title: 9769100149_R02C01

description: Tumor

label: Cy5 and Cy689


title: 9769100098_R06C02

status: Public on Mar 31 2023

type: genomic

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

country: USA

institute: Roswell Park Comprehensive Cancer Center

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
The raw intensity IDATfiles were extracted using GenomeStudio,and processed by the minfi R package
Processed data file contains: Average Beta

label: Cy5 and Cy686

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE breast tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a MasterPure DNA purification kit (Epicentre).

tag: tissue

value: breast tumor

tag: Sex

value: Female


title: 9769100149_R01C01

description: Tumor

label: Cy5 and Cy687


title: 9769100149_R01C02

description: Tumor

label: Cy5 and Cy688


title: 9769100098_R05C01

description: Tumor

label: Cy5 and Cy684


title: 9769100098_R05C02

description: Tumor

label: Cy5 and Cy685


title: 9704031056_R04C01

description: Tumor

label: Cy5 and Cy8


title: 9769100098_R03C02

description: Tumor

label: Cy5 and Cy681


title: 9769100098_R04C01

description: Tumor

label: Cy5 and Cy682


title: 9769100098_R02C01

description: Tumor

label: Cy5 and Cy678


title: 9769100098_R01C02

description: Tumor

label: Cy5 and Cy677


title: 9769100098_R01C01

description: Tumor

label: Cy5 and Cy676


title: 9769100098_R03C01

description: Tumor

label: Cy5 and Cy680


title: 9769100097_R06C01

description: Tumor

label: Cy5 and Cy674


title: 9769100097_R06C02

description: Tumor

label: Cy5 and Cy675


title: 9704031056_R01C01

description: Tumor

label: Cy5 and Cy3


title: 9769100097_R05C02

description: Tumor

label: Cy5 and Cy673


title: 9769100097_R03C02

description: Tumor

label: Cy5 and Cy669


title: 9769100097_R04C01

description: Tumor

label: Cy5 and Cy670


title: 9769100097_R03C01

description: Tumor

label: Cy5 and Cy668


title: 9769100097_R01C02

description: Tumor

label: Cy5 and Cy666


title: 9769100097_R02C01

description: Tumor

label: Cy5 and Cy667


title: 9769100076_R06C02

description: Tumor

label: Cy5 and Cy665


title: 9769100076_R05C02

description: Tumor

label: Cy5 and Cy664


title: 9769100076_R04C02

description: Tumor

label: Cy5 and Cy662


title: 9769100076_R04C01

description: Tumor

label: Cy5 and Cy661


title: 9769100076_R05C01

description: Tumor

label: Cy5 and Cy663


title: 9769100098_R04C02

description: Tumor

label: Cy5 and Cy683


title: 9769100076_R02C02

description: Tumor

label: Cy5 and Cy659


title: 9769100076_R03C01

description: Tumor

label: Cy5 and Cy660


title: 9769100076_R01C02

description: Tumor

label: Cy5 and Cy658


title: 9769100076_R01C01

description: Tumor

label: Cy5 and Cy657


title: 9769100069_R05C02

description: Tumor

label: Cy5 and Cy654


title: 9769100069_R06C01

description: Tumor

label: Cy5 and Cy655


title: 9769100098_R02C02

description: Tumor

label: Cy5 and Cy679


title: 9769100069_R06C02

description: Tumor

label: Cy5 and Cy656


title: 9769100069_R03C01

description: Tumor

label: Cy5 and Cy650


title: 9769100069_R03C02

description: Tumor

label: Cy5 and Cy651


title: 9769100069_R04C02

description: Tumor

label: Cy5 and Cy653


title: 9769100069_R02C01

description: Tumor

label: Cy5 and Cy648


title: 9769100097_R05C01

description: Tumor

label: Cy5 and Cy672


title: 9769100069_R04C01

description: Tumor

label: Cy5 and Cy652


title: 9769100069_R01C02

description: Tumor

label: Cy5 and Cy647


title: 9769100097_R04C02

description: Tumor

label: Cy5 and Cy671


title: 9769100068_R06C02

description: Tumor

label: Cy5 and Cy645


title: 9769100069_R01C01

description: Tumor

label: Cy5 and Cy646


title: 9769100068_R06C01

description: Tumor

label: Cy5 and Cy644


title: 9769100068_R05C01

description: Tumor

label: Cy5 and Cy642


title: 9769100068_R04C02

description: Tumor

label: Cy5 and Cy641


title: 9769100068_R04C01

description: Tumor

label: Cy5 and Cy640


title: 9769100068_R02C02

description: Tumor

label: Cy5 and Cy637


title: 9769100069_R02C02

description: Tumor

label: Cy5 and Cy649


title: 9769100068_R05C02

description: Tumor

label: Cy5 and Cy643


title: 9769100068_R01C01

description: Tumor

label: Cy5 and Cy635


title: 9769100067_R06C02

description: Tumor

label: Cy5 and Cy634


title: 9769100067_R05C02

description: Tumor

label: Cy5 and Cy632


title: 9769100067_R04C02

description: Tumor

label: Cy5 and Cy631


title: 9769100067_R04C01

description: Tumor

label: Cy5 and Cy630


title: 9769100067_R03C01

description: Tumor

label: Cy5 and Cy628


title: 9769100067_R02C01

description: Tumor

label: Cy5 and Cy626


title: 9769100067_R02C02

description: Tumor

label: Cy5 and Cy627


title: 9769100067_R03C02

description: Tumor

label: Cy5 and Cy629


title: 9769100067_R01C01

description: Tumor

label: Cy5 and Cy625


title: 9769100065_R06C02

description: Tumor

label: Cy5 and Cy624


title: 9769100065_R06C01

description: Tumor

label: Cy5 and Cy623


title: 9769100065_R03C02

description: Tumor

label: Cy5 and Cy619


title: 9769100065_R04C02

description: Tumor

label: Cy5 and Cy621


title: 9769100065_R04C01

description: Tumor

label: Cy5 and Cy620


title: 9769100065_R02C01

description: Tumor

label: Cy5 and Cy616


title: 9769100065_R02C02

description: Tumor

label: Cy5 and Cy617


title: 9769100068_R03C02

description: Tumor

label: Cy5 and Cy639


title: 9769100068_R03C01

description: Tumor

label: Cy5 and Cy638


title: 9769100065_R03C01

description: Tumor

label: Cy5 and Cy618


title: 9769100051_R06C01

description: Tumor

label: Cy5 and Cy613


title: 9769100068_R01C02

description: Tumor

label: Cy5 and Cy636


title: 9769100051_R06C02

description: Tumor

label: Cy5 and Cy614


title: 9769100051_R04C01

description: Tumor

label: Cy5 and Cy609


title: 9769100051_R03C02

description: Tumor

label: Cy5 and Cy608


title: 9769100067_R06C01

description: Tumor

label: Cy5 and Cy633


title: 9769100051_R04C02

description: Tumor

label: Cy5 and Cy610


title: 9769100051_R02C01

description: Tumor

label: Cy5 and Cy606


title: 9769100051_R01C02

description: Tumor

label: Cy5 and Cy605


title: 9769100051_R05C01

description: Tumor

label: Cy5 and Cy611


title: 9769100048_R06C02

description: Tumor

label: Cy5 and Cy603


title: 9769100048_R05C02

description: Tumor

label: Cy5 and Cy601


title: 9769100048_R06C01

description: Tumor

label: Cy5 and Cy602


title: 9769100048_R04C02

description: Tumor

label: Cy5 and Cy600


title: 9769100065_R05C02

description: Tumor

label: Cy5 and Cy622


title: 9769100051_R03C01

description: Tumor

label: Cy5 and Cy607


title: 9769100048_R03C01

description: Tumor

label: Cy5 and Cy598


title: 9769100048_R02C02

description: Tumor

label: Cy5 and Cy597


title: 9769100048_R04C01

description: Tumor

label: Cy5 and Cy599


title: 9769100048_R02C01

description: Tumor

label: Cy5 and Cy596


title: 9769100051_R01C01

description: Tumor

label: Cy5 and Cy604


title: 9769100048_R01C01

description: Tumor

label: Cy5 and Cy594


title: 9769100048_R01C02

description: Tumor

label: Cy5 and Cy595


title: 9769100065_R01C01

description: Tumor

label: Cy5 and Cy615


title: 9769100047_R06C02

description: Tumor

label: Cy5 and Cy593


title: 9769100051_R05C02

description: Tumor

label: Cy5 and Cy612


title: 9769100047_R05C02

description: Tumor

label: Cy5 and Cy591


title: 9769100047_R04C01

description: Tumor

label: Cy5 and Cy589


title: 9769100047_R06C01

description: Tumor

label: Cy5 and Cy592


title: 9769100047_R03C02

description: Tumor

label: Cy5 and Cy588


title: 9769100047_R05C01

description: Tumor

label: Cy5 and Cy590


title: 9769100047_R03C01

description: Tumor

label: Cy5 and Cy587


title: 9769100047_R02C01

description: Tumor

label: Cy5 and Cy585


title: 9769100046_R06C02

description: Tumor

label: Cy5 and Cy582


title: 9769100047_R01C02

description: Tumor

label: Cy5 and Cy584


title: 9769100047_R01C01

description: Tumor

label: Cy5 and Cy583


