In addition to cataloging PAC from individual samples, PlantAPAdb also provides the PAC list of pooled samples for bulk download. For the pooled data, different files are available for download to meet the users’ need. The file in bed format records simple information such as chromosome, strand, coordinate, and total number of reads for each PAC. The file in text format tabulates full information of each PAC, including the total read count, the raw and TPM normalized read count in each individul sample and replicate, the respective gene, genomic location (CDS, intron, 3’ UTR, 5’ UTR, intergenic, etc.), distance to neighbor genes (if the PAC is located in intergenic region). Moreover, files of heterogeneous cleavage sites in bed format were also provided, which allows users to inspect the polyadenylation in higher resolution. More...
| Full sample list | This file contains the information of the full sample list in PlantAPAdb, including the SRR id, sample name, environmental condition, plant type, tissue, sequencing protocol, reference, read statistics. | Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| All poly(A) site clusters in BED format |
This file contains all poly(A) site clusters (PACs) with the information of Chromosome, strand, coordinate, and score (raw read count from the pooled samples) for each PAC. Internal priming artifacts were removed. Cleavage sites within 24 nt of each other were grouped into one PAC.
Download |
| All poly(A) site clusters with annotation (raw count) |
This file contains full information of all PACs. The expression level (number of supported reads) for each PAC in each experiment is given. The annotation including the gene, gene type, genomic region, number of cleavage sites etc. for each PAC is also given.
Download |
| All poly(A) site clusters with annotation (TPM count) |
This file contains full information of all PACs and the expression levels were normalized by Tag Per Million.
Download |
| High confidence poly(A) site clusters in BED format |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
| High confidence poly(A) site clusters with annotation (TPM count) |
This file contains only high confidence PACs with full annotation.
Download |
| All cleavage sites |
This file contains all cleavage sites, which has four columns: chromosome, strand, coordinate, and number of supported reads. This file was used for generating poly(A) site clusters.
Download |
| Organisms | Type | Total number | Conserved poly(A) sites |
|---|---|---|---|
| Arabidopsis thaliana | All | 105,421 |
For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs.
Download |
| High confidence | 17,699 |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
|
| Oryza sativa Indica Group | All | 57,940 |
For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs.
Download |
| High confidence | 2,484 |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
|
| Oryza sativa Japonica Group | All | 68,139 |
For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs.
Download |
| High confidence | 2,647 |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
|
| Chlamydomonas reinhardtii | All | 315 |
For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs.
Download |
| High confidence | 121 |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
|
| Trifolium pratense | All | 23,525 |
For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs.
Download |
| High confidence | 6,738 |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |
|
| Medicago truncatula | All | 25,656 |
For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs.
Download |
| High confidence | 4,839 |
This file contains only high confidence PACs which are expressed (TPM>=1) in at least two experiments.
Download |