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chore: table of CCLE cell line info
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@jhrcook
jhrcook committed Jun 22, 2020
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20 changes: 20 additions & 0 deletions src/90_30_synlet-for-shikha.R
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Expand Up @@ -40,6 +40,26 @@ coad_dep_map_ids <- synlet_data %>%
unique()


# Write out table of KRAS mutations in CCLE for Shikha.
ccle_cell_lines %>%
filter(!is.na(cancer)) %>%
left_join(ccle_kras_muts, by = "dep_map_id") %>%
select(dep_map_id, ccle_name, stripped_cell_line_name,
cancer, lineage, lineage_subtype, lineage_sub_subtype,
lineage_molecular_subtype, disease, disease_subtype,
primary_or_metastasis,
sex, age, culture_medium,
kras_allele = allele,
kras_codon = codon,
kras_cn = copy_number) %>%
distinct() %>%
mutate(kras_allele = ifelse(is.na(kras_allele), "WT", kras_allele),
kras_codon = ifelse(is.na(kras_codon), "WT", kras_codon),
kras_copynumber = ifelse(is.na(kras_cn), 2, kras_cn)) %>%
filter(cancer == "COAD") %>%
write_tsv(table_path(TABLES_DIR, "CCLE-cell-line-information.tsv"))


#### ---- Basic statistical testing ---- ####


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83 changes: 83 additions & 0 deletions tables/90_30_synlet-for-shikha/CCLE-cell-line-information.tsv
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dep_map_id ccle_name stripped_cell_line_name cancer lineage lineage_subtype lineage_sub_subtype lineage_molecular_subtype disease disease_subtype primary_or_metastasis sex age culture_medium kras_allele kras_codon kras_cn kras_copynumber
ACH-000003 CACO2_LARGE_INTESTINE CACO2 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma NA Male NA NA WT WT NA 2
ACH-000007 LS513_LARGE_INTESTINE LS513 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male 63 RPMI 1640 + 10% FBS G12D 12 2 2
ACH-000009 C2BBE1_LARGE_INTESTINE C2BBE1 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male 72 D10+ITS+Glu WT WT NA 2
ACH-000089 NCIH684_LARGE_INTESTINE NCIH684 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 55 NA G12D 12 2 2
ACH-000202 COLO320_LARGE_INTESTINE COLO320 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 55 RPMI-1640: 10%FBS WT WT NA 2
ACH-000236 SW1417_LARGE_INTESTINE SW1417 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 53 NA WT WT NA 2
ACH-000249 CL11_LARGE_INTESTINE CL11 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male NA DMEM/F-12 (1:1): 80.0% Q61H 61 2 2
ACH-000249 CL11_LARGE_INTESTINE CL11 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male NA DMEM/F-12 (1:1): 80.0% other WT 2 2
ACH-000252 LS1034_LARGE_INTESTINE LS1034 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male 54 RPMI; 10% FBS A146T 146 2 2
ACH-000253 COLO201_LARGE_INTESTINE COLO201 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 70 RPMI-1640: 90.0% WT WT NA 2
ACH-000286 SNU1033_LARGE_INTESTINE SNU1033 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 45 RPMI-1640: 90.0% G12D 12 2 2
ACH-000296 OUMS23_LARGE_INTESTINE OUMS23 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male NA DMEM; 10% FBS; WT WT NA 2
ACH-000342 CL14_LARGE_INTESTINE CL14 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma NA Male NA NA WT WT NA 2
ACH-000350 COLO678_LARGE_INTESTINE COLO678 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 69 RPMI-1640: 10%FBS G12D 12 2 2
ACH-000360 NCIH508_LARGE_INTESTINE NCIH508 COAD colorectal caecum_adenocarcinoma NA NA colon/colorectal cancer caecum adenocarcinoma Metastasis Male 55 RPMI; 10% FBS WT WT NA 2
ACH-000381 T84_LARGE_INTESTINE T84 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 72 DMEM:F12(1:1); 5%FBS; 2mMGlutamine G13D 13 2 2
ACH-000400 SKCO1_LARGE_INTESTINE SKCO1 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 65 NA G12V 12 2.596629179972775 2.596629179972775
ACH-000403 NCIH747_LARGE_INTESTINE NCIH747 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 69 RPMI; 10% FBS G13D 13 2 2
ACH-000412 SNU1197_LARGE_INTESTINE SNU1197 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male 70 NA G12D 12 2 2
ACH-000421 SW837_LARGE_INTESTINE SW837 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male 53 RPMI; 10% FBS G12C 12 2 2
