title: 13C_M_1332


title: 13C_M_1319

status: Public on May 22 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 13C_M_1327


title: 13C_M_1311


title: 13C_M_1300


title: 13C_M_1306


title: 13C_M_1313


title: 13C_M_1295


title: 13C_M_1293


title: 13C_M_1307


title: 13C_M_1291


title: 13C_M_1299


title: 13C_M_1304


title: 13C_M_1298


title: 13C_M_1292


title: 13C_M_1294


title: 13C_M_1312


title: 13C_M_1316


title: 13C_M_1305


title: 13C_M_1289


title: 13C_M_1318


title: 13C_M_1301


title: 13C_M_1314


title: 13C_M_1310


title: 13C_M_1317


title: 13C_M_1302


title: 13C_M_1303


title: 13C_M_1296


title: 13C_M_1290


title: 13C_M_1315


title: 13C_M_1308


title: 13C_M_1297


title: 13C_M_1309


title: 13C_M_1288


title: 13C_M_1285


title: 13C_M_1287


title: 13C_M_1284


title: 13C_M_1269


title: 13C_M_1270


title: 13C_M_1271


title: 13C_M_1282


title: 13C_M_1280


title: 13C_M_1277


title: 13C_M_1268


title: 13C_M_1283


title: 13C_M_1267


title: 13C_M_1274


title: 13C_M_1263


title: 13C_M_1266


title: 13C_M_1281


title: 13C_M_1265


title: 13C_M_1286


title: 13C_M_1275


title: 13C_M_1262


title: 13C_M_1273


title: 13C_M_1279


title: 13C_M_1278


title: 13C_M_1261


title: 13C_M_1272


title: 13C_M_1260


title: 13C_M_1256


title: 13C_M_1254


title: 13C_M_1259


title: 13C_M_1257


title: 13C_M_1253


title: 13C_M_1252


title: 13C_M_1251


title: 13C_M_1246


title: 13C_M_1247


title: 13C_M_1250


title: 13C_M_1248


title: 13C_M_1245


title: 13C_M_1241


title: 13C_M_1236


title: 13C_M_1240


title: 13C_M_1237


title: 13C_M_1235


title: 13C_M_1229


title: 13C_M_1242


title: 13C_M_1233


title: 13C_M_1232


title: 13C_M_1239


title: 13C_M_1230


title: 13C_M_1244


title: 13C_M_1238


title: 13C_M_1234


title: 13C_M_1243


title: 13C_M_1227


title: 13C_M_1228


title: 13C_M_1226


title: 13C_M_1223


title: 13C_M_1225


title: 13C_M_1224


title: 13C_M_1222


title: 13C_M_1231


title: 13C_M_1220


title: 13C_M_1221


title: 13C_M_1218


title: 13C_M_1219


title: 13C_M_1217


title: 13C_M_1151


title: 13C_M_1145


title: 13C_M_1148


title: 13C_M_1149


title: 13C_M_1150


title: 13C_M_1144


title: 13C_M_1147


title: 13C_M_1143


title: 13C_M_1127


title: 13C_M_1136


title: 13C_M_1142


title: 13C_M_1133


title: 13C_M_1130


title: 13C_M_1137


title: 13C_M_1132


title: 13C_M_1138


title: 13C_M_1131


title: 13C_M_1126


title: 13C_M_1125


title: 13C_M_1124


title: 13C_M_1139


title: 13C_M_1135


title: 13C_M_1134


title: 13C_M_1140


title: 13C_M_1216


title: 13C_M_1122


title: 13C_M_1121


title: 13C_M_1141


title: 13C_M_1120


title: 13C_M_1119


title: 13C_M_1117


title: 13C_M_1116


title: 13C_M_1118


title: 13C_M_1114


title: 13C_M_1113


title: 13C_M_1111


title: 13C_M_1109


title: 13C_M_1107


title: 13C_M_1123


title: 13C_M_1106


title: 13C_M_1104


title: 13C_M_1110


title: 13C_M_1099


title: 13C_M_1103


title: 13C_M_1097


title: 13C_M_1105


title: 13C_M_1098


title: 13C_M_1101


title: 13C_M_1100


title: 13C_M_1096


title: 13C_M_1102


title: 13C_M_1095


title: 13C_M_1093


title: 13C_M_1094


title: 13C_M_1090


title: 13C_M_1089


title: 13C_M_1088


title: 13C_M_765


title: 13C_M_767


title: 13C_M_766


title: 13C_M_763


title: 13C_M_762


title: 13C_M_1108


title: 13C_M_761


title: 13C_M_760


title: 13C_M_758


title: 13C_M_757


title: 13C_M_755


title: 13C_M_1091


title: 13C_M_749


title: 13C_M_747


title: 13C_M_1092


title: 13C_M_742


title: 13C_M_751


title: 13C_M_750


title: 13C_M_753


title: 13C_M_752


title: 13C_M_740


title: 13C_M_744


title: 13C_M_745


title: 13C_M_746


title: 13C_M_743


title: 13C_M_748


title: 13C_M_741


title: 13C_M_759


title: 13C_M_737


title: 13C_M_736


title: 13C_M_734


title: 13C_M_738


title: 13C_M_735


title: 13C_M_733


title: 13C_M_732


title: 13C_M_730


title: 13C_M_731


title: 13C_M_754


title: 13C_M_729


title: 13C_M_727


title: 13C_M_724


title: 13C_M_725


title: 13C_M_722


title: 13C_M_721


title: 13C_M_720


title: 13C_M_712


title: 13C_M_713


title: 13C_M_718


title: 13C_M_723


title: 13C_M_739


title: 13C_M_716


title: 13C_M_714


title: 13C_M_719


title: 13C_M_717


title: 13C_M_711


title: 13C_M_728


title: 13C_M_706


title: 13C_M_699


title: 13C_M_709


title: 13C_M_703


title: 13C_M_702


title: 13C_M_707


title: 13C_M_701


title: 13C_M_726


title: 13C_M_698


title: 13C_M_700


title: 13C_M_710


title: 13C_M_697


title: 13C_M_696


title: 13C_M_708


title: 13C_M_704


title: 13C_M_705


title: 13C_M_692


title: 13C_M_683


title: 13C_M_691


title: 13C_M_682


title: 13C_M_687


title: 13C_M_686


title: 13C_M_689


title: 13C_M_690


title: 13C_M_693


title: 13C_M_685


title: 13C_M_688


title: 13C_M_681


title: 13C_M_674


title: 13C_M_673


title: 13C_M_676


title: 13C_M_675


title: 13C_M_672


title: 13C_M_680


title: 13C_M_678


title: 13C_M_679


title: 13C_M_671


title: 13C_M_669


title: 13C_M_670


title: 13C_M_668


title: 13C_M_694


title: 13C_M_666


title: 13C_M_665


title: 13C_M_664


title: 13C_M_663


title: 13C_M_662


title: 13C_M_658


title: 13C_M_660


title: 13C_M_656


title: 13C_M_654


title: 13C_M_653


title: 13C_M_657


title: 13C_M_659


title: 13C_M_655


title: 13C_M_661


title: 13C_M_667


title: 13C_M_647


title: 13C_M_648


title: 13C_M_652


title: 13C_M_650


title: 13C_M_649


title: 13C_M_646


title: 13C_M_644


title: 13C_M_684


title: 13C_M_651


title: 13C_M_645


title: 13C_M_616


title: 13C_M_615


title: 13C_M_614


title: 13C_M_613


title: 13C_M_612


title: 13C_M_611


title: 13C_M_620


title: 13C_M_627


title: 13C_M_640


title: 13C_M_634


title: 13C_M_621


title: 13C_M_623


title: 13C_M_617


title: 13C_M_643


title: 13C_M_642


title: 13C_M_618


title: 13C_M_631


title: 13C_M_619


title: 13C_M_638


title: 13C_M_641


title: 13C_M_624


title: 13C_M_622


title: 13C_M_633


title: 13C_M_635


title: 13C_M_626


title: 13C_M_628


title: 13C_M_630


title: 13C_M_625


title: 13C_M_632


title: 13C_M_629


title: 13C_M_636


title: 13C_M_637


title: 13C_M_610


title: 13C_M_609


title: 13C_M_607


title: 13C_M_603


title: 13C_M_606


title: 13C_M_602


title: 13C_M_601


title: 13C_M_600


title: 13C_M_597


title: 13C_M_598


title: 13C_M_595


title: 13C_M_599


title: 13C_M_608


title: 13C_M_592


title: 13C_M_582


title: 13C_M_590


title: 13C_M_587


title: 13C_M_585


title: 13C_M_583


title: 13C_M_584


title: 13C_M_589


title: 13C_M_588


title: 13C_M_578


title: 13C_M_591


title: 13C_M_593


title: 13C_M_594


title: 13C_M_579


title: 13C_M_581


title: 13C_M_580


title: 13C_M_605


title: 13C_M_596


title: 13C_M_586


title: 13C_M_577


title: 13C_M_575


title: 13C_M_574


title: 13C_M_576


title: 13C_M_569


title: 13C_M_567


title: 13C_M_572


title: 13C_M_570


title: 13C_M_568


title: 13C_M_571


title: 13C_M_573


title: 13C_M_566


title: 13C_M_563


title: 13C_M_560


title: 13C_M_557


title: 13C_M_556


title: 13C_M_562


title: 13C_M_551


title: 13C_M_564


title: 13C_M_558


title: 13C_M_550


title: 13C_M_549


title: 13C_M_553


title: 13C_M_548


title: 13C_M_555


title: 13C_M_559


title: 13C_M_552


title: 13C_M_546


title: 13C_M_544


title: 13C_M_543


title: 13C_M_545


title: 13C_M_565


title: 13C_M_542


title: 13C_M_561


title: 13C_M_554


title: 13C_M_539


title: 13C_M_541


title: 13C_M_540


title: 13C_M_537


title: 13C_M_538


title: 13C_M_547


title: 13C_M_533


title: 13C_M_530


title: 13C_M_531


title: 13C_M_535


title: 13C_M_534


title: 13C_M_528


title: 13C_M_525


title: 13C_M_526


title: 13C_M_527


title: 13C_M_529


title: 13C_M_520


title: 13C_M_522


title: 13C_M_524


title: 13C_M_519


title: 13C_M_518


title: 13C_M_517


title: 13C_M_514


title: 13C_M_515


title: 13C_M_513


title: 13C_M_512


title: 13C_M_511


title: 13C_M_509


title: 13C_M_510


title: 13C_M_536


title: 13C_M_507


title: 13C_M_506


title: 13C_M_532


title: 13C_M_508


title: 13C_M_521


title: 13C_M_504


title: 13C_M_499


title: 13C_M_505


title: 13C_M_502


title: 13C_M_501


title: 13C_M_498


title: 13C_M_503


title: 13C_M_497


title: 13C_M_500


title: 13C_M_496


title: 13C_M_492


title: 13C_M_516


title: 13C_M_493


title: 13C_M_494


title: 13C_M_495


title: 13C_M_491


title: 13C_M_489


title: 13C_M_487


title: 13C_M_483


title: 13C_M_482


title: 13C_M_485


title: 13C_M_484


title: 13C_M_488


title: 13C_M_486


title: 13C_M_490


title: 13C_M_460


title: 13C_M_467


title: 13C_M_476


title: 13C_M_466


title: 13C_M_475


title: 13C_M_463


title: 13C_M_461


title: 13C_M_468


title: 13C_M_477


title: 13C_M_470


title: 13C_M_480


title: 13C_M_472


title: 13C_M_474


title: 13C_M_465


title: 13C_M_464


title: 13C_M_479


title: 13C_M_481


title: 13C_M_462


title: 13C_M_471


title: 13C_M_459


title: 13C_M_458


title: 13C_M_478


title: 13C_M_457


title: 13C_M_456


title: 13C_M_453


title: 13C_M_454


title: 13C_M_455


title: 13C_M_469


title: 13C_M_452


title: 13C_M_451


title: 13C_M_449


title: 13C_M_448


title: 13C_M_446


title: 13C_M_447


title: 13C_M_442


title: 13C_M_439


title: 13C_M_443


title: 13C_M_445


title: 13C_M_444


title: 13C_M_428


title: 13C_M_434


title: 13C_M_430


title: 13C_M_435


title: 13C_M_429


title: 13C_M_432


title: 13C_M_426


title: 13C_M_438


title: 13C_M_433


title: 13C_M_437


title: 13C_M_431


title: 13C_M_436


title: 13C_M_440


title: 13C_M_441


title: 13C_M_422


title: 13C_M_423


title: 13C_M_424


title: 13C_M_421


title: 13C_M_427


