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Load GWDI strains #118

Open cybersiddhu opened 5 years ago

cybersiddhu commented 5 years ago

55

pfey03 commented 4 years ago

The parent ID for GWDI strains has changed and is now DBS0351471. See the corrected parent annotation in the sample GWDI strain gxcAA- (DBS0351107) http://dictybase.org/db/cgi-bin/dictyBase/phenotype/strain_and_phenotype_details.pl?genotype_id=10791

Thanks!

cybersiddhu commented 3 years ago

The current strain data loads fine but for any changes the data file has to be updated and properly mapped.

pfey03 commented 3 years ago

Annotation of GWDI single intragenic insertion

Example:

From table: Strain descriptor: adkB- Strain name: GWDI_11_E_8 Chr: DDB0232433 Position: 2,004,501 Orientation: + Insert: G1 (GATC) Mutants in well: 1 gene ID: DDB_G0292730

Annotations:

Strain descriptor: adkB- Strain name: GWDI_11_E_8 genotype general: _axeA1,axeB1,axeC1,straindescriptor,[bsRcas],bsR genotype example: axeA1,axeB1,axeC1,adkB-,[bsRcas],bsR Note, the changing aspect in genotypes is that after axeA1,axeB1,axeC1 the strain descriptor is inserted, and then always followed by [bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) adkB- mutant; insertion at position 2,004,501, chr 6, at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, null mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): adkB Reference: doi:10.1101/582072

pfey03 commented 3 years ago

I decided to add the orientation. as it helps people. I also think I add a GWDI info page to the DSC and explain the annotations. The text of the table explanation is quite specific: "6) Insert Orientation We have included the orientation of the insert to reduce the number of PCR reaction you have to set up to validate your mutant. If the orientation is "+", you have to use primer pGWDI1 together with your upstream genomic primer and primer pGWDI2 with your downstream genomic primer. If it's orientation "-", use them the other way around. You can, of course, set up all reactions and use the ones without a band as a negative control."

pfey03 commented 3 years ago

Annotation of GWDI single intergenic insertions general info

These fall into 2 categories, and number 2 has three sup-categories, which change annotations accordingly.

  1. Intergenic insertions that are not in vicinity of an annotated gene and have no gene link
  2. Intergenic insertions that are within 500 bp of the start codon of a gene - they decided that within 500 bp upstream, it's likely in the promoter region. This is an informed assumption, and I will also add that on our GWDI info page.

2.1 Intergenic_up: insertion interrupts promoter of gene upstream (Crick) 2.2 Intergenic_down: iinsertion interrupts promoter of gene downstream (Watson) 2.3 Intergenic_both: promoter regions of two genes overlap; insertion is within 500 bp of the start codon of both genes (genes next to each other, 5' to 5', head_to_head)

Finally, I added strain descriptors for promoter mutants as gene name in brackets. In our other strain descriptors when we add the promoter like act15 we put that in brackets like [act15]. So I did it like that and then added a - to indicate insertion/mutation, like [fhkB]-.

pfey03 commented 3 years ago

Annotation of intergenic insertions that are not in vicinity of an annotated gene

From table: Strain descriptor: GWDI_11_D_10 Strain name: GWDI_11_D_10 Chr: DDB0232428 Position: 423,301 Orientation: - Insert: G1 (GATC) Mutants in well: 1 gene ID: none

Annotations:

Strain descriptor: GWDI_11_D_10 Strain name: GWDI_11_D_10 genotype: axeA1,axeB1,axeC1,GWDI_11_D_10,[bsRcas],bsR Like everywhere, we add the strain descriptor here!

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, not near a known coding region; insertion at position 423,301, chr 1 at GATC genomic sites; - orientation.

