title: KIR3_S247


title: KIR3_S246

status: Public on Mar 08 2022

type: SRA

city: Stanford

first: Mark

last: Davis

state: CA

address: Stanford University

country: USA

institute: Institute for Immunity, Transplantation and Infection

library_source: transcriptomic

data_processing:
FASTQ files for each cell were extracted and generated, distinguished by the unique dual index adaptors.
Reads were aligned to the GRCh38 genome using STAR v2.6.1d.
Transcript abundance was quantified using HTSeq v0.5.4p5.
Genome_build: hg38
Supplementary_files_format_and_content: csv file including transcript abundance quantified by HTSeq for each cell
Supplementary_files_format_and_content: metadata for each cell
Supplementary_files_format_and_content: metadata with TCR information for each cell

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Blood KIR+ CD8+ T cells (Live CD3+CD56–CD8+TCRαβ+KIR+ cells) were sorted into 96-well plates and cDNA synthesis was performed using the Smart-seq2 protocol
Illumina sequencing libraries were prepared using a Mosquito HTS liquid handler (TTP Labtech). In brief, tagmentation was carried out on 0.4 μl double-stranded cDNA using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Amplicon Tagment Mix (Illumina), then incubated at 55°C for 10 min. The reaction was stopped by adding 0.4 μl Neutralize Tagment Buffer (Illumina) and centrifuging at room temperature at 3000 g for 5 min. Indexing PCR reactions were performed by adding 0.8 μl of pre-mixed 5 μM i5 and i7 unique dual indexing primers (IDT, customized) and 1.2 μL of Nextera NPM mix (Illumina). PCR amplification was carried out on a C1000 Touch™ Thermal Cycler with 384-Well Reaction Module (Bio-rad) using the following program: 1) 72°C for 3 min, 2) 95°C for 30 s, 3) 12 cycles of 95°C for 10 s, 55°C for 30 s and 72°C for 1 min, and 4) 72°C for 5 min.

