title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056380_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056383_G1]

status: Public on Mar 09 2022

type: genomic

city: Memphis

first: Zhaoming

last: Wang

state: TN

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

country: USA

institute: St. Jude Children's Research Hospital

description: blood from survivor of childhood cancer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChips using standard Illumina protocal

scan_protocol: Arrays were stained and scanned using the Illumina HiScan system with standard recommended Illumina scanner setting

data_processing:
GenomeStudio V2011.1
Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Standard Illumina Protocal

extract_protocol: DNA extracted from periperihal blood mononuclear cells using the QIAamp DNA Blood Mini Kit (Qiagen cat#51106)

tag: gender

value: Male

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056407_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021939_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056363_G1]

description: blood from survivor of childhood cancer

value: Female


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007141_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021946_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056348_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056347_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056346_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006066_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056357_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004203_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005404_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056352_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056344_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056359_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT056340_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056335_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS056313_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056349_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056330_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004718_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056334_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056333_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001281_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST056345_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEPD056315_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056320_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056325_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005817_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056318_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056341_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056361_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056297_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056353_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056303_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056277_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056276_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS004917_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL056292_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMB056290_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005855_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056251_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056258_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056266_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056265_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006085_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056275_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST056268_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS056250_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056248_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056249_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056238_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056237_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML004332_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056269_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056257_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056243_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056262_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005836_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056236_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056234_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056227_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005081_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGENLK011914_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056247_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006097_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056232_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056230_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056224_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056218_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST056217_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL056207_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056213_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056195_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003527_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056202_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNM056208_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056225_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL022002_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML016538_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056192_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005801_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021997_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL056191_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEPD056209_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL022047_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEPD056206_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056228_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056190_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056200_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056189_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS056172_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056178_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056188_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056169_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056179_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005853_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML016548_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021948_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006071_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML056176_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL022035_G4]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056153_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056154_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056159_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005406_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056136_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056163_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL056144_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056147_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056141_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEPD056155_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056125_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056139_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL056130_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056132_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056117_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056121_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004206_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056133_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMB008030_G4]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL045755_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMB056119_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006101_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL056123_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMB008041_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005397_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056124_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005811_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056110_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056103_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056107_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS056111_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMB056113_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056122_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB056108_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS056101_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005806_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005809_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056098_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJACT056095_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056089_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT056094_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS056075_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL056051_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003419_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056050_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021941_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB005824_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003110_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEPD056041_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006089_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056011_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL056044_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT056102_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM055999_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB056055_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMRT055996_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004774_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS056079_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL055992_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB055985_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB055994_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005411_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMB055974_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS055968_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001233_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML056063_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007106_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB055960_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL055963_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004714_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021915_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003238_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM056025_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003323_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007017_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005422_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL022008_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL055976_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL043963_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041009_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL040997_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005143_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001219_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042755_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042698_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041496_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018547_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003706_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042708_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042694_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL041584_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019091_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL040978_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041509_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJST019851_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041577_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019086_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017916_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT041524_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019079_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041495_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041572_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041460_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHB041013_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL040957_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041578_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT040984_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML041472_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041511_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041506_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041440_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018580_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT019775_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041573_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041426_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS017894_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041436_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018509_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018575_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019432_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041504_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041494_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041626_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041502_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041403_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019435_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJLGG001205_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML018556_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041444_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB040951_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041413_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041376_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041367_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041627_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041361_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041360_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041422_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041418_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041396_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041629_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS017896_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041669_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041624_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041342_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019137_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041712_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041623_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042668_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041439_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041407_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018500_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041364_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041037_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041560_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041341_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041354_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019475_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041711_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041320_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019023_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019480_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041329_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS017947_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041324_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAUL041029_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041299_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041666_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041318_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041303_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041036_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041315_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041617_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017875_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017873_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041620_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019807_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041621_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017878_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018776_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS041639_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041298_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041709_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041028_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041288_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041707_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018459_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018475_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017872_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018458_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041280_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041284_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS017948_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017874_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041267_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041706_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB041015_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL041595_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041660_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041021_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041262_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041658_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041264_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041381_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL041594_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041248_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041653_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042732_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041273_G2]