ACH-000467 HCC56_LARGE_INTESTINE HCC56 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma NA Unknown NA EMEM; 10% FBS G12V 12 2 2
ACH-000470 SW1463_LARGE_INTESTINE SW1463 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 66 RPMI-1640: 10%FBS G12C 12 2 2
ACH-000489 SW1116_LARGE_INTESTINE SW1116 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Male 73 NA G12A 12 2 2
ACH-000491 NCIH716_LARGE_INTESTINE NCIH716 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 33 RPMI; 10% FBS other WT 2 2
ACH-000501 LS123_LARGE_INTESTINE LS123 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 65 NA G12S 12 2 2
ACH-000532 SNU61_LARGE_INTESTINE SNU61 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 48 NA G12D 12 2 2
ACH-000552 HT29_LARGE_INTESTINE HT29 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 44 McCoy's 5A; 10% FBS WT WT NA 2
ACH-000565 RCM1_LARGE_INTESTINE RCM1 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 73 Ham F-12: 40.0%, RPMI-1640: 40.0% G12V 12 2 2
ACH-000651 SW620_LARGE_INTESTINE SW620 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 51 Leibovitz's L-15; 10%FBS G12V 12 3.067188855179383 3.067188855179383
ACH-000680 SW948_LARGE_INTESTINE SW948 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Primary Female 81 RPMI-1640: 90.0% Q61L 61 2 2
ACH-000683 SNU503_LARGE_INTESTINE SNU503 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 52 RPMI;10% FBS; WT WT NA 2
ACH-000708 SNU283_LARGE_INTESTINE SNU283 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Female 62 NA WT WT NA 2
ACH-000722 SNUC1_LARGE_INTESTINE SNUC1 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Male 71 NA WT WT NA 2
ACH-000798 CL40_LARGE_INTESTINE CL40 COAD NA NA NA NA colon/colorectal cancer colorectal carcinoma Primary Female NA DMEM/F-12 (1:1): 80.0% G12D 12 2 2
ACH-000820 SW403_LARGE_INTESTINE SW403 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Female 51 Leibovitz's L-15; 10%FBS G12V 12 2 2
ACH-000842 SW480_LARGE_INTESTINE SW480 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male 50 NA G12V 12 2 2
ACH-000895 CL34_LARGE_INTESTINE CL34 COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Female NA NA WT WT NA 2
ACH-000926 HT55_LARGE_INTESTINE HT55 COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Unknown NA E20+Glu+NEAA WT WT NA 2
ACH-000935 MDST8_LARGE_INTESTINE MDST8 COAD NA NA NA NA colon/colorectal cancer colon carcinoma NA Unknown NA DMEM; 10% FBS;2mM Glutamine WT WT NA 2
ACH-000943 RKO_LARGE_INTESTINE RKO COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Unknown NA MEM10 WT WT NA 2
ACH-000950 LOVO_LARGE_INTESTINE LOVO COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Metastasis Male 56 F12; 10% FBS; 2mMGlutamax-1; 1500mg/L NaHCO3 (2 vols of 100X) G13D 13 2 2
ACH-000955 SNU407_LARGE_INTESTINE SNU407 COAD NA NA NA NA colon/colorectal cancer colon carcinoma Metastasis Male 37 NA G12D 12 2 2
ACH-000957 LS180_LARGE_INTESTINE LS180 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Female 58 EMEM, 10%FBS G12D 12 2 2
ACH-000958 SW48_LARGE_INTESTINE SW48 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Female 82 RPMI-1640: 90.0% WT WT NA 2
ACH-000959 SNUC4_LARGE_INTESTINE SNUC4 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma NA Male 35 RPMI; 10% heat inactive fetal bovine serum (FBS); L-glutamine (300mg/L), 25mM HEPES and 25mM NaHCO3 WT WT NA 2
ACH-000963 CCK81_LARGE_INTESTINE CCK81 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Metastasis Female NA EMEM, 10%FBS WT WT NA 2
ACH-000967 SNUC2A_LARGE_INTESTINE SNUC2A COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Female 43 NA G12D 12 2 2
ACH-000969 KM12_LARGE_INTESTINE KM12 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Unknown NA R10 WT WT NA 2
ACH-000970 SNUC5_LARGE_INTESTINE SNUC5 COAD NA NA NA NA colon/colorectal cancer colorectal adenocarcinoma NA Female 77 NA WT WT NA 2
ACH-000971 HCT116_LARGE_INTESTINE HCT116 COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Male NA NA G13D 13 2 2
ACH-000982 GP2D_LARGE_INTESTINE GP2D COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Female 71 NA G12D 12 2 2
ACH-000985 LS411N_LARGE_INTESTINE LS411N COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Male 32 NA WT WT NA 2
ACH-000986 HT115_LARGE_INTESTINE HT115 COAD NA NA NA NA colon/colorectal cancer colon carcinoma NA Unknown NA DMEM;15%FBS, 2mMGlutamax-1 WT WT NA 2