tag: tissue

value: PBMC

tag: cell type

value: KIR+ CD8 T


title: KIR3_S245


title: KIR3_S244


title: KIR3_S243


title: KIR3_S242


title: KIR3_S262


title: KIR3_S241


title: KIR3_S240


title: KIR3_S239


title: KIR3_S234


title: KIR3_S238


title: KIR3_S232


title: KIR3_S24


title: KIR3_S235


title: KIR3_S233


title: KIR3_S231


title: KIR3_S230


title: KIR3_S226


title: KIR3_S225


title: KIR3_S228


title: KIR3_S224


title: KIR3_S229


title: KIR3_S227


title: KIR3_S223


title: KIR3_S250


title: KIR3_S249


title: KIR3_S222


title: KIR3_S248


title: KIR3_S221


title: KIR3_S220


title: KIR3_S219


title: KIR3_S217


title: KIR3_S218


title: KIR3_S216


title: KIR3_S215


title: KIR3_S212


title: KIR3_S210


title: KIR3_S214


title: KIR3_S237


title: KIR3_S203


title: KIR3_S211


title: KIR3_S204


title: KIR3_S207


title: KIR3_S23


title: KIR3_S21


title: KIR3_S209


title: KIR3_S206


title: KIR3_S201


title: KIR3_S200


title: KIR3_S205


title: KIR3_S20


title: KIR3_S202


title: KIR3_S2


title: KIR3_S197


title: KIR3_S198


title: KIR3_S196


title: KIR3_S22


title: KIR3_S195


title: KIR3_S199


title: KIR3_S193


title: KIR3_S194


title: KIR3_S191


title: KIR3_S19


title: KIR3_S208


title: KIR3_S186


title: KIR3_S184


title: KIR3_S183


title: KIR3_S179


title: KIR3_S178


title: KIR3_S187


title: KIR3_S188


title: KIR3_S177


title: KIR3_S213


title: KIR3_S171


title: KIR3_S176


title: KIR3_S174


title: KIR3_S181


title: KIR3_S180


title: KIR3_S170


title: KIR3_S175


title: KIR3_S169


title: KIR3_S167


title: KIR3_S182


title: KIR3_S192


title: KIR3_S173


title: KIR3_S165


title: KIR3_S185


title: KIR3_S166


title: KIR3_S190


title: KIR3_S164


title: KIR3_S17


title: KIR3_S168


title: KIR3_S161


title: KIR3_S172


title: KIR3_S159


title: KIR3_S18


title: KIR3_S162


title: KIR3_S163


title: KIR3_S156


title: KIR3_S153


title: KIR3_S154


title: KIR3_S150


title: KIR3_S160


title: KIR3_S15


title: KIR3_S157


title: KIR3_S158


title: KIR3_S147


title: KIR3_S16


title: KIR3_S149


title: KIR3_S148


title: KIR3_S145


title: KIR3_S152


title: KIR3_S155


title: KIR3_S146


title: KIR3_S143


title: KIR3_S144


title: KIR3_S140


title: KIR3_S14


title: KIR3_S139


title: KIR3_S142


title: KIR3_S138


title: KIR3_S141


title: KIR3_S136


title: KIR3_S134


title: KIR3_S137


title: KIR3_S135


title: KIR3_S131


title: KIR3_S130


title: KIR3_S129


title: KIR3_S125


title: KIR3_S123


title: KIR3_S151


title: KIR3_S127


title: KIR3_S132


title: KIR3_S126


title: KIR3_S13


title: KIR3_S124


title: KIR3_S122


title: KIR3_S12


title: KIR3_S120


title: KIR3_S121


title: KIR3_S119


title: KIR3_S113


title: KIR3_S116


title: KIR3_S115


title: KIR3_S118


title: KIR3_S117


title: KIR3_S112


title: KIR3_S111


title: KIR3_S110


title: KIR3_S109


title: KIR3_S11


title: KIR3_S108


title: KIR3_S133


title: KIR3_S106


title: KIR3_S105


title: KIR3_S107


title: KIR3_S103


title: KIR3_S101


title: KIR3_S128


title: KIR3_S100


title: KIR3_S1


title: KIR3_S104


title: KIR3_S10


title: KIR2_S99


title: KIR2_S98


title: KIR2_S97


title: KIR2_S382


title: KIR2_S96


title: KIR2_S381


title: KIR2_S380


title: KIR2_S377


title: KIR2_S375


title: KIR2_S378


title: KIR3_S114


title: KIR2_S376


title: KIR2_S372


title: KIR2_S373


title: KIR2_S371


title: KIR2_S370


title: KIR2_S369


title: KIR2_S367


title: KIR2_S363


title: KIR2_S360


title: KIR2_S364


title: KIR2_S365


title: KIR2_S368


title: KIR2_S357


title: KIR2_S358


title: KIR2_S359


title: KIR2_S353


title: KIR2_S349


title: KIR2_S354


title: KIR2_S351


title: KIR2_S352


title: KIR2_S356


title: KIR2_S350


title: KIR2_S379


title: KIR2_S348


title: KIR2_S347


title: KIR2_S344


title: KIR2_S374


title: KIR2_S345


title: KIR2_S236


title: KIR2_S235


title: KIR2_S234


title: KIR2_S232


title: KIR2_S233


title: KIR2_S228


title: KIR2_S226


title: KIR2_S231


title: KIR2_S229


title: KIR2_S227


title: KIR2_S366


title: KIR2_S225


title: KIR2_S222


title: KIR2_S218


title: KIR2_S216


title: KIR2_S220


title: KIR2_S346


title: KIR2_S214


title: KIR2_S230


title: KIR2_S223


title: KIR2_S213


title: KIR2_S237


title: KIR2_S221


title: KIR2_S215


title: KIR2_S217


title: KIR2_S211


title: KIR2_S210


title: KIR2_S208


title: KIR2_S207


title: KIR2_S209


title: KIR2_S206


title: KIR2_S205


title: KIR2_S224


title: KIR2_S201


title: KIR2_S200


title: KIR2_S202


title: KIR2_S197


title: KIR2_S198


title: KIR2_S195


title: KIR2_S196


title: KIR2_S191


title: KIR2_S192


title: KIR2_S194


title: KIR2_S188


title: KIR2_S190


title: KIR2_S187


title: KIR2_S219


title: KIR2_S183


title: KIR2_S181


title: KIR2_S185


title: KIR2_S182


title: KIR2_S180


title: KIR2_S178


title: KIR2_S179


title: KIR2_S177


title: KIR2_S176


title: KIR2_S204


title: KIR2_S203


title: KIR2_S175


title: KIR2_S174


title: KIR2_S173


title: KIR2_S172


title: KIR2_S171


title: KIR2_S170


title: KIR2_S169


title: KIR2_S193


title: KIR2_S167


title: KIR2_S165


title: KIR2_S163


title: KIR2_S160


title: KIR2_S166


title: KIR2_S186


title: KIR2_S164


title: KIR2_S161


title: KIR2_S162


title: KIR2_S184


title: KIR2_S158


title: KIR2_S156


title: KIR2_S159


title: KIR2_S155


