title: Adult_nphx_532


title: Adult_nphx_508

status: Public on Apr 01 2023

type: SRA

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv

library_source: transcriptomic

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs

molecule: total RNA

organism: Mus musculus

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: strain

tag: cell type

value: FACS sorted


title: Adult_nphx_507


title: Adult_nphx_529


title: Adult_nphx_521


title: Adult_nphx_522


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title: Adult_nphx_500


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title: Adult_nphx_62


title: Adult_nphx_63


title: Adult_nphx_84


title: Adult_nphx_64


title: Adult_nphx_61


title: Adult_nphx_60


title: Adult_nphx_59


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title: Adult_nphx_72


title: Adult_nphx_56


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title: Adult_nphx_53


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title: Adult_nphx_54


title: Adult_nphx_52


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title: Adult_nphx_46


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title: Adult_nphx_44


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title: Adult_nphx_42


title: Adult_nphx_38


title: Adult_nphx_40


title: Adult_nphx_37


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title: Adult_nphx_32


title: Adult_nphx_35


title: Adult_nphx_31


title: Adult_nphx_33


title: Adult_nphx_30


title: Adult_nphx_29


title: Adult_nphx_28


title: Adult_nphx_27


title: Adult_nphx_26


title: Adult_nphx_25


title: Adult_nphx_23


title: Adult_nphx_22


title: Adult_nphx_41


title: Adult_nphx_20


title: Adult_nphx_17


title: Adult_nphx_16


title: Adult_nphx_19


title: Adult_nphx_11


title: Adult_nphx_14


title: Adult_nphx_12


title: Adult_nphx_13


title: Adult_nphx_10


title: Adult_nphx_8


title: Adult_nphx_7


title: Adult_nphx_9


title: Adult_nphx_6


title: Adult_nphx_15


title: Adult_nphx_4


title: Adult_nphx_3


title: Adult_nphx_5


title: Adult_nphx_2


title: Adult_nphx_1


title: Aged_nphx_1024

description:
Aged_nphx_lec
Aged_nphx_normalized_expression_matrix.csv


title: Adult_nphx_18


title: Adult_nphx_24


title: Aged_nphx_1019


title: Aged_nphx_1022


title: Aged_nphx_1020


title: Aged_nphx_1023


title: Aged_nphx_1021


title: Adult_nphx_21


title: Aged_nphx_1017


title: Aged_nphx_1025


title: Aged_nphx_1016


title: Aged_nphx_1015


title: Aged_nphx_1018


title: Aged_nphx_1013


title: Aged_nphx_1011


title: Aged_nphx_1014


title: Aged_nphx_1009


title: Aged_nphx_1012


title: Aged_nphx_1005


title: Aged_nphx_1004


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title: Aged_nphx_962


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title: Aged_nphx_961


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title: Aged_nphx_949


title: Aged_nphx_959


title: Aged_nphx_952


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title: Aged_nphx_947


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title: Aged_nphx_923


title: Aged_nphx_921


title: Aged_nphx_924


title: Aged_nphx_946


title: Aged_nphx_922


title: Aged_nphx_920


title: Aged_nphx_936


title: Aged_nphx_919


title: Aged_nphx_916


title: Aged_nphx_917


title: Aged_nphx_915


title: Aged_nphx_912


title: Aged_nphx_910


title: Aged_nphx_911


title: Aged_nphx_909


title: Aged_nphx_927


title: Aged_nphx_907


title: Aged_nphx_908


title: Aged_nphx_905


title: Aged_nphx_903


title: Aged_nphx_902


title: Aged_nphx_900


title: Aged_nphx_906


title: Aged_nphx_901


title: Aged_nphx_896


title: Aged_nphx_897


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title: Aged_nphx_895


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title: Aged_nphx_904


title: Aged_nphx_892


title: Aged_nphx_914


title: Aged_nphx_893


title: Aged_nphx_891


title: Aged_nphx_918


title: Aged_nphx_889


title: Aged_nphx_888


title: Aged_nphx_913


title: Aged_nphx_890


title: Aged_nphx_886


title: Aged_nphx_884


title: Aged_nphx_885


title: Aged_nphx_882


title: Aged_nphx_880


title: Aged_nphx_879


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title: Aged_nphx_876


title: Aged_nphx_878


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title: Aged_nphx_875


title: Aged_nphx_874


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title: Aged_nphx_871


title: Aged_nphx_870


title: Aged_nphx_872


title: Aged_nphx_869


title: Aged_nphx_887


title: Aged_nphx_867


title: Aged_nphx_883


title: Aged_nphx_864


title: Aged_nphx_861


title: Aged_nphx_862


title: Aged_nphx_859


title: Aged_nphx_863


title: Aged_nphx_866


title: Aged_nphx_858


title: Aged_nphx_857


title: Aged_nphx_860


title: Aged_nphx_865


title: Aged_nphx_855


title: Aged_nphx_856


title: Aged_nphx_852


title: Aged_nphx_850


title: Aged_nphx_853


title: Aged_nphx_873


title: Aged_nphx_851


title: Aged_nphx_854


title: Aged_nphx_868


title: Aged_nphx_848


title: Aged_nphx_847


title: Aged_nphx_845


title: Aged_nphx_843


title: Aged_nphx_849


title: Aged_nphx_846


title: Aged_nphx_844


title: Aged_nphx_840


title: Aged_nphx_842


title: Aged_nphx_841


title: Aged_nphx_838


title: Aged_nphx_836


title: Aged_nphx_835


title: Aged_nphx_839


title: Aged_nphx_837


title: Aged_nphx_834


title: Aged_nphx_833


title: Aged_nphx_832


title: Aged_nphx_830


title: Aged_nphx_829


title: Aged_nphx_831


title: Aged_nphx_827


title: Aged_nphx_828


title: Aged_nphx_819


title: Aged_nphx_826


title: Aged_nphx_814


title: Aged_nphx_825


title: Aged_nphx_824


title: Aged_nphx_823


title: Aged_nphx_820


title: Aged_nphx_812


title: Aged_nphx_811


title: Aged_nphx_818


title: Aged_nphx_809


title: Aged_nphx_808


title: Aged_nphx_817


title: Aged_nphx_807


title: Aged_nphx_816


title: Aged_nphx_801


title: Aged_nphx_802


title: Aged_nphx_815


title: Aged_nphx_803


title: Aged_nphx_800


title: Aged_nphx_810


title: Aged_nphx_797


title: Aged_nphx_813


title: Aged_nphx_794


title: Aged_nphx_806


title: Aged_nphx_804


title: Aged_nphx_805


title: Aged_nphx_791


title: Aged_nphx_787


title: Aged_nphx_799


title: Aged_nphx_783


title: Aged_nphx_822


title: Aged_nphx_778


title: Aged_nphx_786


title: Aged_nphx_781


title: Aged_nphx_821


title: Aged_nphx_776


title: Aged_nphx_798


title: Aged_nphx_796


title: Aged_nphx_771


title: Aged_nphx_789


title: Aged_nphx_770


title: Aged_nphx_769


title: Aged_nphx_795


title: Aged_nphx_792


title: Aged_nphx_788


title: Aged_nphx_790


title: Aged_nphx_793


title: Aged_nphx_777


title: Aged_nphx_765


title: Aged_nphx_763


title: Aged_nphx_785


title: Aged_nphx_782


title: Aged_nphx_780


title: Aged_nphx_754


title: Aged_nphx_774


title: Aged_nphx_753


title: Aged_nphx_773


title: Aged_nphx_751


title: Aged_nphx_775


title: Aged_nphx_772


title: Aged_nphx_748


title: Aged_nphx_768


title: Aged_nphx_767


title: Aged_nphx_758


title: Aged_nphx_779


title: Aged_nphx_766


title: Aged_nphx_744


title: Aged_nphx_784


title: Aged_nphx_762


title: Aged_nphx_742


title: Aged_nphx_764


title: Aged_nphx_760


title: Aged_nphx_761


title: Aged_nphx_759


title: Aged_nphx_741


title: Aged_nphx_757


title: Aged_nphx_736


title: Aged_nphx_739


title: Aged_nphx_755


title: Aged_nphx_735


title: Aged_nphx_733


title: Aged_nphx_752


title: Aged_nphx_743


title: Aged_nphx_732


title: Aged_nphx_749


title: Aged_nphx_750


title: Aged_nphx_746


title: Aged_nphx_745


title: Aged_nphx_729


title: Aged_nphx_727


title: Aged_nphx_747


title: Aged_nphx_740


title: Aged_nphx_731


title: Aged_nphx_738


title: Aged_nphx_728


title: Aged_nphx_737


title: Aged_nphx_723


title: Aged_nphx_720


title: Aged_nphx_734


title: Aged_nphx_756


title: Aged_nphx_726


title: Aged_nphx_725


title: Aged_nphx_712


title: Aged_nphx_724


title: Aged_nphx_715


title: Aged_nphx_709


title: Aged_nphx_722


title: Aged_nphx_719


title: Aged_nphx_716


title: Aged_nphx_718


title: Aged_nphx_714


title: Aged_nphx_705


title: Aged_nphx_721


title: Aged_nphx_706


title: Aged_nphx_704


title: Aged_nphx_730


title: Aged_nphx_713


title: Aged_nphx_710


title: Aged_nphx_707


title: Aged_nphx_711


title: Aged_nphx_699


title: Aged_nphx_696


title: Aged_nphx_695


title: Aged_nphx_703


title: Aged_nphx_692


title: Aged_nphx_693


title: Aged_nphx_717


title: Aged_nphx_690


title: Aged_nphx_697


title: Aged_nphx_701


title: Aged_nphx_700


title: Aged_nphx_702


title: Aged_nphx_708


title: Aged_nphx_689


title: Aged_nphx_691


title: Aged_nphx_688


title: Aged_nphx_694


title: Aged_nphx_683


title: Aged_nphx_684


title: Aged_nphx_681


title: Aged_nphx_679


title: Aged_nphx_687


title: Aged_nphx_678