Genetic Modification: exogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): None Reference: doi:10.1101/582072

NOTE: The genetic modification changes hear from endogenous insertion to exogenous insertion!!

pfey03 commented 3 years ago

We could think about eventually linking the the chromosomal location in the Strain Summary to location in JBrowse, an idea for later

pfey03 commented 3 years ago

Annotation of intergenic_up - insertion interrupts promoter of upstream gene

From table: Strain descriptor: [fhkB]- Strain name: GWDI_63_D_11 Chr: DDB0232430 Position: 3,551,949 Orientation: + Insert: G2 (GATC) Mutants in well: 1 gene ID: DDB_G0280599

Annotations:

Strain descriptor: [fhkB]- Strain name: GWDI_63_D_11 genotype: axeA1,axeB1,axeC1,[fhkB]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, insertion is within 500 bp of start codon; nearest gene fhkB is upstream of the insertions site (Crick strand), insertion at position 3,551,949, chr 3 at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): fhkB Reference: doi:10.1101/582072

pfey03 commented 3 years ago

Annotation of intergenic_down - insertion interrupts promoter of downstream gene

From table: Strain descriptor: [panC]- Strain name: GWDI_62_F_11 Chr: DDB0232432 Position: 2,148,474 Orientation: + Insert: G2 (GATC) Mutants in well: 1 gene ID: DDB_G0288935

Annotations:

Strain descriptor: [panC]- Strain name: GWDI_62_F_11 genotype: axeA1,axeB1,axeC1,[panC]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, insertion is within 500 bp of start codon; nearest gene panC is downstream of the insertions site (Watson strand), insertion at position 2,148,474, chr 5 at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): panC Reference: doi:10.1101/582072

pfey03 commented 3 years ago

Annotation of intergenic_both - insertion might interrupt two promoters of neighboring genes

From table: Strain descriptor: [vps45/DDB_G0290215]- Strain name: GWDI_68_G_5 Chr: DDB0232432 Position: 3,805,571 Orientation: + Insert: G2 (GATC) Mutants in well: 1 gene ID: DDB_G0290213,DDB_G0290215

Annotations:

Strain descriptor: [vps45/DDB_G0290215]- Strain name: GWDI_68_G_5 genotype: axeA1,axeB1,axeC1, [vps45/DDB_G0290215]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, insertion is within 500 bp of start codons of two neighboring genes oriented in opposite direction; potentially affected genes are vps45 and _DDBG0290215, insertion at position 3,805,571, chr 5 at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): vps45,DDB_G0290215 Reference: doi:10.1101/582072

pfey03 commented 3 years ago

GWDI Wells with Multiple Mutants general Info

After inspecting those with > 1 clone, they can be handled like all the above as they also have intragenic, intergenic, intergenic_up, intergenic_down, and intergenic_both. The intragenic have usually all different mutants within one gene, and there is only one insertion site given, which is a bit weird. So they are the same and just have an additional part to strain summary, e.g.

"...; this stock contains 14 individual mutants."

Real examples to follow

pfey03 commented 3 years ago

Annotation of GWDI intragenic insertions - Multiple Mutants

Example:

From table: Strain descriptor: aatB- Strain name: GWDI_200_F_1 Chr: DDB0232430 Position: 5,846,444 Orientation: - Insert: C4 (CATG) Mutants in well: 2 gene ID: DDB_G0282493

Annotations:

Strain descriptor: aatB- Strain name: GWDI_200_F_1 genotype: axeA1,axeB1,axeC1,aatB-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) mutants, aatB intragenic insertions; insertion at position 5,846,444, chr 3 at CATG genomic sites; - orientation; this stock contains 2 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, null mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): aatB Reference: doi:10.1101/582072

pfey03 commented 3 years ago

Annotation of intergenic_up insertion - Multiple Mutants

Example:

From table: Strain descriptor: [DDB_G0286487]- Strain name: GWDI_202_B_2 Chr: DDB0232431 Position: 4,555,710 Orientation: - Insert: C6 (CATG) Mutants in well: 9 gene ID: DDB_G0286487

Annotations:

Strain descriptor: [DDB_G0286487]- Strain name: GWDI_202_B_2 genotype: _axeA1,axeB1,axeC1, [DDBG0286487]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) mutants, insertions are within 500 bp of start codon; nearest gene DDB_G0286487 is upstream of the insertions sites (Crick strand); insertion at position 4,555,710, Chr 4 at CATG genomic sites; - orientation; this stock contains 9 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): DDB_G0286487 Reference: doi:10.1101/582072

pfey03 commented 3 years ago

Annotation of intergenic_down insertion - Multiple Mutants

Example:

From table: Strain descriptor: [mdhB]- Strain name: GWDI_203_B_2 Chr: DDB0232433 Position: 1,825,857 Orientation: - Insert: C6 (CATG) Mutants in well: 2 gene ID: DDB_G0292600