title: KIR2_S154


title: KIR2_S152


title: KIR2_S153


title: KIR2_S151


title: KIR2_S149


title: KIR2_S150


title: KIR2_S147


title: KIR2_S145


title: KIR2_S146


title: KIR2_S143


title: KIR2_S141


title: KIR2_S168


title: KIR2_S140


title: KIR2_S142


title: KIR2_S148


title: KIR2_S138


title: KIR2_S139


title: KIR2_S137


title: KIR2_S133


title: KIR2_S134


title: KIR2_S136


title: KIR2_S135


title: KIR2_S130


title: KIR2_S129


title: KIR2_S128


title: KIR2_S127


title: KIR2_S126


title: KIR2_S125


title: KIR2_S124


title: KIR2_S123


title: KIR2_S121


title: KIR2_S122


title: KIR2_S119


title: KIR2_S117


title: KIR2_S118


title: KIR2_S113


title: KIR2_S115


title: KIR2_S114


title: KIR2_S112


title: KIR2_S110


title: KIR2_S109


title: KIR2_S108


title: KIR2_S107


title: KIR2_S106


title: KIR2_S103


title: KIR2_S102


title: KIR2_S132


title: KIR2_S100


title: KIR2_S131


title: KIR2_S105


title: KIR2_S101


title: KIR1_S99


title: KIR1_S97


title: KIR1_S96


title: KIR1_S93


title: KIR1_S92


title: KIR1_S98


title: KIR1_S90


title: KIR1_S9


title: KIR1_S89


title: KIR1_S88


title: KIR2_S116


title: KIR1_S85


title: KIR1_S86


title: KIR1_S82


title: KIR1_S83


title: KIR1_S80


title: KIR1_S81


title: KIR2_S111


title: KIR1_S79


title: KIR1_S77


title: KIR1_S761


title: KIR1_S765


title: KIR1_S760


title: KIR1_S759


title: KIR1_S762


title: KIR1_S76


title: KIR1_S755


title: KIR1_S756


title: KIR1_S757


title: KIR1_S758


title: KIR1_S753


title: KIR1_S91


title: KIR1_S75


title: KIR1_S749


title: KIR1_S748


title: KIR1_S754


title: KIR1_S750


title: KIR1_S87


title: KIR1_S747


title: KIR1_S744


title: KIR1_S743


title: KIR1_S745


title: KIR1_S742


title: KIR1_S741


title: KIR1_S746


title: KIR1_S740


title: KIR1_S8


title: KIR1_S78


title: KIR1_S739


title: KIR1_S737


title: KIR1_S736


title: KIR1_S733


title: KIR1_S734


title: KIR1_S735


title: KIR1_S730


title: KIR1_S729


title: KIR1_S731


title: KIR1_S728


title: KIR1_S727


title: KIR1_S726


title: KIR1_S751


title: KIR1_S723


title: KIR1_S722


title: KIR1_S72


title: KIR1_S718


title: KIR1_S719


title: KIR1_S720


title: KIR1_S717


title: KIR1_S712


title: KIR1_S716


title: KIR1_S714


title: KIR1_S738


title: KIR1_S715


title: KIR1_S713


title: KIR1_S711


title: KIR1_S708


title: KIR1_S705


title: KIR1_S71


title: KIR1_S703


title: KIR1_S710


title: KIR1_S706


title: KIR1_S732


title: KIR1_S700


title: KIR1_S704


title: KIR1_S709


title: KIR1_S70


title: KIR1_S702


title: KIR1_S707


title: KIR1_S699


title: KIR1_S698


title: KIR1_S724


title: KIR1_S696


title: KIR1_S694


title: KIR1_S693


title: KIR1_S697


title: KIR1_S701


title: KIR1_S692


title: KIR1_S721


title: KIR1_S695


title: KIR1_S691


title: KIR1_S69


title: KIR1_S690


title: KIR1_S685


title: KIR1_S688


title: KIR1_S687


title: KIR1_S682


title: KIR1_S689


title: KIR1_S681


title: KIR1_S680


title: KIR1_S677


title: KIR1_S678


title: KIR1_S676


title: KIR1_S686


title: KIR1_S675


title: KIR1_S679


title: KIR1_S68


title: KIR1_S674


title: KIR1_S670


title: KIR1_S669


title: KIR1_S673


title: KIR1_S672


title: KIR1_S67


title: KIR1_S671


title: KIR1_S668


title: KIR1_S666


title: KIR1_S665


title: KIR1_S664


title: KIR1_S661


title: KIR1_S660


title: KIR1_S66


title: KIR1_S659


title: KIR1_S658


title: KIR1_S657


title: KIR1_S656


title: KIR1_S655


title: KIR1_S683


title: KIR1_S653


title: KIR1_S654


title: KIR1_S652


title: KIR1_S650


title: KIR1_S651


title: KIR1_S649


title: KIR1_S648


title: KIR1_S647


title: KIR1_S646


title: KIR1_S642


title: KIR1_S643


title: KIR1_S644


title: KIR1_S645


title: KIR1_S641


title: KIR1_S663


title: KIR1_S640


title: KIR1_S637


title: KIR1_S64


title: KIR1_S636


title: KIR1_S638


title: KIR1_S639


title: KIR1_S662


title: KIR1_S635


title: KIR1_S634


title: KIR1_S633


title: KIR1_S630


title: KIR1_S631


title: KIR1_S63


title: KIR1_S627


title: KIR1_S629


title: KIR1_S626


title: KIR1_S628


title: KIR1_S625


title: KIR1_S622


title: KIR1_S624


title: KIR1_S623


title: KIR1_S65


title: KIR1_S621


title: KIR1_S62


title: KIR1_S617


title: KIR1_S618


title: KIR1_S616


title: KIR1_S612


title: KIR1_S615


title: KIR1_S613


title: KIR1_S614


title: KIR1_S610


title: KIR1_S61


title: KIR1_S609


title: KIR1_S607


title: KIR1_S606


title: KIR1_S632


title: KIR1_S60


title: KIR1_S601


title: KIR1_S602


title: KIR1_S604


title: KIR1_S600


title: KIR1_S603


title: KIR1_S6


title: KIR1_S599


title: KIR1_S598


title: KIR1_S597


title: KIR1_S596


title: KIR1_S595


title: KIR1_S594


title: KIR1_S593


title: KIR1_S592


title: KIR1_S619


title: KIR1_S590


title: KIR1_S59


title: KIR1_S591


title: KIR1_S586


title: KIR1_S589


title: KIR1_S584


title: KIR1_S587


title: KIR1_S585


title: KIR1_S611


title: KIR1_S608


title: KIR1_S583


title: KIR1_S581


title: KIR1_S577


title: KIR1_S58


title: KIR1_S579


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title: KIR1_S576


title: KIR1_S605


title: KIR1_S575


title: KIR1_S574


title: KIR1_S571


title: KIR1_S570


title: KIR1_S569


title: KIR1_S567


title: KIR1_S568


title: KIR1_S566


title: KIR1_S565


title: KIR1_S563


title: KIR1_S564