description: blood from survivor of childhood cancer


title: NC410

type: SRA

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
The standard 10x Genomics cellranger (version 6.0.0) pipeline was used to extract Fastqs and 10X Genomics cellranger (version 6.0.0) pipeline was used to perform data processing.
Sequenced reads were aligned to the 10x Genomics provided mouse reference sequences (refdata-gex-mm10-2020-A).
Genome_build: mm10 (refdata-gex-mm10-2020-A)
Supplementary_files_format_and_content: 10x Genomics filtered h5 files

molecule: total RNA

organism: Mus musculus

source_name: Immune cells

growth_protocol: Samples were isolated by CD45+ enrichment from tumor single cell suspensions

extract_protocol:
Miltenyi CD45 Kit
Libraries were constructed according to 10X Genomics 3' v3.1 dual index
scRNAseq

treatment_protocol: Control, NC410, Bintrafusp alfa, NC410 plus Bintrafusp alfa, NC410 plus anti-PD-L1, NC410 plus TGF-β trap control

tag: strain

tag: tumor model

tag: cell type

value: CD45+ tumor infiltrating cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041243_G2]

description: blood from survivor of childhood cancer


title: Control


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018444_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041247_G2]

description: blood from survivor of childhood cancer


title: TRF2-homozygous-3d-1

city: Shanghai

first: Yilin

last: YING

address: Ruijin No.2 road 197, building11-1110

country: China

institute: Ruijin Hospital Shanghai China

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina HiSeq Xten 2 ×150bp paired-end was used for sequencing. More than 40 million raw reads were obtained.
Raw RNA-seq reads were filtrated by SOAPnkue with default setting to remove adapters and low quality reads and the remaining reads were trimmed into 100bp for downstream analysis.
Reads were aligned using STAR v2.6.1d on zebrafish zv10 release with parameter–quantMode GeneCounts.
Differential expression analysis was performed using DESeq2 R package.
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Embryos

extract_protocol:
Embryos were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

tag: tissue

value: Embryo

value: 3 day post fertilised

tag: genotype

value: terfa-/-


title: NC410 plus TGF-β trap control


title: TRF2-hybrid-3d-3

value: terfa+/-


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041697_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019660_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019282_G1]

description: blood from survivor of childhood cancer


title: NC410 plus Bintrafuap alfa


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018437_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT041514_G2]

description: blood from survivor of childhood cancer


title: TRF2-homozygous-3d-2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041239_G2]

description: blood from survivor of childhood cancer


title: NC410 plus anti-PD-L1


title: WT-3d-2

value: wild type


title: Bintrafusp alfa


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041610_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041235_G2]

description: blood from survivor of childhood cancer


title: TRF2-hybrid-3d-1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018429_G2]

description: blood from survivor of childhood cancer


title: TRF2-hybrid-3d-2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041694_G2]

description: blood from survivor of childhood cancer


title: WT-3d-3


title: SV_salt replicate 2

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Transcript of SA were de novol assembled using Trinity
The function of SA genes were annotated by search the ortholog of SV protein dataset using Blastx. The protein dataset was downloaded from phytozome (https://phytozome.jgi.doe.gov/pz/portal.html)
for SA,  RNA-seq reads were mapped to assembled transcripts to quantify the abundance of transcript using RSEM.And for SV, RNA-seq reads were mapped to cDNA dataset of seteria viridis downloaded from Phytozome.
Call differentiall expressed genes between ctrl and ABA treatments using edgeR package.
Genome_build: txt file contains the transcript abundance of annotated genes

organism: Setaria viridis

source_name: mature leaf

growth_protocol: Trays containing Spartina seedlings were kept indoor at a temperature controlled room of (25-27°C), under fluorescent grow light (80 - 120 μmol m-2 s-1) on a photoperiod of 16/8 hour (light/dark) photoperiod. Then two-month old healthy plants with large expanded leaves where transferred to hydroponic for salt treatment. For S. viridis, the procedure is easier and consists of directly sowing dry seed on wet potted soil and keeps soil wet by spraying water daily on the soil till the seed germinate. Setaria grow in the same photoperiod and temperature conditions as Spartina, even though its optimum light (150 – 200 μmol m-2 s-1) is slightly higher than that of Spartina. Nutrient was added routinely to ensure healthy growing plants before transferring them to hydroponic medium for salt stress treatment.

extract_protocol:
Total RNA was isolated following the protocol of the PureLInkTM RNA Mini (ThermoFisher Scientific)
Next-generation RNA-seq was performed in the Illumina platform in the pair-ended mode with read length150 bp.