title: 9769100047_R02C02

description: Tumor

label: Cy5 and Cy586


title: 9769100046_R06C01

description: Tumor

label: Cy5 and Cy581


title: 9769100046_R05C02

description: Tumor

label: Cy5 and Cy580


title: 9769100046_R05C01

description: Tumor

label: Cy5 and Cy579


title: 9769100046_R04C02

description: Tumor

label: Cy5 and Cy578


title: 9769100046_R03C02

description: Tumor

label: Cy5 and Cy576


title: 9769100046_R02C02

description: Tumor

label: Cy5 and Cy575


title: 9769100046_R01C02

description: Tumor

label: Cy5 and Cy573


title: 9769100046_R04C01

description: Tumor

label: Cy5 and Cy577


title: 9769100034_R06C02

description: Tumor

label: Cy5 and Cy571


title: 9769100046_R02C01

description: Tumor

label: Cy5 and Cy574


title: 9769100034_R05C01

description: Tumor

label: Cy5 and Cy569


title: 9769100046_R01C01

description: Tumor

label: Cy5 and Cy572


title: 9769100034_R03C01

description: Tumor

label: Cy5 and Cy566


title: 9769100034_R04C01

description: Tumor

label: Cy5 and Cy568


title: 9769100034_R02C02

description: Tumor

label: Cy5 and Cy565


title: 9769100034_R03C02

description: Tumor

label: Cy5 and Cy567


title: 9769100017_R06C02

description: Tumor

label: Cy5 and Cy562


title: 9769100034_R02C01

description: Tumor

label: Cy5 and Cy564


title: 9769100017_R06C01

description: Tumor

label: Cy5 and Cy561


title: 9769100034_R01C01

description: Tumor

label: Cy5 and Cy563


title: 9769100017_R05C02

description: Tumor

label: Cy5 and Cy560


title: 9769100017_R05C01

description: Tumor

label: Cy5 and Cy559


title: 9769100017_R04C02

description: Tumor

label: Cy5 and Cy558


title: 9769100017_R04C01

description: Tumor

label: Cy5 and Cy557


title: 9769100017_R01C01

description: Tumor

label: Cy5 and Cy552


title: 9769100014_R06C02

description: Tumor

label: Cy5 and Cy551


title: 9769100017_R01C02

description: Tumor

label: Cy5 and Cy553


title: 9769100014_R06C01

description: Tumor

label: Cy5 and Cy550


title: 9769100014_R05C02

description: Tumor

label: Cy5 and Cy549


title: 9769100014_R03C02

description: Tumor

label: Cy5 and Cy546


title: 9769100034_R06C01

description: Tumor

label: Cy5 and Cy570


title: 9769100014_R02C02

description: Tumor

label: Cy5 and Cy545


title: 9769100014_R04C01

description: Tumor

label: Cy5 and Cy547


title: 9769100014_R04C02

description: Tumor

label: Cy5 and Cy548


title: 9769100014_R02C01

description: Tumor

label: Cy5 and Cy544


title: 9769100014_R01C02

description: Tumor

label: Cy5 and Cy543


title: 9769100014_R01C01

description: Tumor

label: Cy5 and Cy542


title: 9769100012_R05C02

description: Tumor

label: Cy5 and Cy540


title: 9769100012_R04C02

description: Tumor

label: Cy5 and Cy538


title: 9769100012_R06C02

description: Tumor

label: Cy5 and Cy541


title: 9769100012_R05C01

description: Tumor

label: Cy5 and Cy539


title: 9769100012_R04C01

description: Tumor

label: Cy5 and Cy537


title: 9769100012_R03C01

description: Tumor

label: Cy5 and Cy536


title: 9769100012_R01C02

description: Tumor

label: Cy5 and Cy534


title: 9769100011_R05C01

description: Tumor

label: Cy5 and Cy530


title: 9769100012_R02C01

description: Tumor

label: Cy5 and Cy535


title: 9769100011_R04C02

description: Tumor

label: Cy5 and Cy529


title: 9769100011_R06C01

description: Tumor

label: Cy5 and Cy532


title: 9769100011_R05C02

description: Tumor

label: Cy5 and Cy531


title: 9769100017_R02C01

description: Tumor

label: Cy5 and Cy554


title: 9769100011_R06C02

description: Tumor

label: Cy5 and Cy533


title: 9769100011_R04C01

description: Tumor

label: Cy5 and Cy528


title: 9769100017_R03C01

description: Tumor

label: Cy5 and Cy556


title: 9769100017_R02C02

description: Tumor

label: Cy5 and Cy555


title: 9769100011_R03C01

description: Tumor

label: Cy5 and Cy526


title: 9769100011_R02C01

description: Tumor

label: Cy5 and Cy525


title: 9769100011_R03C02

description: Tumor

label: Cy5 and Cy527


title: 9769100011_R01C02

description: Tumor

label: Cy5 and Cy524


title: 9761749166_R06C01

description: Tumor

label: Cy5 and Cy522


title: 9761749166_R05C02

description: Tumor

label: Cy5 and Cy521


title: 9761749166_R04C02

description: Tumor

label: Cy5 and Cy519


title: 9761749166_R06C02

description: Tumor

label: Cy5 and Cy523


title: 9761749166_R05C01

description: Tumor

label: Cy5 and Cy520


title: 9761749166_R03C02

description: Tumor

label: Cy5 and Cy517


title: 9761749166_R04C01

description: Tumor

label: Cy5 and Cy518


title: 9761749166_R02C02

description: Tumor

label: Cy5 and Cy515


title: 9761749166_R03C01

description: Tumor

label: Cy5 and Cy516


title: 9761749166_R01C01

description: Tumor

label: Cy5 and Cy513


title: 9761749166_R02C01

description: Tumor

label: Cy5 and Cy514


title: 9761749150_R06C02

description: Tumor

label: Cy5 and Cy512


title: 9761749150_R05C02

description: Tumor

label: Cy5 and Cy510


title: 9761749150_R05C01

description: Tumor

label: Cy5 and Cy509


title: 9761749150_R04C01

description: Tumor

label: Cy5 and Cy507


title: 9761749150_R04C02

description: Tumor

label: Cy5 and Cy508


title: 9761749150_R01C02

description: Tumor

label: Cy5 and Cy503


title: 9761749150_R03C01

description: Tumor

label: Cy5 and Cy506


title: 9761749150_R01C01

description: Tumor

label: Cy5 and Cy502


title: 9761749148_R04C02

description: Tumor

label: Cy5 and Cy498


title: 9761749148_R06C01

description: Tumor

label: Cy5 and Cy501


title: 9761749150_R02C01

description: Tumor

label: Cy5 and Cy504


title: 9761749150_R02C02

description: Tumor

label: Cy5 and Cy505


title: 9761749150_R06C01

description: Tumor

label: Cy5 and Cy511


title: 9761749148_R05C01

description: Tumor

label: Cy5 and Cy499


title: 9761749148_R03C02

description: Tumor

label: Cy5 and Cy496


title: 9761749148_R05C02

description: Tumor

label: Cy5 and Cy500


title: 9761749148_R03C01

description: Tumor

label: Cy5 and Cy495


title: 9761749148_R04C01

description: Tumor

label: Cy5 and Cy497


title: 9761749148_R01C02

description: Tumor

label: Cy5 and Cy492


title: 9721367122_R05C02

description: Tumor

label: Cy5 and Cy488


title: 9721367122_R06C02

description: Tumor

label: Cy5 and Cy490


title: 9761749148_R01C01

description: Tumor

label: Cy5 and Cy491


title: 9761749148_R02C02

description: Tumor

label: Cy5 and Cy494


title: 9721367122_R05C01

description: Tumor

label: Cy5 and Cy487


title: 9721367122_R06C01

description: Tumor

label: Cy5 and Cy489


title: 9721367122_R04C02

description: Tumor

label: Cy5 and Cy486


title: 9721367122_R04C01

description: Tumor

label: Cy5 and Cy485


title: 9721367122_R03C02

description: Tumor

label: Cy5 and Cy484


title: 9721367122_R01C01

description: Tumor

label: Cy5 and Cy481


title: 9721367106_R05C01

description: Tumor

label: Cy5 and Cy478


title: 9721367106_R02C01

description: Tumor

label: Cy5 and Cy473


title: 9721367106_R04C01

description: Tumor

label: Cy5 and Cy476


title: 9721367076_R06C02

description: Tumor

label: Cy5 and Cy470


title: 9721367076_R05C02

description: Tumor

label: Cy5 and Cy469


title: 9721367106_R02C02

description: Tumor

label: Cy5 and Cy474


title: 9721367106_R01C02

description: Tumor

label: Cy5 and Cy472


title: 9721367106_R01C01

description: Tumor

label: Cy5 and Cy471


title: 9721367076_R05C01

description: Tumor

label: Cy5 and Cy468


title: 9721367076_R03C02

description: Tumor

label: Cy5 and Cy465


title: 9721367076_R04C02

description: Tumor

label: Cy5 and Cy467


title: 9721367106_R04C02

description: Tumor

label: Cy5 and Cy477


title: 9721367076_R04C01

description: Tumor

label: Cy5 and Cy466


title: 9721367076_R03C01

description: Tumor

label: Cy5 and Cy464


title: 9721367106_R03C02

description: Tumor

label: Cy5 and Cy475


title: 9721367076_R02C02

description: Tumor

label: Cy5 and Cy463


title: 9721367076_R02C01

description: Tumor

label: Cy5 and Cy462


title: 9721367076_R01C02

description: Tumor

label: Cy5 and Cy461