title: 13C_M_450


title: 13C_M_419


title: 13C_M_420


title: 13C_M_425


title: 13C_M_418


title: 13C_M_417


title: 13C_M_414


title: 13C_M_413


title: 13C_M_416


title: 13C_M_412


title: 13C_M_408


title: 13C_M_409


title: 13C_M_405


title: 13C_M_400


title: 13C_M_407


title: 13C_M_392


title: 13C_M_394


title: 13C_M_396


title: 13C_M_410


title: 13C_M_388


title: 13C_M_393


title: 13C_M_402


title: 13C_M_406


title: 13C_M_398


title: 13C_M_395


title: 13C_M_389


title: 13C_M_404


title: 13C_M_403


title: 13C_M_387


title: 13C_M_391


title: 13C_M_411


title: 13C_M_401


title: 13C_M_303


title: 13C_M_306


title: 13C_M_312


title: 13C_M_309


title: 13C_M_307


title: 13C_M_305


title: 13C_M_297


title: 13C_M_316


title: 13C_M_308


title: 13C_M_385


title: 13C_M_314


title: 13C_M_317


title: 13C_M_310


title: 13C_M_311


title: 13C_M_301


title: 13C_M_315


title: 13C_M_302


title: 13C_M_299


title: 13C_M_304


title: 13C_M_386


title: 13C_M_384


title: 13C_M_300


title: 13C_M_319


title: 13C_M_294


title: 13C_M_296


title: 13C_M_293


title: 13C_M_318


title: 13C_M_292


title: 13C_M_313


title: 13C_M_295


title: 13C_M_288


title: 13C_M_291


title: 13C_M_287


title: 13C_M_286


title: 13C_M_282


title: 13C_M_274


title: 13C_M_283


title: 13C_M_276


title: 13C_M_280


title: 13C_M_275


title: 13C_M_278


title: 13C_M_268


title: 13C_M_285


title: 13C_M_277


title: 13C_M_266


title: 13C_M_284


title: 13C_M_281


title: 13C_M_272


title: 13C_M_279


title: 13C_M_262


title: 13C_M_267


title: 13C_M_271


title: 13C_M_264


title: 13C_M_261


title: 13C_M_263


title: 13C_M_290


title: 13C_M_269


title: 13C_M_265


title: 13C_M_270


title: 13C_M_260


title: 13C_M_259


title: 13C_M_256


title: 13C_M_3002


title: 13C_M_3003


title: 13C_M_3007


title: 13C_M_3006


title: 13C_M_3001


title: 13C_M_3005


title: 13C_M_3004


title: 13C_M_2995


title: 13C_M_2990


title: 13C_M_2999


title: 13C_M_2993


title: 13C_M_3000


title: 13C_M_2996


title: 13C_M_2994


title: 13C_M_2992


title: 13C_M_2998


title: 13C_M_2997


title: 13C_M_2988


title: 13C_M_2991


title: 13C_M_2989


title: 13C_M_258


title: 13C_M_2986


title: 13C_M_2983


title: 13C_M_2985


title: 13C_M_2987


title: 13C_M_2984


title: 13C_M_2982


title: 13C_M_257


title: 13C_M_2977


title: 13C_M_2979


title: 13C_M_2978


title: 13C_M_2980


title: 13C_M_2971


title: 13C_M_2976


title: 13C_M_2975


title: 13C_M_2973


title: 13C_M_2974


title: 13C_M_2972


title: 13C_M_2963


title: 13C_M_2967


title: 13C_M_2965


title: 13C_M_2970


title: 13C_M_2966


title: 13C_M_2981


title: 13C_M_2968


title: 13C_M_2969


title: 13C_M_2960


title: 13C_M_2955


title: 13C_M_2957


title: 13C_M_2959


title: 13C_M_2956


title: 13C_M_2958


title: 13C_M_2962


title: 13C_M_2961


title: 13C_M_2954


title: 13C_M_2953


title: 13C_M_2952


title: 13C_M_2948


title: 13C_M_2964


title: 13C_M_2949


title: 13C_M_2951


title: 13C_M_2947


title: 13C_M_2946


title: 13C_M_2942


title: 13C_M_2940


title: 13C_M_2945


title: 13C_M_2944


title: 13C_M_2943


title: 13C_M_2939


title: 13C_M_2938


title: 13C_M_2937


title: 13C_M_2936


title: 13C_M_2941


title: 13C_M_2932


title: 13C_M_2933


title: 13C_M_2950


title: 13C_M_2931


title: 13C_M_2928


title: 13C_M_2925


title: 13C_M_2930


title: 13C_M_2926


title: 13C_M_2929


title: 13C_M_2927


title: 13C_M_2935


title: 13C_M_2923


title: 13C_M_2921


title: 13C_M_2922


title: 13C_M_2924


title: 13C_M_2934


title: 13C_M_2918


title: 13C_M_2916


title: 13C_M_2917


title: 13C_M_2913


title: 13C_M_2912


title: 13C_M_2908


title: 13C_M_2909


title: 13C_M_2910


title: 13C_M_2906


title: 13C_M_2911


title: 13C_M_2914


title: 13C_M_2907


title: 13C_M_2904


title: 13C_M_2905


title: 13C_M_2920


title: 13C_M_2919


title: 13C_M_2901


title: 13C_M_2898


title: 13C_M_2900


title: 13C_M_2899


title: 13C_M_2903


title: 13C_M_2902


title: 13C_M_2895


title: 13C_M_2894


title: 13C_M_2896


title: 13C_M_2892


title: 13C_M_2891


title: 13C_M_2915


title: 13C_M_2897


title: 13C_M_2890


title: 13C_M_2888


title: 13C_M_2886


title: 13C_M_2889


title: 13C_M_2883


title: 13C_M_2885


title: 13C_M_2882


title: 13C_M_2881


title: 13C_M_2880


title: 13C_M_2879


title: 13C_M_2887


title: 13C_M_2877


title: 13C_M_2876


title: 13C_M_2893


title: 13C_M_2878


title: 13C_M_2874


title: 13C_M_2875


title: 13C_M_2873


title: 13C_M_2871


title: 13C_M_2872


title: 13C_M_2869


title: 13C_M_2870


title: 13C_M_2884


title: 13C_M_2867


title: 13C_M_2863


title: 13C_M_2866


title: 13C_M_2862


title: 13C_M_2865


title: 13C_M_2868


title: 13C_M_2864


title: 13C_M_2861


title: 13C_M_2860


title: 13C_M_2858


title: 13C_M_2855


title: 13C_M_2857


title: 13C_M_2848


title: 13C_M_2849


title: 13C_M_2856


title: 13C_M_2854


title: 13C_M_2850


title: 13C_M_2846


title: 13C_M_2844


title: 13C_M_2847


title: 13C_M_2843


title: 13C_M_2845


title: 13C_M_2842


title: 13C_M_2841


title: 13C_M_2840


title: 13C_M_2839


title: 13C_M_2837


title: 13C_M_2834


title: 13C_M_2835


title: 13C_M_2836


title: 13C_M_2851


title: 13C_M_2832


title: 13C_M_2833


title: 13C_M_2859


title: 13C_M_2829


title: 13C_M_2838


title: 13C_M_2828


title: 13C_M_2853


title: 13C_M_2827


title: 13C_M_2852


title: 13C_M_2825


title: 13C_M_2826


title: 13C_M_2823


title: 13C_M_2824


title: 13C_M_2822


title: 13C_M_2821


title: 13C_M_2820


title: 13C_M_2819


title: 13C_M_2818


title: 13C_M_2815


title: 13C_M_2816


title: 13C_M_2814


title: 13C_M_2817


title: 13C_M_2813


title: 13C_M_2831


title: 13C_M_2812


title: 13C_M_2811


title: 13C_M_2810


title: 13C_M_2809


title: 13C_M_2807


title: 13C_M_2806


title: 13C_M_2830


title: 13C_M_2808


title: 13C_M_2805


title: 13C_M_2801


title: 13C_M_2804


title: 13C_M_2803


title: 13C_M_2802


title: 13C_M_2799


title: 13C_M_2798


title: 13C_M_2794


title: 13C_M_2789


title: 13C_M_2796


title: 13C_M_2795


title: 13C_M_2790


title: 13C_M_2787


title: 13C_M_2786


title: 13C_M_2792


title: 13C_M_2797


title: 13C_M_2793


title: 13C_M_2788


title: 13C_M_2791


title: 13C_M_2784


title: 13C_M_2782


title: 13C_M_2785


title: 13C_M_2780


title: 13C_M_2783


title: 13C_M_2779


title: 13C_M_2800


title: 13C_M_2778


title: 13C_M_2781


title: 13C_M_2776


title: 13C_M_2774


title: 13C_M_2777


title: 13C_M_2775


title: 13C_M_2770


title: 13C_M_2772


title: 13C_M_2771


title: 13C_M_2769


title: 13C_M_2762


title: 13C_M_2757


title: 13C_M_2764


title: 13C_M_2761


title: 13C_M_2763


title: 13C_M_2759


title: 13C_M_2758


title: 13C_M_2754


title: 13C_M_2773


title: 13C_M_2752


title: 13C_M_2765


title: 13C_M_2767


title: 13C_M_2755


title: 13C_M_2756


title: 13C_M_2686


title: 13C_M_2681


title: 13C_M_2760


title: 13C_M_2679


title: 13C_M_2678


title: 13C_M_2685


title: 13C_M_2687


title: 13C_M_2684


title: 13C_M_2682


title: 13C_M_2753


title: 13C_M_2766


title: 13C_M_2768


title: 13C_M_2680


title: 13C_M_2677


title: 13C_M_2675


title: 13C_M_2674


title: 13C_M_2673


title: 13C_M_2671


title: 13C_M_2676


title: 13C_M_2667


title: 13C_M_2668


title: 13C_M_2658


title: 13C_M_2659


title: 13C_M_2664


title: 13C_M_2666


title: 13C_M_2670


title: 13C_M_2660


title: 13C_M_2657


title: 13C_M_2665


title: 13C_M_2663


title: 13C_M_2669


title: 13C_M_2649


title: 13C_M_2654


title: 13C_M_2656


title: 13C_M_2653


title: 13C_M_2650


title: 13C_M_2645


title: 13C_M_2647


title: 13C_M_2651


title: 13C_M_2646


title: 13C_M_2655


title: 13C_M_2648


title: 13C_M_2672


title: 13C_M_2661


title: 13C_M_2644


title: 13C_M_2643


title: 13C_M_2652


title: 13C_M_2638


title: 13C_M_2635


title: 13C_M_2639


title: 13C_M_2636


title: 13C_M_2637


title: 13C_M_2640


title: 13C_M_2633


title: 13C_M_2641


title: 13C_M_2631


title: 13C_M_2632


title: 13C_M_2625


title: 13C_M_2559


title: 13C_M_2557


title: 13C_M_2624


title: 13C_M_2626


title: 13C_M_2556


title: 13C_M_2627


title: 13C_M_2553


title: 13C_M_2628


title: 13C_M_2555


title: 13C_M_2558


title: 13C_M_2549


title: 13C_M_2550


title: 13C_M_2642


title: 13C_M_2551


title: 13C_M_2548


title: 13C_M_2552


title: 13C_M_2634


title: 13C_M_2630


title: 13C_M_2629


title: 13C_M_2544


title: 13C_M_2547


title: 13C_M_2546


title: 13C_M_2542


title: 13C_M_2543


title: 13C_M_2541


title: 13C_M_2539


title: 13C_M_2540


title: 13C_M_2535


title: 13C_M_2538


title: 13C_M_2536


title: 13C_M_2533


title: 13C_M_2532


title: 13C_M_2537


title: 13C_M_2528


title: 13C_M_2530


title: 13C_M_2524


title: 13C_M_2529


title: 13C_M_2534


title: 13C_M_2525


title: 13C_M_2522


title: 13C_M_2527


title: 13C_M_2526


title: 13C_M_2521


title: 13C_M_2545


title: 13C_M_2519


title: 13C_M_2516


title: 13C_M_2513


title: 13C_M_2518


title: 13C_M_2514


title: 13C_M_2517


title: 13C_M_2511


title: 13C_M_2531


title: 13C_M_2512


title: 13C_M_2508


title: 13C_M_2504


title: 13C_M_2502


title: 13C_M_2506


title: 13C_M_2507


title: 13C_M_2505


title: 13C_M_2500


title: 13C_M_2510


title: 13C_M_2509


title: 13C_M_2501


title: 13C_M_2430


title: 13C_M_2496


title: 13C_M_2499


title: 13C_M_2431


title: 13C_M_2498


title: 13C_M_2428


title: 13C_M_2497


title: 13C_M_2515


title: 13C_M_2426


title: 13C_M_2427


title: 13C_M_2425


title: 13C_M_2424


title: 13C_M_2421


title: 13C_M_2423


title: 13C_M_2420


title: 13C_M_2422


title: 13C_M_2418


title: 13C_M_2419


