Functional mapping of yeast genomes by saturated transposition
- ETH Zurich, Switzerland
- University of Fribourg, Switzerland
Figures
Figure 1 with 3 supplements
Principle of the method.
(A) Outline of the experimental procedure. Left, the transposon (green) can insert either into non-essential DNA (blue) and give rise to a clone, or into essential DNA (orange), in which case no …
Figure 1—figure supplement 1
Size distribution of the colonies appearing on SD +Galactose -Ade.
(A) Histogram of colony area for a randomly chosen sample of 402 colonies. (B) Example of picture of colonies (top) and segmentation thereof (bottom) used to calculate histogram in (A). Scale bar, 1 …
Figure 1—figure supplement 2
Genome-wide analysis of transposon insertion sites.
(A) Frequency plot of nucleotide composition around transposon insertion site. The strand is determined according to the orientation of the transposon insertion. Plot was calculated with a random …
Figure 1—figure supplement 3
Transposon density in essential and non-essential genes.
As in Figure 1D–E, except that, for each gene, the transposon density (i.e. number of transposons divided by length of the gene) is shown.
Figure 2 with 5 supplements
Examples of genes showing partial loss of transposon coverage.
The grey level is proportional to the number of sequencing reads. Known functional domains are indicated. (A) Essential genes for which C-terminal truncations yield a viable phenotype. (B) Essential …
Figure 2—figure supplement 1
Detection of essential protein domains.
Top, algorithm to detect essential protein domains. This algorithm is implemented in Source code 2. For each gene, a score is computed as follows: the longest interval between transposon n and …
Figure 2—figure supplement 2
Transposon maps in the 100 highest scoring genes.
Grey scale indicates the number of sequencing reads as in Figure 2.
Figure 2—figure supplement 3
Transposon maps in the genes scoring 101 to 200.
https://doi.org/10.7554/eLife.23570.011
Figure 2—figure supplement 4
Transposon maps in the genes scoring 201 to 300.
https://doi.org/10.7554/eLife.23570.012
Figure 2—figure supplement 5
Transposon maps in the genes scoring 301 to 400.
https://doi.org/10.7554/eLife.23570.013
Figure 3
TAF3 and PRP45 can be truncated without visible effects on cell growth.
(A) A truncation of TAF3 was generated in a heterozygous diploid strain (left) by introduction of an HA tag and a G418-resistance cassette (HA kanr). The strain was tetrad dissected (middle). …
Figure 4 with 1 supplement
Genetic interaction analyses.
Libraries in panels B, C, E and G are displayed in the same order as in Figure 1C. (A) Comparison of the number of transposons inserted in each of the 6603 yeast CDSs in the wild-type (x-axis) and mm…
Figure 4—figure supplement 1
Volcano plots comparing libraries or combinations of libraries as indicated.
The calculated fold-change in transposon density between the two sets of libraries is plotted in log2 scale on the x-axis. The -log10(p-value) (computed using the Student’s t-test) is plotted on the …
Figure 5
Synthetic rescue of lethal phenotypes.
(A) Transposon coverage of CDC10 in the seven libraries. The coverage is increased in the dpl1Δ psd2Δ library. (B) Tetrad dissection of a PSD2/psd2Δ DPL1/dpl1Δ CDC10/cdc10Δ triple heterozygote at …
Figure 6 with 1 supplement
Detection of rapamycin resistant strains.
(A) Comparison of the number of sequencing reads mapping to each of the 6603 yeast CDSs in rapamycin-untreated (x-axis) and -treated (y-axis) libraries. Note the difference in scale between both …
Figure 6—figure supplement 1
A) Transposon coverage of the PIB2 gene.