title: KIR1_S561


title: KIR1_S562


title: KIR1_S56


title: KIR1_S559


title: KIR1_S588


title: KIR1_S558


title: KIR1_S557


title: KIR1_S556


title: KIR1_S555


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title: KIR1_S580


title: KIR1_S549


title: KIR1_S550


title: KIR1_S551


title: KIR1_S548


title: KIR1_S55


title: KIR1_S546


title: KIR1_S573


title: KIR1_S544


title: KIR1_S545


title: KIR1_S543


title: KIR1_S57


title: KIR1_S541


title: KIR1_S540


title: KIR1_S54


title: KIR1_S537


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title: KIR1_S535


title: KIR1_S534


title: KIR1_S533


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title: KIR1_S529


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title: KIR1_S525


title: KIR1_S528


title: KIR1_S524


title: KIR1_S554


title: KIR1_S527


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title: KIR1_S552


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title: KIR1_S521


title: KIR1_S522


title: KIR1_S52


title: KIR1_S519


title: KIR1_S518


title: KIR1_S517


title: KIR1_S542


title: KIR1_S515


title: KIR1_S514


title: KIR1_S513


title: KIR1_S511


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title: KIR1_S512


title: KIR1_S51


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title: KIR1_S509


title: KIR1_S503


title: KIR1_S504


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title: KIR1_S507


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title: KIR1_S497


title: KIR1_S5


title: KIR1_S498


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title: KIR1_S495


title: KIR1_S492


title: KIR1_S493


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title: KIR1_S489


title: KIR1_S490


title: KIR1_S485


title: KIR1_S49


title: KIR1_S483


title: KIR1_S487


title: KIR1_S482


title: KIR1_S481


title: KIR1_S480


title: KIR1_S48


title: KIR1_S475


title: KIR1_S474


title: KIR1_S479


title: KIR1_S473


title: KIR1_S472


title: KIR1_S471


title: KIR1_S47


title: KIR1_S469


title: KIR1_S468


title: KIR1_S470


title: KIR1_S502


title: KIR1_S466


title: KIR1_S465


title: KIR1_S464


title: KIR1_S462


title: KIR1_S494


title: KIR1_S461


title: KIR1_S460


title: KIR1_S457


title: KIR1_S46


title: KIR1_S456


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title: KIR1_S454


title: KIR1_S453


title: KIR1_S452


title: KIR1_S505


title: KIR1_S451


title: KIR1_S450


title: KIR1_S449


title: KIR1_S45


title: KIR1_S446


title: KIR1_S444


title: KIR1_S445


title: KIR1_S476


title: KIR1_S443


title: KIR1_S442


title: KIR1_S441


title: KIR1_S440


title: KIR1_S44


title: KIR1_S467


title: KIR1_S439


title: KIR1_S438


title: KIR1_S436


title: KIR1_S435


title: KIR1_S434


title: KIR1_S433


title: KIR1_S463


title: KIR1_S432


title: KIR1_S458


title: KIR1_S430


title: KIR1_S431


title: KIR1_S43


title: KIR1_S429


title: KIR1_S428


title: KIR1_S427


title: KIR1_S425


title: KIR1_S426


title: KIR1_S424


title: KIR1_S423


title: KIR1_S422


title: KIR1_S421


title: KIR1_S42


title: KIR1_S447


title: KIR1_S419


title: KIR1_S448


title: KIR1_S418


title: KIR1_S417


title: KIR1_S415


title: KIR1_S416


title: KIR1_S414


title: KIR1_S413


title: KIR1_S41


title: KIR1_S409


title: KIR1_S408


title: KIR1_S437


title: KIR1_S407


title: KIR1_S406


title: KIR1_S405


title: KIR1_S404


title: KIR1_S402


title: KIR1_S400


title: KIR1_S40


title: KIR1_S401


title: KIR1_S4


title: KIR1_S398


title: KIR1_S399


title: KIR1_S396


title: KIR1_S397


title: KIR1_S394


title: KIR1_S395


title: KIR1_S390


title: KIR1_S389


title: KIR1_S39


title: KIR1_S391


title: KIR1_S393


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title: HDFs-Pooled-Input_rep2

city: Lund

first: Evelyn

last: Halitzki

address: Sölvegatan 17

country: Sweden

institute: Lund University

description:
HDFs-Pooled-Input
11-HDFs-Pooled-Input_hg38_rep 2

library_source: genomic

data_processing:
The FASTQ files were mapped to the human hg38 genome using Bowtie 2.
Bigwig files were created from bam files with deeptools v2.5.4.
The mapped output files were processed through MACS v2.1.0 analysis software to determine peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, bed

molecule: genomic DNA

source_name: adult human dermal fibroblast

growth_protocol: HDFs were cultured in gelatine-coated plates in DMEM+10%FBS.

extract_protocol:
Cells were collected together with the other samples.
Cultured cells were fixed in 11 % formaldehyde for 15 min at room temperature on a rotating platform. The formaldehyde was quenched by adding 125 nM glycine. The chromatin was sheared and immunoprecipitated with the antibody of interest. A control sample consisting of sonicated chromatin that was not immunoprecipitated was also sequenced.
Illumina sequencing libraries were prepared from ChIP and Input DNAs by standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single-end).

tag: antibody

tag: cell line

value: HDFa

value: adult human dermal fibroblast

tag: genotype

value: wildtype


title: PIB-HDFs-IRF8_rep2

description:
PIB-HDFs-IRF8
9-PIB-HDFs-IRF8_hg38_rep 2

growth_protocol: After transduction with lentiviral particles encoding PU.1, IRF8 and BATF3, HDFs were cultured in gelatine-coated plates in DMEM+10%FBS.

