|
| Status |
Public on Feb 02, 2021 |
| Title |
Bisulfite_sequencing_Aphid_72hrs_bioreplicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
Rosette leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Columbia 0 wild type
|
| Treatment protocol |
5-week-old plants were infested with 40 wingless M.persicae of second to fourth larval instars and covered with net cage. After 72 hours all aphids were carefully removed by brush and all Arabidopsis rosette leaves were sampled into Falcon tubes extraction bag before being placed in liquid nitrogen. Tissue was collected from all tested mutants. Each frozen plant sample was stored at -70 °C before RNA and DNA extraction.
|
| Growth protocol |
Plants were grown under standard long day conditions at 22 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Life Technologies) following the manufacturer instructions. mRNA for RNA and PARE sequencing was obtained by purification with the NEB mRNA isolation kit (New England Biolabs). RNA for sRNA library preparation was enriched with the mirVana miRNA Isolation Kit (Life Technologies). Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen).
sRNA libraries were produced using the TruSeq Small RNA Sample Preparation Kit (Illumina). PARE libraries were constructed according to Zhai et al (2014). RNA libraries were produced using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Bisulfite DNA libraries were produced and sequenced at Novogene (Hong Kong).
sRNA-sequencing, RNA sequencing, PARE sequencing and Bisulfite sequencing
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Bisulfited genomic DNA
Bisulfite_CpG_context_Aphid_72hrs_bioreplicate_2.bedGraph.gz
Bisulfite_CHG_context_Aphid_72hrs_bioreplicate_2.bedGraph.gz
Bisulfite_CHH_context_Aphid_72hrs_bioreplicate_2.bedGraph.gz
Bisulfite_CpG_context_Aphid_72hrs_bioreplicate_2.bigWig
Bisulfite_CHG_context_Aphid_72hrs_bioreplicate_2.bigWig
Bisulfite_CHH_context_Aphid_72hrs_bioreplicate_2.bigWig
|
| Data processing |
sRNAs, PARE and RNA libraries were trimmed using Trim Galore. For bisulfite sequencing libraries adapters and 10 bases from 5' ends from reads were trimmed using Trimgalore.
All libraries were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. sRNAs were mapped with bowtie allowing 2 mismatches. PARE and RNA seq libaries were mapped using bowtie2 with default parameters. For bisulfite libraries Clean reads were mapped to the reference genome TAIR 10 using bismark, allowing one mismatch per 25 nt seed. Forward and reverse reads were mapped independently. Alignments at the same position were removed using deduplicate_bismark script, including alignments of reads 1 and 2 together.Conversion rate of cytosines were obtained using bismark_methylation_extractor, the first 7 bases from 5' end and 13 from 3' end of each read were ignored.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files were generated using Galaxy. For RNA seq experiments reads were aligned with bowtie with default parameters. SAM files were converted to BAM and count reads per gene or TE were assesed with ht-seq counts. Count files were used to infer differential expression using DESeq2.
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| |
|
| Submission date |
Jan 23, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
German Martinez |
| E-mail(s) |
german.martinez.arias@slu.se
|
| Organization name |
Swedish University of Agricultural Sciences
|
| Department |
Plant Biology
|
| Lab |
Martinez Lab
|
| Street address |
Almas Allé 8
|
| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
750 07 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE144181 |
Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis |
|
| Relations |
| BioSample |
SAMN13911167 |
| SRA |
SRX7625551 |
