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Status |
Public on Mar 02, 2020 |
Title |
Wheat_ATAC_S1_001 |
Sample type |
SRA |
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Source name |
Seedlings
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Organism |
Triticum aestivum |
Characteristics |
genotype: Chinese Spring developmental stage: 14 days old seedlings tissue: shoot
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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).
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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).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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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
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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
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Phone |
769929568
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Organization name |
École Normale Supérieure
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Department |
Institut de Biologie
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Lab |
Plant and Algal Genomics Lab
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Street address |
46 Rue d'Ulm
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City |
Paris |
ZIP/Postal code |
75020 |
Country |
France |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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