extract_protocol:
Cells were transduced overnight twice in consecutive days and media replaced in between. After the second transduction, culture media was replaced by normal growth media and this was considered day 0.
Cells were collected 2 days after viral transduction
Cultured cells were fixed in 11 % formaldehyde for 15 min at room temperature on a rotating platform. The formaldehyde was quenched by adding 125 nM glycine. The chromatin was sheared and immunoprecipitated with the antibody of interest. A control sample consisting of sonicated chromatin that was not immunoprecipitated was also sequenced.
Illumina sequencing libraries were prepared from ChIP and Input DNAs by standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single-end).


title: PIB-HDFs-BATF3_rep2

description:
PIB-HDFs-BATF3
10-PIB-HDFs-BATF3_hg38_rep 2


title: PIB-HDFs-PU-1_rep2

description:
PIB-HDFs-PU-1
8-PIB-HDFs-PU-1_hg38_rep 2


title: HDFs-Pooled-Input_rep1

description:
HDFs-Pooled-Input
7-HDFs-Pooled-Input_hg38


title: BATF3-HDFs-BATF3

description:
BATF3-HDFs-BATF3
6-BATF3-HDFs-BATF3_hg38


title: IRF8-HDFs-IRF8

description:
IRF8-HDFs-IRF8
5-IRF8-HDFs-IRF8_hg38


title: CS1_S409


title: PIB-HDFs-BATF3_rep1

description:
PIB-HDFs-BATF3
3-PIB-HDFs-BATF3_hg38


title: PU.1-HDFs-PU.1

description:
PU.1-HDFs-PU.1
4-PU.1-HDFs-PU.1_hg38


title: PIB-HDFs-IRF8_rep1

description:
PIB-HDFs-IRF8
2-PIB-HDFs-IRF8_hg38


title: Molm13_A2_2

city: Milwaukee

last: Zhu

state: WI

address: 8733 W Watertown Plank Rd

institute: Versiti Blood Research Institute Milwaukee

data_processing:
Library strategy: CUT&Tag
Reads were aligned to the hg19 genome using Bowtie v2.3.5 using the' --local --very-sensitive-local --no-unal --no-discordant --phred33 -I 10 -X 700' settings
Peaks were called for each of the ARID antibody samples using Macs v2.2.7.1 in combination with an IgG control.
IDR analysis was used to obtain replicable Arid2 and Arid1b binding loci from CUT&Tag data. IDR values were calculated using replicate samples using the R implementation of IDR v1.2 and peaks with an IDR value < 0.01 were retained as replicable peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BED files of peak coordinates after IDR analysis with an IDR threshold of 0.01

growth_protocol: MOLM13 cells were cultured in RPMI media supplemented with 10% FBS 1% P/S

extract_protocol:
CUT&Tag was perfomed according to Bench Top CUT&Tag v3 (protocols.io, Hatice S Kaya-Okur,Steven Henikoff)
Libraries were contructed according to Bench Top CUT&Tag v3 (protocols.io, Hatice S Kaya-Okur,Steven Henikoff) using indexed primers described by Buenrostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486 (2015).

value: Acute Myeloid Leukemia

value: ARID2 (A302-229A, Bethyl Lab Inc)


title: PIB-HDFs-PU.1_rep1

description:
PIB-HDFs-PU.1
1-PIB-HDFs-PU.1_hg38


title: Molm13_A1b_2

value: ARID1B (A301-406A, Bethyl Lab Inc)


title: Molm13_A1b_1


title: MDS-23.6_ATAC

city: New York

first: Eirini

middle: P.

last: Papapetrou

address: One Gustave L. Levy Place Box 1044A

institute: Icahn School of Medicine at Mount Sinai

description:
processed data file:
ATAC_norm_counts.txt.gz
ATAC_peaks.txt.gz

data_processing:
RNA alignment: STAR aligner, v2.5.4b
RNA splicing: rMATS, v3.1.0
RNA analysis: R v3.5.2; DESeq2 v1.22.2
ATAC alignment: R v3.5.2, RBowtie2 v1.4.0
ATAC peak calling: MACS2 v2.1.2
ATAC peak filtering: IDR v2.0.4
ATAC analysis: R v3.5.2; DESeq2 v1.22.2
Genome_build: GRCh37
Supplementary_files_format_and_content: RNA: DESeq2-normalized count matrix; txt format
Supplementary_files_format_and_content: ATAC: DESeq2-normalized count matrix; txt format
Supplementary_files_format_and_content: ATAC: ATAC-seq peaks in matrix format; txt format

source_name: iPSC

extract_protocol:
50,000 MACS-sorted CD34+/CD45+ cells from each individual iPSC line were processed as follows: nuclei were isolated by lysis with 50 ul of ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and washed with 1 mL of ATAC wash buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Cell lysates were spun to obtain nuclear pellets, which were subjected to transposase reaction using the Illumina Nextera DNA Sample Preparation Kit according to the manufacturer’s instructions.
The libraries were quantified using the Agilent BioAnalyzer. Sequencing of 75 nucleotide-long paired-end reads was performed in a NextSeq-500 (Illumina).