title: Aged_nphx_676


title: Aged_nphx_685


title: Aged_nphx_686


title: Aged_nphx_682


title: Aged_nphx_673


title: Aged_nphx_680


title: Aged_nphx_670


title: Aged_nphx_675


title: Aged_nphx_669


title: Aged_nphx_674


title: Aged_nphx_698


title: Aged_nphx_665


title: Aged_nphx_666


title: Aged_nphx_659


title: Aged_nphx_664


title: Aged_nphx_668


title: Aged_nphx_667


title: Aged_nphx_672


title: Aged_nphx_671


title: Aged_nphx_658


title: Aged_nphx_662


title: Aged_nphx_663


title: Aged_nphx_660


title: Aged_nphx_653


title: Aged_nphx_649


title: Aged_nphx_677


title: Aged_nphx_657


title: Aged_nphx_647


title: Aged_nphx_656


title: Aged_nphx_646


title: Aged_nphx_654


title: Aged_nphx_655


title: Aged_nphx_643


title: Aged_nphx_644


title: Aged_nphx_645


title: Aged_nphx_650


title: Aged_nphx_648


title: Aged_nphx_641


title: Aged_nphx_639


title: Aged_nphx_638


title: Aged_nphx_652


title: Aged_nphx_661


title: Aged_nphx_635


title: Aged_nphx_634


title: Aged_nphx_636


title: Aged_nphx_631


title: Aged_nphx_633


title: Aged_nphx_630


title: Aged_nphx_632


title: Aged_nphx_629


title: Aged_nphx_628


title: Aged_nphx_627


title: Aged_nphx_651


title: Aged_nphx_623


title: Aged_nphx_625


title: Aged_nphx_626


title: Aged_nphx_640


title: Aged_nphx_622


title: Aged_nphx_620


title: Aged_nphx_618


title: Aged_nphx_621


title: Aged_nphx_617


title: Aged_nphx_616


title: Aged_nphx_612


title: Aged_nphx_610


title: Aged_nphx_609


title: Aged_nphx_615


title: Aged_nphx_614


title: Aged_nphx_637


title: Aged_nphx_619


title: Aged_nphx_605


title: Aged_nphx_607


title: Aged_nphx_606


title: Aged_nphx_611


title: Aged_nphx_642


title: Aged_nphx_603


title: Aged_nphx_601


title: Aged_nphx_624


title: Aged_nphx_597


title: Aged_nphx_613


title: Aged_nphx_600


title: Aged_nphx_594


title: Aged_nphx_598


title: Aged_nphx_592


title: Aged_nphx_593


title: Aged_nphx_595


title: Aged_nphx_599


title: Aged_nphx_591


title: Aged_nphx_608


title: Aged_nphx_583


title: Aged_nphx_587


title: Aged_nphx_589


title: Aged_nphx_578


title: Aged_nphx_604


title: Aged_nphx_579


title: Aged_nphx_577


title: Aged_nphx_580


title: Aged_nphx_576


title: Aged_nphx_588


title: Aged_nphx_584


title: Aged_nphx_575


title: Aged_nphx_602


title: Aged_nphx_581


title: Aged_nphx_572


title: Aged_nphx_574


title: Aged_nphx_573


title: Aged_nphx_571


title: Aged_nphx_582


title: Aged_nphx_586


title: Aged_nphx_590


title: Aged_nphx_585


title: Aged_nphx_570


title: Aged_nphx_568


title: Aged_nphx_567


title: Aged_nphx_566


title: Aged_nphx_569


title: Aged_nphx_564


title: Aged_nphx_563


title: Aged_nphx_561


title: Aged_nphx_560


title: Aged_nphx_558


title: Aged_nphx_557


title: Aged_nphx_596


title: Aged_nphx_559


title: Aged_nphx_555


title: Aged_nphx_553


title: Aged_nphx_554


title: Aged_nphx_552


title: Aged_nphx_556


title: Aged_nphx_550


title: Aged_nphx_551


title: Aged_nphx_549


title: Aged_nphx_548


title: Aged_nphx_547


title: Aged_nphx_546


title: Aged_nphx_565


title: Aged_nphx_542


title: Aged_nphx_543


title: Aged_nphx_544


title: Aged_nphx_562


title: Aged_nphx_539


title: Aged_nphx_538


title: Aged_nphx_541


title: Aged_nphx_537


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title: Aged_nphx_536


title: Aged_nphx_534


title: Aged_nphx_535


title: Aged_nphx_528


title: Aged_nphx_524


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title: Aged_nphx_523


title: Aged_nphx_529


title: Aged_nphx_530


title: Aged_nphx_545


title: Aged_nphx_526


title: Aged_nphx_520


title: Aged_nphx_527


title: Aged_nphx_522


title: Aged_nphx_525


title: Aged_nphx_517


title: Aged_nphx_513


title: Aged_nphx_515


title: Aged_nphx_514


title: Aged_nphx_521


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title: Aged_nphx_519


title: Aged_nphx_518


title: Aged_nphx_508


title: Aged_nphx_507


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title: Aged_nphx_512


title: Aged_nphx_506


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title: Aged_nphx_509


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title: Aged_nphx_505


title: Aged_nphx_498


title: Aged_nphx_499


title: Aged_nphx_502


title: Aged_nphx_495


title: Aged_nphx_492


title: Aged_nphx_500


title: Aged_nphx_501


title: Aged_nphx_489


title: Aged_nphx_490


title: Aged_nphx_493


title: Aged_nphx_504


title: Aged_nphx_494


title: Aged_nphx_491


title: Aged_nphx_485


title: Aged_nphx_497


title: Aged_nphx_482


title: Aged_nphx_486


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title: Aged_nphx_480


title: Aged_nphx_488


title: Aged_nphx_503


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title: Aged_nphx_477


title: Aged_nphx_479


title: Aged_nphx_496


title: Aged_nphx_476


title: Aged_nphx_475


title: Aged_nphx_473


title: Aged_nphx_474


title: Aged_nphx_471


title: Aged_nphx_469


title: Aged_nphx_472


title: Aged_nphx_470


title: Aged_nphx_484


title: Aged_nphx_466


title: Aged_nphx_487


title: Aged_nphx_468


title: Aged_nphx_465


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title: Aged_nphx_460


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title: Aged_nphx_427


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title: Aged_nphx_422


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title: Aged_nphx_187


title: Aged_nphx_202


title: Aged_nphx_183


title: Aged_nphx_181


title: Aged_nphx_180


title: Aged_nphx_177


title: Aged_nphx_178


title: Aged_nphx_185


title: Aged_nphx_176


title: Aged_nphx_179


title: Aged_nphx_175


title: Aged_nphx_172


title: Aged_nphx_170


title: Aged_nphx_173


title: Aged_nphx_167


title: Aged_nphx_174


title: Aged_nphx_168


title: Aged_nphx_166


title: Aged_nphx_165


title: Aged_nphx_162


title: Aged_nphx_163


title: Aged_nphx_160


title: Aged_nphx_161


title: Aged_nphx_158


title: Aged_nphx_156


title: Aged_nphx_154


title: Aged_nphx_155


title: Aged_nphx_157


title: Aged_nphx_153


title: Aged_nphx_151


title: Aged_nphx_149


title: Aged_nphx_150


title: Aged_nphx_171


title: Aged_nphx_169


title: Aged_nphx_148


title: Aged_nphx_147


title: Aged_nphx_146


title: Aged_nphx_145


title: Aged_nphx_164


title: Aged_nphx_144


title: Aged_nphx_143


title: Aged_nphx_142


title: Aged_nphx_159


title: 3_7j_pi_conv

city: Jouy-en-Josas

first: Leyla

last: Slamti

state: État

address: Domaine de Vilvert

department: Micalis

country: France

institute: INRAE

data_processing:
bcl2fastq2-2.18.12 (demultiplex), Cutadapt 1.15 (adapter trimming),
FastQC v0.11.5 (quality control)
mapping (BWA v0.6.2-r126)
FeatureCounts (v1.5.2)
Assembly: GenBank (Assembly: GCA_000306745.1)
Supplementary files format and content: tab-delimited text file including genes and count values for all samples

organism: Bacillus thuringiensis

source_name: extracted from insect cadavers at 7dpi

growth_protocol: in vitro, LB 30°C or extracted from Galleria mellonella cadavers at 7 days-post-infection

extract_protocol:
Trizol RNA-Extraction + DNAse treatment
ribosomal RNA depletion (RiboZero) + Truseq Stranded Total RNA prep

treatment_protocol: Harvested in RNA-later

value: extracted from insect cadavers at 7dpi

tag: genotype

value: WT

tag: growth phase

value: 7 dpi


title: 2_7j_pi_conv


title: Aged_nphx_140


title: Aged_nphx_141


title: 1_7j_pi_conv


title: Aged_nphx_139


title: 3_stat_LB30

source_name: in vitro, LB 30degreeC

value: in vitro, LB 30degreeC

value: early stationnary phase, OD600nm=8


title: Aged_nphx_138


title: 2_stat_LB30


title: Aged_nphx_137


title: 1_stat_LB30


title: Aged_nphx_152


title: 3_expo_LB30

value: exponential growth phase OD600nm=1


title: 2_expo_LB30


title: Aged_nphx_136


title: Aged_nphx_135


title: Aged_nphx_134


title: CD8 spermidine, biological rep2

type: RNA

city: Meguro-ku, Tokyo

first: Sana

last: Hibino

address: T block (56th Bldg.), Komaba 4-6-1

country: Japan

institute: University of Tokyo

description: Gene expression data from in vitro-cultured mouse CD8+ T cells treated with spermidine

hyb_protocol: 2.3 μg of fragmented and labeled cDNA were hybridized for 16 hr at 45℃ on the Clariom S array using GeneChipTM Hybridization Oven 645. Arrays were washed and stained using GeneChipTM Fluidics Station 450.

scan_protocol: Clariom S arrays were scanned using the GeneChipTM Scanner 3000 7G, according to the manufacturer’s protocol (GeneChipTM Command Console (AGCC) 4.0 User Manual, Thermo Fisher Scientific, Inc.).

data_processing: Probe set summarization and initial data quality examination for Clariom S arrays were performed using Expression Console™ Software  (Thermo Fisher Scientific, Inc.). For normalization, SST-RMA algorithm was used.