Top row is the rapamycin-treated library and rows below are presented as in Figures 2–5. The gray scale has been adjusted to account for the large number of sequencing reads mapping in the 5’ region …
Tables
Table 1
Characteristics of the libraries
| Library | Number of colonies | Reads mapped | Transposons mapped | Median read per transposon | Number of MiSeq runs | Overlap between MiSeq runs |
|---|---|---|---|---|---|---|
| Wild-type 1 | ~1.6×106 | 31794831 | 284162 | 22 | 2* | 54%, 88%* |
| Wild-type 2 | ~2.4×106 | 15303285 | 258568 | 12 | 1 | NA |
| VPS13(D716H) | ~4.7×106 | 24958456 | 414114 | 13 | 2† | 41%, 42%† |
| Mmm1Δ VPS13(D716H) | ~1.9×106 | 17799948 | 303323 | 12 | 1 | NA |
| dpl1Δ | ~2.3×106 | 15077156 | 401126 | 8 | 1 | NA |
| dpl1Δ psd2Δ | ~2.9×106 | 11649561 | 363179 | 9 | 1 | NA |
| YEN1on | ~2.8×106 | 9517877 | 495125 | 6 | 1 | NA |
| Wild-type 2 + rapamycin | ~2.4×106 | 9664956 | 169322 | 9 | 1 | NA |
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* The harvested library was grown in two flasks, one at 30°C and the other at 37°C. DNA was extracted separately from the two cultures and sequenced in two separate MiSeq runs
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† The library was harvested as ten subpools, which were grown in ten separate flasks. DNA was extracted separately. In one case, DNA from all ten subpools was pooled and processed to sequencing in one MiSeq run. In the other case, DNAs were kept separate and processed until the PCR step (1 × 100 µl PCR by subpool). PCR products were pooled and sequenced as another MiSeq run.
Table 2
Yeast strains used in this study.
| Name | Parent | Genotype | Reference |
|---|---|---|---|
| CWY1 | BY4723 | MATa his3Δ0 ura3Δ0 ade2:Ds-1 | Weil and Kunze (2000) |
| ByK157 | BY4743 | MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 VPS13(D716H) | Lang et al. (2015b) |
| ByK352 | BY4741 | MATa his3Δ1 leu2Δ0 met17Δ0 ura3Δ0 ade2Δ::HIS3* | This study |
| ByK484 | By4742 | MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 ade2Δ::HIS3* | This study |
| ByK485 | ByK352 and ByK484 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* | This study |
| ByK446 | ByK157 | MATα his3Δ1 leu2Δ0 ura3Δ0 ade2Δ::HIS3* VPS13(D716H) | This study |
| ByK528 | ByK446 | MATα his3Δ1 leu2Δ0 ura3Δ0 ade2Δ::HIS3* VPS13(D716H) mmm1Δ::KanMX6 | This study |
| ByK530 | ByK352 | MATa his3Δ1 leu2Δ0 met17Δ0 ura3Δ0 ade2Δ::NAT* dpl1Δ::KanMX6 | This study |
| ByK533 | ByK352 | MATa his3Δ1 leu2Δ0 met17Δ0 ura3Δ0 ade2Δ::HIS3* psd2Δ::KanMX6 dpl1Δ::NAT | This study |
| ByK576 | ByK485 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* prp45Δ::KanMX6/PRP45 | This study |
| ByK579 | ByK485 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* PRP451-462-HA(KanMX6)/ PRP45 | This study |
| ByK583 | ByK485 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* taf3Δ::KanMX6/TAF3 | This study |
| ByK588 | ByK485 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* TAF31-270-HA(KanMX6)/ TAF3 | This study |
| ByK725 | ByK533 and ByK484 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* psd2Δ::KanMX6/PSD2 dpl1Δ::NAT /DPL1 | This study |
| ByK726 | ByK533 and ByK484 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* psd2Δ::KanMX6/PSD2 dpl1Δ::NAT /DPL1 | This study |
| ByK739 | ByK725 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* psd2Δ::KanMX6/PSD2 dpl1Δ::NAT /DPL1 cdc10Δ::URA3/CDC10 | This study |
| ByK740 | ByK726 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* psd2Δ::KanMX6/PSD2 dpl1Δ::NAT /DPL1 cdc10Δ::URA3/CDC10 | This study |
| ByK741 | ByK726 | MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met17Δ0/MET17 ura3Δ0/ura3Δ0 ade2Δ::HIS3*/ade2Δ::HIS3* psd2Δ::KanMX6/PSD2 dpl1Δ::NAT /DPL1 cdc10Δ::URA3/CDC10 | This study |
| YJM3916 | ByK352 | MATa his3Δ1 leu2Δ0 met17Δ0 ura3Δ0 ade2Δ::HIS3* YEN1on | This study |
| YL516 | BY4741/BY4742 | MATa his3Δ1 leu2Δ0 ura3Δ0 | Binda et al. (2009) |
| MB32 | YL516 | MATa his3Δ1 leu2Δ0 ura3Δ0 gtr1Δ::kanMX | Binda et al. (2009) |
| RKH106 | YL516 | MATa his3Δ1 leu2Δ0 ura3Δ0 pib2Δ::kanMX | This study |
| RKH241 | MB32 | MATa his3Δ1 leu2Δ0 ura3Δ0 gtr1Δ::kanMX gtr2Δ::hphMX4 | This study |
| NMY51 | his3∆200 trp1-901 leu2-3,112 ade2 LYS::(lexAop)4-HIS3 ura3::(lexAop)8- lacZ ade2::(lexAop)8-ADE2 GAL4 | Dualsystems Biotech AG |
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*ADE2 deleted −56 before ATG +62 after STOP with PCR primers #6 and #7 on pFA6a-His3MX6.