tag: cell genotype

value: SF3B1 K700E

tag: patient id

value: iPS-derived hematopoietic stem/progenitor cells


title: Molm13_A2_1


title: Molm13_IgG_1

description:
arid1b_idr.bed
arid2_idr.bed

value: Rabbit IgG (PP64B, Abcam)


title: MDS-23.38_ATAC


title: MDS-23.24_ATAC


title: N-23.13_ATAC

value: wild type


title: N-22.27_ATAC


title: N-22.22_ATAC


title: CS1_S383


title: MDS-22.44_ATAC


title: N-23.5_ATAC


title: N-23.28_ATAC


title: MDS-21.31_ATAC


title: N-21.14_ATAC


title: N-21.6_ATAC


title: MDS-21.16_ATAC


title: MDS-21.29_ATAC


title: miR-130a KD IgG rep1

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

description: KD1 IgG

data_processing:
Library strategy: CUT&RUN
CUT&RUN paired-end data was trimmed using fastp v. 0.19.5 to remove adapters and low quality base pairs with base pair quality score <30 and read length <35 bp.
Trimmed reads were aligned to the hg38 human reference genome using bowtie2 v. 2.3.5. Reads were also aligned to the  S. cerevisiae yeast genome (sacCer3) yeast genome to evaluate the yeast spike-in control for the normalization.
Peaks were called from the pooled replicates against the IgG using MACS2 v. 2.2.5  with normalizing the samples based on the spike-in reads qunatification.
ChipPeakAnnot library in the R package v.3.6.1 was used to determine the overlap between peak sets and determine the shared and specific peaks represented in the Venn diagrams. Minimum peak overlap was set to 100 bp to determine the intersection peaks between the two samples.
Shared peaks between the sets ETO and Flag antibodies in the Control and miR-130a KD samples were used for the downstream analysis. These two sets of shared peaks were intersected again using ChipPeakAnnot library to determine the shared peaks between the two sets and the unique peaks to each of the two sets.
Peaks were annotated to the genomic features of the hg38 human genomes.
HOMER v. 4.8  was used for de novo motif analysis of the sets of peaks.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files

source_name: Flag-tag AML1-ETO Kasumi-1 cell line

growth_protocol: Flag-tagged AML1-ETO Kasumi-1 cells were cultured in RPMI medium + 20% FBS, 1% Pen/Strep.

extract_protocol:
Sorted GFP+ cells (2x10^5) were washed in PBS and CUT&RUN assay was performed as previously described (Skene et al. 2018).
DNA libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to manufacturer’s instructions. AMPure XP beads (Beckman) were used for cleanup of PCR reaction as described in the manufacturer’s protocol. Subsequently, libraries were size selected for 150-400 bp range with Pippen HT and size verified with Bioanalyzer. Samples were sequenced on Illumina NextSeq500 using 75-bp paired-end reads to achieve sequencing depth of approximately 40M reads/sample.

treatment_protocol: Transduction of  Flag-AML1-ETO Kasumi-1 cells was performed at a density of 2x10^6 cells/ml in RPMI medium with 20% FBS, 1% Pen/Strep. Cells were infected in 24-well suspension plates and centrifuged at 1,400 rpm for 60 min at 32°C and fresh medium was added on the next day. Viable, GFP+ cells were sorted 72 hours post-transduction and 2x10^5 cells were used per experimental condition.

value: t(8;21) AML cell line

tag: days post-transduction

value: 3 days post-tranduction

value: Mouse IgG C Thermo Fisher 10400C


title: miR-130a KD IgG rep3

description: KD3 IgG


title: Control IgG rep 2

description: C2 IgG


title: miR-130a KD IgG rep2

description: KD2 IgG


title: Control IgG rep 1

description: C1 IgG


title: Control IgG rep 3

description: C3 IgG


title: miR-130a KD anti-Flag rep2

description: KD2 Flag

value: Flag M2 Sigma F1804


title: Molm13_IgG_2

description:
arid1b_idr.bed
arid2_idr.bed


title: Control anti-Flag rep 3

description: C3 Flag


title: Control anti-Flag rep 1

description: C1 Flag


title: miR-130a KD anti-Flag rep1

description: KD1 Flag


title: Control anti-Flag rep 2

description: C2 Flag


title: miR-130a KD anti-ETO rep2

description: KD2 ETO

value: ETO Santa Cruz sc-134335


title: miR-130a KD anti-ETO rep3

description: KD3 ETO


title: miR-130a KD anti-ETO rep1

description: KD1 ETO


title: R_S10037

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
The fastqs were aligned using STAR 2.5.2a and hg19
The aligned files were processed using PORT gene-based normalization ( https://github.com/itmat/Normalization )
Genome_build: hg19

extract_protocol:
RNA was isolated using the Qiagen RNeasy micro kit (#74034) according to the manufacturer's protocol
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit for Pico Input Mammalian from Clonetech according to the manufacturer's protocol (#635007)