Annotations:

St descriptor: [mdhB]- Strain name: GWDI_203_B_2 genotype: axeA1,axeB1,axeC1,[mdhB]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) mutants, insertions are within 500 bp of start codon; nearest gene mdhB is downstream of the insertions sites (Watson strand); insertion at position 1,825,857, Chr 6 at CATG genomic sites; - orientation; this stock contains 2 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): mdhB Reference: doi:10.1101/582072

pfey03 commented 3 years ago

Annotation of intergenic_both insertion - Multiple Mutants

Example:

From table: Stran descriptor: [DDB_G0283189/DDB_G0283191]- Strain name: GWDI_370_D_5 Chr: DDB0232431 Position: 394,235 Orientation: + Insert: C8 (CATG) Mutants in well: 3 gene ID: DDB_G0283189,DDB_G0283191

Annotations:

Strain descriptor: [DDB_G0283189/DDB_G0283191]- Strain name: GWDI_370_D_5 genotype: _axeA1,axeB1,axeC1,[DDB_G0283189/DDBG0283191]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutants, insertions within 500 bp of start codons of two neighboring genes oriented in opposite direction; potentially affected genes are DDB_G0283189 and DDB_G0283191, insertion at position 3,805,571, chr 4 at CATG genomic sites; + orientation; this stock contains 3 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): DDB_G0283189,DDB_G0283191 Reference: doi:10.1101/582072

pfey03 commented 3 years ago

Annotation of intergenic insertions that are not in vicinity of an annotated gene - Multiple Mutants

From table: Strain descriptor: GWDI_203_D_2 Strain name: GWDI_203_D_2 Chr: DDB0237465 Position: 64,993 Orientation: + Insert: C6 (CATG) Mutants in well: 2 gene ID: none

Annotations:

Strain descriptor: GWDI_203_D_2 Strain name: GWDI_203_D_2 genotype: axeA1,axeB1,axeC1,GWDI_203_D_2, [bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutants, not near a known coding region; insertion at position 64,993, extrachromosomal ribosomal RNA, at GATC genomic sites; + orientation; this stock contains 2 individual mutants.

Genetic Modification: exogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): None Reference: doi:10.1101/582072

NOTES: This is not on chr 1-6, but on ribosomal RNA. Below is a list of chromosomal IDs and how to translate them in strain summary The genetic modification changes hear from endogenous insertion to exogenous insertion!!

pfey03 commented 3 years ago

Chromosome IDs and strain summary translations

The IDs below occur in the GWDI table. In the strain summary, I write the specifics for each, examples are above.

cybersiddhu commented 3 years ago

Annotation of GWDI

Intragenic

Single mutant :heavy_check_mark:

Example

From table: Strain descriptor: adkB- Strain name: GWDI_11_E_8 Chr: DDB0232433 Position: 2,004,501 Orientation: + Insert: G1 (GATC) Mutants in well: 1 gene ID: DDB_G0292730

Annotations:

Strain descriptor: adkB- Strain name: GWDI_11_E_8 genotype general: _axeA1,axeB1,axeC1,straindescriptor,[bsRcas],bsR genotype example: axeA1,axeB1,axeC1,adkB-,[bsRcas],bsR Note, the changing aspect in genotypes is that after axeA1,axeB1,axeC1 the strain descriptor is inserted, and then always followed by [bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) adkB- mutant; insertion at position 2,004,501, chr 6, at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, null mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): adkB Reference: doi:10.1101/582072

Multiple Mutants :heavy_check_mark:

Example

From table: Strain descriptor: aatB- Strain name: GWDI_200_F_1 Chr: DDB0232430 Position: 5,846,444 Orientation: - Insert: C4 (CATG) Mutants in well: 2 gene ID: DDB_G0282493

Annotations

Strain descriptor: aatB- Strain name: GWDI_200_F_1 genotype: axeA1,axeB1,axeC1,aatB-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) mutants, aatB intragenic insertions; insertion at position 5,846,444, chr 3 at CATG genomic sites; - orientation; this stock contains 2 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, null mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): aatB Reference: doi:10.1101/582072

Intergenic

Single mutant

Not in vicinity of an annotated gene :heavy_check_mark:

Example

Strain descriptor: GWDI_11_D_10 Strain name: GWDI_11_D_10 Chr: DDB0232428 Position: 423,301 Orientation: - Insert: G1 (GATC) Mutants in well: 1 gene ID: none

Annotations

Strain descriptor: GWDI_11_D_10 Strain name: GWDI_11_D_10 genotype: axeA1,axeB1,axeC1,GWDI_11_D_10,[bsRcas],bsR Like everywhere, we add the strain descriptor here!