Table 3
Oligonucleotides used in this study.
| # | Original name | Sequence | Purpose |
|---|---|---|---|
| 1 | P5_MiniDs | AATGATACGGCGACCACCGAGATCTACtccgtcccgcaagttaaata | amplify library |
| 2 | MiniDs_P7 | CAAGCAGAAGACGGCATACGAGATacgaaaacgaacgggataaa | amplify library |
| 3 | 688_minidsSEQ1210 | tttaccgaccgttaccgaccgttttcatcccta | sequence library |
| 4 | ADE2Fwd | GGTTCGAGCTCCCTTTTGATGCGGAATTGAC | clone ADE2 MiniDS |
| 5 | ADE2Rev | GACCTGAGCTCTTACTGGATATGTATGTATG | clone ADE2 MiniDS |
| 6 | Ade2PriFwd | GTATAAATTGGTGCGTAAAATCGTTGGATCTCTCTTCTAAcggatccccgggttaattaa | delete ADE2 |
| 7 | Ade2PriRev | TATGTATGAAGTCCACATTTGATGTAATCATAACAAAGCCgaattcgagctcgtttaaac | delete ADE2 |
| 8 | Dpl1_Janke_S1 | AGCAAGTAGGCTAGCTTCTGTAAAGGGATTTTTCCATCTAATACAcgtacgctgcaggtcgac | delete DPL1 |
| 9 | Dpl1_Janke_S2 | GCACTCTCGTTCTTTAAATTATGTATGAGATTTGATTCTATATAGatcgatgaattcgagctcg | delete DPL1 |
| 10 | Psd2_pringle_F | GATGCTGTATCAATTGGTAAAGAATCCTCGATTTTCAGGAGCATCCAACGcgtacgctgcaggtcgac | delete PSD2 |
| 11 | Psd2_pringle_R | CTTGTTTGTACACGCTATAGTCTATAATAAAGTCTGAGGGAGATTGTTCATGatcgatgaattcgagctcg | delete PSD2 |
| 12 | TAF3_R1 | TGGATGAGATAATGACGAAAGAAAATGCAGAAATGTCGTTgaattcgagctcgtttaaac | TAF3 partial deletion |
| 13 | TAF3_aa90_F2 | AGGTATTGTTAAGCCTACGAACGTTCTGGATGTCTATGATcggatccccgggttaattaa | TAF3 partial deletion |
| 14 | Taf3_Fwd | GGCAAGATGTGATCAGGACG | check TAF3 partial deletion |
| 15 | Taf3_Rev | TCTTGAAGAAGCGAAAGTACACT | check TAF3 partial deletion |
| 16 | TAF3_R1 | TGGATGAGATAATGACGAAAGAAAATGCAGAAATGTCGTTgaattcgagctcgtttaaac | TAF3 complete deletion |
| 17 | TAF3_aa1_ F1 | GAAAACAGCGATATCTTTGGGTCAATAGAGTTCCTCTGCTtgaggcgcgccacttctaaa | TAF3 complete deletion |
| 18 | PRP45_R1 | ACTCAAGCACAAGAATGCTTTGTTTTCCTAGTGCTCATCCTGGGCgaattcgagctcgtttaaac | PRP45 partial deletion |
| 19 | PRP45_aa154_F2 | AACGACGAAGTCGTGCCTGTTCTCCATATGGATGGCAGCAATGATcggatccccgggttaattaa | PRP45 partial deletion |
| 20 | PRP45_Fwd | AGGTTGTAGCACCCACAGAA | check PRP45 partial deletion |
| 21 | PRP45_Rev | CAATCATCACACCTCAGCGA | check PRP45 partial deletion |
| 22 | PRP45_R1 | ACTCAAGCACAAGAATGCTTTGTTTTCCTAGTGCTCATCCTGGGCgaattcgagctcgtttaaac | PRP45 complete deletion |
| 23 | PRP45_aa1_F1 | GCTCTGAGCCGAGAGGACGTATCAGCAACCTCAACCAAATtgaggcgcgccacttctaaa | PRP45 complete deletion |
| 24 | CDC10-Ura3_fwd | AAGGCCAAGCCCCACGGTTACTACAAGCACTCTATAAATATATTAtgacggtgaaaacctctgac | CDC10 complete deletion |
| 25 | URA3-CDC10_rev | TTCTTAATAACATAAGATATATAATCACCACCATTCTTATGAGATtcctgatgcggtattttctcc | CDC10 complete deletion |