tag: donor id

tag: Sex

value: Male

tag: age

tag: tumor recurrence 1 year

tag: library preparation group


title: Control anti-ETO rep 3

description: C3 ETO


title: Control anti-ETO rep 1

description: C1 ETO


title: R_S10029

source_name: Tumor

value: No


title: R_S10026


title: R_S10039


title: R_S10019

value: Female


title: N-22.45_ATAC


title: R_S10016


title: R_S10027


title: R_S10009

value: Yes


title: R_S10006


title: R_S657


title: R_S10007


title: R_S655


title: R_S656


title: R_S653


title: R_S654


title: miR-130a KD anti-Flag rep3

description: KD3 Flag


title: R_S652


title: R_S641


title: R_S651


title: R_S640


title: R_S639


title: R_S395


title: R_S394


title: R_S389


title: R_S393


title: Control anti-ETO rep 2

description: C2 ETO


title: R_S388


title: R_S387


title: R_S385


title: R_S366


title: R_S365


title: R_S363


title: R_S362


title: R_S295


title: R_S10017


title: R_S292


title: R_S288


title: R_S289


title: R_S290


title: R_S287


title: R_S285


title: R_S284


title: R_S262


title: R_S282


title: R_S281


title: R_S260


title: R_S642


title: CS2_S10

value: PBMC

value: KIR+ CD8 T


title: R_S8202

description: PBMC Older CD8_BulkNonNaive

data_processing:
The fastqs were aligned using STAR 2.5.2a and hg19
The aligned files were processed using PORT gene-based normalization ( https://github.com/itmat/Normalization )
The differential gene expression was done with Deseq2
Genome_build: hg19
Supplementary_files_format_and_content: text file with DeSeq2 normalized counts for each sample

extract_protocol:
RNA was isolated using the Qiagen RNeasy micro kit (#74034) according to the manufacturer's protocol
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit for Pico Input Mammalian from Clonetech according to the manufacturer's protocol (#635007)
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell

