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.
Last modification: May 26, 2020