title: 13C_M_2417


title: 13C_M_2413


title: 13C_M_2416


title: 13C_M_2414


title: 13C_M_2406


title: 13C_M_2407


title: 13C_M_2408


title: 13C_M_2410


title: 13C_M_2403


title: 13C_M_2409


title: 13C_M_2398


title: 13C_M_2404


title: 13C_M_2402


title: 13C_M_2399


title: 13C_M_2401


title: 13C_M_2395


title: 13C_M_2397


title: 13C_M_2396


title: 13C_M_2393


title: 13C_M_2394


title: 13C_M_2392


title: 13C_M_2389


title: 13C_M_2390


title: 13C_M_2415


title: 13C_M_2411


title: 13C_M_2405


title: 13C_M_2386


title: 13C_M_2385


title: 13C_M_2400


title: 13C_M_2387


title: 13C_M_2384


title: 13C_M_2383


title: 13C_M_2380


title: 13C_M_2375


title: 13C_M_2373


title: 13C_M_2374


title: 13C_M_2381


title: 13C_M_2370


title: 13C_M_2372


title: 13C_M_2371


title: 13C_M_2369


title: 13C_M_2368


title: 13C_M_2365


title: 13C_M_2367


title: 13C_M_2364


title: 13C_M_2363


title: 13C_M_2388


title: 13C_M_2360


title: 13C_M_2359


title: 13C_M_2362


title: 13C_M_2382


title: 13C_M_2378


title: 13C_M_2379


title: 13C_M_2377


title: 13C_M_2429


title: 13C_M_2391


title: 13C_M_2376


title: 13C_M_2356


title: 13C_M_2357


title: 13C_M_2354


title: 13C_M_2355


title: 13C_M_2358


title: 13C_M_2352


title: 13C_M_2353


title: 13C_M_2350


title: 13C_M_2366


title: 13C_M_2349


title: 13C_M_2351


title: 13C_M_2346


title: 13C_M_2347


title: 13C_M_2345


title: 13C_M_2361


title: 13C_M_2348


title: 13C_M_2343


title: 13C_M_2344


title: 13C_M_2342


title: 13C_M_2338


title: 13C_M_2341


title: 13C_M_2337


title: 13C_M_2336


title: 13C_M_2335


title: 13C_M_2334


title: 13C_M_2329


title: 13C_M_2333


title: 13C_M_2332


title: 13C_M_2331


title: 13C_M_2328


title: 13C_M_2327


title: 13C_M_2326


title: 13C_M_2321


title: 13C_M_2322


title: 13C_M_2324


title: 13C_M_2325


title: 13C_M_2323


title: 13C_M_2320


title: 13C_M_2340


title: 13C_M_2318


title: 13C_M_2339


title: 13C_M_2316


title: 13C_M_2315


title: 13C_M_2319


title: 13C_M_2314


title: 13C_M_2317


title: 13C_M_2330


title: 13C_M_2309


title: 13C_M_2307


title: 13C_M_2311


title: 13C_M_2310


title: 13C_M_2312


title: 13C_M_2313


title: 13C_M_2308


title: 13C_M_1983


title: 13C_M_2304


title: 13C_M_2306


title: 13C_M_1980


title: 13C_M_1982


title: 13C_M_1976


title: 13C_M_1974


title: 13C_M_1979


title: 13C_M_1973


title: 13C_M_1970


title: 13C_M_1971


title: 13C_M_1975


title: 13C_M_1967


title: 13C_M_1969


title: 13C_M_1966


title: 13C_M_2305


title: 13C_M_1978


title: 13C_M_1972


title: 13C_M_1959


title: 13C_M_1963


title: 13C_M_1962


title: 13C_M_1965


title: 13C_M_1960


title: 13C_M_1961


title: 13C_M_1981


title: 13C_M_1957


title: 13C_M_1958


title: 13C_M_1968


title: 13C_M_1956


title: 13C_M_1953


title: 13C_M_1952


title: 13C_M_1954


title: 13C_M_1947


title: 13C_M_1948


title: 13C_M_1946


title: 13C_M_2503


title: 13C_M_1945


title: 13C_M_1949


title: 13C_M_1964


title: 13C_M_1943


title: 13C_M_1951


title: 13C_M_1940


title: 13C_M_1950


title: 13C_M_1939


title: 13C_M_1944


title: 13C_M_1942


title: 13C_M_1934


title: 13C_M_1936


title: 13C_M_1955


title: 13C_M_1941


title: 13C_M_1935


title: 13C_M_1933


title: 13C_M_1937


title: 13C_M_1938


title: 13C_M_1932


title: 13C_M_1931


title: 13C_M_1929


title: 13C_M_1930


title: 13C_M_1928


title: 13C_M_1927


title: 13C_M_1924


title: 13C_M_1922


title: 13C_M_1923


title: 13C_M_1855


title: 13C_M_1920


title: 13C_M_1921


title: 13C_M_1853


title: 13C_M_1925


title: 13C_M_1852


title: 13C_M_1854


title: 13C_M_1846


title: 13C_M_1848


title: 13C_M_1850


title: 13C_M_1843


title: 13C_M_1851


title: 13C_M_1844


title: 13C_M_1842


title: 13C_M_1847


title: 13C_M_1845


title: 13C_M_1841


title: 13C_M_1840


title: 13C_M_1926


title: 13C_M_1835


title: 13C_M_1836


title: 13C_M_1838


title: 13C_M_1849


title: 13C_M_1833


title: 13C_M_1832


title: 13C_M_1830


title: 13C_M_1829


title: 13C_M_1828


title: 13C_M_1826


title: 13C_M_1825


title: 13C_M_1827


title: 13C_M_1831


title: 13C_M_1823


title: 13C_M_1837


title: 13C_M_1822


title: 13C_M_1819


title: 13C_M_1824


title: 13C_M_1815


title: 13C_M_1839


title: 13C_M_1834


title: 13C_M_1817


title: 13C_M_1820


title: 13C_M_1818


title: 13C_M_1814


title: 13C_M_1813


title: 13C_M_1811


title: 13C_M_1812


title: 13C_M_1808


title: 13C_M_1807


title: 13C_M_1810


title: 13C_M_1805


title: 13C_M_1821


title: 13C_M_1816


title: 13C_M_1804


title: 13C_M_1803


title: 13C_M_1796


title: 13C_M_1798


title: 13C_M_1801


title: 13C_M_1799


title: 13C_M_1800


title: 13C_M_1802


title: 13C_M_1797


title: 13C_M_1793


title: 13C_M_1795


title: 13C_M_1788


title: 13C_M_1785


title: 13C_M_1789


title: 13C_M_1806


title: 13C_M_1786


title: 13C_M_1790


title: 13C_M_1792


title: 13C_M_1791


title: 13C_M_1784


title: 13C_M_1783


title: 13C_M_1794


title: 13C_M_1787


title: 13C_M_1778


title: 13C_M_1779


title: 13C_M_1780


title: 13C_M_1777


title: 13C_M_1781


title: 13C_M_1769


title: 13C_M_1771


title: 13C_M_1773


title: 13C_M_1776


title: 13C_M_1774


title: 13C_M_1775


title: 13C_M_1768


title: 13C_M_1772


title: 13C_M_1767


title: 13C_M_1762


title: 13C_M_1763


title: 13C_M_1765


title: 13C_M_1764


title: 13C_M_1766


title: 13C_M_1760


title: 13C_M_1782


title: 13C_M_1758


title: 13C_M_1977


title: 13C_M_1759


title: 13C_M_1754


title: 13C_M_1757


title: 13C_M_1755


title: 13C_M_1753


title: 13C_M_1770


title: 13C_M_1756


title: 13C_M_1750


title: 13C_M_1749


title: 13C_M_1748


title: 13C_M_1747


title: 13C_M_1743


title: 13C_M_1751


title: 13C_M_1752


title: 13C_M_1741


title: 13C_M_1745


title: 13C_M_1744


title: 13C_M_1742


title: 13C_M_1746


title: 13C_M_1735


title: 13C_M_1739


title: 13C_M_1740


title: 13C_M_1738


title: 13C_M_1733


title: 13C_M_1737


title: 13C_M_1736


title: 13C_M_1732


title: 13C_M_1734


title: 13C_M_1730


title: 13C_M_1731


title: 13C_M_1729


title: 13C_M_1728


title: 13C_M_1662


title: 13C_M_1663


title: 13C_M_1661


title: 13C_M_1660


title: 13C_M_1657


title: 13C_M_1659


title: 13C_M_1654


title: 13C_M_1650


title: 13C_M_1651


title: 13C_M_1658


title: 13C_M_1656


title: 13C_M_1652


title: 13C_M_1653


title: 13C_M_1646


title: 13C_M_1649


title: 13C_M_1638


title: 13C_M_1648


title: 13C_M_1635


title: 13C_M_1636


title: 13C_M_1642


title: 13C_M_1637


title: 13C_M_1639


title: 13C_M_1643


title: 13C_M_1644


title: 13C_M_1633


title: 13C_M_1634


title: 13C_M_1632


title: 13C_M_1631


title: 13C_M_1655


title: 13C_M_1630


title: 13C_M_1628


title: 13C_M_1629


title: 13C_M_1647


title: 13C_M_1640


title: 13C_M_1627


title: 13C_M_1626


title: 13C_M_1625


title: 13C_M_1624


title: 13C_M_1623


title: 13C_M_1617


title: 13C_M_1620


title: 13C_M_1619


title: 13C_M_1622


title: 13C_M_1607


title: 13C_M_1615


title: 13C_M_1612


title: 13C_M_1614


title: 13C_M_1608


title: 13C_M_1609


title: 13C_M_1606


title: 13C_M_1611


title: 13C_M_1610


title: 13C_M_1605


title: 13C_M_1613


title: 13C_M_1604


title: 13C_M_1603


title: 13C_M_1621


title: 13C_M_1618


title: 13C_M_1616


title: 13C_M_1406


title: 13C_M_1404


title: 13C_M_1602


title: 13C_M_1407


title: 13C_M_1601


title: 13C_M_1600


title: 13C_M_1405


title: 13C_M_1403


title: 13C_M_1401


title: 13C_M_1397


title: 13C_M_1399


title: 13C_M_1398


title: 13C_M_1400


title: 13C_M_1394


title: 13C_M_1396


title: 13C_M_1393


title: 13C_M_1395


title: 13C_M_1385


title: 13C_M_1389


title: 13C_M_1386


title: 13C_M_1387


title: 13C_M_1390


title: 13C_M_1391


title: 13C_M_1388


title: 13C_M_1384


title: 13C_M_1402


title: 13C_M_1383


title: 13C_M_1382


title: 13C_M_1381


title: 13C_M_1378


title: 13C_M_1379


title: 13C_M_1392


title: 13C_M_1375


title: 13C_M_1376


title: 13C_M_1373


title: 13C_M_1374


title: 13C_M_1377


title: 13C_M_1368


title: 13C_M_1369


title: 13C_M_1370


title: 13C_M_1372


title: 13C_M_1366


title: 13C_M_1365


title: 13C_M_1367


title: 13C_M_1362


title: 13C_M_1360


title: 13C_M_1361


title: 13C_M_1359


title: 13C_M_1358


title: 13C_M_1356


title: 13C_M_1355


title: 13C_M_1354


title: 13C_M_1352


title: 13C_M_1353


title: 13C_M_1371


title: 13C_M_1351


title: 13C_M_1348


title: 13C_M_1349


title: 13C_M_1364


title: 13C_M_1347


title: 13C_M_1363


title: 13C_M_1345


title: 13C_M_1213


title: 13C_M_1211


title: 13C_M_1215


title: 13C_M_1212


title: 13C_M_1210


title: 13C_M_1214


title: 13C_M_1346


title: 13C_M_1357


title: 13C_M_1208


title: 13C_M_1344


title: 13C_M_1207


title: 13C_M_1209


title: 13C_M_1202


title: 13C_M_1200


title: 13C_M_1204


title: 13C_M_1203


title: 13C_M_1206


title: 13C_M_1199


title: 13C_M_1198


title: 13C_M_1197


title: 13C_M_1195


title: 13C_M_1196


title: 13C_M_1193


title: 13C_M_1194


title: 13C_M_1191


title: 13C_M_1192


title: 13C_M_1205


title: 13C_M_1190


title: 13C_M_1189


title: 13C_M_1186


title: 13C_M_1201


title: 13C_M_1180


title: 13C_M_1183


title: 13C_M_1182


title: 13C_M_1181


title: 13C_M_1179


title: 13C_M_1185


title: 13C_M_1177


title: 13C_M_1184


title: 13C_M_1174


title: 13C_M_1175


title: 13C_M_1173


title: 13C_M_1166


title: 13C_M_1170


title: 13C_M_1167


title: 13C_M_1165


title: 13C_M_1171


title: 13C_M_1172


title: 13C_M_1169


title: 13C_M_1187


title: 13C_M_1168


title: 13C_M_1188


title: 13C_M_1164


title: 13C_M_1163


title: 13C_M_1162


title: select_wt_replicate2_tile14 (56)

