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Sample GSM4055233 Query DataSets for GSM4055233
Status Public on Jun 05, 2020
Title Tassel_MNase_seq_rep2_light_digest
Sample type SRA
 
Source name Tassel primordia nuclei
Organism Zea mays
Characteristics genotype: B73
developmental stage: Tassel 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 from small fragments (0-130bp) for tassel at the 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 SAMN12662336
SRA SRX6783812

Supplementary file Size Download File type/resource
GSM4055233_Tassel_MNaselightdigest_rep2.bw 946.2 Mb (ftp)(http) BW
GSM4055233_Tassel_light_small_rep2_iSeg_bc_2.0.bed.gz 10.5 Mb (ftp)(http) BED
GSM4055233_Tassel_light_small_rep2_iSeg_bc_3.0.bed.gz 6.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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