treatment_protocol: For SV salt stress was performed by treating with 250mM NaCL, and for SA salt stress was perfomed by treating with 50 mM NaCL.

value: mature leaf

tag: treatment

value: salt stress


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041237_G2]

description: blood from survivor of childhood cancer


title: SV_salt replicate 1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041228_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS041636_G2]

description: blood from survivor of childhood cancer


title: SV_salt replicate 3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041234_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS041692_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041225_G2]

description: blood from survivor of childhood cancer


title: WT-3d-1


title: SA_salt replicate 2

organism: Sporobolus alterniflorus


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS018800_G2]

description: blood from survivor of childhood cancer


title: SV_control  replicate 2

value: control


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT041513_G2]

description: blood from survivor of childhood cancer


title: SA_salt replicate 1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041551_G2]

description: blood from survivor of childhood cancer


title: SA_control replicate 2


title: SV_control  replicate 1


title: SV_control  replicate 3


title: SA_salt replicate 3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041216_G2]

description: blood from survivor of childhood cancer


title: SA_control replicate 1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041207_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041206_G2]

description: blood from survivor of childhood cancer


title: HEK293_YAP knockout TNF treated_rep3

type: RNA

city: Saint-Priest-en-Jarez

first: Robin

last: Caire

address: 10 rue de la Marandière

department: Biology

country: France

institute: Université Jean Monnnet Saint-Etienne

description: sample date 2020-08-10

hyb_protocol: 70µl of hybridization buffer was added to the reporter codeset to create Mastermix which was aliquoted (8µl) in 12 tubes. 5µl of samples at 10ng/µl were added to each tube. 2µl of capture Probeset was added to each tube. Tubes were placed for 16 hours at 65°C in thermocycler.

scan_protocol: Instrument: nCounter SPRINT, used with standard procedure

data_processing: Data were processed with Nanostring nSolver 4.0 software. All quality controled were performed. Negative threshold was performed based on negative controls +2 Standard deviation. Normalization was performed using 2 housekeeping and 3 endogenous genes (ACAD9,AP2S1,CFLAR,CUL1,PPIA).

label: Nanostring CodeSet

source_name: HEK293 cells

label_protocol: 50 ng of total RNA per sample was labeled with Nanostring CodeSet, which are target specific reporter (color coded) and capture probes.

growth_protocol: HEK293 cells were cultivated in Dulbecco’s modified Eagle’s medium (DMEM, Sigma) with 10% fetal bovine serum (FBS), 1% non-essential amino acid solution and 2% penicillin and streptomycin (PS). HEK293 YAP-/- were generated using specific CRISPR cas-9 and homology direct repair plasmid targeting YAP sequence (Santa Cruz Biotechnology), CRISPR clones generation was done following manufacturer instructions, and validated by western blot and DNA sequencing. 12 well plates were coated with fibronectin (1:100, Sigma) for 2 hours at 37°C before seeding. HEK293 WT (n=6) or YAP-/- (n=6) were plated at high cell density (100,000 cells/cm2).

extract_protocol: RNA was extracted using Allprep RNA/protein kit (Qiagen Inc.). Quality and quantity of RNA were assessed by Experion RNA analysis (BioRad) and QuantIT RiboGreen RNA assay (Thermo Fisher Scientifc), respectively.

treatment_protocol: 24 hours after seeding, 3 wells for WT cells and 3 wells for YAP-/- cells were treated with TNF at 10 ng/ml  (R&D system). TNF treatment was performed for 48 hours. 3 wells for WT cells and 3 wells for YAP-/- cells were used as controls.

tag: cell line

value: YAP knockout

value: TNF treated


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041651_G2]

description: blood from survivor of childhood cancer

tag: gender


title: SA_control replicate 3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041203_G2]

description: blood from survivor of childhood cancer

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018967_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: HEK293_YAP knockout control_rep1

description: sample date 2020-08-10

value: Control


title: HEK293_YAP knockout TNF treated_rep1

description: sample date 2020-08-10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041212_G2]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041197_G2]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041218_G2]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041211_G2]

description: blood from survivor of childhood cancer

tag: vincristine


title: HEK293_Wild type TNF treated_rep3

description: sample date 2020-08-10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT041512_G2]

description: blood from survivor of childhood cancer

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL018734_G1]

description: blood from survivor of childhood cancer

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041326_G2]