city: Copenhagen N

first: Sarah

last: Gersing

address: Ole Maaløes vej 5

country: Denmark

institute: University of Copenhagen

description: Amino acid positions 438-465

library_source: other

data_processing:
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads were aligned and variants called using the TileSeq mutation count pipeline (https://github.com/RyogaLi/tileseq_mutcount) version 0.5.9
Variant calls from the TileSeq mutation count pipeline were then used for calling protein-level amino acid changes and for calculating the enrichment of variants using the TileSeqMave pipeline (https://github.com/jweile/tileseqMave) version 1.1.0
Reference sequence:  sequence.txt on the Series record contains the sequence used for read alignment.
Library strategy: Tile-Seq

molecule: other

organism: synthetic construct

source_name: Yeast cells

growth_protocol: Following library transformations, yeast cells were expanded in SC-URA medium until saturation. Then, cells for the nonselect condition were harvested and stored at -20C prior to plasmid DNA extraction. In addition, yeast cells were washed and grown on solid SC+leucine+methionine+histidine medium with 100 µg/mL methotrexate and 1 mM sulfanilamide at 37C for four days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

extract_protocol:
For all conditions, plasmid DNA was extracted from 9 OD units of yeast cells using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen).
The Gateway entry libraries were previously constructed (Gersing et al., 2022, bioRxiv) and were cloned into the pDEST-DHFR-PCA Gateway destination vector.

tag: yeast strain

tag: selection

value: yes

tag: molecule subtype

value: plasmid


title: 13C_M_1176


title: select_wt_replicate2_tile11 (53)

description: Amino acid positions 338-370


title: select_wt_replicate2_tile12 (54)

description: Amino acid positions 371-404


title: 13C_M_1178


title: 13C_M_1157


title: 13C_M_1161


title: 13C_M_1156


title: 13C_M_1158


title: 13C_M_1160


title: select_wt_replicate2_tile13 (55)

description: Amino acid positions 405-437


title: select_wt_replicate2_tile10 (52)

description: Amino acid positions 305-337


title: 13C_M_1159


title: select_wt_replicate2_tile9 (51)

description: Amino acid positions 273-304


title: select_wt_replicate2_tile8 (50)

description: Amino acid positions 241-272


title: 13C_M_1155


title: select_wt_replicate2_tile7 (49)

description: Amino acid positions 207-240


title: 13C_M_1154


title: 13C_M_1152


title: 13C_M_1153


title: select_wt_replicate2_tile4 (46)

description: Amino acid positions 104-137


title: 13C_M_1086


title: select_wt_replicate2_tile3 (45)

description: Amino acid positions 70-103


title: select_wt_replicate2_tile6 (48)

description: Amino acid positions 172-206


title: select_wt_replicate2_tile2 (44)

description: Amino acid positions 38-69


title: select_wt_replicate2_tile5 (47)

description: Amino acid positions 138-171


title: 13C_M_1084


title: 13C_M_1085


title: select_wt_replicate2_tile1 (43)

description: Amino acid positions 2-37


title: 13C_M_1080


title: 13C_M_1081


title: select_wt_replicate1_tile12 (40)

description: Amino acid positions 371-404


title: 13C_M_1079


title: 13C_M_1082


title: select_wt_replicate1_tile14 (42)

description: Amino acid positions 438-465


title: select_wt_replicate1_tile13 (41)

description: Amino acid positions 405-437


title: select_wt_replicate1_tile10 (38)

description: Amino acid positions 305-337


title: select_wt_replicate1_tile11 (39)

description: Amino acid positions 338-370


title: 13C_M_1083


title: select_wt_replicate1_tile9 (37)

description: Amino acid positions 273-304


title: 13C_M_1078


title: 13C_M_1087


title: select_wt_replicate1_tile7 (35)

description: Amino acid positions 207-240


title: select_wt_replicate1_tile6 (34)

description: Amino acid positions 172-206


title: select_wt_replicate1_tile5 (33)

description: Amino acid positions 138-171


title: select_wt_replicate1_tile4 (32)

description: Amino acid positions 104-137


title: select_wt_replicate1_tile3 (31)

description: Amino acid positions 70-103


title: select_wt_replicate1_tile8 (36)

description: Amino acid positions 241-272


title: 13C_M_1076


title: 13C_M_1067


title: 13C_M_1068


title: 13C_M_1071


title: 13C_M_1069


title: 13C_M_1070


title: 13C_M_1072


title: 13C_M_1075


title: 13C_M_1074


title: 13C_M_1066


title: 13C_M_1077


title: 13C_M_1073


title: 13C_M_1064


title: 13C_M_1063


title: 13C_M_1065


title: 13C_M_1062


title: 13C_M_1061


title: nonselect_wt_replicate2_tile8 (22)

description: Amino acid positions 241-272

value: no


title: nonselect_wt_replicate2_tile6 (20)

description: Amino acid positions 172-206


title: nonselect_wt_replicate2_tile14 (28)

description: Amino acid positions 438-465


title: select_wt_replicate1_tile2 (30)

description: Amino acid positions 38-69


title: select_wt_replicate1_tile1 (29)

description: Amino acid positions 2-37


title: nonselect_wt_replicate2_tile12 (26)

description: Amino acid positions 371-404


title: 13C_M_1060


title: nonselect_wt_replicate2_tile13 (27)

description: Amino acid positions 405-437


title: nonselect_wt_replicate2_tile11 (25)

description: Amino acid positions 338-370


title: nonselect_wt_replicate2_tile10 (24)

description: Amino acid positions 305-337


title: nonselect_wt_replicate2_tile9 (23)

description: Amino acid positions 273-304


title: nonselect_wt_replicate2_tile5 (19)

description: Amino acid positions 138-171


title: nonselect_wt_replicate2_tile3 (17)

description: Amino acid positions 70-103


title: nonselect_wt_replicate1_tile13 (13)

description: Amino acid positions 405-437


title: nonselect_wt_replicate2_tile2 (16)

description: Amino acid positions 38-69


title: nonselect_wt_replicate2_tile1 (15)

description: Amino acid positions 2-37


title: nonselect_wt_replicate1_tile14 (14)

description: Amino acid positions 438-465


title: 13C_M_1057


title: 13C_M_1058


title: 13C_M_1055


title: 13C_M_1053


title: nonselect_wt_replicate2_tile7 (21)

description: Amino acid positions 207-240


title: nonselect_wt_replicate1_tile12 (12)

description: Amino acid positions 371-404


title: 13C_M_1059


title: 13C_M_1056


title: 13C_M_1051


title: 13C_M_1054


title: nonselect_wt_replicate1_tile8 (8)

description: Amino acid positions 241-272


title: nonselect_wt_replicate2_tile4 (18)

description: Amino acid positions 104-137


title: nonselect_wt_replicate1_tile10 (10)

description: Amino acid positions 305-337


title: 13C_M_1049


title: 13C_M_1050


title: nonselect_wt_replicate1_tile6 (6)

description: Amino acid positions 172-206


title: 13C_M_1047


title: 13C_M_1048


title: nonselect_wt_replicate1_tile5 (5)

description: Amino acid positions 138-171


title: nonselect_wt_replicate1_tile7 (7)

description: Amino acid positions 207-240


title: nonselect_wt_replicate1_tile9 (9)

description: Amino acid positions 273-304


title: 13C_M_1045


title: 13C_M_1052


title: 13C_M_1044


title: 13C_M_1042


title: nonselect_wt_replicate1_tile4 (4)

description: Amino acid positions 104-137


title: 13C_M_1046


title: nonselect_wt_replicate1_tile3 (3)

description: Amino acid positions 70-103


title: nonselect_wt_replicate1_tile2 (2)

description: Amino acid positions 38-69


title: nonselect_wt_replicate1_tile1 (1)

description: Amino acid positions 2-37


title: nonselect_wt_replicate1_tile11 (11)

description: Amino acid positions 338-370


title: select_library_replicate2_tile13 (111)

description: Amino acid positions 405-437


title: select_library_replicate2_tile11 (109)

description: Amino acid positions 338-370


title: select_library_replicate2_tile14 (112)

description: Amino acid positions 438-465


title: select_library_replicate2_tile9 (107)

description: Amino acid positions 273-304


title: 13C_M_1040


title: 13C_M_1039


title: 13C_M_1035


title: 13C_M_1036


title: select_library_replicate2_tile12 (110)

description: Amino acid positions 371-404


title: 13C_M_1038


title: 13C_M_1037


title: 13C_M_1041


title: select_library_replicate2_tile8 (106)

description: Amino acid positions 241-272


title: select_library_replicate2_tile6 (104)

description: Amino acid positions 172-206


title: 13C_M_1032


title: select_library_replicate2_tile5 (103)

description: Amino acid positions 138-171


title: 13C_M_1034


title: select_library_replicate2_tile4 (102)

description: Amino acid positions 104-137


title: 13C_M_1030


title: select_library_replicate2_tile7 (105)

description: Amino acid positions 207-240


title: 13C_M_1031


title: 13C_M_1043


title: select_library_replicate2_tile2 (100)

description: Amino acid positions 38-69


title: 13C_M_1027


title: select_library_replicate2_tile3 (101)

description: Amino acid positions 70-103


title: 13C_M_1028


title: select_library_replicate2_tile10 (108)

description: Amino acid positions 305-337


title: select_library_replicate2_tile1 (99)

description: Amino acid positions 2-37


title: 13C_M_1026


title: 13C_M_1029


title: 13C_M_1024


title: 13C_M_1022


title: select_library_replicate1_tile11 (95)

description: Amino acid positions 338-370


title: select_library_replicate1_tile12 (96)

description: Amino acid positions 371-404


title: 13C_M_1023


title: 13C_M_1025


title: select_library_replicate1_tile13 (97)

description: Amino acid positions 405-437


title: 13C_M_1021


title: 13C_M_1020


title: select_library_replicate1_tile14 (98)

description: Amino acid positions 438-465


title: select_library_replicate1_tile9 (93)

description: Amino acid positions 273-304


title: select_library_replicate1_tile8 (92)

description: Amino acid positions 241-272


title: select_library_replicate1_tile10 (94)

description: Amino acid positions 305-337


title: select_library_replicate1_tile7 (91)

description: Amino acid positions 207-240


title: select_library_replicate1_tile6 (90)

description: Amino acid positions 172-206


title: 13C_M_1017


title: 13C_M_1019


title: select_library_replicate1_tile5 (89)

description: Amino acid positions 138-171


title: 13C_M_1018


title: 13C_M_1014


title: select_library_replicate1_tile3 (87)

description: Amino acid positions 70-103


title: select_library_replicate1_tile4 (88)

description: Amino acid positions 104-137


title: 13C_M_1015


title: 13C_M_1016


title: nonselect_library_replicate2_tile14 (84)

description: Amino acid positions 438-465


title: select_library_replicate1_tile2 (86)

description: Amino acid positions 38-69


title: select_library_replicate1_tile1 (85)

description: Amino acid positions 2-37


title: 13C_M_1013


title: 13C_M_1011


title: 13C_M_1012


title: nonselect_library_replicate2_tile13 (83)

description: Amino acid positions 405-437


title: nonselect_library_replicate2_tile12 (82)

description: Amino acid positions 371-404


title: 13C_M_1010


title: 13C_M_1009


title: 13C_M_1008


title: nonselect_library_replicate2_tile8 (78)

description: Amino acid positions 241-272


title: 13C_M_1006


title: nonselect_library_replicate2_tile7 (77)

description: Amino acid positions 207-240


title: 13C_M_1005


title: nonselect_library_replicate2_tile6 (76)

description: Amino acid positions 172-206


title: 13C_M_1004


title: 13C_M_1002


title: nonselect_library_replicate2_tile5 (75)

description: Amino acid positions 138-171


title: nonselect_library_replicate2_tile3 (73)

