragments (<131bp). All fragments (0-500bp).
Peak calling with iSeg. Selection based on biological cutoff (bc) thresholds 2.0, 3.0 and 4.0 as described in Girimurugan et al., BMC Bioinformatics 2018.
AGP B73_v3
Supplementary_files_format_and_content: bed and bw files
|
| |
|
| Submission date |
Aug 30, 2019 |
| Last update date |
Jun 05, 2020 |
| Contact name |
Andrea Eveland |
| E-mail(s) |
AEveland@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Andrea L. Eveland
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE136685 |
The regulatory landscape of early maize inflorescence development |
|
| Relations |
| BioSample |
SAMN12662339 |
| SRA |
SRX6783809 |