ACH-000989 SNU175_LARGE_INTESTINE SNU175 COAD NA NA NA NA colon/colorectal cancer colorectal carcinoma, mucinous Metastasis Female 56 RPMI; 10% FBS other WT 2 2
ACH-000991 SNU81_LARGE_INTESTINE SNU81 COAD NA NA NA NA colon/colorectal cancer colorectal adenocarcinoma NA Male 53 NA A146T 146 2 2
ACH-000997 HCT15_LARGE_INTESTINE HCT15 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male NA NA G13D 13 2 2
ACH-000998 CW2_LARGE_INTESTINE CW2 COAD NA NA NA NA colon/colorectal cancer colorectal carcinoma Primary Female 55 RPMI;10% FBS; other WT 2 2
ACH-000999 SNU1040_LARGE_INTESTINE SNU1040 COAD NA NA NA NA colon/colorectal cancer colorectal carcinoma NA Male 34 RPMI; 10% FBS WT WT NA 2
ACH-001039 COLO205_LARGE_INTESTINE COLO205 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Metastasis Male 70 NA WT WT NA 2
ACH-001061 DLD1_LARGE_INTESTINE DLD1 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male NA RPMI 1640 + 10% FBS WT WT NA 2
ACH-001081 HCC2998_LARGE_INTESTINE HCC2998 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer NA NA Unknown NA NA A146T 146 2 2
ACH-001084 HCT8_LARGE_INTESTINE HCT8 COAD NA NA NA NA colon/colorectal cancer colorectal adenocarcinoma NA Male 67 NA WT WT NA 2
ACH-001091 HRT18_LARGE_INTESTINE HRT18 COAD NA NA NA NA colon/colorectal cancer colorectal adenocarcinoma NA Male 67 NA other WT 2 2
ACH-001091 HRT18_LARGE_INTESTINE HRT18 COAD NA NA NA NA colon/colorectal cancer colorectal adenocarcinoma NA Male 67 NA G13D 13 2 2
ACH-001199 SNUC2B_LARGE_INTESTINE SNUC2B COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma NA Female 43 NA G12D 12 2 2
ACH-001345 GP5D_LARGE_INTESTINE GP5D COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Female 71 DMEM + 10% FBS G12D 12 2 2
ACH-001399 SW626_LARGE_INTESTINE SW626 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer NA Metastasis Female 46 NA G12V 12 2 2
ACH-001454 C10_LARGE_INTESTINE C10 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male 71 scove_s Modified Dulbecco_s Medium, + 10% Fetal Bovine Serum (FBS) + 2 mM Glutamine WT WT NA 2
ACH-001456 C125PM_LARGE_INTESTINE C125PM COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Unknown NA NA K117N 117 2 2
ACH-001458 C75_LARGE_INTESTINE C75 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male 56 Iscove_s Modified Dulbecco_s Medium, + 10% Foetal Bovine Serum (FBS) + 2 mM Glutamine WT WT NA 2
ACH-001459 C80_LARGE_INTESTINE C80 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male 69 IMDM 10%FBS+ 2 mM Glutamine A146V 146 2 2
ACH-001460 C84_LARGE_INTESTINE C84 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male 67 IMDM; 10% FBS; 1% Glutamax G12A 12 2 2
ACH-001461 C99_LARGE_INTESTINE C99 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Male 69 Iscove_s Modified Dulbecco_s Medium, + 10% Foetal Bovine Serum (FBS) + 2 mM Glutamine WT WT NA 2
ACH-001786 SNU1544_LARGE_INTESTINE SNU1544 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma Primary Female 38 RPMI 1640 + 10% FBS with L-glutamine (300mg/L), 25mM HEPES and 25mM NaHCO3; Penicillin-streptomycin were added to culture media (final concentration, 100 U/mL) WT WT NA 2
ACH-001825 SW527_LARGE_INTESTINE SW527 COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma NA NA NA NA WT WT NA 2
ACH-002022 PMFKO14_LARGE_INTESTINE PMFKO14 COAD NA NA NA NA colon/colorectal cancer colon carcinoma Primary Female 51 NA WT WT NA 2
ACH-002023 TGBC18TKB_LARGE_INTESTINE TGBC18TKB COAD NA NA NA NA colon/colorectal cancer adenocarcinoma, papillotubular Primary Female 79 NA WT WT NA 2
ACH-002219 COLO320HSR_LARGE_INTESTINE COLO320HSR COAD NA NA NA NA colon/colorectal cancer colon adenocarcinoma NA Female 55 NA WT WT NA 2
ACH-002233 DIFI_LARGE_INTESTINE DIFI COAD NA NA NA NA colon/colorectal cancer colorectal carcinoma Metastasis NA NA NA WT WT NA 2
ACH-002287 NCIH630_LARGE_INTESTINE NCIH630 COAD NA NA NA NA colon/colorectal cancer colorectal carcinoma NA NA NA NA WT WT 22.533299999937693 22.533299999937693
ACH-002345 CAR1_LARGE_INTESTINE CAR1 COAD colorectal colorectal_adenocarcinoma NA NA colon/colorectal cancer adenocarcinoma Metastasis Unknown NA NA WT WT NA 2
ACH-002394 GEO_LARGE_INTESTINE GEO COAD NA NA NA NA colon/colorectal cancer colon carcinoma NA NA NA NA G12A 12 2 2

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