description: Amino acid positions 70-103


title: 13C_M_1001


title: 13C_M_1000


title: nonselect_library_replicate2_tile4 (74)

description: Amino acid positions 104-137


title: nonselect_library_replicate2_tile1 (71)

description: Amino acid positions 2-37


title: 13C_M_999


title: nonselect_library_replicate2_tile2 (72)

description: Amino acid positions 38-69


title: 13C_M_998


title: 13C_M_997


title: 13C_M_996


title: nonselect_library_replicate1_tile13 (69)

description: Amino acid positions 405-437


title: nonselect_library_replicate1_tile14 (70)

description: Amino acid positions 438-465


title: nonselect_library_replicate2_tile10 (80)

description: Amino acid positions 305-337


title: nonselect_library_replicate2_tile11 (81)

description: Amino acid positions 338-370


title: 13C_M_1007


title: nonselect_library_replicate1_tile12 (68)

description: Amino acid positions 371-404


title: nonselect_library_replicate2_tile9 (79)

description: Amino acid positions 273-304


title: 13C_M_995


title: nonselect_library_replicate1_tile11 (67)

description: Amino acid positions 338-370


title: nonselect_library_replicate1_tile9 (65)

description: Amino acid positions 273-304


title: 13C_M_993


title: 13C_M_1003


title: 13C_M_994


title: nonselect_library_replicate1_tile8 (64)

description: Amino acid positions 241-272


title: nonselect_library_replicate1_tile10 (66)

description: Amino acid positions 305-337


title: 13C_M_991


title: 13C_M_990


title: nonselect_library_replicate1_tile7 (63)

description: Amino acid positions 207-240


title: nonselect_library_replicate1_tile6 (62)

description: Amino acid positions 172-206


title: 13C_M_989


title: 13C_M_987


title: nonselect_library_replicate1_tile5 (61)

description: Amino acid positions 138-171


title: nonselect_library_replicate1_tile4 (60)

description: Amino acid positions 104-137


title: 13C_M_986


title: 13C_M_984


title: 13C_M_985


title: nonselect_library_replicate1_tile1 (57)

description: Amino acid positions 2-37


title: nonselect_library_replicate1_tile3 (59)

description: Amino acid positions 70-103


title: 13C_M_983


title: 13C_M_982


title: 13C_M_980


title: 13C_M_992


title: 13C_M_981


title: 1365_wt_HC_DH_S9_R1_001

city: Los Angeles

first: Sita

last: Reddy

state: California

address: HMR 702A, 2011 Zonal Avenue

institute: University of Southern California

library_source: transcriptomic

data_processing:
cutadapt (v1.18)  - flanking Ns were trimmed from the reads (command - "--trim-n")
Filter by quality (Galaxy version 1.0.0) - Reads with low quality score are filtered out (parameters - quality cut-off value - 20, Percent of bases in sequence that must have quality equal to / higher than cut-off value - 50)
Bowtie2 (Galaxy version 2.3.4.2) - Reads are aligned to the a PolyA database and only unaligned reads are used in the analysis downstream. (Parameters - all default except Write unaligned reads (in fastq format) to separate file(s) - Yes, Single or paired - single, Number of mismatches allowed - 0, Sets of length of seed substrings to align during multiseed alignment -25
Tophat2 (Galaxy version 2.1.1) - Reads were mapped to the mm10 genome (Parameters - Default except - max realign edit distance - 0, Library type - FR unstranded, Final read mismatches - 2, Max number of alignments to be allowed - 1, Minimum length of read segments - 25)
HTSeq (htseq-count Galaxy version 0.9.1) - Counts per gene for each sample is obtained using HTSeq in intersection (strict) setting and DESeq2 (v 1.18.1) was used to obtained the fold changes (log2).
Assembly: mm10
Supplementary files format and content: .tabular files for each of the 12 samples with counts per gene obtained from HTSeq
Supplementary files format and content: .txt files with expression levels (log2 Fold changes) for 4 comparisons WT_HC vs WT_TR, KO_HC vs KO_TR, WT_HC vs KO_HC, WT_TR vs KO_TR obtained from DESeq2

molecule: total RNA

source_name: dorsal hippocampus

extract_protocol:
Total RNA from the dorsal hippocampus of mice was isolated by using the RNeasy Mini kit in accordance with the manufacturer’s protocol. 1 µg RNA per sample was used for polyA mRNA preparation by using NEBNext Poly(A) mRNA Magnetic Isolation.
RNA libraries for RNA-seq were generated by using NEBNext Ultra II RNA Library Prep kit according to the manufacturer’s instructions

tag: tissue

value: dorsal hippocampus

tag: genotype

value: Mbnl2 WT

tag: Sex

value: Male

tag: treatment

value: House Control


title: 13C_M_979


title: 1359_ko_TR_DH_S12_R1_001

value: Mbnl2 KO

value: Trained


title: 1238_ko_TR_DH_S7_R1_001


title: 13C_M_977


title: 1192_ko_HC_DH_S6_R1_001


title: 13C_M_978


title: 13C_M_976


title: 1357_ko_HC_DH_S11_R1_001


title: 1231_wt_TR_DH_S4_R1_001


title: nonselect_library_replicate1_tile2 (58)

description: Amino acid positions 38-69


title: 1194_wt_HC_DH_S2_R1_001


title: 13C_M_975


title: 13C_M_972


title: 13C_M_973


title: 1240_ko_TR_DH_S8_R1_001


title: 1189_ko_HC_DH_S5_R1_001


title: 1188_wt_HC_DH_S1_R1_001


title: 13C_M_969


title: 1364_wt_TR_DH_S10_R1_001


title: 13C_M_970


title: GFP

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

description: purified RNA

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Raw NGS reads (FASTQ files) were aligned to the mm9 mouse reference genome using topHat (version 2.0.6); aligned reads are stored in BAM files.
ChIP-seq narrow peaks were called against the input using MACS2 software (version 2.0.9, p-value threshold = 1e-5, --mfold=7,30). For RNAPII samples, MACS2 was also used to call broad peaks.
Genome_build: mm9
Supplementary_files_format_and_content: text files with peaks identified by the macs2 software. For each peak, genomic coordinates (chromosome, start, end, length, summit), number of tags falling within, and confidence scores (-10*log10(pvalue), fold_enrichment and FDR(%)) are reported

source_name: mouse muscle

growth_protocol: C2C12 myoblasts (ATCC, CRL-1772) were maintained in growth medium (high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) (v/v) (Gibco), 2% glutamine (v/v) (Thermo Scientific), 2% pen/strep (v/v) (Thermo Scientific) and in 37°C, 5% CO2 and 90% humidified atmosphere.

extract_protocol:
At complete confluency, cells were suspended in 1000ul of RIP lysis buffer (50mM tris HCl pH 7.4, 150mM NaCl, 1mM EDTA, 1% NP-40), kept in ice for 20min and vortex frequently. Samples were then centrifuged at 10000g for 10min at 4°C and supernatant were saved. Meanwhile, 40µl of agarose-Flag Ab beads (Sigma Aldrich, A2220) were washed in 380µl of TBS and centrifuged at 8000g for 1min at 4°C. Beads were suspended in 40µl with RIP lysis buffer and added to each RIP sample at equal volume. Samples were then incubated through constant rotation for 2 hr at 4°C. After extensive washes, 1/50 of each mixture was saved for IP western blot validation. Finally, beads were centrifuged and suspended in 300µl of pureZOL for subsequent bound RNAs isolation. Total RNA was subsequently quantified on 2100 Bioanalyzer (Agilent).
SMART-seq2 protocol adapted from (Picelli et al., 2014b) was used to retrotranscribe 10ng total RNA into full-length cDNA with oligo(dT) primers and LNA-containing template-switching oligo (TSO). Purified cDNA was tagmented with Tn5 transposase and enriched by PCR to create the final library for sequencing on an Illumina HiSeq2000 platform.

treatment_protocol: Zc3h10 overexpression in C2C12 myoblasts and myotubes was performed by exposing cells to adenoviral vectors for 48 hr (Human Adenovirus Type 5 dE1/dE3). Validated adenoviral vector carried mouse Zc3h10 cDNA fused together with a Flag-tag to the N-terminal portion (Flag-Zc3) controlled by a CMV promoter (Vector Biolabs, ADV-276549). As control, we used the same construct expressing the GFP under the control of CMV promoter (Vector Biolabs, 1768). Flag-Zc3h10 and GFP were overexpressed at a multiplicity of infection (MOI) of 5

tag: cell line

tag: cell type

value: myoblasts

value: wildtype with GFP expression

tag: antibody


title: 13C_M_968


title: Zc3h10

description: purified RNA

value: agarose-Flag Ab beads (Sigma Aldrich, A2220)


title: 13C_M_967


title: RNA_total_WT_rep3

description: total RNA

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Reads were aligned on the mouse reference genome (NCBI 37, MM9) with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded
Gene annotations and read counts have been made using the “make_annotation” and “make_ie_counts.R” functions available at https://github.com/ste-depo/Audano2017code. Briefly, exons are retrieved from the TxDb.Mmusculus.UCSC.mm9.knownGene R/Bioconductor package and introns are obtained by removing the annotated exons from transcripts coordinates. For genes with multiple transcripts metagenes models are created that aggregates exons from all isoforms. Reads are mapped to exon features first and then to intron features solving ambiguities in favour of exons in case of reads mapping to both exon and intron features. Eventually for each gene sample and data type (nascent and total mRNA) the counts of exonic and intronic reads are determined.
Genome_build: mm9
Supplementary_files_format_and_content: text files with read counts distinguishing for exons and introns of each gene

growth_protocol:
C2C12 myoblasts (ATCC, CRL-1772) were maintained in growth medium (high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) (v/v) (Gibco), 2% glutamine (v/v) (Thermo Scientific), 2% pen/strep (v/v) (Thermo Scientific) and in 37°C, 5% CO2 and 90% humidified atmosphere.
genotype: Zc3h10 targeted silencing used a validated adenoviral construct contained specific short hairpin RNA sequence under a U6 promoter (shADV-276549), while control vector contained a scrambled sequence (Vector Biolabs, 1122). Both constructs were transduced using a MOI of 100 in C2C12 cells.

extract_protocol:
Cells were rinsed in 1 ml of ice-cold PBS. Total RNA was isolated using silica column approach (NucleoSpin® RNA extraction kit, Macherey-Nagel, 740955.250). Briefly, cells were washed in ice-cold PBS and lysed in 350 of lysis buffer supplemented with 1% β-mercaptoethanol. After adding 100µl of chloroform, mouse samples were centrifuged at 10,000g at 4°C for 15 min. Upper polar phases and cell samples were then transferred to silica columns and spun 11,000g for 30 seconds. Total RNA was then isolated by following manufacturer’s instructions and eluted from columns with 50µl of RNase free water.
4-thiouridine (Sigma Aldrich, T4509) and RNA-seq were performed as previously described (Rabani et al., 2011). Briefly, 300μM 4-thiouridine was used for 30 minutes labeling in confluent scramble and ShZc3h10 myoblasts. After labelling, cells were harvested in 10ml of ice-cold PBS, of which 250μl were saved for total RNA-seq. 50μg of RNA were conjugated to biotin-HPDP (Abcam) and precipitated with 50μl of streptavidin (MyOne Steptavidin T1, Invitrogen) for 4sU-tagged RNA isolation. RNA samples were eluted in 50µl of water, quantified by UV spectrophotometry (NanoDrop 1000 Spectrophotometer, Thermo Scientific) and saved at -80°C. We then removed rRNA from total RNA samples by Ribo-Zero Magnetic Kit (Illumina, Mrzh116) following manufacturer’s instructions.
SMART-seq2 protocol adapted from Picelli and colleagues (Picelli et al., 2014b) was used to generate full-length cDNA with modified random priming (5’-AAGCAGTGGTATCAACGCAGAGTACNNNNNN-3’). Purified cDNA was tagmented with Tn5 transposase produced in-house following described protocol (Picelli et al., 2014a) . cDNA fragments were enriched by PCR to create the final library and sequenced on an Illumina HiSeq2000 platform.   SMART-seq2 protocol adapted from Picelli and colleagues (Picelli et al., 2014b) was used to generate full-length cDNA with modified random priming (5’-AAGCAGTGGTATCAACGCAGAGTACNNNNNN-3’). Purified cDNA was tagmented with Tn5 transposase produced in-house following described protocol (Picelli et al., 2014a) . cDNA fragments were enriched by PCR to create the final library and sequenced on an Illumina HiSeq2000 platform.

