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Sample GSM3929160 Query DataSets for GSM3929160
Status Public on Mar 02, 2020
Title Wheat_ATAC_S1_001
Sample type SRA
 
Source name Seedlings
Organism Triticum aestivum
Characteristics genotype: Chinese Spring
developmental stage: 14 days old seedlings
tissue: shoot
Growth protocol Seeds were surface sterilized with bayrochlore and ethanol, sown on MS agar plates, placed at 4°C in the dark for 2 days and then grown in a growth chamber for 14 days (long day conditions, 18°C).
Extracted molecule genomic DNA
Extraction protocol 100 mg of 14-d-old seedlings were ground and nuclei were isolated with 4°C Buffer (0,25M Sucrose, 10mM Tris-HCl, 10mM MgCL2, 1% Triton, 5mM beta-mercaptoethanol) containing proteinase inhibitor cocktail (Roche) and filtered in 63µm.
DNA libraries were amplified for a total of 8 cycles as described by Buenrostro et al., (2013) and Jégu et al., (2017).
100 mg of 14-d-old seedlings were ground and nuclei were isolated with 4°C Buffer (0,25M Sucrose, 10mM Tris-HCl, 10mM MgCL2, 1% Triton, 5mM beta-mercaptoethanol) containing proteinase inhibitor cocktail (Roche) and filtered in 63µm. Nuclei were resuspended in 1X TD Buffer (Illumina FC-121-1030) and 2.5 μL of Tn5 Transposes (Illumina FC-121-1030) were added. Transposition reaction was performed at 37°C for 30min, and DNA was purified using a Qiagen MinElute Kit. DNA libraries were amplified for a total of 8 cycles as described by Buenrostro et al., (2013) and Jégu et al., (2017).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Adapters trimming: Sequencing reads were trimmed with trim_galore v0.4.4 with the following command "trim_galore --fastqc --paired --nextera --dont_gzip"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.3 with the following setting "bowtie2 --very-sensitive" against the genome of Triticum aestivum (iwgsc_1.0).
Filtering step: Mapped reads were sorted with sambamba view v.0.6.6 with the command "sambamba view -F "mapping_quality >= 10 --format bam"
Bigwig generation: read density was scored over 100-bp non-overlapping bins with deepTools v.3.1.0 with the command "bamCoverage --binSize 100 --smoothLength 2100 --centerReads -of bigwig"
peak calling: peaks of read density were called with macs2 2.1.1.20160309 with the command "macs2 callpeak --qvalue 0.01 --format BAMPE --keep-dup all --gsize 1.46e10 --nomodel --shift -100 --extsize 200"
Genome_build: iwgsc_1.0
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.
Supplementary_files_format_and_content: narrowPeak file from macs2
 
Submission date Jul 05, 2019
Last update date Mar 02, 2020
Contact name Lorenzo Concia
E-mail(s) colore@gmail.com, concia@bio.ens.psl.eu
Phone 769929568
Organization name École Normale Supérieure
Department Institut de Biologie
Lab Plant and Algal Genomics Lab
Street address 46 Rue d'Ulm
City Paris
ZIP/Postal code 75020
Country France
 
Platform ID GPL26889
Series (2)
GSE133879 Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ATAC)
GSE133885 Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories
Relations
BioSample SAMN12219945
SRA SRX6408585

Supplementary file Size Download File type/resource
GSM3929160_Wheat_ATAC_S1_001.q10.qval0.01_peaks.narrowPeak.gz 12.0 Mb (ftp)(http) NARROWPEAK
GSM3929160_Wheat_ATAC_S1_001.q10.smooth_2kb.bigwig 24.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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