title: 9721367074_R06C02

description: Tumor

label: Cy5 and Cy459


title: 9761749148_R02C01

description: Tumor

label: Cy5 and Cy493


title: 9721367076_R01C01

description: Tumor

label: Cy5 and Cy460


title: 9721367074_R06C01

description: Tumor

label: Cy5 and Cy458


title: 9721367074_R05C02

description: Tumor

label: Cy5 and Cy457


title: 9721367122_R02C02

description: Tumor

label: Cy5 and Cy483


title: 9721367106_R06C01

description: Tumor

label: Cy5 and Cy479


title: 9721367106_R06C02

description: Tumor

label: Cy5 and Cy480


title: 9721367122_R02C01

description: Tumor

label: Cy5 and Cy482


title: 9721367074_R04C02

description: Tumor

label: Cy5 and Cy455


title: 9721367074_R04C01

description: Tumor

label: Cy5 and Cy454


title: 9721367074_R03C02

description: Tumor

label: Cy5 and Cy453


title: 9721367074_R02C02

description: Tumor

label: Cy5 and Cy452


title: 9721367074_R01C01

description: Tumor

label: Cy5 and Cy449


title: 9721367073_R05C02

description: Tumor

label: Cy5 and Cy447


title: 9721367073_R06C01

description: Tumor

label: Cy5 and Cy448


title: 9721367074_R02C01

description: Tumor

label: Cy5 and Cy451


title: 9721367074_R01C02

description: Tumor

label: Cy5 and Cy450


title: 9721367073_R04C02

description: Tumor

label: Cy5 and Cy445


title: 9721367073_R05C01

description: Tumor

label: Cy5 and Cy446


title: 9721367073_R03C02

description: Tumor

label: Cy5 and Cy443


title: 9721367073_R02C02

description: Tumor

label: Cy5 and Cy441


title: 9721367073_R01C01

description: Tumor

label: Cy5 and Cy438


title: 9721367073_R02C01

description: Tumor

label: Cy5 and Cy440


title: 9721367073_R04C01

description: Tumor

label: Cy5 and Cy444


title: 9721367073_R03C01

description: Tumor

label: Cy5 and Cy442


title: 9721367073_R01C02

description: Tumor

label: Cy5 and Cy439


title: 9721367064_R06C02

description: Tumor

label: Cy5 and Cy437


title: 9721367064_R03C02

description: Tumor

label: Cy5 and Cy432


title: 9721367064_R03C01

description: Tumor

label: Cy5 and Cy431


title: 9721367064_R04C02

description: Tumor

label: Cy5 and Cy434


title: 9721367064_R05C02

description: Tumor

label: Cy5 and Cy435


title: 9721367064_R06C01

description: Tumor

label: Cy5 and Cy436


title: 9721367064_R04C01

description: Tumor

label: Cy5 and Cy433


title: 9721367074_R05C01

description: Tumor

label: Cy5 and Cy456


title: 9721367064_R02C02

description: Tumor

label: Cy5 and Cy430


title: 9721367064_R02C01

description: Tumor

label: Cy5 and Cy429


title: 9721367064_R01C02

description: Tumor

label: Cy5 and Cy428


title: 9721367063_R06C01

description: Tumor

label: Cy5 and Cy425


title: 9721367063_R06C02

description: Tumor

label: Cy5 and Cy426


title: 9721367063_R05C02

description: Tumor

label: Cy5 and Cy424


title: 9721367064_R01C01

description: Tumor

label: Cy5 and Cy427


title: 9721367063_R04C01

description: Tumor

label: Cy5 and Cy423


title: 9721367063_R03C01

description: Tumor

label: Cy5 and Cy421


title: 9721367063_R02C02

description: Tumor

label: Cy5 and Cy420


title: 9721367063_R02C01

description: Tumor

label: Cy5 and Cy419


title: 9721367063_R01C02

description: Tumor

label: Cy5 and Cy418


title: 9721367063_R01C01

description: Tumor

label: Cy5 and Cy417


title: 9721367047_R06C02

description: Tumor

label: Cy5 and Cy416


title: 9721367047_R06C01

description: Tumor

label: Cy5 and Cy415


title: 9721367047_R05C01

description: Tumor

label: Cy5 and Cy413


title: 9721367063_R03C02

description: Tumor

label: Cy5 and Cy422


title: 9721367047_R03C01

description: Tumor

label: Cy5 and Cy409


title: 9721367047_R01C02

description: Tumor

label: Cy5 and Cy407


title: 9721367047_R01C01

description: Tumor

label: Cy5 and Cy406


title: 9721367040_R04C01

description: Tumor

label: Cy5 and Cy401


title: 9721367040_R06C01

description: Tumor

label: Cy5 and Cy404


title: 9721367040_R03C02

description: Tumor

label: Cy5 and Cy400


title: 9721367040_R01C02

description: Tumor

label: Cy5 and Cy397


title: 9721367040_R02C01

description: Tumor

label: Cy5 and Cy398


title: 9721367040_R03C01

description: Tumor

label: Cy5 and Cy399


title: 9721367027_R05C02

description: Tumor

label: Cy5 and Cy394


title: 9721367027_R06C02

description: Tumor

label: Cy5 and Cy395


title: 9721367047_R04C02

description: Tumor

label: Cy5 and Cy412


title: 9721367047_R02C02

description: Tumor

label: Cy5 and Cy408


title: 9721367040_R06C02

description: Tumor

label: Cy5 and Cy405


title: 9721367027_R05C01

description: Tumor

label: Cy5 and Cy393


title: 9721367027_R04C01

description: Tumor

label: Cy5 and Cy392


title: era_N2_2

status: Public on Feb 08 2023

type: SRA

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

library_source: transcriptomic

data_processing:
Genome_build: genome of Ath TAIR10
genome mapping and counts of reads by gene locus are done with Tophat2/HTSeqcount; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: Media=poting soil,Hygrometry 50%,24 day and 19°C night, 100 µmol.m-2.s-1 Light

extract_protocol:
era_N2_2(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx

treatment_protocol: N2-abiotic stress-nitrogen-nitrate nutritionquantity 2mM

tag: genotype

value: era1 - mutant=knock-out,insertional mutagen,T-DNA-AT5G66470

tag: developmental stage

value: rosette


title: era_N2_3

extract_protocol:
era_N2_3(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: 9721367047_R05C02

description: Tumor

label: Cy5 and Cy414


title: era_N2_1

extract_protocol:
era_N2_1(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: 9721367047_R04C01

description: Tumor

label: Cy5 and Cy411


title: 9721367047_R03C02

description: Tumor

label: Cy5 and Cy410


title: era_N10_2

extract_protocol:
era_N10_2(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx

treatment_protocol: N10-abiotic stress-nitrogen-nitrate nutritionquantity 10mM


title: 9721367040_R05C02

description: Tumor

label: Cy5 and Cy403


title: 9721367040_R04C02

description: Tumor

label: Cy5 and Cy402


title: era_N10_1

extract_protocol:
era_N10_1(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: era_N10_3

extract_protocol:
era_N10_3(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: WT_N2_3

extract_protocol:
WT_N2_3(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx

value: wild type (WT)


title: era_N0_2

extract_protocol:
era_N0_2(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx

treatment_protocol: N0-abiotic stress-nitrogen-nitrate nutritionquantity 0mM


title: WT_N2_1

extract_protocol:
WT_N2_1(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: WT_N2_2

extract_protocol:
WT_N2_2(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: era_N0_3

extract_protocol:
era_N0_3(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: WT_N0_2

extract_protocol:
WT_N0_2(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: WT_N10_1

extract_protocol:
WT_N10_1(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: WT_N0_3

extract_protocol:
WT_N0_3(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: era_N0_1

extract_protocol:
era_N0_1(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: 9721367040_R01C01

description: Tumor

label: Cy5 and Cy396


title: WT_N0_1

extract_protocol:
WT_N0_1(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: WT_N10_2

extract_protocol:
WT_N10_2(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: nlp2_T0_3

data_processing:
Genome_build: transcriptome of TAIR10
transcriptome mapping and counts of reads by gene locus are done with bowtie2; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,gene_length,counts_SEreads

extract_protocol:
nlp2_T0_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Nitrate treatment/deprivation-compound based treatment-nitrogen concentration-nitrogen deprivation 10 days old seedling (No treatment) were N-starved during 3 days (Nitrate Stravation treatment) , and nitrate (3 mM) was then applied (13 days old seedlings) during 30 (Nitrate Induction treatment).