value: Scrambled short hairpin


title: RNA_total_WT_rep1

description: total RNA


title: RNA_total_SH_rep3

description: total RNA

value: Zc3h10 targeted short hairpin


title: 13C_M_965


title: RNA_total_WT_rep2

description: total RNA


title: 13C_M_964


title: 13C_M_974


title: 1196_wt_TR_DH_S3_R1_001


title: 13C_M_962


title: 13C_M_963


title: 13C_M_961


title: RNA_labeled_WT_rep2

description: labeled RNA

tag: 4su labeling time

value: 30 minutes


title: RNA_total_SH_rep2

description: total RNA


title: 13C_M_960


title: RNA_labeled_WT_rep1

description: labeled RNA


title: RNA_total_SH_rep1

description: total RNA


title: RNA_labeled_SH_rep3

description: labeled RNA


title: 13C_M_959


title: 13C_M_957


title: 13C_M_958


title: RNA_labeled_SH_rep1

description: labeled RNA


title: genomic DNA from control CEPH [CEPH]

type: genomic

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

country: France

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

description: normal blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Average Beta

label: Cy5 and Cy5

organism: Homo sapiens

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: Gentra DNA extraction kit (Qiagen)

value: blood


title: 13C_M_955


title: 13C_M_956


title: genomic DNA from cord blood [97C]

description: normal blood sample

label: Cy5 and Cy4

source_name: cord blood

value: cord blood


title: genomic DNA from maternal blood (1st trimester) [97A]

description: normal blood sample

label: Cy5 and Cy3

source_name: maternal blood 1

value: maternal blood 1


title: 13C_M_953


title: 13C_M_952


title: 13C_M_951


title: 13C_M_950


title: genomic DNA from maternal blood (3rd trimester) [89B]

description: normal blood sample

source_name: maternal blood 3

value: maternal blood 3


title: genomic DNA from maternal blood (1st trimester) [89A]

description: normal blood sample


title: 13C_M_948


title: genomic DNA from cord blood [83C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [83B]

description: normal blood sample


title: 13C_M_949


title: genomic DNA from maternal blood (1st trimester) [83A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [75B]

description: normal blood sample


title: 13C_M_945


title: genomic DNA from cord blood [75C]

description: normal blood sample


title: 13C_M_944


title: 13C_M_946


title: 13C_M_947


title: RNA_labeled_SH_rep2

description: labeled RNA


title: genomic DNA from cord blood [63C]

description: normal blood sample


title: 13C_M_942


title: genomic DNA from maternal blood (3rd trimester) [97B]

description: normal blood sample


title: 13C_M_954


title: genomic DNA from maternal blood (1st trimester) [63A]

description: normal blood sample


title: genomic DNA from cord blood [55C]

description: normal blood sample


title: genomic DNA from cord blood [89C]

description: normal blood sample


title: 13C_M_940


title: 13C_M_941


title: 13C_M_939


title: genomic DNA from maternal blood (3rd trimester) [55B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [55A]

description: normal blood sample


title: 13C_M_938


title: 13C_M_937


title: genomic DNA from cord blood [48C]

description: normal blood sample


title: 13C_M_936


title: genomic DNA from maternal blood (1st trimester) [48A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [48B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [75A]

description: normal blood sample


title: 13C_M_935


title: 13C_M_934


title: 13C_M_943


title: genomic DNA from maternal blood (3rd trimester) [63B]

description: normal blood sample


title: 13C_M_933


title: 13C_M_931


title: genomic DNA from maternal blood (1st trimester) [478A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [478B]

description: normal blood sample


title: 13C_M_932


title: genomic DNA from maternal blood (1st trimester) [471A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [471B]

description: normal blood sample


title: genomic DNA from cord blood [471C]

description: normal blood sample


title: 13C_M_929


title: 13C_M_928


title: 13C_M_930


title: genomic DNA from maternal blood (3rd trimester) [465B]

description: normal blood sample


title: genomic DNA from cord blood [465C]

description: normal blood sample


title: 13C_M_927


title: genomic DNA from maternal blood (1st trimester) [465A]

description: normal blood sample


title: 13C_M_925


title: genomic DNA from cord blood [455C]

description: normal blood sample


title: 13C_M_924


title: genomic DNA from maternal blood (3rd trimester) [455B]

description: normal blood sample


title: genomic DNA from cord blood [451C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [455A]

description: normal blood sample


title: 13C_M_922


title: genomic DNA from maternal blood (3rd trimester) [451B]

description: normal blood sample


title: 13C_M_921


title: 13C_M_920


title: genomic DNA from maternal blood (1st trimester) [451A]

description: normal blood sample


title: 13C_M_926


title: genomic DNA from maternal blood (1st trimester) [448A]

description: normal blood sample


title: 13C_M_919


title: genomic DNA from cord blood [446C]

description: normal blood sample


title: 13C_M_918


title: genomic DNA from maternal blood (3rd trimester) [446B]

description: normal blood sample


title: 13C_M_917


title: genomic DNA from maternal blood (1st trimester) [446A]

description: normal blood sample


title: 13C_M_916


title: genomic DNA from cord blood [442C]

description: normal blood sample


title: 13C_M_914


title: 13C_M_915


title: 13C_M_913


title: genomic DNA from maternal blood (1st trimester) [442A]

description: normal blood sample


title: 13C_M_912


title: genomic DNA from maternal blood (3rd trimester) [439B]

description: normal blood sample


title: 13C_M_911


title: genomic DNA from maternal blood (1st trimester) [439A]

description: normal blood sample


title: 13C_M_910


title: 13C_M_923


title: genomic DNA from cord blood [439C]

description: normal blood sample


title: genomic DNA from cord blood [478C]

description: normal blood sample


title: 13C_M_909


title: 13C_M_908


title: genomic DNA from maternal blood (3rd trimester) [428B]

description: normal blood sample


title: genomic DNA from cord blood [423C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [428A]

description: normal blood sample


title: 13C_M_907


title: 13C_M_906


title: 13C_M_904


title: genomic DNA from maternal blood (3rd trimester) [442B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [423B]

description: normal blood sample


title: 13C_M_903


title: genomic DNA from maternal blood (3rd trimester) [422B]

description: normal blood sample


title: 13C_M_902


title: 13C_M_900


title: genomic DNA from maternal blood (1st trimester) [422A]

description: normal blood sample


title: 13C_M_898


title: 13C_M_899


title: genomic DNA from maternal blood (1st trimester) [42A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [42B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [418B]

description: normal blood sample


title: 13C_M_897


title: genomic DNA from cord blood [428C]

description: normal blood sample


title: genomic DNA from cord blood [418C]

description: normal blood sample


title: 13C_M_893


title: 13C_M_895


title: 13C_M_894


title: genomic DNA from maternal blood (1st trimester) [418A]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [423A]

description: normal blood sample


title: 13C_M_892


title: genomic DNA from maternal blood (1st trimester) [409A]

description: normal blood sample


title: genomic DNA from cord blood [422C]

description: normal blood sample


title: 13C_M_891


title: 13C_M_901


title: 13C_M_890


title: genomic DNA from maternal blood (3rd trimester) [409B]

description: normal blood sample


title: genomic DNA from cord blood [403C]

description: normal blood sample


title: genomic DNA from cord blood [42C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [403B]

description: normal blood sample


title: 13C_M_888


title: 13C_M_887


title: 13C_M_886


title: 13C_M_889


title: 13C_M_885


title: genomic DNA from maternal blood (1st trimester) [4A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [398B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [398A]

description: normal blood sample


title: genomic DNA from cord blood [398C]

description: normal blood sample


title: 13C_M_884


title: 13C_M_883


title: genomic DNA from cord blood [394C]

description: normal blood sample


title: 13C_M_881


title: genomic DNA from maternal blood (3rd trimester) [394B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [394A]

description: normal blood sample


title: 13C_M_880


title: genomic DNA from cord blood [392C]

description: normal blood sample


title: 13C_M_882


title: 13C_M_879


title: 13C_M_878


title: genomic DNA from maternal blood (3rd trimester) [392B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [403A]

description: normal blood sample


title: 13C_M_876


title: genomic DNA from maternal blood (1st trimester) [392A]

description: normal blood sample


title: genomic DNA from cord blood [4C]

description: normal blood sample


title: 13C_M_875


title: 13C_M_877


title: genomic DNA from maternal blood (3rd trimester) [4B]

description: normal blood sample


title: genomic DNA from cord blood [387C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [387B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [387A]

description: normal blood sample


title: 13C_M_873


title: 13C_M_872


title: genomic DNA from cord blood [386C]

description: normal blood sample


title: 13C_M_874


title: genomic DNA from maternal blood (3rd trimester) [386B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [386A]

description: normal blood sample


title: 13C_M_869


title: genomic DNA from maternal blood (3rd trimester) [382B]

description: normal blood sample


title: 13C_M_868


title: 13C_M_867


title: genomic DNA from maternal blood (1st trimester) [374A]

description: normal blood sample


title: 13C_M_865


title: genomic DNA from maternal blood (3rd trimester) [372B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [382A]

description: normal blood sample


title: 13C_M_864


title: 13C_M_866


title: 13C_M_863


title: 13C_M_861


title: genomic DNA from maternal blood (3rd trimester) [374B]

description: normal blood sample


title: genomic DNA from cord blood [374C]

description: normal blood sample


title: genomic DNA from cord blood [371C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [372A]

description: normal blood sample


title: genomic DNA from cord blood [372C]

description: normal blood sample


title: 13C_M_862


title: 13C_M_860


title: 13C_M_859


title: genomic DNA from maternal blood (1st trimester) [371A]

description: normal blood sample


title: 13C_M_858


title: 13C_M_857


title: genomic DNA from cord blood [382C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [371B]

description: normal blood sample


title: 13C_M_870


title: genomic DNA from maternal blood (3rd trimester) [369B]

description: normal blood sample


title: genomic DNA from cord blood [369C]

description: normal blood sample


title: 13C_M_856


title: 13C_M_855


title: genomic DNA from maternal blood (1st trimester) [369A]

description: normal blood sample


title: genomic DNA from cord blood [368C]

description: normal blood sample


title: 13C_M_853


title: genomic DNA from maternal blood (1st trimester) [368A]

description: normal blood sample


title: 13C_M_849


title: 13C_M_851


title: genomic DNA from cord blood [354C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [354B]

description: normal blood sample


title: 13C_M_848


title: genomic DNA from maternal blood (3rd trimester) [368B]

description: normal blood sample


title: 13C_M_852


title: 13C_M_854


title: genomic DNA from maternal blood (3rd trimester) [350B]

description: normal blood sample


title: genomic DNA from cord blood [350C]

description: normal blood sample


title: 13C_M_871


title: 13C_M_846


title: genomic DNA from maternal blood (1st trimester) [350A]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [354A]

description: normal blood sample


title: 13C_M_844


title: 13C_M_843


title: genomic DNA from cord blood [346C]

description: normal blood sample


title: 13C_M_845


title: genomic DNA from maternal blood (3rd trimester) [346B]

description: normal blood sample


title: 13C_M_840


title: 13C_M_839


title: genomic DNA from cord blood [330C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [346A]

description: normal blood sample


title: 13C_M_838


title: 13C_M_837


title: genomic DNA from maternal blood (1st trimester) [330A]

description: normal blood sample


title: genomic DNA from cord blood [329C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [329A]

description: normal blood sample


title: genomic DNA from cord blood [318C]

description: normal blood sample


title: 13C_M_836


title: 13C_M_835


title: 13C_M_834


title: genomic DNA from maternal blood (1st trimester) [318A]

description: normal blood sample


title: 13C_M_842


title: 13C_M_830


title: 13C_M_833


title: 13C_M_832


title: genomic DNA from maternal blood (3rd trimester) [316B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [316A]

description: normal blood sample


title: genomic DNA from cord blood [305C]

description: normal blood sample


title: 13C_M_829


title: genomic DNA from maternal blood (3rd trimester) [330B]

description: normal blood sample


title: genomic DNA from cord blood [316C]

description: normal blood sample


title: 13C_M_827


title: genomic DNA from maternal blood (1st trimester) [305A]

description: normal blood sample


title: 13C_M_826


title: 13C_M_828


title: 13C_M_825


title: genomic DNA from maternal blood (3rd trimester) [305B]

description: normal blood sample


title: 13C_M_824


title: 13C_M_823


title: genomic DNA from maternal blood (3rd trimester) [329B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [300B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [318B]

description: normal blood sample


title: 13C_M_822


title: genomic DNA from maternal blood (1st trimester) [300A]

description: normal blood sample


title: genomic DNA from cord blood [299C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [299B]