description: blood from survivor of childhood cancer

tag: chestrt


title: HEK293_Wild type TNF treated_rep2

description: sample date 2020-08-10


title: HEK293_YAP knockout control_rep2

description: sample date 2020-08-10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT019220_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST019239_G2]

description: blood from survivor of childhood cancer


title: HEK_Hneg_ONT

city: Trento

first: Alessia

last: Del Piano

state: Trento

address: Via Sommarive 18

country: Italy

institute: IMMAGINA BioTECHNOLOGY

description: ribosome profiling with circAID-p-seq from HEK293T cells, transiently transfected with GFP plasmid

data_processing:
Library strategy: circAID-p-seq
circAID-p-seq basecalling : Guppy 3.6.1
circAID-p-seq consensus generation: CircAidMe pipeline
Ribo-seq data from all the library construction were aligned on GRCh38.p13 for HEK293T and GRCm38.p6 for mouse tissue using Botwie 2
Alignment files were processed with Samtools version 1.9 and analyzed with the RiboWaltz R package
Genome_build: Human: GRCh38.p13 -  Mouse:GRCm38.p6
Supplementary_files_format_and_content: Excel files including a brief annotation and transcript-specific counts of ribosome protected fragments

source_name: control HEK293T cells, circAID-p-seq/ONT

growth_protocol: Young adult wild-type FVB mice were obtained from breeding stocks at the University of Edinburgh. HEK293 (H. Sapiens, RRID: CVCL_0045) cells were seeded at 1.5x106 cells/dish and kept in culture until reaching 80% of confluence

extract_protocol:
Oxford nanopore libraries for RPFs from HEK293T and mouse liver were prepared according to circAID-p-seq protocol. Briefly, upon 5′ phosphorylation of RPFs, library preparation was performed starting from 10 pmol of ADR12 used for ligation, followed by RNA self circularization and RT-RCA. The final libraries were loaded on a R9.4 flow cell and sequenced with a MinION sequencer.
HEK298T cell lysates were obtained using a hypotonic lysis buffer. A total of 1.7 a.u. (A260 nm) were digested using . RPFs were generated by treating 1.7a.u. of lysate with 12.7 U of RNase I at room temperature for 45 min (as described in Clamer et al., 2018). ). Liver tissues were dissected immediately following sacrifice and pulverized under liquid nitrogen using a pestle and a mortar and the lysates obtained according to Bernabò et al.2017. Lysates were treated with RNAse I and the 80S with RPFs were isolated using sucrose gradient separation. The RPFs were purified using acidic phenol/chloroform extraction followed by PAGE extraction.
Libraries from RPFs isolated from HEK293T cells were prepared using the SMARTer® smRNA-Seq Kit for Illumina  and sequenced with 50 cycles single-read on an Illumina NovaSeq 6000 sequencer. Illumina libraries for RPFs from mouse liver tissue were prepared according to Ingolia et al., 2012 and were sequenced with 50 cycles single-read on an Illumina HiSeq2500 sequencer.
Oxford nanopore libraries for RPFs from HEK293T and mouse liver were prepared according to circAID-p-seq protocol. Briefly, upon 5′ phosphorylation of RPFs, library preparation was performed starting from 10 pmol of ADR12 used for ligation, followed by RNA self circularization and RT-RCA. The final libraries were loaded on a R9.4 flow cell and sequenced with a MinION sequencer.

treatment_protocol: HEK293T cells were  treated with or without harringtonine (2 µg/mL) for 3 min, followed by CHX (10 μg/mL) for 5 min at 37°C.

value: HEK293T, GFP transfected, cell line

tag: replicate

tag: rna fraction

value: Ribo-seq

value: circAID-p-seq

tag: sequencing platform

value: Oxford nanopore technology

value: Treated with CHX for 5 min before cell lysis


title: HEK293_YAP knockout control_rep3

description: sample date 2020-08-10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL041529_G2]

description: blood from survivor of childhood cancer

value: Male


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041199_G2]

description: blood from survivor of childhood cancer


title: HEK293_YAP knockout TNF treated_rep2

description: sample date 2020-08-10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041201_G2]

description: blood from survivor of childhood cancer

value: Female


title: HEK293_Wild type control_rep3

description: sample date 2020-08-10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB041668_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041188_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041191_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018403_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018402_G1]

description: blood from survivor of childhood cancer


title: HEK_Hpos_ONT

description: ribosome profiling with circAID-p-seq from HEK293T cells, transiently transfected with GFP plasmid and treated with Harringtoine drug

