LabxDB seq tables
Project table
| Column | Description |
|---|---|
| Project ref | Project reference (ID), i.e. AGPxxx (Two initials + P) |
| Project name | Project name. A computer-oriented name: short, no space. Used by post-processing pipelines folder names etc. |
| Short label | As short as possible label (to fit small spaces such as genome track label). Use abbreviations. Populated while creating the annotation structure. |
| Long label | More descriptive label. Longer than short label. No abbreviation. Include all conditions, genotypes, timepoints and treatments. |
| Scientist | Scientist initials. |
| External scientist | In case this project is imported (from SRA for example) or in collaboration, enter that scientist name. |
| SRA ref | SRPxxx ID (for project imported from SRA). |
Sample table
| Column | Type | Description |
|---|---|---|
| Sample ref | Sample reference (ID), i.e. AGSxxx (Two initials + S) | |
| Project ref | Project reference (ID). Structure column: which project this sample belongs to. | |
| Short label | Short label using abbreviation. Include genotype, timepoint and condition. | |
| Long label | Long label without abbreviation. Expands short label. | |
| Species | fish | Species (danRer, homSap, droMel etc). |
| Maternal strain | fish | Genotype of mother if not wild-type. |
| Paternal strain | fish | Genotype of father if not wild-type. |
| Genotype | fish | “WT” or specific genotype. |
| Ploidy | fish | “2n” if diploid or “n” if haploid. |
| Age (hpf) | fish | Age in hours post-fertilization. |
| Stage | fish | Developmental stage embryos were collected. |
| Tissue | fish | If specific tissue was collected. |
| Condition | library | If experiment is done in pair (or more) such as CLIP/input, CLIP/IgG or RPF/input, enter the condition. |
| Treatment | library | Chemical treatment applied such as morpholino, cycloheximide. |
| Selection | library | Selection or purification of library such as poly(A) (abbreviated “pA”), ribo-zero (abbreviated “r0”) or antibodies. |
| Molecule | library | Sequenced molecule: “mRNA” for mRNA-seq, “RNA” for CLIP or “DNA” for ChIP-seq. |
| Library protocol | library | Protocol used to prepared the library such as dUTP or sRNA (small RNA). |
| Adapter 5' | library | Name of 5’ adapter. |
| Adapter 3' | library | Name of 3’ adapter. |
| Track priority | Genome track priority. Track with lowest number comes first. | |
| Track color | Genome track color name. | |
| SRA ref | SISxxx ID (for SRA Imported Sample). | |
| Notes | Any information not input in other columns. |
Replicate table
| Column | Description |
|---|---|
| Replicate ref | Replicate reference (ID), i.e. AGNxxx (Two initials + N) |
| Replicate order | Number. First, second or third (etc) replicates. |
| Sample ref | Sample reference (ID). Structure column: which sample this replicate belongs to. |
| Short label | Short label using abbreviation. Include genotype, timepoint and condition. Include replicate number (for example with B1, B2). |
| Long label | Long label without abbreviation. Expands short label. Include replicate number. |
| SRA ref | SINxxx ID (for SRA Imported Replicate). |
| Publication ref | If replicate has been published, name of publication. |
| Notes | Any information not input in other columns. |
Run table
| Column | Description |
|---|---|
| Run ref | Run reference (ID), i.e. AGRxxx (Two initials + R) |
| Run order | Number. First, second or third (etc) runs. |
| Replicate ref | Replicate reference (ID). Structure column: which replicate this run belongs to. |
| Tube label | Label used on tube sent to sequencing facility. Filename of FASTQ files. |
| Barcode | Illumina barcode if samples were multiplexed. |
| Second barcode | Internal barcode if samples were multiplexed using a second barcode. |
| Request | Internal reference for sequencing request. |
| Request date | Date of internal sequencing request. |
| Failed | Did this sequencing run failed? |
| Flowcell | Flowcell reference. |
| Platform | Name of platform used for sequencing. For example “Illumina NovaSeq 6000”. |
| Quality scores | Quality scores coding within FASTQ files. Most recent scores are coded with “Illumina 1.8”. |
| Directional | Is read direction (5’ to 3’ for example) preserved during library preparation? |
| Paired | Single-end or paired-end sequencing. |
| Read1 strand | If read is directional, what is the orientation of read 1. Example: mRNA-seq prepared with dUTP is “-” or antisense. CLIP or small-RNA-seq are “+” or sense. Most DNA sequencing is “u” unstranded. Important for read mapping. |
| Spots | Number of spots. |
| Max read length | Length of longest read in run. |
| SRA ref | SRRxxx ID (for run imported from SRA). |
| Notes | Any information not input in other columns. |