tag: nitrate treatment

value: nlp2-2 - mutant=knock-out,insertional mutagen,T-DNA-AT4G35270

tag: dates

value: seedling


title: nlp2_T30_1

extract_protocol:
nlp2_T30_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: nlp2_T30_3

extract_protocol:
nlp2_T30_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: nlp2_ctrl_2

extract_protocol:
nlp2_ctrl_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: ctrl


title: nlp2_T0_2

extract_protocol:
nlp2_T0_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_ctrl_3

extract_protocol:
Col4_ctrl_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: wild type (Col-4)


title: nlp2_T0_1

extract_protocol:
nlp2_T0_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_ctrl_2

extract_protocol:
Col4_ctrl_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_T30_3

extract_protocol:
Col4_T30_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_ctrl_1

extract_protocol:
Col4_ctrl_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_T30_2

extract_protocol:
Col4_T30_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_T30_1

extract_protocol:
Col4_T30_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_T0_3

extract_protocol:
Col4_T0_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Col4_T0_2

extract_protocol:
Col4_T0_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: nlp2_ctrl_3

extract_protocol:
nlp2_ctrl_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT_N10_3

extract_protocol:
WT_N10_3(100mg)
rna_selection:selection polyA(3'seq), single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx


title: T3

status: Public on Dec 31 2022

city: Shijiazhuang

first: Shuang

state: Hebei

address: No.215 Heping West Road

department: Neurology

country: China

institute: The Second Hospital of Hebei Medical University

description: Administered with liraglutide

data_processing:
Basecalling was performed using default software offered by Illumina NovaSeq6000.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm10 whole genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) by default parameters.
Fragments Per Kilobase per Million (FPKM) were calculated.
Genome_build: mm10
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.

molecule: polyA RNA

organism: Mus musculus

source_name: Lumbar Spinal Cord

extract_protocol:
Lumbar spinal cord of EAE mice and liraglutide treated EAE mice were removed on disease peak, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Agilent 2100 Bioanalyzer was used to evaluate the quality of RNA. Oligo(dT) magnetic bead was used to purify the mRNA in total RNA, then mRNA was split into 300 bp fragments and reverse transcribed into cDNA library for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: LIRA+EAE

tag: strain

value: Lumbar Spinal Cord


title: T1

description: Administered with liraglutide


title: T2

description: Administered with liraglutide


title: C2

description: Administered with saline

value: EAE


title: Eomes iKO cIEL P14 CD8+ T cells ADT

status: Public on Dec 28 2022

city: San Diego

first: John

last: Chang

state: CA

address: UCSD

institute: UC San Diego

description:
3_19_NE_CIEL_CD45_1_barcodes.tsv.gz
3_19_NE_CIEL_CD45_1_features.tsv.gz
3_19_NE_CIEL_CD45_1_matrix.mtx.gz

library_source: other

data_processing:
Cell Ranger (v6.0.1) was used to process sequencing information and single cell barcodes.
Gene and cell filtering, clustering, differential and average expression using Seurat (v4.1.1)
Cell Ranger output was converted to .loom files with velocyto (v0.17.17) for velocity analysis.
Velocity and latent time anlysis using scVelo (v0.2.4).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Colon IEL

extract_protocol:
Control and Eomes iKO P14 CD8+T cells were harvested from the siIEL, siLPL, cIEL, and cLPL tissue compartments from recipient mice infected more than 21 days prior, FACS-isolated, and prepared for single-cell libraries.
Libaries were constructed using the Chromium Next GEM Single Cell 3’Kit v3.1 (10xGenomics).

value: Colon IEL

tag: cell type

value: T cells


title: C1

description: Administered with saline


title: Eomes iKO cLPL P14 CD8+ T cells ADT

description:
3_19_NE_CLPL_CD45_1_barcodes.tsv.gz
3_19_NE_CLPL_CD45_1_features.tsv.gz
3_19_NE_CLPL_CD45_1_matrix.mtx.gz

source_name: Colon LPL

value: Colon LPL


title: Eomes iKO cLPL P14 CD8+ T cells RNA


title: nlp2_ctrl_1

extract_protocol:
nlp2_ctrl_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Control cLPL P14 CD8+ T cells ADT

description:
3_19_NE_CLPL_CD45_1_2_barcodes.tsv.gz
3_19_NE_CLPL_CD45_1_2_features.tsv.gz
3_19_NE_CLPL_CD45_1_2_matrix.mtx.gz


title: nlp2_T30_2

extract_protocol:
nlp2_T30_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Control cLPL P14 CD8+ T cells RNA


title: Eomes iKO cIEL P14 CD8+ T cells RNA


title: Control cIEL P14 CD8+ T cells RNA

description:
3_19_NE_CIEL_CD45_1_2_barcodes.tsv.gz
3_19_NE_CIEL_CD45_1_2_features.tsv.gz
3_19_NE_CIEL_CD45_1_2_matrix.mtx.gz


title: Eomes iKO si LPL P14 CD8+ T cells ADT

description:
3_19_NE_SILPL_CD45_1_barcodes.tsv.gz
3_19_NE_SILPL_CD45_1_features.tsv.gz
3_19_NE_SILPL_CD45_1_matrix.mtx.gz

source_name: Small intestine LPL

value: Small intestine LPL


title: Eomes iKO si LPL P14 CD8+ T cells RNA


title: Control cIEL P14 CD8+ T cells ADT


title: Control siLPL P14 CD8+ T cells RNA

description:
3_19_NE_SILPL_CD45_1_2_barcodes.tsv.gz
3_19_NE_SILPL_CD45_1_2_features.tsv.gz
3_19_NE_SILPL_CD45_1_2_matrix.mtx.gz


title: Eomes iKO siIEL P14 CD8+ T cells ADT

description:
3_19_NE_SIIEL_CD45_1_barcodes.tsv.gz
3_19_NE_SIIEL_CD45_1_features.tsv.gz
3_19_NE_SIIEL_CD45_1_matrix.mtx.gz

source_name: Small intestine intraepithelial lymphocytes


title: Eomes iKO siIEL P14 CD8+ T cells RNA

value: Small intestine intraepithelial lymphocytes


title: Col4_T0_1

extract_protocol:
Col4_T0_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Control siIEL P14 CD8+ T cells RNA

description:
3_19_NE_SIIEL_CD45_1_2_barcodes.tsv.gz
3_19_NE_SIIEL_CD45_1_2_features.tsv.gz
3_19_NE_SIIEL_CD45_1_2_matrix.mtx.gz


title: SI_LPL P14 CD8+ T cells

library_source: transcriptomic single cell

data_processing:
Cell Ranger ATAC (v6.0.1) was used to process sequencing information and single cell barcodes.
Cellranger outputs were analyzed in R using Signac (v1.6.0)
Annotation, quality control, dimensional reduction, and UMAPcreationwerecompleted using the standard Signac workflow.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files used: filtered_peak_bc_matrix.h5, singlecell.csv, fragments.tsv.gz, peaks.bed

extract_protocol:
P14 CD8+ T cells were harvested from the siIEL, siLPL, cIEL, and cLPL tissue compartments from recipient mice infected more than 21 days priorandpurifiedbyFACS
Nuclei wereisolated and preparedfor single-cell libraries using the ChromiumNext GEM SingleCell ATAC Library & Gel Bead Kit v1.1


title: Control siIEL P14 CD8+ T cells ADT


title: C3

description: Administered with saline


title: SI_IEL P14 CD8+ T cells


title: CLPL P14 CD8+ T cells


title: 72hpi_Pc273_YW_3

status: Public on Oct 24 2022

data_processing:
Genome_build: genome of Pcapsici (Pc107+Pc273)
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

organism: Capsicum annuum

growth_protocol: Media:on 11-week-old plants in potting soil;hygrometry:50 to 80%;temperature:24°C day/22°C night;Light:12h day/12h night

extract_protocol:
72hpi_Pc273_YW_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 72hpi_Pc273-biotic stress-infection-pcapsici pc273time 72hour  Pc273 inoculation - RNA extraction 72hours post-inoculation

value: wild type (Yolo Wonder (YW, PM0031))

value: stem


title: CIEL P14 CD8+ T cells


title: 0week, WT2, retina

status: Public on Nov 25 2022

city: Guangzhou

first: Min

last: Fu

address: No. 253, Industrial Avenue Middle, Haizhu District

institute: The Second Clinical School, Southern Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: retina

extract_protocol:
Animals that were considered diabetic were maintained on a high-sugar diet, and tail vein blood samples were collected and measured regularly for assessment of glucose levels. The rats in the experimental group (2 weeks, 4 weeks, 8 weeks) and the control group were anesthetized by intraperitoneal injection and fixed in the supine position. First, the eyeballs were removed, and then the corneoscleral limbus was cut. The eyeballs were radially incised, the anterior segment and vitreous were removed, and the iris structure was slowly separated from the intact retina and placed in protective solution.  The tissues were transported in sterile culture dishes with 10 ml of 1x Dulbecco's phosphate-buffered saline (DPBS; Thermo Fisher, Cat. No. 14190144) on ice. The residual tissue storage solution was removed, and the tissues were then minced on ice. We used 0.25% trypsin (dissociation enzyme; Thermo Fisher, Cat. No. 25200-072) and 10 µg/mL DNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% fetal bovine serum (FBS; Thermo Fisher, Cat. No. SV30087.02) to digest the tissues. The tissues were dissociated at 37°C with a shaking speed of 50 RPM for approximately 40 min. We repeatedly collected the dissociated cells at intervals of 20 min to increase cell yield and viability. The cell suspensions were filtered using a 40 µm nylon cell strainer, and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. No. 00-4333-57). The dissociated cells were washed with 1x DPBS containing 2% FBS. The cells were stained with 0.4% Trypan Blue (Thermo Fisher, Cat. No. 14190144), and viability was assessed on a Countess® II Automated Cell Counter (Thermo Fisher).
Beads with unique molecular identifiers (UMIs) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in gel beads-in-emulsion (GEMs). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. The beads were retrieved into a single tube for reverse transcription. In cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of the messenger RNA transcript) with the UMI and a cell label indicating its cell of origin. Briefly, 10× beads were subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ ends of the transcripts linked with the cell barcodes and UMIs. All the remaining procedures, including library construction, were performed according to the standard manufacturer’s protocol (CG000206 Rev D). The sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and with a Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on a NovaSeq6000 instrument (Illumina) in 2 x 150 bp mode.

