More shared resources, please refer to public ftp server: ftp://nandesyn.single-cell.cn/pub/.

 

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)