description: normal blood sample


title: 13C_M_820


title: 13C_M_819


title: 13C_M_831


title: 13C_M_821


title: genomic DNA from cord blood [299A]

description: normal blood sample


title: 13C_M_818


title: genomic DNA from maternal blood (1st trimester) [297A]

description: normal blood sample


title: 13C_M_817


title: genomic DNA from maternal blood (3rd trimester) [297C]

description: normal blood sample


title: genomic DNA from cord blood [300C]

description: normal blood sample


title: 13C_M_814


title: 13C_M_815


title: 13C_M_813


title: genomic DNA from maternal blood (3rd trimester) [289B]

description: normal blood sample


title: genomic DNA from cord blood [289C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [28B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [28A]

description: normal blood sample


title: genomic DNA from cord blood [28C]

description: normal blood sample


title: 13C_M_812


title: genomic DNA from maternal blood (1st trimester) [289A]

description: normal blood sample


title: genomic DNA from cord blood [279C]

description: normal blood sample


title: 13C_M_811


title: 13C_M_810


title: genomic DNA from maternal blood (3rd trimester) [279B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [279A]

description: normal blood sample


title: 13C_M_807


title: 13C_M_806


title: genomic DNA from maternal blood (1st trimester) [267A]

description: normal blood sample


title: 13C_M_804


title: genomic DNA from cord blood [26C]

description: normal blood sample


title: genomic DNA from cord blood [267C]

description: normal blood sample


title: 13C_M_803


title: 13C_M_802


title: 13C_M_801


title: genomic DNA from maternal blood (1st trimester) [26A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [26B]

description: normal blood sample


title: 13C_M_816


title: genomic DNA from maternal blood (3rd trimester) [258B]

description: normal blood sample


title: genomic DNA from cord blood [258C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [258A]

description: normal blood sample


title: genomic DNA from cord blood [254C]

description: normal blood sample


title: 13C_M_809


title: genomic DNA from maternal blood (3rd trimester) [254B]

description: normal blood sample


title: 13C_M_808


title: genomic DNA from maternal blood (1st trimester) [254A]

description: normal blood sample


title: 13C_M_797


title: 13C_M_796


title: 13C_M_795


title: 13C_M_794


title: genomic DNA from cord blood [248C]

description: normal blood sample


title: 13C_M_799


title: 13C_M_798


title: genomic DNA from maternal blood (3rd trimester) [248B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [267B]

description: normal blood sample


title: 13C_M_790


title: 13C_M_793


title: genomic DNA from cord blood [241C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [248A]

description: normal blood sample


title: 13C_M_791


title: genomic DNA from maternal blood (1st trimester) [241A]

description: normal blood sample


title: 13C_M_792


title: 13C_M_789


title: 13C_M_787


title: genomic DNA from maternal blood (3rd trimester) [240B]

description: normal blood sample


title: genomic DNA from cord blood [240C]

description: normal blood sample


title: 13C_M_788


title: genomic DNA from maternal blood (3rd trimester) [241B]

description: normal blood sample


title: genomic DNA from cord blood [24C]

description: normal blood sample


title: 13C_M_785


title: 13C_M_786


title: genomic DNA from maternal blood (3rd trimester) [24B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [24A]

description: normal blood sample


title: genomic DNA from cord blood [238C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [238B]

description: normal blood sample


title: 13C_M_781


title: genomic DNA from maternal blood (1st trimester) [238A]

description: normal blood sample


title: 13C_M_800


title: 13C_M_782


title: 13C_M_780


title: 13C_M_779


title: genomic DNA from cord blood [212C]

description: normal blood sample


title: 13C_M_778


title: genomic DNA from maternal blood (1st trimester) [212A]

description: normal blood sample


title: genomic DNA from cord blood [210C]

description: normal blood sample


title: 13C_M_777


title: genomic DNA from maternal blood (3rd trimester) [210B]

description: normal blood sample


title: 13C_M_776


title: 13C_M_775


title: 13C_M_774


title: 13C_M_773


title: genomic DNA from maternal blood (1st trimester) [240A]

description: normal blood sample


title: genomic DNA from cord blood [2C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [210A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [2B]

description: normal blood sample


title: 13C_M_784


title: 13C_M_772


title: 13C_M_783


title: 13C_M_771


title: genomic DNA from cord blood [192C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [192B]

description: normal blood sample


title: 13C_M_770


title: 13C_M_769


title: genomic DNA from cord blood [189C]

description: normal blood sample


title: 13C_M_768


title: genomic DNA from maternal blood (3rd trimester) [189B]

description: normal blood sample


title: 13C_M_382


title: 13C_M_381


title: 13C_M_383


title: genomic DNA from maternal blood (3rd trimester) [212B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [189A]

description: normal blood sample


title: 13C_M_380


title: genomic DNA from maternal blood (3rd trimester) [187B]

description: normal blood sample


title: genomic DNA from cord blood [187C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [187A]

description: normal blood sample


title: 13C_M_378


title: 13C_M_376


title: 13C_M_377


title: 13C_M_375


title: genomic DNA from maternal blood (1st trimester) [2A]

description: normal blood sample


title: 13C_M_373


title: genomic DNA from maternal blood (3rd trimester) [182B]

description: normal blood sample


title: genomic DNA from cord blood [182C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [182A]

description: normal blood sample


title: genomic DNA from cord blood [18C]

description: normal blood sample


title: 13C_M_374


title: genomic DNA from maternal blood (1st trimester) [192A]

description: normal blood sample


title: 13C_M_372


title: genomic DNA from maternal blood (3rd trimester) [18B]

description: normal blood sample


title: 13C_M_370


title: 13C_M_369


title: 13C_M_371


title: genomic DNA from cord blood [165C]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [18A]

description: normal blood sample


title: 13C_M_368


title: genomic DNA from maternal blood (1st trimester) [165A]

description: normal blood sample


title: genomic DNA from cord blood [163C]

description: normal blood sample


title: 13C_M_367


title: 13C_M_379


title: genomic DNA from maternal blood (1st trimester) [163A]

description: normal blood sample


title: genomic DNA from cord blood [161C]

description: normal blood sample


title: 13C_M_363


title: 13C_M_364


title: 13C_M_365


title: genomic DNA from maternal blood (3rd trimester) [161B]

description: normal blood sample


title: 13C_M_366


title: genomic DNA from maternal blood (1st trimester) [161A]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [150A]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [150B]

description: normal blood sample


title: 13C_M_359


title: genomic DNA from maternal blood (3rd trimester) [165B]

description: normal blood sample


title: 13C_M_362


title: 13C_M_360


title: 13C_M_361


title: genomic DNA from cord blood [150C]

description: normal blood sample


title: genomic DNA from cord blood [148C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [163B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [148B]

description: normal blood sample


title: 13C_M_358


title: 13C_M_356


title: genomic DNA from cord blood [146C]

description: normal blood sample


title: 13C_M_357


title: genomic DNA from maternal blood (3rd trimester) [146B]

description: normal blood sample


title: 13C_M_355


title: genomic DNA from maternal blood (1st trimester) [146A]

description: normal blood sample


title: genomic DNA from cord blood [145C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [145B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [145A]

description: normal blood sample


title: 13C_M_353


title: genomic DNA from cord blood [143C]

description: normal blood sample


title: 13C_M_350


title: genomic DNA from maternal blood (3rd trimester) [143B]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [141B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [148A]

description: normal blood sample


title: 13C_M_346


title: 13C_M_347


title: genomic DNA from maternal blood (1st trimester) [143A]

description: normal blood sample


title: genomic DNA from cord blood [141C]

description: normal blood sample


title: 13C_M_344


title: 13C_M_340


title: genomic DNA from maternal blood (1st trimester) [131A]

description: normal blood sample


title: 13C_M_343


title: 13C_M_339


title: genomic DNA from cord blood [131C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [131B]

description: normal blood sample


title: 13C_M_338


title: genomic DNA from cord blood [129C]

description: normal blood sample


title: 13C_M_337


title: genomic DNA from maternal blood (3rd trimester) [129B]

description: normal blood sample


title: 13C_M_354


title: 13C_M_341


title: 13C_M_349


title: 13C_M_336


title: 13C_M_348


title: genomic DNA from maternal blood (1st trimester) [129A]

description: normal blood sample


title: 13C_M_352


title: 13C_M_334


title: 13C_M_335


title: genomic DNA from maternal blood (1st trimester) [127A]

description: normal blood sample


title: 13C_M_333


title: genomic DNA from maternal blood (3rd trimester) [127B]

description: normal blood sample


title: genomic DNA from cord blood [115C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [115B]

description: normal blood sample


title: 13C_M_332


title: 13C_M_330


title: genomic DNA from maternal blood (3rd trimester) [114B]

description: normal blood sample


title: genomic DNA from cord blood [114C]

description: normal blood sample


title: 13C_M_331


title: 13C_M_328


title: genomic DNA from cord blood [103C]

description: normal blood sample


title: genomic DNA from maternal blood (3rd trimester) [103B]

description: normal blood sample


title: genomic DNA from maternal blood (1st trimester) [114A]

description: normal blood sample


title: 13C_M_329


title: 13C_M_327


title: 13C_M_325


title: 13C_M_324


title: genomic DNA from maternal blood (1st trimester) [103A]

description: normal blood sample


title: genomic DNA from cord blood [127C]

description: normal blood sample


title: 13C_M_323


title: 13C_M_321


title: 13C_M_322


title: 13C_M_320


title: 13C_M_255


title: genomic DNA from maternal blood (1st trimester) [115A]

description: normal blood sample


title: 13C_M_254


title: 13C_M_253


title: 13C_M_326


title: N20

city: San Francisco

first: Harish

last: Vasudevan

address: 1450 3rd street

institute: UCSF

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
All methylation array data was analyzed using the minfi Bioconductor package using standard parameters
Average Beta or normalized (provide the normalization method) Average Beta

label: Cy3 and Cy5

source_name: Peripheral nerve tumor

label_protocol: standard Illumina protocol

extract_protocol: DNA isolation and prepared for Illumina EPIC methylation array per manufacter instructions

