|
| Status |
Public on Nov 10, 2023 |
| Title |
set2, AagrOXF 4week thalli, H3K4me3, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
thalli
|
| Organism |
Anthoceros agrestis |
| Characteristics |
strain: Oxford
tissue: thalli
age: 4 weeks
genotype: wild type
chip antibody: H3K4me3
|
| 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 |
Tissues were fixed with 1% paraformaldehyde for 10 minutes. After quenching and tissue lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the Ovation® Ultralow Library Systems V2. 1-10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12-15 cycles on the thermocycler. Libraries were validated using the fragment analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TH_Aa_ChIP11
|
| Data processing |
Self-ligated adaptor sequences were removed by using catadapt with a option --minimum-length 1.
ChIP-seq reads were aligned to the Anthoceros agrestis Oxford genome using Bowtie2 version 2.3.4.2 with options --sensitive -p 8 -N 0 --trim5 0 --trim3 0. Reads with MAPQ less than ten were removed with Samtools v1.9 and duplicates were removed with Picard v2.18.27.
Bigwig files were generated using the bamCoverage function of deepTools v3.3.1 with options --normalizeUsing RPGC --effectiveGenomeSize 122905886 --binSize=10.
Bigwig files of log2 ratio of each mark to input sample were generated using the bamConpare function of deepTools v3.3.1 with options--scaleFactorsMethod readCount --binSize=10.
Peaks were called using MACS2 v2.2.5 with options --nomodel --nolambda -q 0.01 --broad --broad-cutoff 0.1.
Aligned BAM files of each replicate were merged using SAMtools v1.9. These merged BAM files were used to generate bigwig files and MACS2 peak files (used the same method described above)
Assembly: Anthoceros agrestis Oxford
Supplementary files format and content:
macs2 broadPeak (except for Input sample)
bigwig files for coverage of each mark.
bigwig files for log2 ratio of each mark normalized with input sample.
genome fasta file; Gene and TE annotations in gff3 format
log2r bigwig files of each mark made from merged bam files of each replicate
macs2 broadpeak files of each mark made from merged bam files of each replicate
|
| |
|
| Submission date |
Nov 28, 2022 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Tetsuya Hisanaga |
| E-mail(s) |
hisanaga.tetsuya@naist.ac.jp
|
| Phone |
+81 743 72 5563
|
| Organization name |
Nara Institute of Science and Technology
|
| Lab |
Nakajima Lab
|
| Street address |
Takayama 8916-5
|
| City |
Ikoma |
| State/province |
Nara |
| ZIP/Postal code |
630-0192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL32890 |
| Series (2) |
| GSE218878 |
Chromatin profile of Anthoceros agrestis |
| GSE218880 |
5-methyl cytosine profile and chromatin profile of Anthoceros agrestis |
|
| Relations |
| BioSample |
SAMN31891377 |
| SRA |
SRX18397592 |