value: retina

value: SD

value: retinal cells

value: The control group


title: 0week, WT1, retina

description: 10x Genomics


title: 72hpi_Pc273_YW_2

extract_protocol:
72hpi_Pc273_YW_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc273_YW_1

extract_protocol:
72hpi_Pc273_YW_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc107_YW_2

extract_protocol:
72hpi_Pc107_YW_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 72hpi_Pc107-biotic stress-infection-pcapsici pc107time 72hour  Pc107 inoculation - RNA extraction 72hours post-inoculation


title: 72hpi_Pc107_YW_1

extract_protocol:
72hpi_Pc107_YW_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc273_CM334_1

extract_protocol:
72hpi_Pc273_CM334_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: wild type (Criollo de Morelos 334 (CM334, PM0702))


title: 72hpi_Pc273_CM334_3

extract_protocol:
72hpi_Pc273_CM334_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc273_CM334_2

extract_protocol:
72hpi_Pc273_CM334_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc107_YW_3

extract_protocol:
72hpi_Pc107_YW_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc107_CM334_2

extract_protocol:
72hpi_Pc107_CM334_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 72hpi_Pc107_CM334_3

extract_protocol:
72hpi_Pc107_CM334_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: Control siLPL P14 CD8+ T cells ADT

extract_protocol:
Control and Eomes iKO P14 CD8+T cells were harvested from the siIEL, siLPL, cIEL, and cLPL tissue compartments from recipient mice infected more than 21 days prior, FACS-isolated, and prepared for single-cell libraries.
Libaries were constructed using the Chromium Next GEM Single Cell 3’Kit v3.1 (10xGenomics).


title: 24hpi_Pc273_YW_2

extract_protocol:
24hpi_Pc273_YW_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 24hpi_Pc273-biotic stress-infection-pcapsici pc273time 24hour  Pc273 inoculation - RNA extraction 24hours post-inoculation


title: 24hpi_Pc273_CM334_1

extract_protocol:
24hpi_Pc273_CM334_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 24hpi_Pc273_CM334_2

extract_protocol:
24hpi_Pc273_CM334_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 24hpi_Pc273_CM334_3

extract_protocol:
24hpi_Pc273_CM334_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 24hpi_Pc273_YW_1

extract_protocol:
24hpi_Pc273_YW_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 24hpi_Pc107_CM334_3

extract_protocol:
24hpi_Pc107_CM334_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 24hpi_Pc107-biotic stress-infection-pcapsici pc107time 24hour  Pc107 inoculation - RNA extraction 24hours post-inoculation


title: 24hpi_Pc107_YW_2

extract_protocol:
24hpi_Pc107_YW_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 24hpi_Pc107_CM334_2

extract_protocol:
24hpi_Pc107_CM334_2(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 24hpi_Pc107_CM334_1

extract_protocol:
24hpi_Pc107_CM334_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: MOCK_30Min_3

status: Public on Jun 21 2022

data_processing:
Genome_build: transcriptome of 32926 genes Physcomitrella patens
transcriptome mapping and counts of reads by gene locus are done with bowtie2; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,gene_length,counts_SEreads,counts_PEreads

organism: Physcomitrium patens

growth_protocol: Moss colonies were initiated from 1 mm2 spot cultures and cultivated in sterile Magenta GA-7 tissue culture vessels (Bioworld, Dublin, OH, USA) on BCDAT medium (250 mg/L MgSO4.7H2O, 250 mg/L KH2PO4 (pH 6.5), 1010 mg/L KNO3, 12.5 mg/L, FeSO4.7H2O, 0.001% Trace Element Solution (0.614 mg/L H3BO3, 0.055 mg/L AlK(SO4)2.12H2O, 0.055 mg/L CuSO4.5H2O, 0.028 mg/L KBr, 0.028 mg/L LiCl, 0.389 mg/L MnCl2.4H2O, 0.055 mg/L CoCl2.6H2O, 0.055 mg/L ZnSO4.7H2O, 0.028 mg/L KI and 0.028 mg/L SnCl2.2H2O), 0.92 g/L di-ammonium tartrate (C4H12N2O6) and 8 g/L agar with CaCl2 added to a 1 mM concentration after autoclaving, at 23°C under a 16h light/8h dark cycle, at 50-150 umol.m-2.s-1 in MLR-352 growth cabinets (PHCbi, Etten-Leur, The Netherlands).

extract_protocol:
MOCK_30Min_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: MOCK-compound based treatment-none-mock Mock solvent for 30 min

value: wild type (Gransden strain)

value: gametophore


title: MOCK_30Min_2

extract_protocol:
MOCK_30Min_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: non informed,gametophore


title: IAA_30Min_3

extract_protocol:
IAA_30Min_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: 10µmIAAT30Min-compound based treatment-hormone-auxinquantity 10uM time 30min

value: gametophoren informed


title: CUT_TO_2

growth_protocol: Moss colonies were initiated from 1 mm2 spot cultures and cultivated in sterile Magenta GA-7 tissue culture vessels (Bioworld, Dublin, OH, USA) on BCDAT medium (250 mg/L MgSO4.7H2O, 250 mg/L KH2PO4 (pH 6.5), 1010 mg/L KNO3, 12.5 mg/L, FeSO4.7H2O, 0.001% Trace Element Solution (0.614 mg/L H3BO3, 0.055 mg/L AlK(SO4)2.12H2O, 0.055 mg/L CuSO4.5H2O, 0.028 mg/L KBr, 0.028 mg/L LiCl, 0.389 mg/L MnCl2.4H2O, 0.055 mg/L CoCl2.6H2O, 0.055 mg/L ZnSO4.7H2O, 0.028 mg/L KI and 0.028 mg/L SnCl2.2H2O), 0.92 g/L di-ammonium tartrate (C4H12N2O6) and 8 g/L agar with CaCl2 added to a 1 mM concentration after autoclaving, at 23°C under a 16h light/8h dark cycle, at 50-150 umol.m-2.s-1 in MLR-352 growth cabinets (PHCbi, Etten-Leur, The Netherlands). For each biological replicate and condition, RNA were pooled from 5-10 gametophores collected from 4 week-old colonies.

extract_protocol:
CUT_TO_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: decap T0h-decap t0h-decap t0h-decap t0h


title: CUT_TO_3

extract_protocol:
CUT_TO_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: MOCK_30Min_1

extract_protocol:
MOCK_30Min_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: IAA_30Min_1

extract_protocol:
IAA_30Min_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: CUT_T6_2

extract_protocol:
CUT_T6_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: decap T6h-decap t6h-decap t6h-decap t6h


title: CUT_TO_1

extract_protocol:
CUT_TO_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: IAA_30Min_2

extract_protocol:
IAA_30Min_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: 24hpi_Pc273_YW_3

extract_protocol:
24hpi_Pc273_YW_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: CUT_T6_1

extract_protocol:
CUT_T6_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: 72hpi_Pc107_CM334_1

extract_protocol:
72hpi_Pc107_CM334_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: CUT_T2_1

extract_protocol:
CUT_T2_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: decap T2h-decap t2h-decap t2h-decap t2h


title: 24hpi_Pc107_YW_3

extract_protocol:
24hpi_Pc107_YW_3(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: CUT_T24_3

extract_protocol:
CUT_T24_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: decap T24h-decap t24h,biotic stress-decap t24h-decap t24h


title: CUT_T24_2

extract_protocol:
CUT_T24_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: CUT_T2_3

extract_protocol:
CUT_T2_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: CUT_T2_2

extract_protocol:
CUT_T2_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Dranse_DRA-13_2

data_processing:
Genome_build: transcriptome of Populus trichocarpa
Mapping and counts of reads by locus gene (tophat2/bowtie2). If PE reads, count only consistent PE reads
type:count file (txt); content:gene ID,length of Gene,nb single reads,nb PE reads

organism: Populus nigra

growth_protocol: Trees were pruned 2 times after the initial planting (in 2005). Planting space was organized in 4 blocks. The harvest date for RNA extraction was 4 years after the last pruning in winter 2011-2012.

extract_protocol:
Dranse_DRA-13_2(5ug)
rna_selection:selection polyA, single-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: no treatment

tag: population

value: Dranse

tag: age

value: cambium,xylem


title: CUT_T12_3

extract_protocol:
CUT_T12_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: decap T12h-decap t12h-decap t12h-decap t12h


title: Adour_AST-010_2

extract_protocol:
Adour_AST-010_2(5ug)
rna_selection:selection polyA, single-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: Adour


title: Ovarian cancer tumor, patient 1, C1D1 [RNA-Seq]

status: Public on Jun 20 2022

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
QC: fastqc  alignment: STAR (GRCh38)  expression count calculation: rsem (expected count)  filter to 70%+ samples with non-zero counts   differential expression: DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: expected_count  TPM     FPKM

source_name: tumor biopsy sample

extract_protocol:
RNA was extracted from tumor biopsies using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia CA) according to the manufacturer instructions.
Libraries were prepared with a NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs Inc., Ipswich, MA) as described in the manufacturer’s protocol.