label: biotin

label_protocol: Biotinylated cDNA were prepared from 250 ng total RNA by using GeneChipTM WT PLUS Reagent Kit, according to the manufacturer’s protocol (GeneChipTM WT PLUS Reagent Kit User Manual, Thermo Fisher Scientific, Inc) .

growth_protocol: Mouse CD8+ T cells  were stimulated with Dynabeads Mouse T-Activator CD3/CD28 (Thermo Fisher Scientific), along with expansion in culture medium containing IL-2  for 3 days.

extract_protocol: Total RNA was extracted using ReliaPrep RNA Cell Miniprep System (Promega), according to the manufacturer's instructions.

treatment_protocol: Spermidine (25μM) was added to the culture medium.

value: mouse CD8+ T cells isolated from spleens and lymph nodes of C57/BL6 mice


title: CD8 spermidine, biological rep1

source_name: mouse CD8+ T cells treated with spermidine


title: Aged_nphx_133


title: Aged_nphx_132


title: CD8 control, biological rep1

description: Gene expression data from in vitro-cultured mouse CD8+ T cells

source_name: mouse CD8+ T cells left untreated


title: 1_expo_LB30


title: Aged_nphx_131


title: CD8 control, biological rep2


title: Aged_nphx_130


title: ROMA

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

library_source: genomic

data_processing:
Illumina platform used for base calling
TASSEL5 GBSv2 pipeline was used for identification of tags at cut sites and SNPs located across reference genome.
The fastq files were aligned against the tomato reference genome using the Bowtie2 tool version 2.2.9. The .sam file created from the Bowtie2 aligner program was used through SAMToGBSdbPlugin()
DiscoverySNPCallerPluginV2 took a GBSv2 database file as input and identified SNPs from the aligned tags.
Assembly: mm9
Supplementary files format and content: The VCF file generated from tassel pipeline was generated.
Supplementary files format and content: After filtration SNPs were retained provided in hapmap (hmp) format.

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: Leaf

extract_protocol:
gDNA was isolated from leaf samples by using Xcelgen Plant gDNA Isolation Kit (XG2611-01) as per the protocol described. The DNA was eluted in 50µl Nuclease-Free Water. The samples were quantified using Qubit Fluorometer. For determining A260/280 ratio, 1µl of sample was loaded in Nanodrop8000 spectrophotometer. The quality of samples was checked in 0.8% Agarose gel electrophoresis along with Hind III marker for the presence of intact bands.
To 100ng of gDNA, barcoded adapters (~0.1pM) were added and digested with Apek1 enzyme for 12h at 75oC. The barcoded and common adapters were ligated to the sticky ends of the digested DNA with T4 DNA Ligase enzyme at 22oC for 180 mins, followed by heat inactivation. The ligated products were pooled into 12 groups of 12 samples each group. The pool was PCR amplified to generate the final library pool.
High Sensitivity (HS) DNA chip and library pool was sequenced on Illumina platform to generate ~ 3 million reads/sample.

tag: domestication

value: Cultivated

tag: tissue

value: Leaf


title: PUSA SHEETAL


title: EC-145057


title: Aged_nphx_220


title: EC-914112


title: Aged_nphx_127


title: Aged_nphx_128


title: WIR-13708


title: Aged_nphx_126


title: IARI-4


title: IIHR-2201


title: EC-914091


title: Aged_nphx_125


title: EC-808922


title: S-22


title: Aged_nphx_124


title: Aged_nphx_123


title: Aged_nphx_122


title: Aged_nphx_121


title: SHALIMAR 1


title: Aged_nphx_120


title: MORTGAGE LIFTER


title: LOCALS2


title: Aged_nphx_119


title: EC-914092


title: Aged_nphx_129


title: Aged_nphx_118


title: EC-914108


title: EC-914106


title: STUPICE


title: IARI-3


title: Aged_nphx_116


title: Aged_nphx_117


title: EC-164334


title: SUB-ARCTIC


title: Aged_nphx_113


title: Aged_nphx_114


title: Aged_nphx_115


title: EC-914103


title: Aged_nphx_112


title: IARI-7


title: TOLCV-32


title: Aged_nphx_111


title: Aged_nphx_110


title: Aged_nphx_109


title: LOCAL PULWAMA


title: Aged_nphx_108


title: BLACK PLUM


title: SHALIMAR-2


title: Aged_nphx_106


title: Aged_nphx_105


title: EC-914113


title: Aged_nphx_103


title: Aged_nphx_104


title: EC-620438


title: Aged_nphx_102


title: EC-249574


title: IARI-1


title: Aged_nphx_100


title: Aged_nphx_101


title: EC-617047


title: COLD SET


title: Aged_nphx_98


title: Aged_nphx_97


title: TOLCV-16


title: EC-620402


title: Aged_nphx_99


title: EC-521047


title: VRT-01


title: Aged_nphx_95


title: POLISH TOMATO


title: Aged_nphx_96


title: Aged_nphx_94


title: Aged_nphx_92


title: Aged_nphx_90


title: Aged_nphx_107


title: xct1SpXAP5_biorep_2

city: DAVIS

first: Stacey

middle: L

last: Harmer

state: California

address: 1002 Green Hall, One Shields Ave.

department: Plant Biology

country: USA

institute: UC Davis

data_processing:
Raw reads generated by the PacBio Sequel II sequencer were imported into PacBio SMRT Link v 8.0 for Circular Consensus Sequence (CCS) calling and demultiplexing.
Next, poly(A) tails and concatemers were removed using the refine command from isoseq3 package via Bioconda (v 3.10) with the option ‘--require-polya’.
Then the fastq files containing full-length non-concatemer reads were mapped to Arabidopsis TAIR 10 genome assembly using minimap2 (v 2.17) with the parameter ‘-ax splice -t 30 -uf --secondary=no -C5’.
For differential splicing analysis, counts of exonic regions and known/novel splice junctions were generated using QoRTs software package (v 1.3.6; Hartley and Mullikin, 2015) with the parameter ‘--stranded --singleEnded --stranded_fr_secondstrand --keepMultiMapped’. To adapt to the long-read data, the ‘maxPhredScore’ was set to 93 and the ‘maxReadLength’ was adjusted manually for each library. To increase the power of detecting novel splice junctions, the '--minCount' threshold was set to 5.
The raw count data was then loaded to JunctionSeq R package (v 1.5.4; Hartley and Mullikin, 2016) to determine differential usage of exons or splice junctions relative to the overall expression of the gene with a false discovery rate (FDR) of 0.05.
Assembly: Arabidopsis TAIR 10 genome assembly
Supplementary files format and content: The raw count files are gzip compressed tab-delimited text files that include raw counts for each exon/known junction/novel junction
Supplementary files format and content: The normalized abundance files are gzip compressed tab-delimited text files that include normalized expression levels, statistic significance of the differential usage and corresponding location information of each of each exon/known junction/novel junction

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seeds were surface sterilized in 70% ethanol prepared in 0.1% (v/v) Triton X-100 (Sigma) for 5 minutes and then in 100% Ethanol for 20 minutes. After air drying, seeds were plated on 1x Murashige and Skoog (MS) growth media containing 0.7% agar, pH 5.7. After 3d stratification in dark at 4˚C, plates were transferred to a growth chamber with constant light (55 µmol m-2 s-1) and temperature (22˚C) to germinate.

extract_protocol:
Samples were flash-frozen in liquid nitrogen, and ground into fine powder using a beadbeater. Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) followed by purification using the RNA Clean & Concentrator Kit (Zymo Research). Purified RNAs were quantified using a Nanodrop (ThermoFisher) and quality control was performed by an Agilent Bioanalyzer 2100.
PacBio Sequel II library preparation and RNA-sequencing (Iso-Seq) was performed by UC Davis DNA Technologies & Expression Analysis Core (https://dnatech.genomecenter.ucdavis.edu/pacbio-library-prep-sequencing/).
PacBio Sequel II

treatment_protocol: At day 11, approximately 60 mg of whole seedlings of each genotype were collected every 2h over 24 hours and pooled. Three independent biological replicates were collected for each genotype.

value: whole seedling

tag: developmental stage

value: xct-1 XCT::SpXAP5

tag: treatment

value: constant light (55 umol m-2 s-1) and temperature (22 C)

tag: time

value: sampled every 2h over 24 hours and pooled


title: xct1SpXAP5_biorep_3


title: prl1_biorep_2


title: prl1_biorep_1


title: xct1SpXAP5_biorep_1


title: xct2XCT_biorep_3

value: xct-2 XCT::XCT


title: Aged_nphx_89


title: GLACIER


title: Aged_nphx_91


title: prl1_biorep_3


title: Aged_nphx_87


title: Aged_nphx_88


title: xct2XCT_biorep_2


title: Aged_nphx_86


title: Aged_nphx_85


title: xct2_biorep_2


title: Aged_nphx_84


title: Aged_nphx_83


title: xct2_biorep_1


title: Aged_nphx_93


title: Aged_nphx_82


title: xct1_biorep_2


title: Aged_nphx_81


title: xct1_biorep_1


title: Aged_nphx_80


title: Aged_nphx_79


title: Aged_nphx_78


title: Col_biorep_3


title: Col_biorep_2


title: Aged_nphx_77


title: media and ORF and empty vector, replicate 5

city: Tucson

first: Syed Shujaat Ali

last: Zaidi

address: 1656 E Mabel St

department: Department of Immunobiology

institute: University of Arizona

data_processing:
double-stranded cDNA was synthesized using SuperScript III Reverse Transcriptase (Invitrogen) with random hexamers. RNA integrity number >9 was confirmed using the Agilent 4200 TapeStation system (Agilent Technologies). RNAseq on the shRNA-treated iNs was performed by Functional Genomics Core at the University of Arizona at a depth of 30 million single-end reads (100 bp long). The RNAseq data was QCed and processed with the same steps as outlined in the Methods section “ROSMAP RNAseq, data processing, and quality control”.
Supplementary files format and content: counts

organism: Homo sapiens

extract_protocol: Cell were lysed, at least 250 ng of total RNA input was oligo(dT) purified using the PureLink RNA Mini Kit (Invitrogen),

