|
| Status |
Public on Nov 10, 2023 |
| Title |
AagrOXF 4 week thalli, EMseq, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
thalli
|
| Organism |
Anthoceros agrestis |
| Characteristics |
strain: Oxford
tissue: thalli
age: 4 weeks
genotype: wild type
|
| Growth protocol |
Plants were cultured on 0.5 Gamborg’s B5 medium solidified with 1% agar under continuous white light at 22°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 100 mg of 4-week-old gametophyte tissue of A. agrestis using Nucleon PhytoPure (cytiva). Sequencing libraries for genome-wide DNA methylation profiles were generated from 200 ng of genomic DNA using NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs). These libraries were sequenced on a Illumina NextSeq 2000 to generate 100 bp paired end reads.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
TH_AaEM02
EM-seq
|
| Data processing |
The bam files of EM-seq reads were sorted with SAMtools v1.9 and converted to fastq format using bamtofastq function of BEDTools v2.27.1, then trimmed with Trim Galore.
Bisulfite converted reference genome was prepared from A. agrestis Oxford strain genome sequence using Bismark.
Trimmed reads were mapped to the bisulfite genome using the Bowtie2 option of Bismark. Duplicates were removed using the deduplicate function in Bismark.
Cytosine methylation reports were created from deduplicated reads using the bismark_methylation_extractor function in Bismark.
Each cytosine which is covered by at least four reads was used for further analyses. Methylation ratio of each cytosine was calculated and summarized to a bed file.
Bam files of each replicate were merged using SAMtools v1.9 and processed using the same method described above.
Cytosines which are covered by at least ten reads was used to calculate methylation levels. Methylation levels of each cytosine context were summarized to bed files.
Assembly: Anthoceros agrestis Oxford
Supplementary files format and content: Cytosine methylation reports.
Supplementary files format and content: bedgraph files for methylation ratio of each cytosine per each context.
|
| |
|
| Submission date |
Nov 28, 2022 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Tetsuya Hisanaga |
| E-mail(s) |
tetsuya.hisanaga@gmi.oeaw.ac.at
|
| Phone |
+43 1 79044-9814
|
| Organization name |
Gregor Mendel Institute
|
| Lab |
Berger lab
|
| Street address |
Dr.Bohr-gasse 3
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL32889 |
| Series (2) |
| GSE218877 |
5-methyl cytosine profile of Anthoceros agrestis |
| GSE218880 |
5-methyl cytosine profile and chromatin profile of Anthoceros agrestis |
|
| Relations |
| BioSample |
SAMN31891388 |
| SRA |
SRX18397601 |
