In EricEdwardBryant/rothfreezer: Freezer database for the Rothstein Lab

Quick Links

• Strains
• Primers
• Freezer

Tables

Freezer Addresses

Table name: addresses

Fields:

Field Description

---

freezer Freezer name temp Freezer temperature shelf Shelf number (starting with 1 at top of freezer) rack Rack number (starting with 1 on left of shelf) pullout Pullout number (starting with 1 at top of rack) insert Insert number (starting with 1 at front of pullout) row Row letter (starting with A at top of insert) column Column number (starting with 1 at left of insert) pullout_label Label on Pullout box_label Label on Box description Description of item type Type of item (computed from other tables in database) item_id ID of item (must match a strain_id, plasmid_id, or primer_id)

Allele-Item mappings

Table name: allele_item

Fields:

Field Description

---

allele_id An allele ID (must be present in alleles table) item_id ID of item (must match a strain_id, plasmid_id, or primer_id)

Allele annotation

Table name: alleles

Fields:

Field Description

---

allele_id An allele ID allele_name Name of allele allele_type Type of allele (e.g. disruption, point mutation...) allele_description Description of allele dna_changes Mutations relative to WT reference DNA aa_changes Mutations relative to WT reference amino acid sequence

Antibodies

Table name: antibodies

Fields:

Field Description

---

antibody_id An antibody ID antibody_name Name of antibody antibody_description Description of antibody

Drugs

Table name: drugs

Fields:

Field Description

---

drug_id A drug ID drug_name Name of drug drug_description Description of drug

Gene annotation

Table name: genes

Fields:

Field Description

---

gene_id SGD ID orf_id ORF ID gene_name Official gene name (from SGD) gene_alias Gene aliases (separaged by |) gene_description Gene descritpion

Plasmids

Table name: plasmids

Fields:

Field Description

---

plasmid_id ID of plasmid (e.g. pWJ#) plasmid_name Name of plasmid plasmid_description Description of plasmid promoter Promoter source (e.g. GAL1) allele_id An allele ID gene_id A gene ID insert_gene
insert_orf yeast_marker yeast_propagation bact_marker bact_propagation plasmid_parent plasmid_owner plasmid_address Soon to be removed plasmid_date plasmid_notes viability Soon to be removed

Primers

Table name: primers

Fields:

Field Description

---

primer_id ID of primer alias Alias of primer sequence Sequence of primer description Description of primer owner Owner of primer notes Notes on primer

Strain Collections

Table name: strain_collections

Fields:

Field Description

---

strain_collection_id ID of strain collection strain_id Strain ID plate Plate number row Row letter column Column number plate_control Is the strain to be treated as a plate control? (T/F) strain_collection_notes Notes on the strain in this particular collection

Strains

Table name: strains

Fields:

Field Description

---

strain_id Strain ID strain_name Strain name strain_description Strain description allele_id
gene_id genotype mat background strain_notes

EricEdwardBryant/rothfreezer documentation built on Nov. 27, 2020, 11:02 a.m.