tag: cell line

value: iPSC-derived neuron

value: media and ORF and empty vector

value: RNAi


title: Col_biorep_1


title: media and ORF and empty vector, replicate 4


title: media and ORF and empty vector, replicate 3


title: Aged_nphx_75

value: FACS sorted


title: Aged_nphx_74


title: Aged_nphx_73


title: xct2XCT_biorep_1


title: xct2_biorep_3


title: Aged_nphx_72


title: Aged_nphx_71


title: media and ORF and empty vector, replicate 2


title: media and no vector, replicate-4

value: media and no vector


title: Aged_nphx_70


title: xct1_biorep_3


title: media and no vector, replicate-2


title: media and no vector, replicate-1


title: Aged_nphx_68


title: Aged_nphx_69


title: Aged_nphx_67


title: Aged_nphx_76


title: media and empty vector, replicate 2

value: media and empty vector


title: Aged_nphx_66


title: Aged_nphx_65


title: media and empty vector, replicate 1


title: Aged_nphx_64


title: YWHAZ knockdown, replicate 3

value: YWHAZ knockdown


title: YWHAZ knockdown, replicate 2


title: YWHAZ knockdown, replicate 1


title: media and ORF and empty vector, replicate 1


title: Aged_nphx_62


title: Aged_nphx_63


title: STXBP1 knockdown, replicate 2

value: STXBP1 knockdown


title: media and no vector, replicate-3


title: Aged_nphx_61


title: RHBDD2 knockdown, replicate 3

value: RHBDD2 knockdown


title: STXBP1 knockdown, replicate 1


title: Aged_nphx_59


title: Aged_nphx_60


title: RHBDD2 knockdown, replicate 2


title: Aged_nphx_57


title: RBM4 knockdown, replicate 1

value: RBM4 knockdown


title: RBM4 knockdown, replicate 3


title: Aged_nphx_56


title: Aged_nphx_55


title: Aged_nphx_51


title: Aged_nphx_54


title: STXBP1 knockdown, replicate 3


title: RAB9A knockdown, replicate 3

value: RAB9A knockdown


title: RAB9A knockdown, replicate 2


title: Aged_nphx_52


title: Aged_nphx_50


title: RBM4 knockdown, replicate 2


title: RAB3A knockdown, replicate 1

value: RAB3A knockdown


title: Aged_nphx_58


title: Aged_nphx_49


title: NUDT2 knockdown, replicate 3

value: NUDT2 knockdown


title: RAB3A knockdown, replicate 2


title: Aged_nphx_46


title: NUDT2 knockdown, replicate 2


title: Aged_nphx_47


title: NUDT2 knockdown, replicate 1


title: Aged_nphx_45


title: RHBDD2 knockdown, replicate 1


title: NDRG4 knockdown, replicate 3

value: NDRG4 knockdown


title: Aged_nphx_43


title: NSF knockdown, replicate 1

value: NSF knockdown


title: NDRG4 knockdown, replicate 2


title: RAB3A knockdown, replicate 3


title: Aged_nphx_42


title: Aged_nphx_53


title: Aged_nphx_41


title: Aged_nphx_40


title: JMJD6 knockdown, replicate 3

value: JMJD6 knockdown


title: Aged_nphx_39


title: NDRG4 knockdown, replicate 1


title: Aged_nphx_38


title: Aged_nphx_48


title: JMJD6 knockdown, replicate 2


title: ICA knockdown, replicate 3

value: ICA knockdown


title: JMJD6 knockdown, replicate 1

value: iPSC-derived neuron


title: ICA knockdown, replicate 1


title: NSF knockdown, replicate 3


title: HP1BP3 knockdown, replicate 3

value: HP1BP3 knockdown


title: ICA knockdown, replicate 2

value: RNAi


title: Aged_nphx_36

value: FACS sorted


title: Aged_nphx_35


title: Aged_nphx_33


title: HP1BP3 knockdown, replicate 2


title: Aged_nphx_34


title: Aged_nphx_30


title: Aged_nphx_31


title: Aged_nphx_44


title: HP1BP3 knockdown, replicate 1


title: GABARAP knockdown, replicate 1

value: GABARAP knockdown


title: Aged_nphx_32


title: FMNL2 knockdown, replicate 3

value: FMNL2 knockdown


title: Aged_nphx_26


title: FIBP knockdown, replicate 3

value: FIBP knockdown


title: FMNL2 knockdown, replicate 1


title: Aged_nphx_25


title: Aged_nphx_37


title: FIBP knockdown, replicate 1


title: DCAF12 knockdown, replicate 2

value: DCAF12 knockdown


title: GABARAP knockdown, replicate 2


title: Aged_nphx_21


title: GABARAP knockdown, replicate 3


title: Aged_nphx_20


title: Aged_nphx_28


title: FMNL2 knockdown, replicate 2


title: CIRBP knockdown, replicate 3

value: CIRBP knockdown


title: Aged_nphx_27


title: Aged_nphx_18


title: CIRBP knockdown, replicate 1


title: ATP6V1A knockdown, replicate 3

value: ATP6V1A knockdown


title: Aged_nphx_16


title: DCAF12 knockdown, replicate 3


title: Aged_nphx_22


title: ATP6V1A knockdown, replicate 1


title: Aged_nphx_17


title: DCAF12 knockdown, replicate 1


title: Aged_nphx_23


title: Aged_nphx_29


title: Aged_nphx_19


title: Aged_nphx_24


title: Aged_nphx_15


title: FIBP knockdown, replicate 2


title: ATP1B1 knockdown, replicate 1

value: ATP1B1 knockdown


title: Aged_nphx_14


title: ATP1B1 knockdown, replicate 3


title: ATP6V1A knockdown, replicate 2


title: MGAcell

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description: 20211104_2, 20211104_3, 20211104_4, 20211104_5, 20211104_6, 20211104_7, 20211104_8, 20211104_9, 20211104_10, 20211104_11, 20211104_13, 20211104_14, 20211104_15, 20211104_16, 20211104_17, 20211104_18, 20211104_19, 20211104_20, 20211104_21, 20211027_2, 20211027_3, 20211027_4, 20211027_5, 20211027_6, 20211027_7, 20211027_8, 20211027_9, 20211027_10, 20211027_11, 20211027_12, 20211027_13, 20211027_14, 20211027_15, 20211027_16, 20211027_17, 20211027_18, 20211027_19, 20211027_20, 20211027_21, 20211020_1, 20211020_2, 20211020_3, 20211020_4, 20211020_5, 20211020_6, 20211020_7, 20211020_8, 20211020_9, 20211020_10, 20211020_11, 20211020_12, 20211020_13, 20211020_14, 20211020_15, 20211020_16, 20211020_17, 20211020_18, 20211020_19, 20211020_20, P1_1, P1_2, P1_3, P1_4, P1_5, P1_6, P1_7, P1_8, P1_9, P1_10, P1_11, P1_12, P2_1, P2_2, P2_3, P2_4, P2_5, P2_6, P2_7, P2_8, P2_9, P2_10, P2_11, P2_12, P3_1, P3_2, P3_3, P3_4, P3_5, P3_6, P3_7, P3_8, P3_9, P3_10, P3_11, P3_12, Empty

data_processing:
FASTQ files were demultiplexed and read alignment was done using STAR to the human genome (hg19, annotation: UCSC known genes),
Assembly: hg19, annotation (UCSC known genes)
Supplementary files format and content: .txt files of count matrix

source_name: Human cell lines

extract_protocol:
For acute slice-cultures, slices were transferred to OCT and frozen into blocks. Tissue from each slice was isolated for RNA extraction using the QiaSymphony extraction method. Total RNA was quantified using Nanodrop measurements, and 150ng of RNA from each slice/condition was loaded into a well of a 96 well plate. Automated liquid-handling was used to introduce lysis buffer, capture polyadenylated mRNA with an oligo(dT)-grafted plate, and deliver well-specific, barcoded oligo(dT) primers to every sample in the plate. After reverse transcription, the cDNA in each well contains a specific barcode sequence on its 5’-end and a common adapter and can then be combined into a single pool for purification and concentration. Pooled second-strand synthesis was performed from adapter-linked random primers with Klenow Large Fragment, which lacks strand-displacement and 5’-to-3’ exonuclease activities. Therefore, each cDNA molecule produces at most, one second-strand synthesis product containing the sample barcode. Finally, the pooled library is enriched in a single PCR prior to sequencing. The resulting libraries represent the 3’-ends of mRNAs and are sequenced to a depth of 0.5-2 million raw reads per sample.
Sequencing of the resultant libraries was done on Illumina NextSeq 500.

