8 research outputs found

    Premessa

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    Additional file 1: Table S1. The chromosome, position, reference and alternative bases for the 193 SNVs and 17 indels that were verified as being true somatic calls are listed here. The variant read frequency observed in the verification sequencing is also listed here

    Additional file 2: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

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    Figure S1. PTEN protein abundance of breast cancer cell lines. (A) Western blots showing PTEN and actin (loading control) abundance in 19 breast cancer cell lines. (B) Scatter plot of RPPA-measured PTEN abundance reported by Marcotte et al. [17] versus PTEN abundance that we quantified through densitometric analysis of western blot bands in (A). Cell lines were categorized as PTEN-expressing (in black) or PTEN-deficient (in red) based on PTEN protein abundance. (PNG 201 kb

    Additional file 1: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

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    Table S1. Growth media for breast cancer cell lines used in study. Table S2. PTEN protein abundance in cell lines quantified by western blot. Table S3. Classification of breast cancer cell lines as PTEN+ or PTEN- based on PTEN protein abundance. Table S4. Primary screen results and hits. Table S5. Details of shRNA library used in secondary screen. Table S6. shRNA barcode counts from secondary screen in 11 cell lines. Table S7. Fold-change in shRNA barcode count for 11 cell lines. Table S8. shRNAs used in ATARiS gene solutions, with ATARiS consistency scores per shRNA. Table S9. ATARiS gene level scores for 11 cell lines. Table S10. Secondary screen results and hits. Table S11. Screen results (zGARP scores) from Breast Functional Genomics Dataset. Table S12. Screen results (DEMETER scores) from Cancer Dependency Map Dataset. Table S13. Screen results (z scores) from Kinase Dependency Profiles Dataset. (XLSX 22688 kb

    <i>USP9X</i> splice site mutation in Patient 3.

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    <p>(A) IGV snapshot of c.1986-1G>T variant in <i>USP9X</i> (Chr X:41025124, hg19). (B) Sanger sequencing confirmation of c.1986-1G>T variant (NM_001039590.2) in Patient 3. (C) Partial cDNA sequence showing expression of both the wild type and low level mutant allele with the 13 bp deletion. (D) Partial cDNA sequence of control patient. (E) Partial genomic DNA sequence of exon 15 (uppercase, blue) and intron 14 (lowercase, red) of <i>USP9X</i> gene showing the c.1986-1G>T variant (arrow) and the 13 bp deletion (r.1986_1998delATTTTTATTGAAG) which is underlined.</p

    <i>L1CAM</i> splice site mutation in Patient 1.

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    <p>(A) IGV snapshot of c.3458-1G>A variant in the <i>L1CAM</i> gene (Chr X:153129005, hg19). (B) Sanger sequencing confirmation of c.3458-1G>A variant (NM_000425.3) (C) Partial cDNA sequence showing the mutant allele with the 5 bp deletion.</p
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