treatment_protocol: See overall design

tag: group

value: Baseline (control)

tag: responder

value: Non-Responder (NR)

tag: disease

value: ovarian cancer


title: Fetal cerebellum scRNA-seq

status: Public on Oct 08 2022

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

institute: CCHMC

description: The raw data for GSM5952337 was removed. SRX14462060/SRR18324534/SRR18324535 were withdrawn. Submitters do not have permission to make this human data public.

data_processing:
For the scRNA-seq data, we used Cellranger v5.0.1 to align reads to the human reference sequence.
The raw base call files were demultiplexed into FASTQ files.
The FASTQ files were aligned to the reference human genome GRCH38 to generate raw gene-barcode count matrices. SoupX (https://xuranw.github.io/MuSiC/articles/MuSiC.html) was used to remove the cells with ambient RNA contamination, and using the criteria based on the cell with <500 genes expression and >20 % mitochondrial gene content to remove the dying cells. Doublets were detected and filtered using the R package DoubletFinder v.2.0.2 with default settings. The cells with low-abundance genes or genes expressed in <3 cells were also removed from the datasets. By defaulting in Seurat, we employ a global-scaling normalization method 'LogNormalize' that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result. Next, we apply a linear transformation ('scaling') that is a standard pre-processing step using all genes or variable genes. Then, we perform principal component analysis (PCA) to get the linear dimensional reduction after the data scaling.
Doublets were detected and filtered using the R package DoubletFinder v.2.0.2 with default settings. The cells with low-abundance genes or genes expressed in <3 cells were also removed from the datasets. By defaulting in Seurat, we employ a global-scaling normalization method 'LogNormalize' that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result. Next, we apply a linear transformation ('scaling') that is a standard pre-processing step using all genes or variable genes. Then, we perform principal component analysis (PCA) to get the linear dimensional reduction after the data scaling.
We re-grouped the "UBC/GCP-progenitors" into "UBC-progenitor" and "GCP-progenitor" and change the name of the previous not clear cell type "15XXX" into "Brainstem".
Assembly: hg38
Supplementary files format and content: Seurat format

source_name: human fetal cerebellum

growth_protocol: hNSCs and MB004 cells were cultured in complete NPC medium (Neurobasal medium containing B27 supplement, N2 supplement, 2 mM L-glutamine, 20 ng/ml EGF, 20 ng/ml bFGF, 2 mg/ml Heparin and 50 μg/ml BSA). Spheres were dissociated at a diameter of 100-200 μm and were changed with complete NPC medium every 3 days to maintain cell metabolic activity.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: no treatment for the 2 cell lines

value: human fetal cerebellum


title: CUT_T12_2

extract_protocol:
CUT_T12_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: no,gametophore

value: stem


title: Ovarian cancer tumor, patient 17, C1D1 [RNA-Seq]


title: CUT_T12_1

extract_protocol:
CUT_T12_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 15, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 16, C1D1 [RNA-Seq]

value: Responder


title: CUT_T6_3

extract_protocol:
CUT_T6_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 10, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 11, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 5, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 6, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 4, C1D1 [RNA-Seq]


title: CUT_T24_1

extract_protocol:
CUT_T24_1(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 13, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 3, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 8, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 6, C2D8 [RNA-Seq]

value: Treated


title: Ovarian cancer tumor, patient 9, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 5, C2D8 [RNA-Seq]


title: Ovarian cancer tumor, patient 4, C2D8 [RNA-Seq]


title: Ovarian cancer tumor, patient 14, C1D1 [RNA-Seq]


title: Ovarian cancer tumor, patient 2, C2D8 [RNA-Seq]


title: Ovarian cancer tumor, patient 9, C2D8 [RNA-Seq]


title: Ovarian cancer tumor, patient 8, C2D8 [RNA-Seq]


title: Ovarian cancer tumor, patient 7, C2D8 [RNA-Seq]


title: withDex_2

status: Public on May 18 2022

data_processing:
Genome_build: transcriptome of TAIRv10
transcriptome mapping and counts of reads by gene locus are done with bowtie2; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,gene_length,counts_SEreads,counts_PEreads

growth_protocol: Arabidopsis growth medium in vitro/ 21°C / LD

extract_protocol:
withDex_2(10ug)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: Dex-treatment-compound based treatment-compound addition-dexamethasonequantity 10ul time 6hour  Plantlets grown in 10 ml of liquid medium were treated either with 10µL of DEX for 6 hours prior being snap frozen in liquid nitrogen

value: seedling


title: Ovarian cancer tumor, patient 3, C2D8 [RNA-Seq]


title: noDex_2

extract_protocol:
noDex_2(10ug)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: noDex_3

extract_protocol:
noDex_3(10ug)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: noDex_1

extract_protocol:
noDex_1(10ug)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: boyes 1.02


title: withDex_1

extract_protocol:
withDex_1(10ug)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: H2O_6H_3

status: Public on May 06 2022

data_processing:
Genome_build: genome of TAIR10+AIRPORT11
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

growth_protocol: Long Days, temperature 20°C , HR+70%

extract_protocol:
H2O_6H_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: wild type (WT)

value: seed

value: no treatment


title: H2O_6H_2

extract_protocol:
H2O_6H_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: H2O_24H_3

extract_protocol:
H2O_24H_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: H2O_24H_1

extract_protocol:
H2O_24H_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: H2O_24H_2

extract_protocol:
H2O_24H_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 12, C1D1 [RNA-Seq]


title: H2O_16H_3

extract_protocol:
H2O_16H_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: H2O_16H_2

extract_protocol:
H2O_16H_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: DRY_OH_2

extract_protocol:
DRY_OH_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: DRY_OH_3

extract_protocol:
DRY_OH_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: C2H4_6H_3

extract_protocol:
C2H4_6H_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: C2H4-6h-abiotic stress-ethylene imbibition 6hours


title: C2H4_6H_2

extract_protocol:
C2H4_6H_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 1, C2D8 [RNA-Seq]

extract_protocol:
RNA was extracted from tumor biopsies using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia CA) according to the manufacturer instructions.
Libraries were prepared with a NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs Inc., Ipswich, MA) as described in the manufacturer’s protocol.


title: C2H4_6H_1

extract_protocol:
C2H4_6H_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 2, C1D1 [RNA-Seq]


title: C2H4_24H_2

extract_protocol:
C2H4_24H_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: C2H4-24h-abiotic stress-ethylene imbibition 24hours


title: C2H4_24H_1

extract_protocol:
C2H4_24H_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Ovarian cancer tumor, patient 7, C1D1 [RNA-Seq]


title: NB15 (RNA-seq)

status: Public on May 05 2022

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

description: [Updated on April 29, 2025] Changed from Title N14 to NB15, age 108 to 76.

data_processing:
Demultiplexing of bcl files into .fastq files was performed using cellranger 3.0.1 mkfastq software (10x Genomics) and alignments to the human (GRCh38) genome reference sequences were performed using cellranger count. The reference included all protein coding genes as well as mitochondrial genes for downstream analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count matrix in csv

source_name: neuroblastoma

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Fresh tissue obtained from surgery was collected in Media 199 (Gibco) supplemented with 2% (v/v) FBS on ice. Single cell suspensions of the tumors were obtained by cutting the tumor in to small pieces (1mm3) followed by enzymatic dissociation for 45 minutes at 37°C with shaking at 120 rpm using Collagenase I, Collagenase II, Collagenase III, Collagenase IV (all at a concentration of 1 mg/ml; Worthington Biochemical) and Dispase (2mg/ml; Thermo Fisher) in the presence of DNAse I solution (Thermo Fisher Scientific; 1:100) and RNase Out (Thermo Fisher; 1:1000). Cells were then resuspended in fetal bovine serum (FBS) with 5% DMSO and cryopreserved in liquid nitrogen.Cryopreserved cells from neuroblastoma samples were thawed and stained with anti-CD235-PE (Biolegend) and Calcein AM (Thermo Fisher) for 30 minutes at 4°C.  Cells were washed twice with Media199 containing 2% FBS followed by DAPI and/or 7AAD staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI/7AAD-negative, Calcein AM-positive, CD235-negative) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument.