value: Human cell lines


title: Aged_nphx_13


title: Aged_nphx_7


title: AVS144

source_name: GBM Tissue

value: GBM Tissue


title: Aged_nphx_12


title: ATP1B1 knockdown, replicate 2


title: Aged_nphx_11


title: Aged_nphx_9


title: AVS146


title: CIRBP knockdown, replicate 2


title: AVS138


title: Aged_nphx_8


title: AVS145


title: Aged_nphx_1


title: MGAslice

description: MGA001, MGA002, MGA003, MGA004, MGA005, MGA006, MGA007, MGA008, MGA009, MGA010, MGA011, MGA012, MGA013, MGA014, MGA015, MGA016, MGA017, MGA018, MGA019, MGA020, MGA021, MGA022, MGA023, MGA024, MGA025, MGA026, MGA027, MGA028, MGA029, MGA030, MGA031, MGA032, MGA033, MGA034, MGA035, MGA036, MGA037, MGA038, MGA039, MGA040, MGA041, MGA042, MGA043, MGA044, MGA045, MGA046, MGA047, MGA048, MGA049, MGA050, MGA051, MGA052, MGA053, MGA054, MGA055, MGA056, MGA057, MGA058, MGA059, MGA060, MGA061, MGA062, MGA063, MGA064, MGA065, MGA066, MGA067, MGA068, MGA069, MGA070, MGA071, MGA072, MGA073, MGA074, MGA075, MGA076, MGA077, MGA078, MGA079, MGA080, MGA081, MGA082, MGA083, MGA084, MGA085, MGA086, MGA087, MGA088, MGA089, MGA090, MGA091, MGA092, MGA093, MGA094, MGA095, MGA096


title: AVS142


title: Adult_nphx_1535


title: AVS139


title: Aged_nphx_2


title: Aged_nphx_6


title: Aged_nphx_5


title: AVS133


title: AVS135


title: Aged_nphx_4


title: Aged_nphx_3


title: AVS131


title: Aged_nphx_10


title: AVS132


title: Adult_nphx_1533


title: AVS137


title: AVS136


title: Adult_nphx_1532


title: Adult_nphx_1536


title: AVS127


title: Adult_nphx_1531


title: Adult_nphx_1529


title: AVS130


title: AVS141


title: Adult_nphx_1524


title: Adult_nphx_1530


title: AVS129


title: AVS122


title: AVS123


title: AVS121


title: Adult_nphx_1523


title: AVS119


title: Adult_nphx_1528


title: AVS125


title: Adult_nphx_1527


title: AVS124


title: Adult_nphx_1518


title: Adult_nphx_1534


title: Adult_nphx_1517


title: AVS115


title: Adult_nphx_1516


title: Adult_nphx_1526


title: Adult_nphx_1525


title: AVS112


title: Adult_nphx_1522


title: Adult_nphx_1514


title: Adult_nphx_1521


title: AVS126


title: AVS120


title: Adult_nphx_1520


title: AVS117


title: AVS108


title: Adult_nphx_1519


title: Adult_nphx_1511


title: AVS118


title: Adult_nphx_1510


title: H3K79me2_creAF10_rep2

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
Reads were aligned mm9 mouse genome with Bowtie2
Samtools-1.2 was used to convert .sam files into .bam files using “view” and then sort .bam files with the “sort” command.
Spike-in normalization was calculated by isolating reads that did not align to the mouse genome from sorted bam files with Sam-1.2 “view -f4”. These unmapped reads were converted to fastq files with Samtools-1.2 “bam2fq” and aligned to hg19 using the Bowtie2 and Samtools-1.2 as above. Samtools-1.2 “flagstat” was used to calculate the number of reads that uniquely map to the human genome, which was used as a scaling factor for generation of bigwig files.
Peaks were called against a MEF DNA input using MACS2 with the parameters: --broad -p 0.0001 (H3K79me2) and --broad -p 0.001 (H3K79me1). Peaks were annotated with HOMER to the mm9 genome using annotatePeaks.pl
Deeptools was used to generate bigwig files that were normalized to the human spike-in scaling factor with: bamCoverage --binSize 10 --scaleFactor  --ignoreForNormalization chrX, and used to make metaplots.
H3K79me enrichment per gene body was calculated with BEDTools2.0 “multibamCov”. Reads were normalized per human spike-in scaling factor, and then per kilobase of gene length.
Assembly: mm9
Supplementary files format and content: bigwig
Supplementary files format and content: broadPeak

source_name: Mouse embryonic fibroblast

growth_protocol: MEFs were maintained in MEF media (DMEM, 10% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, and 2-Mercaptoethanol - 4 μl/500ml) and reprogramming cells were grown in ESC media (knock-out DMEM, 15% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, 2-Mercaptoethanol - 4 μl/525ml, and leukemia inhibitory factor) on plates coated with 0.1% porcine gelatin and DR4 feeder MEFs. All cells were maintained in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed for 10 minutes with 1% formaldehyde, in solution, rotating at room temperature. Fixing was quenched with 0.14 M glycine for 5 minutes, and the cells were spun down at 300xg for 3 minutes. Cells were washed 3 times with PBS and flash frozen. 25-30 million cells were resuspended in 1 mL lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA, 1x cOmplete (Roche, 4693132001) protease inhibitor), and sonicated on a Covaris S220 Focused-ultrasonicator with the following parameters: 21 cycles of 45 seconds ON (peak 170, duty factor 5, cycles/burst 200), 45 seconds OFF (rest) in 6-8°C degassed water to generate fragments of 200-400 bp. Sonicated DNA was quantified with Qubit dsDNA HS (ThermoFisher Scientific, Q32854), aliquoted, and stored at -80°C. The immunoprecipitation was set up with 7.1 ug of assay chromatin plus 1:53 (133 ng) of human 293T spike in chromatin, generated as above. Chromatin was diluted 1:10 with dilution buffer (16.7 mM Tris-HCl pH 8, 0.01% SDS, 1.1% Trition-X, 1.2 mM EDTA, and 167 mM NaCl), and immunoprecipitated with 5 ug H3K79me1 (Abcam, ab2886, Lot GR274715-4) or H3K79me2 (Active Motif, 39143, Lot 16918002) antibody for 16 hours, rotating at 4°C. 25 μL of Protein A (ThermoFisher Scientific, 10002D) and 25 μL of Protein G (ThermoFisher Scientific, 10004D) Dynabeads that were washed once in PBS, 0.02% Tween-20 and once in dilution buffer, were added. Chromatin was incubated, rotating, with beads for 2 hours at 4°C. Beads were washed twice, rotating at 4°C for 5 minutes, with 1 mL of each of the following buffers: Low salt (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1 mM EDTA pH 8.0, 140 mM NaCl), High salt (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1 mM EDTA pH 8.0, 500 mM NaCl), LiCl (20 mM Tris-HCl pH 8, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA pH 8.0, 250 mM LiCl), and TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8) using a magnetic rack. Beads were incubated with 250 μL elution buffer (50 mM Tris-HCl pH 8, 1 mM EDTA pH 8, 1% SDS) for 10 minutes at 65°C, shaking. 200 μL of TE with 0.67% SDS was added, and incubated shaking at 65°C for 10 minutes. 10 μg RNase A was added and incubated at 37°C for 30 minutes. 40 μg of Proteinase K was added, and incubated for 12-16 hours at 65°C to reverse crosslinks. DNA was cleaned with phenol-chloroform phase separation with phase lock tubes (VWR, 10847-802). DNA was precipitated with 1 volume isopropanol, 1/10th volume of 3M NaActate, and 20 μg glycogen, and washed with 70% ethanol. DNA was dissolved in 30 μL ultrapure water and concentrated to 5 μL using a SpeedVac for library preparation.
The entire ChIP sample was used as starting material for library construction with Ovation Ultralow System V2 using reagents at 0.5x and adapters diluted 1/5 in water, following the manufacturer’s instructions (NuGEN, 0344). The libraries were separated on an 1.5% agarose gel, cut from 200-400 bp for an additional size selection step. The gel fragment was purified using the MinElute Gel Extraction Kit (Qiagen, 28604).

treatment_protocol: Cells were infected with Cre recombinase (Ad5-CMV-Cre) and empty control (Ad5-CMV-Empty) purchased from the Vector Development Lab (Baylor College of Medicine) to delete AF10. 2.4e9 pfu of virus was resuspended in 5 mL of serum-free DMEM and added to 1-2 million MEFs in a 10-cm dish. Virus containing media was removed after 1 hour and replaced with MEF media. Reprogramming was initiated 2 days post-transduction with with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), and replaced every 48 hours.

value: Mouse embryonic fibroblast

value: Conditional AF10

value: Day 4 reprogramming

value: AF10 -/-, OSKM, rtTA

value: CRE, dox

tag: chip antibody

value: H3K79me2, Active Motif, 39143


title: H3K79me2_creAF10_rep1


title: AVS116


title: Adult_nphx_1509


title: Adult_nphx_1515


title: AVS111


title: Adult_nphx_1508


title: AVS110


title: AVS113


title: AVS107


title: AVS106


title: Adult_nphx_1513


title: Adult_nphx_1512


title: Adult_nphx_1506


title: H3K79me2_fl_rep2

value: AF10 fl/fl, OSKM, rtTA

value: Control, dox


title: AVS103


title: H3K79me2_fl_rep1


title: H3K79me1_creAF10_rep2

value: H3K79me1, Abcam, ab2886


title: Adult_nphx_1504

value: FACS sorted


title: Adult_nphx_1503


title: AVS102


title: Adult_nphx_1505


title: H3K79me1_creAF10_rep1


title: Adult_nphx_1502


title: Adult_nphx_1501


title: AVS101


title: Adult_nphx_1499


title: AVS99


title: Adult_nphx_1500


title: H3K79me1_fl_rep2


title: Adult_nphx_1498


title: AVS98


title: Adult_nphx_1497


title: Adult_nphx_1496


title: Adult_nphx_1495


title: H3K79me1_fl_rep1


title: KTM

city: stony brook

first: Fu

last: Luo

state: New York

address: 100 Nicholls Road

institute: Stony Brook University

description: Single cell RNA-seq results from minor NPK clones

data_processing:
For single cell RNA-seq samples, FASTQ files were processed using the entire Cell Ranger (v3.0.2) single-cell analysis pipeline (10x Genomics). This pipeline includes both a ‘count’ and ‘aggregate’ step. Briefly, data were aligned with the 10x Genomics pre-built mouse genome for filtering, barcode counting, and UMI counting using default parameters.
For bulk RNA-seq samples, RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.17) for conversion of BCL to fastq format, coupled with adaptor trimming. Reads were mapped to the mouse genome (UCSC/mm10) using STAR (2.5.2b) and FeatureCounts (v1.5.0-p3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample or every cell

molecule: polyA RNA

source_name: Prostate luminal cancer cells

extract_protocol:
RNA libraries were prepared with 10x Genomics Chromium Single Cell 3′ Library & Gel Bead Kit v3 according to the manufactures protocols
Briefly, mouse prostate tissue from AP lobes was dissected in cold phosphate buffered saline (PBS) and minced with scissors, followed by incubation in DMEM/F12 (Gibco) supplemented with 5% FBS and 0.1% collagenase/hyaluronidase (STEMCELL Technologies) at 37°C for 2 hours. Dissociated tissues were spun at 350 g for 5 min and resuspended in TrypLE (Gibco), followed by incubation at 37°C for 20 minutes. After centrifugation at 350 g, pelleted cells were resuspended with pre-warmed 5 mg/ml dispase (STEMCELL Technologies) and, if necessary, incubated for an additional 20 minutes at 37°C. The cell suspension was then supplemented with 1:10 dilution of 1 mg/ml DNase I (STEMCELL Technologies) and triturated vigorously for 2 min. Enzymes were deactivated and diluted by addition of HBSS/2% FBS. Finally, the resulting cell suspension was passed through a 40 μm cell strainer (Falcon) to remove any large clumps of cells remaining. Filtered single cells were resuspended in Opti-MEM (Gibco) and flow sorted based on RFP, CFP or YFP expression on a BD FACS Aria II instrument. The Confetti+ FACS sorted cells were processed for single cell RNAseq on a 10x Genomics platform. Similarly collected cells were also flash-frozen in liquid nitrogen and stored at −80 °C for subsequent RNA processing.
Protocols applicable to each sample are included in the SAMPLES section

