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Sample GSM7881934 Query DataSets for GSM7881934
Status Public on Apr 23, 2024
Title H3K27me3, WT, 1 DAI, rep2
Sample type SRA
Source name 1-day-old seedling
Organism Arabidopsis thaliana
Characteristics tissue: 1-day-old seedling
genotype: Col-0
treatment: 1% sucrose
Extracted molecule genomic DNA
Extraction protocol Chromatins were fixed and extracted according to a published protocol (Song et al., 2016). Then, cross-linked DNA molecules with all proteins were fragmented by sonication using a Bioruptor Plus (Diagenode, Denville, NJ, USA) for 15 cycles, with each cycle consisting of 30 seconds ON and 90 seconds OFF at the HIGH setting. Sonicated chromatin was diluted by ChIP Dilution Buffer and then incubated overnight with HA antibody (CST, Danvers, MA, USA, 3724, 1:100 v/v dilution) and H3K27me3 antibody (Active Motif, Carlsbad, CA, USA, 61018, 1:100 v/v dilution) for precipitation of 3xHA-AtSDR4L-3xFLAG and H3K27me3 bound chromatin fragments, respectively. The captured chromatin was eluted in 200 μl Elution Buffer and then reserve crosslinked at 65°C for 6 h, followed by treatment of 100 μg/mL proteinase K at 55°C for 2 h before the phenol: chloroform: IAA (25:24:1 v/v, pH 8.0) extraction. DNA was precipitated and double‐size selected using 0.6 vol. and 1.3 vol. AMPure XP beads (Beckman Coulter, Brea, CA, USA, A63881)
ChIP-seq libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA, E7645S)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Data processing Basecalling was performed on NovaSeq 6000 with the built-in software RTA3 and Demultiplexing was performed using bcl2fastq v2.19.
Low-quality reads were filtered, and adapters were trimmed by fastp version 0.23.4
Reads were aligned to the Arabidopsis genome (TAIR10) with Botiew2 version 2.2.5 with the default parameters. Subsequently, the aligned reads were converted to BAM format and filtered for mapping quality scores greater than 10 by Samtools version 1.6. Alignment files of mock IgG controls from wild-type and mutant backgrounds were concatenated to form a common control for peak calling of H3K27me3 libraries.
Peaks were called by MACS2 version for H3K27me3 ChIP using the combined mock IP as a control and “--broad” argument to call broad peaks. For native promoter-driven AtSDR4L ChIP, peak calling was performed on MACS2 version 2.2.6 using Col-0 wildtype as control. For both peak callings, the argument “-f BAMPE” was used to specify the pair-end library as well as “-g 1.2e8 -q 0.1". The argument "--call-summits" was used for native promoter-driven AtSDR4L peak calling.
The TDFs were created from BAM by igvtools version 2.5.3 for native promoter-driven AtSDRL libraries and version 2.14.1 for H3K27me3 libraries, with the maximum zoom level of 5 for precomputing, window size of 10 bp for averaging coverage, and “includeDuplicates” option enabled.
Assembly: TAIR10
Supplementary files format and content: broadpeak and narrowPeak files (MACS2 output)
Supplementary files format and content: tiled data files,TDF (igvtools output)
Submission date Nov 03, 2023
Last update date Apr 23, 2024
Contact name Liang Song
Organization name University of British Columbia
Department Botany
Lab Song Lab
Street address 2231-6270 UNIVERSITY BLVD
State/province British Columbia
ZIP/Postal code V6T 1Z4
Country Canada
Platform ID GPL26208
Series (1)
GSE246997 AtSDR4L and DIG1 interact with VAL2 to promote seed-to-seedling transition
BioSample SAMN38094108
SRA SRX22366761

Supplementary file Size Download File type/resource
GSM7881934_S004_02_L1_peaks.broadPeak.gz 156.4 Kb (ftp)(http) BROADPEAK
GSM7881934_filtered_S004_02_L1.sorted.tdf 52.8 Mb (ftp)(http) TDF
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