More shared resources, please refer to https://ftp.nandesyn.single-cell.cn/.
List of epigenomic datasets:
| Level | Type | Condition | Replicates | NCBI BioProject | NCBI SRA Accessions | Data size |
|---|---|---|---|---|---|---|
| DNA methylation | 5mC | HC | 3 | PRJNA769619 | SRR16250976, SRR16250977, SRR16250978 | 3.7 Gb |
| LC | 3 | PRJNA769619 | SRR16250973, SRR16250974, SRR16250975 | 5.6 Gb | ||
| Histone modification | H3K4me2 | HC | 2 | PRJNA769792 | SRR16267483, SRR16267484 | 8.2 Gb |
| LC | 2 | PRJNA769792 | SRR16267481, SRR16267482 | 11.3 Gb | ||
| H3K9ac | HC | 2 | PRJNA769792 | SRR16267487, SRR16267488 | 8.4 Gb | |
| LC | 2 | PRJNA769792 | SRR16267471, SRR16267476 | 11.9 Gb | ||
| H3K27ac | HC | 2 | PRJNA769792 | SRR16267469, SRR16267470 | 4.0 Gb | |
| LC | 2 | PRJNA769792 | SRR16267467, SRR16267468 | 3.3 Gb | ||
| Kcr | HC | 2 | PRJNA769792 | SRR16267465, SRR16267466 | 5.6 Gb | |
| LC | 2 | PRJNA769792 | SRR16267485, SRR16267486 | 2.4 Gb | ||
| H3K9me3 | HC | 2 | PRJNA769792 | SRR16288283, SRR16288284 | 7.8 Gb | |
| LC | 2 | PRJNA769792 | SRR16288281, SRR16288282 | 10.6 Gb | ||
| H3K27me3 | HC | 1 | PRJNA769792 | SRR16288288 | 2.0 Gb | |
| LC | 1 | PRJNA769792 | SRR16288287 | 1.1 Gb | ||
| H2A.Z | HC | 1 | PRJNA769792 | SRR16288286 | 1.6 Gb | |
| LC | 1 | PRJNA769792 | SRR16288285 | 1.2 Gb | ||
| Input1 | HC | 2 | PRJNA769792 | SRR16267479, SRR16267480 | 13.1 Gb | |
| LC | 2 | PRJNA769792 | .SRR16267477, SRR16267478 | 11.0 Gb | ||
| Input2 | HC | 2 | PRJNA769792 | SRR16267474, SRR16267475 | 9.3 Gb | |
| LC | 2 | PRJNA769792 | SRR16267472, SRR16267473 | 6.8 Gb | ||
| H3K4me2 | M4 | 3 | PRJNA769958 | SRR16278139, SRR16278141, SRR16278143 | 10.9 Gb | |
| M4_Input | 3 | PRJNA769958 | SRR16278140, SRR16278142, SRR16278137 | 9.6 Gb | ||
| M6 | 3 | PRJNA769958 | SRR16278132, SRR16278134, SRR16278136 | 13.3 Gb | ||
| M6_Input | 3 | PRJNA769958 | SRR16278131, SRR16278133, SRR16278135 | 13.3 Gb | ||
| WT | 3 | PRJNA769958 | SRR16278124, SRR16278145, SRR16278147 | 9.6 Gb | ||
| WT_Input | 3 | PRJNA769958 | SRR16278144, SRR16278146, SRR16278148 | 9.4 Gb | ||
| Nucleosome occupancy | MNase-Seq | HC | 2 | PRJNA769749 | SRR16265741, SRR16265742 | 6.8 Gb |
| LC | 2 | PRJNA769749 | SRR16265739, SRR16265740 | 5.6 Gb | ||
| Chromosome architecture | Hi-C | HC | 2 | PRJNA513887 | SRR8420587, SRR16268661 | 121.1 Gb |
| LC | 2 | PRJNA513887 | SRR16268659, SRR16268660 | 115.7 Gb | ||
| Transcriptome | mRNA-Seq | M4 | 3 | PRJNA769958 | SRR16278128, SRR16278129, SRR16278130 | 19.3 Gb |
| M6 | 3 | PRJNA769958 | SRR16278125, SRR16278126, SRR16278127 | 19.7 Gb | ||
| WT | 3 | PRJNA769958 | SRR16278138, SRR16278149, SRR16278150 | 20.8 Gb |
Nannochloropsis oceanica IMET1 version 2: |
|
| Genome assembly FASTA: | IMET1v2.fasta |
| Gene structure annotation GFF3: | IMET1v2.gene.gff3 |
| Gene synonyms: | IMET1v2all.synonym.txt |
| Repeat annotations: | IMET1v2.fasta.RM.tar.gz |
| Protein sequences: | IMET1v2.protein.fa |
| 6mA methylation: | IMET1v2_m6A.gff |
| Conversion with IMET1v1: | IMET1v2.synonym.txt |
| tRNA annotation: | IMET1v2_tRNA.zip |
Nannochloropsis salina CCMP1776: |
|
| Genome assembly FASTA: | N_salina.genome.fasta |
| Gene structure annotation GTF: | N_salina.gtf |
| mRNA sequences: | N_salina.mRNA.fasta |
| MiRNA: | N_salina.miRNAs.gff3 |
| CircRNA: | N_salina.circRNAs.bed |
N. salina CCMP537 contigs: |
GCA_004335465.1_ASM433546v1_genomic.fna |
Collection of genome assemblies from QIBEBT: |
database.tar.bz2 |
Collection of PGDBs: |
pgdbs.tar.gz |
Sister groups of algae deployed in NanDeSyn:
Monodopsis sp. C141 FASTA GFF Contact: Fay-Wei Li (fl329@cornell.edu)
Monodopsis sp. C73 FASTA GFF Contact: Fay-Wei Li (fl329@cornell.edu)
Vischeria sp. C74 FASTA GFF Contact: Fay-Wei Li (fl329@cornell.edu)