value: prostate

value: Nkx3.1CreERT2/+; Ptenflox/flox; K-RasLSLG12D/+; R26r-Confetti

tag: age

value: 3 month


title: AVS92


title: Adult_nphx_1507


title: KTD

description: Single cell RNA-seq results from dominant NPK clones


title: Adult_nphx_1494


title: AVS91


title: Adult_nphx_1493


title: AVS85


title: Kasumi1-AR2-Cat

city: Singapore

first: Henry

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
The paired-end RNA-seq reads are mapped by STAR to the human reference genome GRCh38 (hg38).
Alignments with mapping quality below 20 are filtered out. Normalization between the samples was based on the proportionality of the numbers of the mapped reads. featureCounts was used to summarize the counts for each transcripts.
Assembly: hg38
Supplementary files format and content: presented in RKPM for each transcript

source_name: blood

growth_protocol: Kasumi 1 (ATCC, cat.no. CRL 2724) cells were maintained in RPMI 1640 medium (Biowest, cat.no. L0500) supplemented with 20% FBS.

extract_protocol:
Cells were lysed with Trizol, RNAs were isolated using phenol-chloroform extraction.
Libraries were prepared using a TruSeq stranded total RNA library preparation kit (Illumina)  according to the manufacturer's instructions.

treatment_protocol: To generate Kasumi 1 cells stably expressing ADAR2, ADAR2 mutants, and wildtype or edited forms of COPA and COG3, 4.5 µg VSV G and 4.5 µg expression constructs were co transfected into GP2 293 cells cultured in T75 flasks for virus generation. Supernatants containing retrovirus were harvested and filtered using 0.45 µm syringe filters (Sartorius, cat.no. 16537) at 48 and 72 hours after transfection. These two portions of supernatant were mixed and aliquoted for virus transduction or stored in -80°C for subsequent usage. Virus transduction was performed using RetroNectin® Recombinant Human Fibronectin Fragment (Takara, cat.no. T100A/B) according to the manufacturer’s instructions (with centrifugation). At 72 hours after virus transduction, cells were selected using puromycin (1 µg/ml) for 72 hours or by fluorescence-activated cell sorting (FACS).

value: human AML

value: blood

value: adult


title: Kasumi1-AR2-dsRBD


title: Adult_nphx_1490


title: AVS83

value: GBM Tissue


title: Adult_nphx_1492


title: Adult_nphx_1491


title: Kasumi1-ADAR2


title: Adult_nphx_1489


title: AVS82


title: Adult_nphx_1488


title: Kasumi1-EV


title: Adult_nphx_1487


title: AVS81


title: Adult_nphx_1486


title: Adult_nphx_1485


title: Sinomenine (40mg/kg) treated group_4

city: xiamen

first: Yan

last: Li

state: Fujian

address: Zhenhai road

country: China

institute: Xiamen University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat (http://tophat.cbcb.umd.edu/, version2.1.1) software. The mapping criteria of bowtie was as follows: sequencing reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions. Then the region of gene were expanded following depths of sites and the operon was obtained. In addition, the whole genome was split into multiple 15kb windows that share 5kb. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html)[3] was utilized for differential expression analysis.  In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS 2.1.1 (http://kobas.cbi.pku.edu.cn/download.php)
Supplementary files format and content: tab-delimited text files include counts for each Sample

organism: Rattus norvegicus

source_name: Sinomenine (40mg/kg) treated group

growth_protocol: The male inbred SD rats, 6-8 weeks old, weighing 200±20g, after adaptive feeding, all rats were randomly distributed into four groups: normal group; DN group; SIN (20mg/kg) administration group; SIN (40mg/kg) administration group.

extract_protocol:
Total RNA was extracted from the XX tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer's instructions (Illumina, San Diego, CA). RNA-seq transcriptome librariy was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. Libraries were size selected for cDNA target fragments of 200-300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina Novaseq 6000 (2X150bp read length).

treatment_protocol: We used 0.1M citrate buffer (pH 4.5) to prepare streptozotocin (STZ, Sigma) and injected the freshly prepared STZ to overnight fasting rats at a 45 mg/kg dose. After one week, rats with a blood glucose level over 16.7 mmol/L were selected in subsequent experiments. In normal group, equal volume of sodium citrate buffer was injected. The rats in normal group were fed in normal diet, while the remaining groups were administered with high-glucose and high-fat diet. In addition, SIN (20mg/kg) administration group was treated with SIN (20mg/kg) per day and SIN (40mg/kg) administration group was treated with SIN (40mg/kg) per day.

value: Sprague Dawley

value: kidney

tag: Sex

value: male

value: high-fat and high-sugar treatment and sinomenine (40mg/kg) treatment


title: Adult_nphx_1483


title: Sinomenine (40mg/kg) treated group_3


title: Adult_nphx_1484


title: AVS80


title: Adult_nphx_1482


title: Adult_nphx_1481


title: Adult_nphx_1480


title: Adult_nphx_1479


title: AVS78


title: Sinomenine (40mg/kg) treated group_2


title: Sinomenine (40mg/kg) treated group_1


title: AVS76


title: Adult_nphx_1477


title: Sinomenine (20mg/kg) treated group_4

source_name: Sinomenine (20mg/kg) treated group

value: high-fat and high-sugar treatment and sinomenine (20mg/kg) treatment


title: AVS75


title: Adult_nphx_1476


title: Adult_nphx_1474


title: AVS74


title: Sinomenine (20mg/kg) treated group_3


title: Adult_nphx_1473


title: Sinomenine (20mg/kg) treated group_2


title: AVS73


title: Adult_nphx_1475


title: Sinomenine (20mg/kg) treated group_1


title: Adult_nphx_1472


title: AVS79


title: Adult_nphx_1471


title: Adult_nphx_1469


title: Adult_nphx_1470


title: Adult_nphx_1468


title: AVS66


title: Diabetic nephropathy group_4

source_name: Diabetic nephropathy group

value: high-fat and high-sugar treatment


title: Adult_nphx_1478


title: Adult_nphx_1467


title: Diabetic nephropathy group_3


title: AVS65


title: Adult_nphx_1465


title: Adult_nphx_1466


title: Diabetic nephropathy group_2


title: Adult_nphx_1464


title: AVS62


title: AVS61


title: Adult_nphx_1461


title: Diabetic nephropathy group_1


title: Adult_nphx_1462


title: Normal group_4

source_name: Normal group

value: sham


title: Adult_nphx_1460


title: AVS69


title: Adult_nphx_1459


title: AVS60


title: Normal group_3


title: AVS59


title: Adult_nphx_1457


title: Adult_nphx_1458


title: Normal group_2


title: Adult_nphx_1456


title: Adult_nphx_1455


title: Normal group_1


title: Adult_nphx_1453


title: Adult_nphx_1452


title: Adult_nphx_1451


title: RNAseq5

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

country: Canada

institute: McGill University

description: RNAseq

data_processing:
Illumina Novaseq 6000,Casava software used for basecalling.
Adaptor sequences and low-quality score containing bases (Phred score < 30) were trimmed from reads using Cutadapt v2.8 (-j 8 -u 4 -u -4 -Z  -o) Noncoding RNAs were removed by custom scripts following mapping these contaminant reads using Bowtie2 v2.3.5 ( --phred33 --very-sensitive) . The unmapped reads were aligned to reference rat genome (Rnor_6.0.94) using STAR v2.7.3a (54) with options ( --twopassMode Basic --twopass1readsN -1 -- seedSearchStartLmax 15 --outSJfilterOverhangMin 15 8 8 8 -- outFilterMismatchNoverReadLmax 0.1). QuantMode with STAR was used to obtain transcript coordinates.
Assigning RPF reads to genomic features (CDS, UTRs) was based on Genome annotation (Rnor_6.0.94). Only a single transcript isoform, with the highest APPRIS score , was considered per gene.
Genome_build: Rnor6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: BedGraph files were generated using Deeptools Scores represent normalized read count