value: human peripheral nerve tumor


title: N19


title: N11


title: N16


title: MPNST47


title: N22


title: N15


title: N12


title: N23


title: N7


title: N21


title: 13C_M_251


title: 13C_M_248


title: 13C_M_249


title: VS11


title: 13C_M_250


title: 13C_M_246


title: 13C_M_247


title: N1


title: VS10


title: 13C_M_245


title: VS8


title: VS6


title: 13C_M_244


title: 13C_M_243


title: VS3


title: 13C_M_242


title: 13C_M_252


title: N3


title: VS1


title: VS69


title: VS30


title: VS57


title: VS31


title: 13C_M_241


title: 13C_M_239


title: VS38


title: 13C_M_238


title: VS55


title: 13C_M_236


title: VS29


title: VS56


title: 13C_M_235


title: 13C_M_234


title: VS12


title: 13C_M_237


title: VS68


title: VS54


title: 13C_M_232


title: 13C_M_233


title: VS28


title: VS53


title: 13C_M_228


title: 13C_M_229


title: VS52


title: VS35


title: 13C_M_230


title: 13C_M_226


title: 13C_M_224


title: VS51


title: 13C_M_225


title: VS64


title: VS27


title: VS6 #2


title: VS67


title: 13C_M_223


title: 13C_M_220


title: 13C_M_218


title: VS9 #2


title: 13C_M_222


title: VS48


title: VS50


title: 13C_M_219


title: 13C_M_221


title: 13C_M_240


title: 13C_M_231


title: VS47


title: VS46


title: VS26


title: VS14


title: 13C_M_215


title: 13C_M_214


title: VS49


title: 13C_M_227


title: VS36


title: 13C_M_212


title: 13C_M_213


title: 13C_M_217


title: 13C_M_211


title: 13C_M_210


title: 13C_M_216


title: VS13


title: VS21


title: VS58 #2


title: 13C_M_207


title: 13C_M_209


title: 13C_M_208


title: 13C_M_204


title: 13C_M_206


title: VS43


title: VS22


title: VS23


title: VS20


title: 13C_M_205


title: VS45


title: VS44


title: VS1 #2


title: 13C_M_202


title: 13C_M_201


title: VS19


title: VS34


title: VS24


title: 13C_M_200


title: 13C_M_198


title: VS61 #3


title: VS61 #1


title: 13C_M_199


title: 13C_M_197


title: 13C_M_196


title: 13C_M_203


title: VS37


title: VS63


title: VS66


title: 13C_M_191


title: 13C_M_194


title: VS42


title: 13C_M_195


title: VS41


title: 13C_M_192


title: 13C_M_193


title: 13C_M_189


title: VS40


title: VS59 #2


title: 13C_M_188


title: VS39


title: 13C_M_190


title: 13C_M_187


title: VS18


title: VS60 #2


title: 13C_M_185


title: 13C_M_186


title: VS65


title: VS17


title: 13C_M_183


title: VS16


title: 13C_M_184


title: VS15


title: 13C_M_182


title: MPNST9


title: MPNST8


title: VS62


title: MPNST7


title: MPNST6


title: 13C_M_180


title: 13C_M_179


title: 13C_M_178


title: 13C_M_181


title: MPNST5


title: MPNST43


title: 13C_M_177


title: 13C_M_176


title: MPNST4


title: 13C_M_175


title: MPNST40


title: MPNST39


title: 13C_M_174


title: 13C_M_173


title: MPNST37


title: MPNST38


title: 13C_M_170


title: 13C_M_172


title: 13C_M_171


title: MPNST36


title: MPNST35


title: MPNST34


title: 13C_M_168


title: MPNST33


title: MPNST32


title: MPNST31


title: 13C_M_166


title: 13C_M_167


title: MPNST30


title: 13C_M_164


title: 13C_M_165


title: 13C_M_163


title: MPNST29


title: 13C_M_162


title: MPNST28


title: 13C_M_161


title: MPNST27


title: 13C_M_160


title: 13C_M_159


title: MPNST26


title: VS60 #1


title: 13C_M_156


title: 13C_M_155


title: 13C_M_158


title: 13C_M_157


title: MPNST25


title: MPNST23


title: 13C_M_169


title: MPNST24


title: MPNST20


title: 13C_M_154


title: MPNST2


title: MPNST19


title: 13C_M_153


title: MPNST3


title: 13C_M_151


title: MPNST17


title: MPNST18


title: MPNST16


title: 13C_M_148


title: MPNST15


title: 13C_M_149


title: MPNST13


title: 13C_M_147


title: MPNST14


title: 13C_M_146


title: MPNST22


title: 13C_M_144


title: MPNST12


title: 13C_M_145


title: 13C_M_142


title: MPNST10


title: 13C_M_143


title: 13C_M_141


title: MPNST1


title: 13C_M_140


title: 13C_M_152


title: 13C_M_150


title: 13C_M_137


title: 13C_M_139


title: 13C_M_136


title: 13C_M_135


title: EWS-502 SCR H3K27me3 (Diagenode)

city: Aurora

first: Heide

last: Ford

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

data_processing:
CUT&RUN reads were quality assessed by FastQC (v.0.11.8), MultiQC (v.1.8) and filtered with BBDuk (v.38.87).
ChIPseq reads were aligned to the hg38 human genome assembly using Bowtie2 (v2.3.4.3).
Samtools (v.1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool (v.2.21.1).
The normalization ratio for each sample was calculated by dividing the number of uniquely mapped human reads of the sample with the lowest number of reads by the number of uniquely mapped human reads of each sample. These normalization ratios were used to randomly sub-sample reads to obtain the same number of reads for each sample using using samtools view -s.
Bedtools genomecov (v.2.27.1) was used to create bedgraph files from the bam files.
Bigwig files were created using deepTools bamCoverage (v.3.2.1) and visualized using IGV (v.2.8.2).
Peaks were called using MACS2 (v2.1.2).
IDR (v.2. 0.3) was used to identify the reproducible peaks between the replicates.
Further processing of the peak data was performed in R, using in particular the following tools: valR (v.0.6.4), and DiffBind (v.3.6.2).
Average profiles and heatmaps were generated using ngs.plot (v.2.61).
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&RUN

growth_protocol: EWS-502 cells were maintained in DMEM High Glucose supplemented with 10% FBS, 1% Sodium Pyruvate, 1% NEAAs, and 1% HEPES in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were adsorbed onto activated Concavalin A beads and then incubated with antibodies O/N at 4°C. pAG-MNase was added to each sample to produce chromatin fragments under targets.
Fragmentation was terminated with the addition of STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 ug/mL RNaseA, 50 μg/mL Glycogen) and 0.5ng/ulE.colispike-in DNA. DNA was purified using a columnpurificationkit and used for library assembly.
CUT&RUN libraries were assembled using the NEBNext II Ultra Library Prep kit and dual-index primers following manufacturer protocols

treatment_protocol: Cells were maintained in 1ug/ml Puromycin after shRNA transduction

value: Ewing sarcoma

tag: cut and_run_antibody

value: Rb H3K27me3 (Diagenode C15410069)


title: EWS-502 shSIX1 KD4, SIX1 (Atlas)

value: Rb SIX1 (Atlas Antibodies HPA0011893)


title: EWS-502 SCR, SIX1 (Atlas)


title: EWS-502 SCR, FLI1 (Abcam)

value: Rb FLI1 (Abcam ab133485)


title: EWS-502 shSIX1 KD4 H3K27me3 (Diagenode)


title: EWS-502 shSIX1 KD5, IgG (Epicypher)

value: Rb igG (Epicypher 13-0042k)


title: 13C_M_134


title: EWS-502 shSIX1 KD5 H3K27me3 (Diagenode)


title: EWS-502 shSIX1 KD4, IgG (Epicypher)


title: MPNST11


title: EWS-502  SCR, IgG (Epicypher)


title: 13C_M_132


title: 13C_M_131


title: 13C_M_130


title: 13C_M_129


title: 13C_M_138


title: vascularized-kidney-organoid-d18

city: Pittsburgh

middle: C.

last: Maggiore

state: PA

institute: University of Pittsburgh

description:
10x Genomics
barcodes.tsv
genes.tsv
matrix.mtx

library_source: transcriptomic single cell

data_processing:
Raw reads were processed using Partek® Flow® software, v10.0 and aligned to the GRCh38 human reference genome.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC derived kidney organoid

growth_protocol: Day 18 kidney organoids were generated using a previously published kidney organoid protocol. The methodology was modified in order to incorporate a genetically engineered cell line

extract_protocol:
Day 18 kidney organoids were washed in DPBS once, then transferred into 37°C 0.25% trypsin-EDTA (Gibco, 15400054) and incubated with intermittent agitation for 10 minutes to obtain single cells. Cells were then centrifuged at 800rpm for 5 minutes and resuspended in DPBS and filtered through a 40mm cell filter (pluriSelect, 43-50040-51). 10X Genomics CG000365 Demonstrated Protocol was then adapted to isolate nuclei. In summary, cells were treated with chilled Multiome Lysis Buffer on ice for 5 minutes to obtain nuclei. Nuclei were centrifuged at 500 rcf for 5 minutes, supernatant was removed and resuspended in Wash Buffer. Nuclei were washed and centrifuged 3 additional times. Finally, supernatant was removed and nuclei were resuspended in Nuclei Buffer. Composition of all buffers can be found in Supplementary Table 4, 5 and 6. Using Trypan Blue, a live cell count was performed to identify dead cells. Following counting, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 1000 nuclei for analysis, accounting for predicted cell loss and doublets as laid out in 10X Genomics Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index), User Guide, CG000315.
After generation of GEMs, the cDNA library was prepared by University of Pittsburgh Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to UPMC Genome Center for sequencing on a NovaSeq 6000.

value: iPSC derived kidney organoid

value: MANZ2-2 + iETV2-PGP1

value: Wildtype MANZ2-2 + iETV2-PGP1

value: Doxycycline days 5-18


title: control-kidney-organoid-d18

growth_protocol: Day 18 kidney organoids were generated using a previously published kidney organoid protocol. The methodology was modified in order to incorporate a genetically engineered cell line/

value: Wildtype


title: EWS-502 shSIX1 KD6, SIX1 (Atlas)


title: 13C_M_128


title: 13C_M_127


title: 13C_M_126


title: PalboNTC_1

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

description:
non-targeting shRNA control
Chris_Palbo_RNA_matrix.txt

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads with default parameter. Only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to human genome reference combining the GRCh38.  STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were measured using the featureCounts.
Assembly: GRCh38
Supplementary files format and content: Chris_THBD_featurecount_matrix.txt: Reads mapped to human GRCh38, featurecount was used to count reads per gene per sample, tab-delimited txt file
Supplementary files format and content: Chris_Palbo_featurecount_matrix.txt: Reads mapped to human GRCh38, featurecount was used to count reads per gene per sample, tab-delimited txt file

source_name: Liver

growth_protocol: IMR-90 cells were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% FBS, 1X glutamine, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, and 1X penicillin streptomycin. To establish replicative senescence, IMR90 cells were passaged for 90 days. Huh7 cells were cultured Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using an RNAeasy kit (Qiagen) and dissolved in RNase-free water. RNA samples were sequenced by Novogene Corporation. In brief, RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer Spectrophotometer (IMPLEN). RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Clustering of index-coded samples was performed on an Illumina NovaSeq sequencer

treatment_protocol: non-target control, and shTHBD knock down in IMR-90 cells,shTHBD knock down in Palbocilcib-induced senescent Huh7 cells

value: Liver

value: Non-target control

value: Palbociclib-inducedsenescentHuh7cells infected withnon-targeting control


title: PalboNTC_2


title: Palbo53925_3

description:
THBD knock down in Huh7 cell line
Chris_Palbo_RNA_matrix.txt

value: shTHBD


title: 13C_M_125


title: 13C_M_133


title: Palbo53925_1


title: 13C_M_122


title: 13C_M_121


title: 13C_M_123


title: shTHBD22

description:
THBD knock down in IMR90 cell line
Chris_THBD_featurecount_matrix.txt

source_name: Lung

value: Lung

value: Human lung fibroblasts cell line

value: THBD knockdown HRAS G12V-induced senescent IMR90 cells


title: 13C_M_120


title: shTHBD13


title: shTHBD12


title: shTHBD23

description:
THBD knock down in Huh7 cell line
Chris_THBD_featurecount_matrix.txt


title: 13C_M_119


title: 13C_M_118


title: shTHBD11


title: PalboNTC_3


title: shNTC1_2

description:
non-targeting shRNA control
Chris_THBD_featurecount_matrix.txt

value: non-targeting shRNA control (NTC) HRAS G12V-induced senescent IMR90 cells


title: shNTC1_3


title: 13C_M_117


title: 13C_M_116


title: shNTC1_1


title: 13C_M_115


title: 13C_M_113


title: 13C_M_114


title: 13C_M_124


title: 13C_M_112


title: 13C_M_111


title: 13C_M_110


title: shTHBD21


title: Palbo53925_2


title: 13C_M_109


title: 13C_M_107


title: 13C_M_98


title: 13C_M_102


title: 13C_M_105


title: 13C_M_101


title: 13C_M_104


title: 13C_M_99


title: 13C_M_106


title: 13C_M_97


title: 13C_M_96


title: 13C_M_94


title: 13C_M_95


title: 13C_M_92


title: 13C_M_93


title: 13C_M_90


title: 13C_M_89


title: 13C_M_88


title: 13C_M_85


title: 13C_M_108


title: 13C_M_86


title: 13C_M_83


title: 13C_M_82


title: 13C_M_84


title: 13C_M_81


title: 13C_M_103


title: 13C_M_100


title: T112B

city: Long Beach

first: Ling

last: Gao

email: ling.gao@va.gov, lingg3@hs.uci.edu

address: 5901 E.7th Street

institute: Department of Veterans Affairs

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics  Cloud  Analysis platform (https://www.10xgenomics.com/products/cloud-analysis). FASTQ files were aligned to GRCh38 human reference genome using Cell Ranger Count v6.1.2. The number of average mapped reads per cell across the libraries were thereafter normalized using Cell Ranger Aggr function. Output files from Cell Ranger were imported to R and analyzed further using Seurat.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: scRNA-seq on paired MCC tumor resected from lymph node of a treatment naïve female patient

extract_protocol:
Resected patient tumors were dissociated followed by red blood cell lysis, washed, and passed through 22µm sterile filters to obtain single-cell suspensions. Dead cells were excluded by SYTOX staining and live cells were collected by the FACSAria Fusion flow cytometer (BD Biosciences) and BD FACSDiva (v8.0.1). Sorted cells were washed with PBS containing 0.04% BSA and resuspended at a final density of ~1000 cells/µL.
Libraries were created targeting ~10,000 cells/sample for capture using Chromium Single Cell 3’ Reagent Kits following the CG00052 Rev B. user guide. Each library was subsequently sequenced on the Illumina NovaSeq 6000 platform to targeting an average of ~50,000 reads/cell.

value: Merkel cell carcinoma tumor

value: Resected tumor from lymph node

tag: mcpyv status

value: MCPyV positive


title: 13C_M_80


title: 13C_M_78