| 26 | OJM370 | ATGGGTGTCTCACAAATATGGG | Amplify YEN1 |
| 27 | OJM371 | TTCAATAGTGCTACTGCTATCAC | Amplify YEN1 |
| 28 | OJM372 | TTCAATAGTGCTACTGCTATCACTGTCACAGGCTCAAACCGGTCGACTG TTCGTACGCTGCAGGTCGAC | Delitto perfetto on YEN1 |
| 29 | OJM373 | ATGGGTGTCTCACAAATATGGGAATTTTTGAAGCCATATCTGCAAGATTCCCGCGCGTTGGCCGATTCAT | Delitto perfetto on YEN1 |
| 30 | o3958 | gacggtatcgataagcttgatatcgGCGCTGGCATCTTTAATCTC | PIB2 cloning |
| 31 | o3959 | actagtggatcccccgggctgcaggTGCTTGGATCCTTCTTGGTC | PIB2 cloning |
| 32 | o3224 | TAATA CGACT CACTA TAGGG | various PIB2 truncations |
| 33 | o3225 | ATTAA CCCTC ACTAA AGGGA A | various PIB2 truncations |
| 34 | o4034 | atctagttcagggttcgacattctggtctccactac | PIB2165-635 truncation |
| 35 | o4010 | gtagtggagaccagaatgtcgaaccctgaactagat | PIB2165-635 truncation |
| 36 | o4012 | tagtggagaccagaatgttaccgcagcctgct | PIB2304-635 truncation |
| 37 | o4035 | tcaaattagaactagcattcattctggtctccactacaactgtg | PIB2221-635 truncation |
| 38 | o4011 | cacagttgtagtggagaccagaatgaatgctagttctaatttga | PIB2221-635 truncation |
| 39 | o4062 | atagttggtattaagttgattctcattctggtctccactacaactg | PIB2426-635 truncation |
| 40 | o3996 | cagttgtagtggagaccagaatgagaatcaacttaataccaactat | PIB2426-635 truncation |
| 41 | o4063 | cgtgtttgcgttatggttgtcgctgttcggaataga | PIB2Δ426-532 truncation |
| 42 | o3997 | tctattccgaacagcgacaaccataacgcaaacacg | PIB2Δ426-532 truncation |
| 43 | o4064 | cacagagccgataacactcgtggttgaaaggttctc | PIB2Δ533-620 truncation |
| 44 | o3998 | gagaacctttcaaccacgagtgttatcggctctgtg | PIB2Δ533-620 truncation |
| 45 | o4065 | gtctcgcaaaaaatgttcatcagcccaaaacatcattaccttct | PIB21-620 truncation |
| 46 | o3999 | agaaggtaatgatgttttgggctgatgaacattttttgcgagac | PIB21-620 truncation |
| 47 | o1440 | GCTAGAGCGGCCATTACGGCCCCGGAGATTTATGGACCTC | KOG1 cloning into pPR3N |
| 48 | o1442 | CGATCTCGGGCCGAGGCGGCCTCAAAAATAATCAATTCTCTCGTC | KOG1 cloning into pPR3N |
| 49 | o3787 | GCTAGAGCGGCCATTACGGCC GAATTGTACAAATCTAGAACTAGT | cloning PIB2 fragments into pCabWT* |
| 50 | o3788 | CGATCTCGGGCCGAGGCGGCCAA GAAACTACTCCAATTCCAGTTTGC | cloning PIB2 fragments into pCabWT* |
| 51 | o3872 | CGATCTCGGGCCGAGGCGGCCAAGCCCAAAACATCATTACCTTCTTCT | cloning PIB2 fragments into pCabWT* |
| 52 | o3871 | CGATCTCGGGCCGAGGCGGCCAAATCTTCGCCCTCCTCAACGT | cloning PIB2 fragments into pCabWT* |
| 53 | o3870 | CGATCTCGGGCCGAGGCGGCCAAGTTGATTCTGTCGCTGTTCG | cloning PIB2 fragments into pCabWT* |
| 54 | o3933 | GCTAGAGCGGCCATTACGGCCAGGAAGAAATTACGCAATTACTAC | cloning PIB2 fragments into pCabWT* |