source_name: whole brain

extract_protocol:
Five P5 rat brains were homogenized in RNA Granule Buffer (20 mM TRIS-HCl pH 7.4, 150 mM NaCl, 2.5 mM MgCl2 supplemented with 1 mM DTT , 1 mM EGTA and Roche EDTA-free protease inhibitor in the presence or absence of 100 ug/ml cycloheximide. This homogenate was used for RNA-SEQ libraries. For Footprinting libraries, homogenate was centrifuged 15 minutes in a Thermo Scientific T865 fixed angle rotor at 9200 rpm (6117 RCF) at 4˚C to spin down cellular debris. The supernatant was treated with 1% IGEPAL CA-630 for 5 minutes at 4˚C on a rocker. The sample was then loaded onto a 2 ml 60% sucrose] cushion (dissolved in supplemented RNA Granule Buffer) in a Sorvall 36 ml tube, filled to top with additional RNA Granule Buffer and centrifuged for 2 hours in a Thermo Scientific AH-629 swing-bucket rotor at 28500 rpm (56660 RCF) at 4˚C to achieve the polysome pellet. The pellet was re-suspended in RNA Granule Buffer, gently dounced and loaded over a 15-60% linear sucrose gradient (gradient was made with RNA Granule Buffer) and centrifuged for 45 minutes at 28500 rpm (56660 RCF) at 4˚C in an AH-629 swing bucket rotor. Fractions of 3.5 ml were then collected from the top, and the remaining pellet was rinsed once and then resuspended using RNA Granule Buffer. For treatments with salt, the suspension was incubated with 400 mM NaCl for 10 minutes at 4˚C on a rocker and then NaCl-free RNA granule buffer was added for a final concentration of 150 mM NaCl. The sample was then treated with 100 U of RNase I [100 U/µl; Ambion AM2294, Thermo Fisher] for 30 minutes at 4˚C on a rocker. The nuclease was quenched with 100 U of SuperaseIN [20 U/µl; Invitrogen #AM2696, Thermo Fisher], and the samples were re-run on a fresh 15-60% sucrose gradient to separate mononsomes. Either Fraction 2 or homoegnates (for RNA-SEQ) was precipitated overnight at -20 ˚C by adding 7 ml of chilled 100% ethanol.
Precipitates were centrifuged at 4,444 x g at 4 °C for 60 min, the isopropanol taken off, the pellet air-dried, and re-suspended in 10 mM Tris-HCl pH 7. We then proceeded with a standard hot phenol-acid extraction (Acid Phenol:Chloroform mix 125:24:1, Invitrogen, AM9722). SI All samples were depleted of ribosomal RNA using the Ribo-Zero Gold (Human/Mouse/Rat) Kit (Illumina) (replicates 1-3 and cycloheximide treated ) or the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat)(E6350, NEB) (replicates 4-5 and no salt treatment) The footprint samples were size-selected using the 17 and 34 nt markers as a guide on a 15% TBE-Urea polyacrylamide gel (Thermo Scientific), while total RNA samples were randomly heat fragmented by incubating at 95 °C in an alkaline fragmentation solution (50 mM NaCO3 pH 9.2, 2 mM EDTA) for 40 min, yielding comparably sized fragments to footprints. All samples were de-phosphorylated using PNK (T4, NEB). The quality and concentration of samples was assessed by running an Agilent Small RNA chip (Agilent Technologies), and sequencing libraries were generated using the NEXTflex™ Small RNA Sequencing Kit v3 (PerkinElmer, NOVA-5132-06), according to the manufacturer’s instructions.

value: whole brain

value: post natal day 5

value: Control


title: RNAseq4

description: RNAseq


title: Adult_nphx_1450

value: FACS sorted


title: AVS53


title: Adult_nphx_1449


title: Adult_nphx_1448


title: Adult_nphx_1447


title: Adult_nphx_1463


title: AVS52


title: RNAseq3

description: RNAseq


title: RNAseq2

description: RNAseq


title: Adult_nphx_1446


title: AVS51


title: Adult_nphx_1445


title: AVS49


title: RNAseq1

description: RNAseq


title: AVS58


title: Adult_nphx_1444


title: AVS56


title: Adult_nphx_1442


title: granuleVEH5

description: Ribosome-protected mRNA fragments

value: Vehicle


title: Adult_nphx_1441


title: AVS46


title: AVS55


title: Adult_nphx_1440


title: Adult_nphx_1454


title: granuleVEH4

description: Ribosome-protected mRNA fragments


title: AVS41


title: AVS42


title: granuleSALT2

description: Ribosome-protected mRNA fragments

value: Salt


title: Adult_nphx_1439


title: AVS40


title: Adult_nphx_1433


title: Adult_nphx_1437


title: Adult_nphx_1438


title: Adult_nphx_1432


title: Adult_nphx_1436


title: granuleSALT1

description: Ribosome-protected mRNA fragments


title: granuleCHX2

description: Ribosome-protected mRNA fragments

value: cycloheximide


title: Adult_nphx_1430


title: AVS37


title: granuleCHX1

description: Ribosome-protected mRNA fragments


title: Adult_nphx_1431


title: Adult_nphx_1435


title: Adult_nphx_1434


title: Adult_nphx_1428


title: AVS36


title: Adult_nphx_1427


title: granuleVEH3

description: Ribosome-protected mRNA fragments


title: Adult_nphx_1443


title: Adult_nphx_1429


title: AVS43


title: Adult_nphx_1426


title: granuleVEH2

description: Ribosome-protected mRNA fragments


title: granuleCHX3

description: Ribosome-protected mRNA fragments


title: Adult_nphx_1425


title: Adult_nphx_1424


title: Adult_nphx_1423


title: AVS34


title: AVS33


title: TE5_NUP153

city: kanazawa city

first: Masaharu

last: Hazawa

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with the default parameters. Only tags that uniquely mapped to the genome were used for further analysis.
PCR duplicates were removed using picard tools
Peak annotation was processed with the homer annotatePeaks.pl script
Bigwig files were generated using the deepTools bamCoverage function with --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --binSize 1.
Assembly: hg19
Supplementary files format and content: bigwig files representing signal normalized to per million reads
Supplementary files format and content: peak bed

growth_protocol: TE5 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% Penicillin and Streptomycin. KYSE150 cells were RPMI-1640 medium supplemented with 5% FBS, 1% Penicillin and Streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, chromatin received enzymatic digestion by following manufacturer's protocols  (CST, SimpleChIP plus enzymatic chromatin IP kit).
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit. 10 ng of DNA was used as starting material for ip samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Esophageal squamous cell carcinoma


title: C3_1

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by sequencing service company (Novogene)
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, version 20101214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

source_name: root

extract_protocol:
protocol from Plant Total RNA Mini Kit, QIAGEN
performed by sequencing service company (Novogene)

value: root

tag: biological replicates

value: all root tip cell types

value: EST 5uM

tag: treatment time

value: 2 h

tag: growth conditions

value: Plants grew in growth chamber for 5 days. Conditions were 23°C by day (16 h), 18°C by night (8 h), light intensity of 120 μmol photons m-2 s-1, 60 % humidity.


title: 5-aza-dc

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
After quality check of the obtained raw paired-end sequence reads (150bp×2 paired-end) using FastQC (Version 0.11.7), low quality bases (>20) or adapter sequences were trimmed using TrimGalore (Version 0.5.0) with "-q 20 --phred33 --rrbs --paired --non_directional" options.
After alignment to the reference genome of the trimmed reads using Bismark (Version 0.20.0) with the "--non_directional" option, the Bismark-resultant .sam files were converted into .bam files with Samtools (Version 1.9).
Methylated positions were called with the processBismarkAln of methylKit (Version 1.10.0) and the number of methylated cytosines in 1000 bases of non-overlapping windows across the whole genome was estimeted by using the tileMethylCounts function from the methylKit package.
After normalization with the normalizeCoverage function in methylKit, bases having below 10 read coverage and bases with more than 99.9th percentile of coverage in each sample (likely PCR artifacts with abnormally high coverage) were removed using the filterByCoverage function of methylKit.
All the samples were then merged with using the unite function in methylKit with the destrand = FALSE option.
Assembly: hg38
Supplementary files format and content: Tab-separated values files including methylation retes at all sites in each sample
Supplementary files format and content: Matrix files including  methylation rates at all sites in all samples and information about these sites

source_name: HPS0063 (Riken BRC, 201B7)

growth_protocol: The iPSCs were maintained under feeder-free condition using mTeSR1 (STEMCELL Technologies, Vancouver, Canada) in a dish coated with 0.5 μg/cm2 of Laminin511-E8 (iMatrix-511, Nippi, Tokyo, Japan).

extract_protocol:
Total genomic DNA was extracted from treated-human iPSCs using DNeasy Blood & Tissue Kit (QIAGEN, Hilden, Germany).
Library of each sample was prepared using Zymo Research Zymo-Seq RRBS Library Kit (ZYMO RESEARCH, D5461, Ver. 1.0.0) according to the manufacturer’s protocol. Then, sequences of the library samples (FASTQ files) were obtained using a Illumina NovaSeq 6000 (Illumina).

treatment_protocol: iPS cells were exposed to chemical substances at the proper concentrations for 48 hours.

value: HPS0063 (Riken BRC, 201B7)

value: pluripotent stem cell

value: WT

value: 10 nM 5-aza-dc


title: AVS38

value: GBM Tissue


title: C2_2


title: AVS31


title: AVS32


title: Theophylline

value: 1 uM theophylline


title: Adult_nphx_1420


title: C2_1


title: Propyl gallate

value: 1 uM propyl gallate


title: Adult_nphx_1419

value: FACS sorted


title: Adult_nphx_1421


title: Etoposide

value: 1 nM etoposide


title: AVS27


title: Control

value: 0.1 % DMSO


title: C1_1


title: C1_2


title: AVS29


title: Adult_nphx_1418


title: AVS35


title: AVS21


title: Adult_nphx_1422


title: C3_2


title: granuleVEH1

description: Ribosome-protected mRNA fragments

value: Sprague Dawley

value: whole brain

value: post natal day 5

value: Vehicle


title: Adult_nphx_1417


title: B3_2

value: root

value: all root tip cell types

value: heatshock 37°C

value: 40 min + 80 min recovery


title: B3_1

value: Plants grew in growth chamber for 5 days. Conditions were 23°C by day (16 h), 18°C by night (8 h), light intensity of 120 μmol photons m-2 s-1, 60 % humidity.