source_name: Treated HEK293T cells, circAID-p-seq/ONT

tag: tissue

value: Treated with harringtonine for 3 min, followed by CHX for 5 min before cell lysis


title: HEK293_Wild type control_rep1

description: sample date 2020-08-10

tag: genotype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041179_G2]

description: blood from survivor of childhood cancer


title: CB 2 blast (K16/2902)

city: Gent

first: Barbara

last: Depreter

state: Not in US

address: C. Heymanslaan 10

department: Internal Medicine and Pediatrics

country: Belgium

institute: University of Ghent

hyb_protocol: Labeled RNA was hybridized to the array in combination with CGH blocking to reduce background signaling.

scan_protocol: Micro-arrays were analyzed using an Agilent micro-array scanner and Feature Extraction software (v12.0).

data_processing: Probe intensities were background subtracted, quantile-normalized and log2-based probe intensities were calculated. A target was present if the log2 expression value exceeded the cut-off set at 6.75, based on the dark corner control probe value plus 1.

source_name: cord blood

label_protocol: Amplified RNA (Complete Whole Transcriptome Amplification Kit, Sigma-Aldrich) was labelled using the Genomic DNA ULS Labeling Kit (Agilent).

growth_protocol: At diagnosis, mononuclear cells were isolated from bone marrow or peripheral blood by Ficoll density gradient (Axis-shield) and cryopreserved in 90% fetal calf serum and 10% dimethylsulfoxide. Samples were thawed, followed by 30 min incubation at room temperature (RT) in 20 mL RPMI with 20% FCS, 200 µL DNase I (1 mg/mL, grade II bovine pancreas) and 200 µL MgCl2 (1 M) (Sigma-Aldrich). After incubation, cells were spinoculated (10 min, 400 rpm) and washed once more with RPMI/20% fetal calf serum.

extract_protocol: RNA was extracted using the miRNeasy Mini Kit (Qiagen) in combination with on-column DNase I digestion (RNase-Free DNase set, Qiagen) according to manufacturer’s instructions.

treatment_protocol: Mononuclear cells collected from AML patients and healthy controls were used to sort CD34+CD38+ and CD34+CD38- populations. If the number of CD34-positive cells concerned less than 50% of the total white blood cell population, CD34-isolation was performed using the CD34 MicroBead Kit (Milteny). The immature myeloid compartment was defined by CD34, CD45 and scatter properties. CD34+CD38+ blasts and CD34+CD38- stem cells were gated using lymphocytes and fluorescence-minus-one controls to determine CD38 expression cut-offs. Lymphocytes were sorted based on high CD45 expression and low SSC-A. Delineated cell populations were backgated on SSC-A/FSC-A and SSC-A/CD45 scatter plots to exclude non-specific events. Sorted cells were collected in RPMI supplemented with 50% fetal calf serum and a post-sort purity of >90% was reached. Following, cells were spun down (10 min, 3000 rpm, 4° C) and resuspended in TRIzol for RNA and/or DNA extraction.

tag: flt3 mutational status

value: FLT3 WT

tag: phenotype

value: Not applicable

tag: core-binding factor leukemia

value: Negative

tag: wt1 overexpression

tag: cell type

value: blast


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB017943_G2]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: anthracyclines

tag: alkylating agent,classic


title: pedAML 3 LSC (K16/2924)

source_name: patient pediatric AML

value: Positive

value: LSC


title: pedAML 1 lymphocytes (K16/2932)

value: lymphocytes


title: CB 1 HSC (K16/2883)

value: HSC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041178_G2]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018932_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt


title: HEK293_Wild type TNF treated_rep1

description: sample date 2020-08-10

tag: cell line

value: wild type

tag: treatment

value: TNF treated


title: CB 3 blast (K16/2884)

tag: flt3 mutational status


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018878_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041176_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041168_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018921_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041174_G2]

description: blood from survivor of childhood cancer


title: HEK293_Wild type control_rep2

description: sample date 2020-08-10

tag: genotype

value: Control


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL041590_G2]

description: blood from survivor of childhood cancer


title: pedAML 4 LSC (K16/2930)

tag: phenotype

tag: core-binding factor leukemia

value: CBFB-MYH11 (inv(16))