tag: risk group

value: High

tag: tumor type

value: Primary


title: C2H4_16H_2

extract_protocol:
C2H4_16H_2(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: C2H4-16h-abiotic stress-ethylene imbibition 16hours


title: DRY_OH_1

extract_protocol:
DRY_OH_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: C2H4_16H_3

extract_protocol:
C2H4_16H_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: C2H4_16H_1

extract_protocol:
C2H4_16H_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: C2H4-16h-abiotic stress- ethylene imbibition 16hours


title: pi4kB1B2_root_3

status: Public on May 04 2022

data_processing:
Genome_build: genome of TAIR11
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

growth_protocol: 7 days old seedlings, cultivated on MS/2 media supplemented with 0.8% agar and 1% sucrose, 22°C, 16h/8h light)

extract_protocol:
pi4kB1B2_root_3(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: pi4k{beta}1{beta}2 - mutant=knock-out,insertional mutagen,T-DNA-

value: roots


title: pi4kB1B2_root_2

extract_protocol:
pi4kB1B2_root_2(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: pi4kB1B2_root_1

extract_protocol:
pi4kB1B2_root_1(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: H2O_6H_1

extract_protocol:
H2O_6H_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: pi4kB1B2_leaf_1

extract_protocol:
pi4kB1B2_leaf_1(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: leaf


title: WT_root_3

extract_protocol:
WT_root_3(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: H2O_16H_1

extract_protocol:
H2O_16H_1(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT_root_2

extract_protocol:
WT_root_2(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT_root_1

extract_protocol:
WT_root_1(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT_leaf_3

extract_protocol:
WT_leaf_3(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT_leaf_2

extract_protocol:
WT_leaf_2(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: C2H4_24H_3

extract_protocol:
C2H4_24H_3(100ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t2_50_3

status: Public on Jan 26 2022

data_processing:
Genome_build: genome of Brassica napus
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

organism: Brassica napus

growth_protocol: Controled conditions (greenhouse) Media: PremierTech sandy compost Hygrometry: 80% field capacity (Fc) Temperature: 25°C day / 20°C night Light: 500 µmol.m².s-1

extract_protocol:
control_t2_50_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: wild type (Trezzor)


title: WT_leaf_1

extract_protocol:
WT_leaf_1(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t2_50_1

extract_protocol:
control_t2_50_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t2_50_2

extract_protocol:
control_t2_50_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t2_25_3

extract_protocol:
control_t2_25_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t2_25_1

extract_protocol:
control_t2_25_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t1_50_2

extract_protocol:
control_t1_50_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t2_25_2

extract_protocol:
control_t2_25_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t1_50_1

extract_protocol:
control_t1_50_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: pi4kB1B2_leaf_3

extract_protocol:
pi4kB1B2_leaf_3(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t1_50_3

extract_protocol:
control_t1_50_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: pi4kB1B2_leaf_2

extract_protocol:
pi4kB1B2_leaf_2(4ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t2_25_2

extract_protocol:
WD_t2_25_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: water shortage-environmental treatment-water shortage,abiotic stress-water deficit In a greenhouse, 30 days after sowing with a growth at 80% field capacity (FC) level, irrigation was kept for control or was stopped until all pots per condition reached a level below 50% of FC (harvest t1_50) and thereafter 25% FC (harvest t1_25). Once theses levels were reached, plant were kept respectively at 50% FC or 25% FC during 12 days before final harvest (havest t2_ 50 and t2_25 respectively). Each harvest consisted to sample leaf blade which has been growing during water shortage for the control condition and the water deficient condition.


title: control_t1_25_2

extract_protocol:
control_t1_25_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t1_25_1

extract_protocol:
control_t1_25_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t2_50_1

extract_protocol:
WD_t2_50_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: control_t1_25_3

extract_protocol:
control_t1_25_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t2_25_3

extract_protocol:
WD_t2_25_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t2_25_1

extract_protocol:
WD_t2_25_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t1_50_3

extract_protocol:
WD_t1_50_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t1_50_1

extract_protocol:
WD_t1_50_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t1_25_3

extract_protocol:
WD_t1_25_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t1_25_2

extract_protocol:
WD_t1_25_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t2_50_3

extract_protocol:
WD_t2_50_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t1_25_1

extract_protocol:
WD_t1_25_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t2_50_2

extract_protocol:
WD_t2_50_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M5_LN_3

status: Public on Jan 24 2022

data_processing:
Genome_build: genome of Hordeum vulgare genome_R2
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

organism: Hordeum vulgare

growth_protocol: Light:110-130 µE/cm2/s-1 day=23°C, twilight=20°C, night=19°C 8 hours night/16 hours day

extract_protocol:
M5_LN_3(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Barley responses to nitrate limitation 0.5mM-abiotic stress-abiotic stress-nitratequantity 0.5mM  Nitrate applied 14 days after sowing

value: wild type (Oussama)

value: aerial

value: 0.5mM  Nitrate


title: M5_LN_2

extract_protocol:
M5_LN_2(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M5_LN_1

extract_protocol:
M5_LN_1(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WD_t1_50_2

extract_protocol:
WD_t1_50_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M5_HN_3

extract_protocol:
M5_HN_3(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Barley responses to nitrate limitation 5mM-abiotic stress-15n for 24 h before sampling-nitratequantity 5mM  Nitrate apllied 14 days after sowing

value: 5mM  Nitrate


title: M5_HN_1

extract_protocol:
M5_HN_1(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M4_LN_4

extract_protocol:
M4_LN_4(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: wild type (Laanaceur)


title: M5_HN_2

extract_protocol:
M5_HN_2(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M4_LN_1

extract_protocol:
M4_LN_1(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M4_LN_3

extract_protocol:
M4_LN_3(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M4_HN_4

extract_protocol:
M4_HN_4(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M4_HN_2

extract_protocol:
M4_HN_2(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: M4_HN_1

extract_protocol:
M4_HN_1(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: GP_LN_3

extract_protocol:
GP_LN_3(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: wild type (Golden Promise)


title: GP_LN_2

extract_protocol:
GP_LN_2(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: GP_LN_1

extract_protocol:
GP_LN_1(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: GP_HN_4

extract_protocol:
GP_HN_4(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: GP_HN_2

extract_protocol:
GP_HN_2(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: GP_HN_1

extract_protocol:
GP_HN_1(30mg)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: SRC013T1_Tc_S5

status: Public on Dec 29 2021

city: San Francisco

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

data_processing:
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Genome_build: GRCh38

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Sarcoma tumor specimen

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified   cDNA using Tecan Ovation RNA-Seq System V2 kit, following the manufacturer protocol.
The dsDNA went through tagmentation, amplification and clean up with   AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration

value: leg

tag: sorted compartment

value: tcell

value: Sarcoma


title: SRC014_T1_rna_tcell_S40

tag: tissue

value: arm


title: SRC001T1_Tc_S59

value: buttock


title: PNET014T1_Tc_S38

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Brain Neuroendocrine tumor specimen

value: Brain

value: Pancreatic neuroendocrine cancer


title: IPIMEL353T1_rna_tcell_S32

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Melanoma tumor specimen

value: Skin

value: Melanoma


title: PDAC037T1_Tc_S58

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Pancreatic tumor specimen

value: Pancreas

value: Pancreatic cancer


title: MELB003T1_Tc_S44


title: SRC004T1_Tc_S15


title: IPIMEL343_T1_rna_Tcell_S23


title: PNET009T1Tc_S47


title: PNET005T1Tc_S42


title: IPIMEL348_T1_rna_tcell_S39


title: 24hpi_Pc107_YW_1

extract_protocol:
24hpi_Pc107_YW_1(30mg)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: wild type (Yolo Wonder (YW, PM0031))

value: stem


title: MEL271T1Tc_S43_S47

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a metastatic Melanoma tumor specimen


title: MEL274T1Tc_S28


title: MEL288T1Tc_S53


title: MEL321T1Tc_S61


title: MEL252T1Tc_S35


title: MEL283T1Tc_S29


title: MEL221T1Tc_S15


title: MEL212T1Tc_S234


title: SRC003T1_Tc_S40


title: LUNG085T1Tc_S66

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Lung tumor specimen

value: Lung

value: Lung cancer


title: MEL108T1_Tc_S54


title: LUNG076T1Tc_S20


title: LUNG081T1Tc_S51


title: SRC012T1_Tc_S43


title: LUNG077T1Tc_S39


title: LUNG055T1Tc_S50


title: LUNG062T1Tc_S6


title: LUNG069_T1_rna_tcells_S35


title: LUNG054T1Tc_S8


title: LUNG052T1Tc_S6


title: LUNG051T1Tc_S43


title: withDex_3

extract_protocol:
withDex_3(10ug)
rna_selection:selection polyA, paired-end, stranded:no, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: seedling


title: LUNG058T1Tc_S31


title: LUNG070_T1_rna_tcell_S22


title: LUNG049T1Tc_S26


title: LUNG015_T1_rna_tcell_S18


title: MEL069T1Tc_S7

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a Metastic Melanoma tumor specimen


title: LUNG030T1_Tc_S47


title: LUNG011_T1_rna_tcells_S51


title: LUNG014_T1_rna_tcell_S7


title: LUNG021T1_Tc_S37


title: LUNG009_T1_rna_tcell_S35


title: IPIKID108T1_rna_tcells4_S63

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Kidney tumor specimen

value: Kidney

value: Kidney cancer


title: IPIKID106T1_rna_tcells_S36

value: tcell


title: IPIKID104_T1_rna_Tcell_S22


title: IPIKID102_T1_rna_Tcell_S35


title: LUNG008_T1_rna_tcell_S27


title: IPIKID103_T1_rna_Tcell_S7


title: IPIKID109T1_rna_tcellsP3_S26


title: IPIKID100_T1_rna_tcell_S23


title: IPIKID099_T1_rna_tcell_S62


title: IPIKID098_T1_rna_tcell_S24


title: LUNG066_T1_rna_tcells_S46


title: KID094T1_Tc_S46


title: IPIKID095_T1_rna_tcell_S8


title: KID092T1_Tc_S79


title: KID093T1_Tc_S26


title: KID091T1_Tc_S13


title: IPIKID097_T1_rna_tcell_S47


title: LUNG013_T1_rna_tcells_S37


title: IPIKID110T1_rna_tcells_S68


title: KID085T1_Tc_S37


title: KID083T1_Tc_S7


title: KID078T1Tc_S63


title: KID077T1Tc_S60


title: KID071_T1_rna_tcell_S49


title: KID076T1Tc_S32


title: KID062_T1_rna_tcells_S25


title: KID074_T1_rna_tcells_S34


title: KID061_T1_rna_tcells_S33


title: KID060_T1_rna_tcell_S20


title: KID067T1Tc_S58


title: KID052T1Tc_S47


title: KID050_T1_rna_tcells_S10


title: KID049T1Tc_S92_S6


title: KID051T1Tc_S8


title: KID057T1Tc_S235


title: KID089T1_Tc_S6


title: KID086T1_Tc_S29


title: KID079T1Tc_S8


title: KID048T1Tc_S74_S51


title: IPIHNSC079T1_rna_tcell_S30

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary tumor specimen in the Head and Neck region