title: Adult_nphx_1416


title: ST3A1

description: 10X Genomics

data_processing:
snRNA samples were processed with 10X genomics software Cell Ranger
Alignment was done using the CellRanger pipeline (10X Genomics) to GRCh38.p12 (refdata-cellranger-GRCh38-1.2.0 file provided by 10x genomics). Count matrices were generated from BAM files using default parameters of the DropEst pipeline (Petukhov V et al. 2018).
Filtering and QC was done using the scater package (3). Nuclei with percent exonic reads from all reads in the range of 25-75% were included. Nuclei with percent mitochondrial reads aligning to mitochondria genes of more than 19% were excluded.
Genes were filtered by keeping features with >10 counts per row in at least in 31 cells. Further filtering of low quality cells was done to include cells with at least 400 detected genes and 10,000 reads.
Assembly: GRCh38 Ensemble 91
Supplementary files format and content: .txt files of count matrix
Library strategy: snRNA-seq

extract_protocol:
Briefly, frozen tissue samples measuring from 5 x 4 x 3 mm to 10 x 6 x 3 mm were homogenized using a dounce homogenizer in ice-cold 30% sucrose 0.1% Triton-X 100 based homogenization buffer. 10-15 strokes of the loose dounce pestle were followed by 10-15 strokes of the tight dounce pestle on ice. Mixing using a P1000 pipette followed before filtration through a BD Falcon 40um filters.  Filtration was repeated after a 10-minute spin at 1000g at 4c. A cleanup step followed using a density gradient step as described in [41]. The nuclear pellet was suspended in 1% BSA in PBS resuspension buffer containing RNAse inhibitors. A final filtration step using 20um Flowmi ™ filters followed before dilution to 700-1200 nuclei per ul in resuspension buffer. The nuclear suspensions were processed by the Chromium Controller (10x Genomics) using single Cell 3’ Reagent Kit v2 or v3 (Chromium Single Cell 3’ Library & Gel Bead Kit v2, catalog number: 120237; Chromium Single Cell A Chip Kit, 48 runs, catalog number: 120236; 10x Genomics).
Sequencing of the resultant libraries was done on Illumina NOVAseq 6000 platformV4 150bp paired end reads.

value: F

tag: disease state

value: Primary


title: ST3B1

description: 10X Genomics

value: GBM Tissue


title: AVS19


title: Adult_nphx_1415

tag: strain


title: B2_2

tag: cell type


title: Adult_nphx_1414


title: B2_1

tag: genotype


title: AVS18


title: Adult_nphx_1413


title: ST1C1

description: 10X Genomics

value: Recurrent


title: B1_2


title: AVS16


title: B1_1


title: ST1D1

description: 10X Genomics


title: ST2C1

description: 10X Genomics


title: Adult_nphx_1412


title: ST1B1

description: 10X Genomics


title: AVS15


title: Adult_nphx_1410


title: AVS20


title: AVS13


title: A3_2

value: PEO-IAA 10uM

value: 20 min


title: A3_3

value: mock


title: ST1A1

description: 10X Genomics


title: Adult_nphx_1409

value: FACS sorted


title: Adult_nphx_1411


title: Molm-14 cells untreated, replicate #3

city: Houston

first: Zheng

last: Yin

state: TX

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

institute: Houston Methodist Cancer Center

description:
Molm_14_UT_3
Genes_fpkm_expression.xlsx, Column AE, FPKM values
Genes_fpkm_expression.xlsx, Column AT, Raw Counts

data_processing:
Used Cutadapt to remove low quality bases, followed by FastQC
Used HISAT2 to map reads to reference genome
Used StringTie for read assembly
Used gffcompare to reconstruct the transcriptome
Used StringTie and edgeR to estimate expression levels for all transcripts
Assembly: Release 101 (August 2020) of the Homo Sapiens reference genome from Ensemble
Supplementary files format and content: Excel file including PRKM and raw count for each gene in each sample

extract_protocol:
Following treatment, the cells were washed with PBS, and RNA extraction was performed with a QIAGEN RNA extraction kit according to the manufacturer’s protocol.
A poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: FLT3-mutated AML cells were cultured and treated with TP-0184 at 200 nM for 48 h

value: AML cell

value: FLT3 mutated

value: Untreated


title: Adult_nphx_1408

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)


title: Molm-14 cells untreated, replicate #1

description:
Molm_14_UT_1
Genes_fpkm_expression.xlsx, Column AC, FPKM values
Genes_fpkm_expression.xlsx, Column AR, Raw Counts


title: A2_3


title: PRV2

city: Guro-gu

first: Jae Kyung

last: Lee

state: Seoul

address: 148 Gurodong-ro

institute: Korea University

data_processing:
Sequence reads mapped by bowtie2 software to obtain alignment file.
Read counts mapped on mature miRNA sequence extracted from alignment file using bedtools (v2.25.0) and R (version 3.2.2).
Read counts used to determine miRNA expression levels.
Assembly: Mature miRNA sequences available on miRBase was used as reference for mapping.
Supplementary files format and content: Excel files contain gene symbol, fold change, normalized data, raw data, mature id, start, end, width, strand, type, alias, derives from, sequence, and target prediction based on miRBase search.

source_name: Placenta

growth_protocol: JEG-3 cells were maintained in growth media (DMEM supplemented with 10% FBS and 1% antibiotics).

extract_protocol:
Small extracellular vesicles were isolated using ExoSpin kit according to the manufacturer protocol. Total RNA from the small extracellular vesicles were extracted using Trizol reagent.
NEBNext Multiplex Small RNA Library Prep Kit

treatment_protocol: JEG-3 cells  seeded in 100mm dishes using serum-free media supplemented with exosome-free FBS were infected with ZIKV. After 2 hours, virus was removed and cells were incubated for 48 hours in serum-free media.

value: Placenta

value: Epithelial

tag: disease

value: choriocarcinoma

value: ZIKV infection


title: PRV1


title: Adult_nphx_1407

city: Daejeon

first: Myung Jin

institute: Institute for Basic Science


title: A3_1

value: root

value: all root tip cell types

value: IAA 10nM


title: A2_1

value: Plants grew in growth chamber for 5 days. Conditions were 23°C by day (16 h), 18°C by night (8 h), light intensity of 120 μmol photons m-2 s-1, 60 % humidity.


title: Molm-13 cells untreated, replicate #3

description:
Molm_13_UT_3
Genes_fpkm_expression.xlsx, Column AB, FPKM values
Genes_fpkm_expression.xlsx, Column AW, Raw Counts


title: Molm-13 cells untreated, replicate #2

description:
Molm_13_UT_2
Genes_fpkm_expression.xlsx, Column AA, FPKM values
Genes_fpkm_expression.xlsx, Column AV, Raw Counts


title: mock1

value: mock infection


title: AVS17

value: GBM Tissue


title: A1_3


title: A2_2

value: PEO-IAA 10uM


title: AVS12


title: Molm-13 cells untreated, replicate #1

description:
Molm_13_UT_1
Genes_fpkm_expression.xlsx, Column Z, FPKM values
Genes_fpkm_expression.xlsx, Column AU, Raw Counts


title: Adult_nphx_1404


title: A1_2

value: 20 min


title: MV4-11 cells untreated, replicate #3

description:
MV4_11_UT_3
Genes_fpkm_expression.xlsx, Column Y, FPKM values
Genes_fpkm_expression.xlsx, Column AK, Raw Counts


title: Molm-14 cells untreated, replicate #2

description:
Molm_14_UT_2
Genes_fpkm_expression.xlsx, Column AD, FPKM values
Genes_fpkm_expression.xlsx, Column AS, Raw Counts


title: Vehicle2

city: Charlottesville

first: Agnieszka

last: Swiatecka-Urban

state: VA

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia School of Medicine

data_processing:
The microRNA sequencing data were analyzed using the GeneGlobe Data Analysis bioinformatics pipeline from Qiagen
The raw QIAseq miRNA sequencing files were uploaded to GeneGlobe Data Analysis Center (Qiagen) for quality control, alignment to the human reference genome (GRCh38), and expression quantification.
Briefly, 3’adapter and low-quality bases were trimmed off from reads using Cutadapt. Reads with less than 16 bp insert sequences or with less than 10 bp unique molecular identifier (UMI) sequences were discarded. The remaining reads were collapsed to UMI counts and aligned to miRBase (release v21) mature and hairpin databases sequentially using Bowtie v1.2. All reads assigned to a particular miRNA or piRNA ID were counted and the associated UMIs were clustered to count unique molecules.
The primary analysis output file was downloaded from GeneGlobe.
Assembly: GRCh38
Supplementary files format and content: Differential analysis results in an excel file.

source_name: Parental CFBE 41o-Cells, HCL+BSA, 24hrs

extract_protocol:
Total RNA was isolated by using Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. An on-column DNase (Zymo Research) treatment was added to remove contamination with genomic DNA
The starting material, 100 ng of total RNA was used with the QIAseqTM miRNA Library Kit (Qiagen, Maryland, MD, USA), following the manufacturer’s instruction. The RNA quantity and quality were verified by Qubit 2.0 Fluorometer, and Agilent Bioanalyzer Tapestation 2200. In short, 3’ and 5’ adapters were ligated to total input RNA. Reverse transcription, followed by PCR, was used to create cDNA constructs. This process selectively enriches those fragments that have adapter molecules on both ends. PCR was performed with primers that anneal to the ends of the adapters. Quality was examined using Agilent Bioanalyzer Tapestation 2200 and Qubit 2.0 Fluorometer with miRNA library pre-sequencing QC protocol mentioned in the QIAseqTM miRNA Library Kit. The cDNA libraries were pooled at a final concentration of 2.5 pM
Cluster generation and 75 base-pair (bp) single-read single-indexed sequencing was performed on Illumina NextSeq 500

value: Parental CFBE 41o-Cells

value: Epithelial Cells

value: WT

value: HCL+BSA


title: A1_1


title: Vehicle1


title: Adult_nphx_1403

last: Yang

value: FACS sorted


title: mock2

value: Placenta


title: MV4-11 cells untreated, replicate #2

description:
MV4_11_UT_2
Genes_fpkm_expression.xlsx, Column X, FPKM values
Genes_fpkm_expression.xlsx, Column AJ, Raw Counts

value: AML cell

value: FLT3 mutated

value: Untreated


title: Adult_nphx_1402


title: MV4-11 cells untreated, replicate #1

description:
MV4_11_UT_1
Genes_fpkm_expression.xlsx, Column W, FPKM values
Genes_fpkm_expression.xlsx, Column AI, Raw Counts


title: Adult_nphx_1406

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv


title: Adult_nphx_1405


title: Adult_nphx_1401


title: Treatment2

source_name: Parental CFBE 41o-Cells, TGF-beta, 24hrs

value: TGF-beta


title: Molm-14 cells treated by TP-0184, replicate #3

description:
Molm_14_Treated_3
Genes_fpkm_expression.xlsx, Column V, FPKM values
Genes_fpkm_expression.xlsx, Column AQ, Raw Counts

value: TP-0184 at 200nM for 48 hours


title: Treatment3


title: Vehicle3


title: Adult_nphx_1399


title: Adult_nphx_1400