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018929_G2]

description: blood from survivor of childhood cancer


title: pedAML 4 blast (K16/2928)

tag: wt1 overexpression

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL044976_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS044973_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic


title: RNA-Seq_dALKBH5dFTO_rep3

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

data_processing:
Trimming was performed with cutadapt v2.10 with "-j 24 --minimum-length 20 --nextseq-trim=20" parameters.
Mapping to the hg38 genome assembly with GENCODE v29 genome annotation (modified to include spike-ins) was performed with STAR v2.7.6a (default parameters).
Gene-level read counting was performed with featureCounts (countMultiMappingReads = FALSE) from RsubRead (v.2.0.1) available in Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated plain text file with read counts per gene including spike-ins.

source_name: Human embryonic kidney

growth_protocol: Cells were cultivated in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum, 2 mM glutamine, 1x Antibiotic-Antimycotic (Gibco) at 37°C in a humidified atmosphere containing 5% CO2 and passaged by standard methods.

extract_protocol:
ALKBH5 and FTO double knockout was performed with CRISPR/Cas9. The cells were lysed in buffer containing 20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide (Sigma-Aldrich), 25 U/ml TURBO DNase (Ambion). Cell lysates were incubated on ice for 10 min, triturated ten times through a 26-G needle, and centrifuged at 20,000 g at +4°C for 10 min. Total RNA was isolated using TRIzol LS Reagent (Thermo Fisher Scientific) and was subsequently purified on columns Direct-zol RNA Miniprep (Zymo Research).
Libraries were prepared according to the manufacturer’s protocol using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) and RiboMinus Eukaryote System v2 (Thermo Fisher Scientific) for rRNA depletion. During library preparation, 1 µg of the total RNA was supplemented with in vitro transcribed spike-in RNAs (7 pg GFP mRNA and 1.2 pg FLuc mRNA, see [PMID:31944153]).

value: ALKBH5 and FTO double knockout


title: RNA-Seq_dALKBH5dFTO_rep2


title: pedAML 3 lymphocytes (K16/2923)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL044972_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS044975_G1]

description: blood from survivor of childhood cancer

tag: vincristine

tag: platinum


title: RNA-Seq_dALKBH5dFTO_rep1


title: RNA-Seq_wt_rep3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL044970_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt


title: pedAML 1 LSC (K16/2933)


title: RNA-Seq_wt_rep1

tag: cell line


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB044969_G1]

description: blood from survivor of childhood cancer


title: CB 1 HSC (K16/2886)

tag: flt3 mutational status


title: pedAML 2 lymphocytes (K16/2935)


title: pedAML 3 blast (K16/2216)


title: CB 2 blast (K16/2899)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS044968_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS044979_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL044967_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-Selinexor, 0.030, 24, Replicate2

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

description:
ACAAGTCT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

data_processing:
Alignment with STARv2.5.3 to GRCh38
Gene-level raw counts summarization with STARv2.5.3 quant-mode.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and metaviper analysis as described in manuscript.
Genome_build: GRCh38.v90
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for gene expression signatures and VIPER analysis of differential protein activity for perturbation samples.
RNAseq: Raw Counts (aligned to GRCh38v90 with STAR)
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt: Raw Counts (aligned to GRCh38v90 with STAR)
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt: PLATESeq sample map cell lines samples treated with selinexor and vehicle control (from A204, G401,KPMRT-RY,KPMRT-NS)
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt: Differential gene expression signature selinexor vs. DMSO control in MRT cell lines; signatures are computed against reference samples from the same matched cell line only.
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt: VIPER assessed differential protein activity selinexor vs. DMSO control in MRT cell lines; signatures are computed against reference samples from the same matched cell line only; the analysis was integrated across networks using metaVIPER

source_name: KP-MRT-RY Malignant Rhabdoid Tumor Cell Line

growth_protocol: The cells were grown in logarithomic phase till treatment

extract_protocol:
mRNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500

treatment_protocol: Drug perturbations profiles in cell lines were done at 6 and/or 24 hours after introducing drug, as indicated by appropriate column names in the sample plate maps and processed data files

value: KP-MRT-RY

value: Malignant Rhabdoid Tumor Cell

tag: treatment

value: Selinexor 0.030 uM at 24 hours


title: KP-MRT-RY-Selinexor, 0.003, 24, Replicate3

description:
TCGAACAT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Selinexor 0.003 uM at 24 hours


title: pedAML 2 blast (K16/2224)

tag: phenotype

value: Male


title: pedAML 1 blast (K16/2183)