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, not near a known coding region; insertion at position 423,301, chr 1 at GATC genomic sites; - orientation.

Genetic Modification: exogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): None Reference: doi:10.1101/582072

NOTE: The genetic modification changes hear from endogenous insertion to exogenous insertion!!

intergenic_up - insertion interrupts promoter of upstream gene :heavy_check_mark:

Example

Strain descriptor: [fhkB]- Strain name: GWDI_63_D_11 Chr: DDB0232430 Position: 3,551,949 Orientation: + Insert: G2 (GATC) Mutants in well: 1 gene ID: DDB_G0280599

Annotations

Strain descriptor: [fhkB]- Strain name: GWDI_63_D_11 genotype: axeA1,axeB1,axeC1,[fhkB]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, insertion is within 500 bp of start codon; nearest gene fhkB is upstream of the insertions site (Crick strand), insertion at position 3,551,949, chr 3 at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): fhkB Reference: doi:10.1101/582072

intergenic_down - insertion interrupts promoter of downstream gene :heavy_check_mark:

Example

Strain descriptor: [panC]- Strain name: GWDI_62_F_11 Chr: DDB0232432 Position: 2,148,474 Orientation: + Insert: G2 (GATC) Mutants in well: 1 gene ID: DDB_G0288935

Annotations

Strain descriptor: [panC]- Strain name: GWDI_62_F_11 genotype: axeA1,axeB1,axeC1,[panC]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, insertion is within 500 bp of start codon; nearest gene panC is downstream of the insertions site (Watson strand), insertion at position 2,148,474, chr 5 at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): panC Reference: doi:10.1101/582072

intergenic_both - insertion might interrupt two promoters of neighboring genes :heavy_check_mark:

Example

Strain descriptor: [vps45/DDB_G0290215]- Strain name: GWDI_68_G_5 Chr: DDB0232432 Position: 3,805,571 Orientation: + Insert: G2 (GATC) Mutants in well: 1 gene ID: DDB_G0290213,DDB_G0290215

Annotations

Strain descriptor: [vps45/DDB_G0290215]- Strain name: GWDI_68_G_5 genotype: axeA1,axeB1,axeC1, [vps45/DDB_G0290215]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutant, insertion is within 500 bp of start codons of two neighboring genes oriented in opposite direction; potentially affected genes are vps45 and _DDBG0290215, insertion at position 3,805,571, chr 5 at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): vps45,DDB_G0290215 Reference: doi:10.1101/582072

Multiple mutants

intergenic_up insertion :heavy_check_mark:

Example

Strain descriptor: [DDB_G0286487]- Strain name: GWDI_202_B_2 Chr: DDB0232431 Position: 4,555,710 Orientation: - Insert: C6 (CATG) Mutants in well: 9 gene ID: DDB_G0286487

Annotations

Strain descriptor: [DDB_G0286487]- Strain name: GWDI_202_B_2 genotype: _axeA1,axeB1,axeC1, [DDBG0286487]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) mutants, insertions are within 500 bp of start codon; nearest gene DDB_G0286487 is upstream of the insertions sites (Crick strand); insertion at position 4,555,710, Chr 4 at CATG genomic sites; - orientation; this stock contains 9 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): DDB_G0286487 Reference: doi:10.1101/582072

intergenic_down insertion :heavy_check_mark:

Example

From table: Strain descriptor: [mdhB]- Strain name: GWDI_203_B_2 Chr: DDB0232433 Position: 1,825,857 Orientation: - Insert: C6 (CATG) Mutants in well: 2 gene ID: DDB_G0292600