| 55 | o3934 | GCTAGAGCGGCCATTACGGCC AGTGTTATCGGCTCTGTGCC | cloning PIB2 fragments into pCabWT* |
| 56 | o3868 | CGATCTCGGGCCGAGGCGGCCAAATTAGTGCTCGAAGCAGGCT | cloning PIB2 fragments into pCabWT* |
| 57 | o3867 | CGATCTCGGGCCGAGGCGGCCAAGTCATCCGTGAATGGCAACG | cloning PIB2 fragments into pCabWT* |
| 58 | o3866 | CGATCTCGGGCCGAGGCGGCCAAGCCTGCCCCTGTTGAGCTCT | cloning PIB2 fragments into pCabWT* |
| 59 | o3865 | CGATCTCGGGCCGAGGCGGCCAAGTCAGCACCGCTTTCCTCAT | cloning PIB2 fragments into pCabWT* |
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Oligonucleotides #1 and #2, ordered as PAGE-purified and lyophilized, are resuspended at 100 μM in water. Oligonucleotide #3, ordered as HPLC-purified and lyophilized, is resuspended at 100 μM in water and distributed into single-use aliquots.
Table 4
Plasmids used in this study.
| Name | Parent | Description | Reference |
|---|---|---|---|
| pBK257 | pWL80R_4x | CEN/URA3, carries MiniDs in ADE2 and hyperactive Ac transposase under GAL1 promoter | This study |
| pWL80R_4x | CEN/URA3, carries hyperactive Ac transposase under GAL1 promoter | Lazarow et al. (2012) | |
| pCORE-UH | Delitto pefetto URA3 cassette | Storici and Resnick (2003) | |
| pJM7 | pENTRY-YEN1ON | This study | |
| pRS413 | CEN/HIS3, empty vector | Sikorski and Hieter, 1989 | |
| pRS415 | CEN/LEU2, empty vector | Sikorski and Hieter, 1989 | |
| pRS416 | CEN/URA3, empty vector | Sikorski and Hieter, 1989 | |
| p1822 | pRS413 | CEN/HIS3, GTR1 | This study |
| p1451 | pRS415 | CEN/LEU2, GTR2 | This study |
| p1821 | pRS413 | CEN/HIS3, GTR1Q65L | This study |
| p1452 | pRS415 | CEN/LEU2, GTR2S23L | This study |
| p3084 | pRS416 | CEN/URA3, PIB2 | This study |
| p3099 | p3084 | CEN/URA3, PIB2165-635 | This study |
| p3097 | p3084 | CEN/URA3, PIB2304-635 | This study |
| p3101 | p3084 | CEN/URA3, PIB2221-635 | This study |
| p3253 | pRS426 | 2 μ/URA3, PIB2 | This study |
| p3255 | pRS426 | 2 μ/URA3, PIB2165-635 | This study |
| p3163 | p3084 | CEN/URA3, PIB2426-635 | This study |
| p3153 | p3084 | CEN/URA3, PIB2Δ426-532 | This study |
| p3154 | p3084 | CEN/URA3, PIB2Δ533-620 | This study |
| p3156 | p3084 | CEN/URA3, PIB21-620 | This study |
| pPR3N | 2 μ/TRP1, NubG-HA | Dualsystems Biotech AG | |
| pCabWT | CEN/LEU2, Aβ-Cub-LexA-VP16 | Dualsystems Biotech AG | |
| p3081 | pPR3N | 2 μ/TRP1, NubG-HA-KOG1 | This study |
| p2966 | pCabWT | CEN/LEU2, Aβ-PIB2-Cub-LexA-VP16 | This study |
| p3002 | pCabWT | CEN/LEU2, Aβ-PIB21-620-Cub-LexA-VP16 | This study |
| p3007 | pCabWT | CEN/LEU2, Aβ-PIB21-550-Cub-LexA-VP16 | This study |