value: FLT3 WT

value: Female

tag: core-binding factor leukemia


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS044977_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-Selinexor, 0.003, 24, Replicate1

description:
CGATAGCC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043907_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-Selinexor, 0.030, 24, Replicate3

description:
CGCTAAGG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM044978_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-Selinexor, 0.003, 24, Replicate2

description:
CACGTCAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM044164_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-DMSO, 0, 24, Replicate3

description:
TACTGCCT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: DMSO at 24 hours


title: KP-MRT-RY-DMSO, 0, 24, Replicate2

description:
GCATCCTG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004720_G2]

description: blood from survivor of childhood cancer


title: RNA-Seq_wt_rep2

tag: genotype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL044971_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-DMSO, 0, 24, Replicate1

description:
CACGAGAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL044965_G1]

description: blood from survivor of childhood cancer

tag: gender


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043913_G1]

description: blood from survivor of childhood cancer

tag: age


title: KP-MRT-RY-MOCK, 0, 24, Replicate3

description:
TTGGGTTT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Untreated at 24 hours


title: KP-MRT-RY-MOCK, 0, 24, Replicate1

description:
TTTACGAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-RY-Selinexor, 0.030, 6, Replicate3

description:
CAGCTTAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Selinexor 0.030 uM at 6 hours


title: KP-MRT-RY-MOCK, 0, 24, Replicate2

description:
TGCCTGTG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL043896_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003422_G3]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic


title: KP-MRT-RY-Selinexor, 0.030, 24, Replicate1

description:
AGCGACCT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML016555_G2]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: KP-MRT-RY-Selinexor, 0.030, 6, Replicate2

description:
GGGCTTCT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004194_G2]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: KP-MRT-RY-Selinexor, 0.030, 6, Replicate1

description:
TGAAGTAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS043950_G1]

description: blood from survivor of childhood cancer

tag: vincristine


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021945_G2]

description: blood from survivor of childhood cancer

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043895_G1]

description: blood from survivor of childhood cancer

tag: brainrt


title: KP-MRT-RY-Selinexor, 0.003, 6, Replicate2

description:
AGGCGGTA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Selinexor 0.003 uM at 6 hours


title: KP-MRT-RY-DMSO, 0, 6, Replicate3

description:
TGTTTGCT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: DMSO at 6 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL044964_G1]

description: blood from survivor of childhood cancer

tag: chestrt


title: KP-MRT-RY-Selinexor, 0.003, 6, Replicate1

description:
CTTGAGCT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

tag: cell line


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043910_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043904_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005426_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-MOCK, 0, 6, Replicate3

description:
AGCACTAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Untreated at 6 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004210_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-DMSO, 0, 6, Replicate1

description:
CGGATCAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005319_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-MOCK, 0, 6, Replicate1

description:
TATGCAGC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041421_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML016547_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-MOCK, 0, 6, Replicate2

description:
GATGAGGT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-Selinexor, 0.030, 24, Replicate3

description:
GACTGCAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: KP-MRT-NS Malignant Rhabdoid Tumor Cell Line

value: KP-MRT-NS


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005424_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005403_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-Selinexor, 0.030, 24, Replicate1

description:
CTGCTTGC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-Selinexor, 0.003, 24, Replicate3

description:
CATCCTTA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-Selinexor, 0.003, 24, Replicate1

description:
CCAGAAGG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-Selinexor, 0.030, 24, Replicate2

description:
GTGATGAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM044962_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043908_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-Selinexor, 0.003, 24, Replicate2

description:
GATTGACA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-RY-Selinexor, 0.003, 6, Replicate3

description:
CTCCAGAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML016477_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004768_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043967_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-RY-DMSO, 0, 6, Replicate2

description:
CGTAAGCG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-DMSO, 0, 24, Replicate1

description:
AGTCATTC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043952_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043953_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-MOCK, 0, 24, Replicate3

description:
GGCCATGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-MOCK, 0, 24, Replicate1

description:
AATCGAGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043906_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043902_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043939_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-Selinexor, 0.030, 6, Replicate3

description:
GGTCTTGG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL044960_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-Selinexor, 0.030, 6, Replicate2

description:
CACCCTAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043968_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL021966_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-Selinexor, 0.003, 6, Replicate3

description:
AGCATGCC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-Selinexor, 0.003, 6, Replicate2

description:
CACTGGTA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003128_G2]

description: blood from survivor of childhood cancer