Annotations

St descriptor: [mdhB]- Strain name: GWDI_203_B_2 genotype: axeA1,axeB1,axeC1,[mdhB]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) mutants, insertions are within 500 bp of start codon; nearest gene mdhB is downstream of the insertions sites (Watson strand); insertion at position 1,825,857, Chr 6 at CATG genomic sites; - orientation; this stock contains 2 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): mdhB Reference: doi:10.1101/582072

intergenic_both insertion :heavy_check_mark:

Example

Stran descriptor: [DDB_G0283189/DDB_G0283191]- Strain name: GWDI_370_D_5 Chr: DDB0232431 Position: 394,235 Orientation: + Insert: C8 (CATG) Mutants in well: 3 gene ID: DDB_G0283189,DDB_G0283191

Annotations

Strain descriptor: [DDB_G0283189/DDB_G0283191]- Strain name: GWDI_370_D_5 genotype: _axeA1,axeB1,axeC1,[DDB_G0283189/DDBG0283191]-,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutants, insertions within 500 bp of start codons of two neighboring genes oriented in opposite direction; potentially affected genes are DDB_G0283189 and DDB_G0283191, insertion at position 3,805,571, chr 4 at CATG genomic sites; + orientation; this stock contains 3 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): DDB_G0283189,DDB_G0283191 Reference: doi:10.1101/582072

intergenic insertions that are not in vicinity of an annotated gene :heavy_check_mark:

Example

Strain descriptor: GWDI_203_D_2 Strain name: GWDI_203_D_2 Chr: DDB0237465 Position: 64,993 Orientation: + Insert: C6 (CATG) Mutants in well: 2 gene ID: none

Annotations

Strain descriptor: GWDI_203_D_2 Strain name: GWDI_203_D_2 genotype: axeA1,axeB1,axeC1,GWDI_203_D_2, [bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) intergenic mutants, not near a known coding region; insertion at position 64,993, extrachromosomal ribosomal RNA, at GATC genomic sites; + orientation; this stock contains 2 individual mutants.

Genetic Modification: exogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s): None Reference: doi:10.1101/582072

NOTES: This is not on chr 1-6, but on ribosomal RNA. Below is a list of chromosomal IDs and how to translate them in strain summary The genetic modification changes hear from endogenous insertion to exogenous insertion!!

cybersiddhu commented 3 years ago

Records with following lines are skipped "GWDI_11_E_2","DDB0237465","84,913","G1","3","-","NA","NA","#N/A"

pfey03 commented 3 years ago

the N/A mutants I will add manually once it's possible. Or maybe by adding a table, that would be cool

pfey03 commented 3 years ago

NA Mutants

1. Single NA mutant :heavy_check_mark:

From table: Strain descriptor: GWDI_18_F_9 Strain name: GWDI_18_F_9 Chr: DDB0237465 Position: 84,913 Orientation: + Insert: G1 (GATC) Mutants in well: 1 gene ID: NA

Annotations:

Strain descriptor: GWDI_18_F_9 Strain name: GWDI_18_F_9 genotype: _axeA1,axeB1,axeC1,GWDI_18_F9,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) GWDI_18_F_9 mutant; insertion at position 84,913, extrachromosomal ribosomal RNA, at GATC genomic sites; + orientation.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s):
Reference: doi:10.1101/582072

2. Multiple N/A Mutant :heavy_check_mark:

From table: Strain descriptor: GWDI_11_E_2 Strain name: GWDI_11_E_2 Chr: DDB0237465 Position: 84,913 Orientation: + Insert: G1 (GATC) Mutants in well: 3 gene ID: -

Annotations

Strain descriptor: GWDI_11_E_2-c Strain name: GWDI_11_E_2 genotype: _axeA1,axeB1,axeC1,GWDI_11_E2-c,[bsRcas],bsR

Strain summary: Genome Wide Dictyostelium Insertion bank (GWDI) GWDI_11_E_2-c mutant; insertion at position 84,913, extrachromosomal ribosomal RNA, at GATC genomic sites; + orientation; this stock contains 3 individual mutants.

Genetic Modification: endogenous insertion Strain Characteristics: blasticidin resistant, axenic, mutant Parental strain: AX4(DBS0351471) Plasmid: Blasticidin S resistance cassette Mutagenesis Method: Restriction Enzyme-Mediated Integration Species: Dictyostelium discoideum Depositor: Amy Baldwin (Hardwood and Thompson labs) Associated gene(s):
Reference: doi:10.1101/582072