| p3001 | pCabWT | CEN/LEU2, Aβ-PIB21-428-Cub-LexA-VP16 | This study |
| p3051 | pCabWT | CEN/LEU2, Aβ-PIB2440-550-Cub-LexA-VP16 | This study |
| p3054 | pCabWT | CEN/LEU2, Aβ-PIB2556-620-Cub-LexA-VP16 | This study |
| p3052 | pCabWT | CEN/LEU2, Aβ-PIB2621-635-Cub-LexA-VP16 | This study |
| p3000 | pCabWT | CEN/LEU2, Aβ-PIB21-312-Cub-LexA-VP16 | This study |
| p2987 | pCabWT | CEN/LEU2, Aβ-PIB2304-635-Cub-LexA-VP16 | This study |
| p2999 | pCabWT | CEN/LEU2, Aβ-PIB21-162-Cub-LexA-VP16 | This study |
| p2986 | pCabWT | CEN/LEU2, Aβ-PIB2165-635-Cub-LexA-VP16 | This study |
| p2998 | pCabWT | CEN/LEU2, Aβ-PIB21-101-Cub-LexA-VP16 | This study |
| p2991 | pCabWT | CEN/LEU2, Aβ-PIB2102-635-Cub-LexA-VP16 | This study |
| p2997 | pCabWT | CEN/LEU2, Aβ-PIB21-49-Cub-LexA-VP16 | This study |
| p2990 | pCabWT | CEN/LEU2, Aβ-PIB250-635-Cub-LexA-VP16 | This study |
Additional files
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Supplementary file 1
Processed dataset containing (1) the position and number of reads for all transposons in each library (in the WIG format),
Processed dataset - Dpl1del.wig
Processed dataset - Mmm1Del_Vps13D716H.wig
Processed dataset - Psd2Del_Dpl1del.wig
Processed dataset - V13D716H.wig
Processed dataset - WildType1.wig
Processed dataset - WildType2.wig
Processed dataset - WT_plus_rapamycin.wig
Processed dataset - Yen1on.wig
summaries of the number of transposon and number of reads per gene, for all genes in each library (in the TXT format).
Processed dataset - Dpl1del_pergene.txt
Processed dataset - Mmm1Del_Vps13D716H_pergene.txt
Processed dataset - Psd2Del_Dpl1del_pergene.txt
Processed dataset - V13D716H_pergene.txt
Processed dataset - WildType1_pergene.txt
Processed dataset - WildType2_pergene.txt
Processed dataset - WT_plus_rapamycin_pergene.txt
Processed dataset - Yen1on_pergene.txt
- https://doi.org/10.7554/eLife.23570.023
-
Supplementary file 2
Table of genes appearing as essential in our analysis (i.e., their density of transposon is below 1/400 bp), but were not previously annotated as essential.
The likely explanation for the low transposon density is written in column B for each gene.
- https://doi.org/10.7554/eLife.23570.024
-
Supplementary file 3
Data computed to draw the volcano plots (Figure 4—figure supplement 1)
- https://doi.org/10.7554/eLife.23570.025
-
Source code 1
MatLab Script 1.
- https://doi.org/10.7554/eLife.23570.026
-
Source code 2
MatLab Script 2.
- https://doi.org/10.7554/eLife.23570.027