value: Head & Neck

value: Head & Neck cancer


title: KID070T1_Tc_S48


title: KID047_T1_rna_tcell_S12


title: IPIHNSC075_T1_rna_tcell_S2


title: IPIHNSC078T1_rna_tcell_S30


title: HNSC070T1_Tc_S28


title: IPIHNSC074_T1_rna_tcell_S10


title: KID066T1_Tc_S51


title: HNSC063T1Tc_S7_S1


title: HNSC062T1Tc_S59_S58


title: KID084T1_Tc_S14


title: HNSC061T1_Tc_S53


title: HNSC060T1Tc_S37


title: HNSC069T1_Tc_S34


title: HNSC057T1Tc_S36_S8


title: HNSC056_T1_rna_tcells_S30


title: HNSC030T1Tc_S33


title: HEP016T1Tc_S19

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a Metastatic Liver tumor specimen

value: Liver

value: Hepatobiliary cancer


title: IPIGYN116T1_rna_tcells_S18

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Gynecologic tumor specimen

value: Uterus & adnexa

value: Gynecologic cancer


title: IPIGYN110_T1_rna_Tcell_S20


title: KID030_T1_rna_tcell_S15


title: HEP003_T1_rna_tcell_S47

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Liver tumor specimen


title: HEP013T1Tc_S40


title: IPIHNSC077T1_rna_tcell_S17


title: IPIGYN124T1_rna_tcells_S20


title: IPIGYN109T1_rna_tcells_S25


title: IPIGYN125T1_rna_tcells_S58


title: HEP017T1_Tc_S73


title: IPIGYN099_T1_rna_Tcell_S11


title: GYN089T1_Tc_S22


title: GYN093T1_Tc_S57


title: GYN088T1_Tc_S1


title: HNSC054T1Tc_S7


title: GYN086T1_Tc_S46


title: GYN098_T1_rna_tcells_S20


title: GYN085T1_Tc_S37


title: GYN083T1Tc_S34


title: IPIGYN105_T1_rna_Tcell_S39


title: IPIGYN103_T1_rna_tcell_S38


title: GYN091T1_Tc_S36


title: IPIGYN064T1_rna_tcells_S8


title: IPIGYN107T1_rna_tcells_S38


title: GYN082T1Tc_S45


title: GYN078T1Tc_S13


title: GYN059T1Tc_S35


title: GYN015T1_Tc_S25


title: GYN040_T1_rna_tcells_S22


title: IPIGYN069T1_rna_tcell_S47


title: GYN013T1_Tc_S13_L001


title: IPIGYN104_T1_rna_tcell_S7


title: IPIGYN048T1_rna_tcells_S10


title: GYN011T1_Tc_S31_L004


title: IPIGBM006T1_rna_tcells_S33

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Brain tumor specimen

value: Brain

value: Glioblastoma


title: IPICRC077_T1_rna_Tcell_S15

description:
IPICRC077.T1
GSE179975

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Colorectal tumor specimen

value: Colon & Rectum

value: Colorectal cancer


title: IPICRC079_T1_rna_Tcell_S27


title: IPICRC076_T1_rna_tcell_S14


title: IPICRC080T1_rna_tcell_S19


title: IPIGYN106_T1_rna_Tcell_S24


title: IPICRC074_T1_rna_tcell_S34


title: IPICRC075_T1_rna_tcell_S53

description:
IPICRC075.T1
GSE179975


title: IPICRC073_T1_rna_tcell_S41


title: IPICRC072_T1_rna_Tcell_S55

description:
IPICRC072.T1
GSE179975


title: GYN060T1Tc_S4


title: IPICRC087T1_rna_tcell_S23

description:
IPICRC087.T1
GSE179975


title: CRC070_T1_rna_tcells_S15


title: IPICRC089T1_rna_tcell_S40


title: CRC063T1_Tc_S34


title: CRC067T1_Tc_S27


title: GYN043T1Tc_S17


title: CRC058T1_Tc_S36

description:
IPICRC058.T1
GSE179975


title: CRC064T1_Tc_S70

description:
IPICRC064.T1
GSE179975


title: CRC062T1_Tc_S14

description:
IPICRC062.T1
GSE179975


title: GYN027T1Tc_S4


title: CRC035T1Tc_S38

description:
IPICRC035.T1
GSE179975


title: CRC039T1Tc_S1_S36

description:
IPICRC039.T1
GSE179975


title: IPIBLAD034T1_rna_tcells_S46

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Bladder tumor specimen

value: Bladder

value: Bladder cancer


title: CRC048T1Tc_S39

description:
IPICRC048.T1
GSE179975


title: IPIBLAD036T1_rna_tcell_S28


title: BLAD030T1Tc_S35


title: BLAD029T1Tc_S55


title: BLAD028T1Tc_S32


title: BLAD026T1Tc_S67


title: BLAD020T1Tc_S33


title: Shoot apex, RNAi_3

status: Public on Nov 22 2021

data_processing:
Mapping and counts of reads by locus gene STAR tool (exact multihits are removed). If PE reads, count only consistent PE reads
Genome_build: genome of Hybrid Populus alba + tremula
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,no_stranded,forward,reverse

organism: Populus tremula x Populus alba

extract_protocol:
RNAi_3(200ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Drought-environmental treatment-abiotic stress-water deficit Control and RNAi lines were subjected to drought stress for three weeks followed by one week of re-watering

value: hybrid 717-1B4 - mutant=knock-down,RNAi,siRNA-DDM1 GENE

value: shoot apex


title: BLAD013T1Tc_S45


title: BLAD006T1Tc_S10


title: BLAD019T1Tc_S29


title: Shoot apex, RNAi_1

extract_protocol:
RNAi_1(200ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Shoot apex, CTRL_3

extract_protocol:
CTRL_3(200ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: wild type (hybrid 717-1B4)


title: Shoot apex, CTRL_2

extract_protocol:
CTRL_2(200ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: BLAD014T1Tc_S236


title: Carence_Mn_1

status: Public on Nov 17 2021

growth_protocol: Media : control nutrient solution Hygrometry : hydroponics Temperature : 25°C day / 20°C night Light : 350 μmol m-2 s-1

extract_protocol:
Carence_Mn_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Mn nutriment deprivation-nutriment deprivation,environmental treatment-nutriment deprivation,abiotic stress-manganese This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.

value: wild type (Trezzor)

value: roots


title: Control_22days_3

extract_protocol:
Control_22days_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Control_ no nutriment deprivation-no nutriment deprivation,environmental treatment-no nutriment deprivation,abiotic stress-no nutriment deprivation This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.


title: CRC055T1Tc_S42

description:
IPICRC055.T1
GSE179975

value: tcell


title: Carence_Mn_3

extract_protocol:
Carence_Mn_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_Mn_2

extract_protocol:
Carence_Mn_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_Co_3

extract_protocol:
Carence_Co_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Co nutriment deprivation-nutriment deprivation,environmental treatment-nutriment deprivation,abiotic stress-cobalt This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.


title: Shoot apex, CTRL_1

extract_protocol:
CTRL_1(200ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_Cl_3

extract_protocol:
Carence_Cl_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Cl nutriment deprivation-nutriment deprivation,environmental treatment-nutriment deprivation,abiotic stress-chlorine This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.


title: Carence_Cl_1

extract_protocol:
Carence_Cl_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_Co_2

extract_protocol:
Carence_Co_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Control_22days_2

extract_protocol:
Control_22days_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_Co_1

extract_protocol:
Carence_Co_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_Cl_2

extract_protocol:
Carence_Cl_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Control_22days_1

extract_protocol:
Control_22days_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_P_3

extract_protocol:
Carence_P_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: P nutriment deprivation-nutriment deprivation,environmental treatment-nutriment deprivation,abiotic stress-phosphore This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.


title: BLAD024T1Tc_S42

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified   cDNA using Tecan Ovation RNA-Seq System V2 kit, following the manufacturer protocol.
The dsDNA went through tagmentation, amplification and clean up with   AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration


title: Carence_S_3

extract_protocol:
Carence_S_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: S nutriment deprivation-nutriment deprivation,environmental treatment-nutriment deprivation,abiotic stress-sulfur This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.


title: Carence_S_1

extract_protocol:
Carence_S_1(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_S_2

extract_protocol:
Carence_S_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Carence_P_2

extract_protocol:
Carence_P_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf