Table 1.
Chlamydomonas sequence data collected for the ChlamyCyc web-portal
| Name | Type | Source | Mapping |
| Genomic sequence data | |||
| Chlre3_1_genome_scaffolds | DNA genomic scaffolds (all1) | JGI2 | - |
| JGI 4.0 genome_scaffolds | DNA genomic scaffolds | JGI3 | - |
| Chlamy chloroplast | DNA complete genome sequence (. NC_005353) | Genbank | - |
| Chlamy mitochondrion | DNA complete genome sequence (. NC_001638) | Genbank | - |
| Chlamy GSS | DNA (15574 GSS sequences from Genbank4) | PlantGDB5 | razerS12 |
| Chlamy STS | DNA (8 STS sequences from Genbank7) | PlantGDB5 | razerS12 |
| Chlamy HTG | DNA (2 HTG sequences from Genbank8) | PlantGDB5 | razerS12 |
| Transcript sequence data | |||
| Chlre3_1.GeneCatalog_2007_09_13.transcripts | mRNA transcripts (frozen gene catalog 3.1) | JGI2 | GFF (from JGI) |
| Chlamy Chlre3.1M dna | mRNA transcripts (Science paper) | JGI2 | GFF (from JGI) |
| Chlre3_1_allESTs.fasta | mRNA transcripts | JGI2 | gmap6 |
| Chlre3_1_ESTcluster.cr.171 | mRNA transcripts | JGI2 | gmap6 |
| Chlre3_1_ESTcluster.cr.210 | mRNA transcripts | JGI2 | gmap6 |
| Chlamy ESTs | mRNA (202044 EST sequences from Genbank) | PlantGDB4 | gmap6 |
| Chlamy ESTcontigs | mRNA (50380 EST assembly sequences) | PlantGDB4 | gmap6 |
| RNA data | |||
| microRNAs | RNA (microRNAs) | MirBase10 | GFF (from JGI) |
| Cresi-RNAdb | RNA (small RNAs) | cresi-RNA11 | razerS12 |
| Chlamydomonas_reinhardtii.scRNA.PLN | RNA (1 scRNA from Genbank) | Genbank | razerS12 |
| Chlamydomonas_reinhardtii.snRNA.PLN | RNA (5 snRNAs from Genbank) | Genbank | razerS12 |
| Chlamydomonas_reinhardtii.tRNA.PLN | RNA (7 tRNA sequences from Genbank) | Genbank | razerS12 |
| Chlamydomonas_reinhardtii.RNA.PLN | RNA (4182 RNA sequences from PLN nucleotides) | Genbank | razerS12 |
| Protein sequence data | |||
| Chlre3_1.GeneCatalog_2007_09_13.proteins | Protein (Frozen gene catalog 3.1) | JGI2 | GFF (from JGI) |
| Chlamy Chlre3.1M.pep | Protein (Science Paper) | JGI2 | GFF (from JGI) |
| allChlre3.proteins | Proteins (alternative gene models) | JGI2 | GFF (from JGI) |
| Chlamy cp aa | Proteins (chloroplast) | Genbank | Genbank |
| Chlamy mt aa | Proteins (mitochondrion) | Genbank | Genbank |
| Chlamy peptides | Proteins (experimental identified peptides) | JGI3 | JGI |
1Assembly v.3.1 scaffolds and scaffolds excluded from v.3.1 assembly file based on blast hits or manual examination
2http://genome.jgi-psf.org/Chlre3/Chlre3.download.ftp.html
3Personal communication
4http://www.ncbi.nlm.nih.gov/dbGSS/
5http://www.plantgdb.org/search/misc/plantlistconstruction.php?mySpecies=Chlamydomonas%20reinhardtii
6http://www.gene.com/share/gmap/
7http://www.ncbi.nlm.nih.gov/dbSTS/
8http://www.ncbi.nlm.nih.gov/HTGS/
9http://www.ncbi.nlm.nih.gov/dbEST/
10http://microrna.sanger.ac.uk/