tag: donor type

value: Older

tag: cmv serostatus

tag: cell subset

tag: sample acquisition location

value: NIA


title: R_S8260

description: PBMC Older CD8_PD1+CD39+


title: R_S8212

description: PBMC Older CD8_BulkNonNaive


title: R_S8207

description: PBMC Older CD8_Naive


title: R_S8211

description: PBMC Older CD8_BulkNaive


title: R_S8240

description: PBMC Older CD8_PD1+CD39+


title: R_S8201

description: PBMC Older CD8_BulkNaive


title: R_S8230

description: PBMC Older CD8_PD1+CD39+


title: R_S392


title: R_S8140

description: PBMC Older CD4_Treg


title: R_S8136

description: PBMC Older CD4_Treg

value: UPenn


title: R_S8134

description: PBMC Older CD4_BulkNonNaive


title: R_S8133

description: PBMC Older CD4_BulkNaive


title: R_S8138

description: PBMC Older CD4_BulkNonNaive


title: R_S8128

description: PBMC Older CD4_Treg

value: Negative


title: R_S8132

description: PBMC Older CD4_Treg


title: R_S8126

description: PBMC Older CD4_BulkNonNaive


title: R_S8129

description: PBMC Older CD4_BulkNaive


title: R_S8130

description: PBMC Older CD4_BulkNonNaive


title: R_S364


title: R_S8125

description: PBMC Older CD4_BulkNaive


title: R_S8120

description: PBMC Older CD4_Treg


title: R_S8118

description: PBMC Older CD4_BulkNonNaive


title: R_S8117

description: PBMC Older CD4_BulkNaive


title: R_S8114

description: PBMC Older CD4_BulkNonNaive


title: R_S280


title: R_S8113

description: PBMC Older CD4_BulkNaive


title: R_S8112

description: PBMC Older CD4_Treg


title: R_S8219

description: PBMC Older CD8_SCM-R3-


title: R_S8101

description: PBMC Older CD4_BulkNaive


title: R_S8110

description: PBMC Older CD4_BulkNonNaive


title: R_S8105

description: PBMC Older CD4_BulkNaive


title: R_S8102

description: PBMC Older CD4_BulkNonNaive


title: R_S8109

description: PBMC Older CD4_BulkNaive


title: R_S8096

description: PBMC Older CD8_CM


title: R_S8095

description: PBMC Older CD8_EM1


title: R_S8106

description: PBMC Older CD4_BulkNonNaive


title: R_S8086

description: PBMC Older CD8_CM


title: R_S8093

description: PBMC Older CD8_EMRA


title: R_S8087

description: PBMC Older CD8_Naive


title: R_S8094

description: PBMC Older CD8_EM2


title: R_S8091

description: PBMC Older CD8_BulkNaive


title: R_S8084

description: PBMC Older CD8_EM2


title: R_S8085

description: PBMC Older CD8_EM1


title: R_S8092

description: PBMC Older CD8_BulkNonNaive


title: R_S8082

description: PBMC Older CD8_BulkNonNaive


title: R_S8083

description: PBMC Older CD8_EMRA


title: R_S8076

description: PBMC Older CD8_CM


title: R_S8078

description: PBMC Older CD8_SCM-R3+


title: R_S8081

description: PBMC Older CD8_BulkNaive


title: R_S8075

description: PBMC Older CD8_EM1


title: R_S8072

description: PBMC Older CD8_BulkNonNaive


title: R_S8073

description: PBMC Older CD8_EMRA


title: R_S8116

description: PBMC Older CD4_Treg


title: R_S8071

description: PBMC Older CD8_BulkNaive


title: R_S8069

description: PBMC Older CD8_SCM-R3-


title: R_S8070

description: PBMC Older CD8_PD1+CD39+


title: R_S8068

description: PBMC Older CD8_SCM-R3+


title: R_S8067

description: PBMC Older CD8_Naive


title: R_S8065

description: PBMC Older CD8_EM1


title: R_S8062

description: PBMC Older CD8_BulkNonNaive


title: R_S8064

description: PBMC Older CD8_EM2


title: R_S8066

description: PBMC Older CD8_CM


title: R_S8047

description: PBMC Older CD8_Naive


title: R_S8061

description: PBMC Older CD8_BulkNaive


title: R_S8046

description: PBMC Older CD8_CM


title: R_S8044

description: PBMC Older CD8_EM2


title: R_S8063

description: PBMC Older CD8_EMRA


title: R_S8041

description: PBMC Older CD8_BulkNaive


title: R_S8045

description: PBMC Older CD8_EM1


title: R_S8097

description: PBMC Older CD8_Naive


title: R_S8050

description: PBMC Older CD8_PD1+CD39+


title: R_S8035

description: PBMC Older CD8_EM1


title: R_S8104

description: PBMC Older CD4_Treg


title: R_S8037

description: PBMC Older CD8_Naive


title: R_S8042

description: PBMC Older CD8_BulkNonNaive


title: R_S8033

description: PBMC Older CD8_EMRA


title: R_S8031

description: PBMC Older CD8_BulkNaive


title: R_S8025

description: PBMC Older CD8_EM1


title: R_S8024

description: PBMC Older CD8_EM2


title: R_S8026

description: PBMC Older CD8_CM


title: R_S8023

description: PBMC Older CD8_EMRA


title: R_S8074

description: PBMC Older CD8_EM2


title: R_S8022

description: PBMC Older CD8_BulkNonNaive


title: R_S8021

description: PBMC Older CD8_BulkNaive


title: R_S8016

description: PBMC Older CD8_CM


title: R_S8012

description: PBMC Older CD8_BulkNonNaive


title: R_S8015

description: PBMC Older CD8_EM1


title: R_S8013

description: PBMC Older CD8_EMRA


title: R_S8011

description: PBMC Older CD8_BulkNaive


title: R_S8006

description: PBMC Older CD8_CM


title: R_S8014

description: PBMC Older CD8_EM2


title: R_S8007

description: PBMC Older CD8_Naive


title: R_S7140

description: PBMC Young CD4_Treg

value: Young


title: R_S8005

description: PBMC Older CD8_EM1


title: R_S7139

description: PBMC Young CD4_Tfh


title: R_S8001

description: PBMC Older CD8_BulkNaive


title: R_S8002

description: PBMC Older CD8_BulkNonNaive


title: R_S7137

description: PBMC Young CD4_BulkNaive


title: R_S8003

description: PBMC Older CD8_EMRA


title: R_S7138

description: PBMC Young CD4_BulkNonNaive


title: R_S7130

description: PBMC Young CD4_BulkNonNaive


title: R_S7132

description: PBMC Young CD4_Treg


title: R_S8043

description: PBMC Older CD8_EMRA


title: R_S7129

description: PBMC Young CD4_BulkNaive


title: R_S7128

description: PBMC Young CD4_Treg

value: Positive


title: R_S8032

description: PBMC Older CD8_BulkNonNaive


title: R_S7126

description: PBMC Young CD4_BulkNonNaive


title: R_S7125

description: PBMC Young CD4_BulkNaive


title: R_S7127

description: PBMC Young CD4_Tfh


title: R_S7124

description: PBMC Young CD4_Treg


title: R_S7122

description: PBMC Young CD4_BulkNonNaive


title: R_S7121

description: PBMC Young CD4_BulkNaive


title: R_S7120

description: PBMC Young CD4_Treg


title: R_S7117

description: PBMC Young CD4_BulkNaive


title: R_S7119

description: PBMC Young CD4_Tfh


title: R_S7118

description: PBMC Young CD4_BulkNonNaive


title: R_S7116

description: PBMC Young CD4_Treg


title: R_S7114

description: PBMC Young CD4_BulkNonNaive


title: R_S7110

description: PBMC Young CD4_BulkNonNaive


title: R_S7111

description: PBMC Young CD4_Tfh


title: R_S7112

description: PBMC Young CD4_Treg


title: R_S7108

description: PBMC Young CD4_Treg


title: H3K36me3_iswi_N6171

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
MNase-seq
Paired-end sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with the option “-q -p 4 -X 250 --no-discordant --no-mixed --no-unal” (Paired-end alignment reads with maximum 250bp distance gap between them were used in subsequent analysis. This length correspond to mono-nucleosome)
Only correctly aligned paired-end alignment reads were filtered using samtools (version 1.5) commands “samtools view –hf 0x2 input.bam | grep –v “XS:i:” “
Dyad Coverage was calculated using the scripts (03_PNA_SDE.R) from Baldi et al (Baldi, S. et al. Genome-wide Rules of Nucleosome Phasing in Drosophila. Mol. Cell 72, 661-672.e4 (2018))
The spectral density (SD) score correspond to periods of 182bp was calculated using the scripts (cov2spec.R) from Baldi et al. SD score was normalized as Z-score :  (log2(SD score) – average) / standard deviation.
Regions with the average Z-score threshold of 2 were defined as the domain of a regular nucleosome array.
Genome_build: neurospora crassa genome (OR74A)
Supplementary_files_format_and_content: bigwig of dyad coverage and spectral density
ChIP-seq
Sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with default option.
Reads with low mapping quality (MapQ < 10) and from repetitive seuqnces were discarded.
Pileup score were calculated using Homer software (version 4.10.1).
ChIP-seq scores correspond to the total number of mapped tags after normalizing to 10 million reads.
Genome_build: neurospora crassa genome (OR74A)
Supplementary_files_format_and_content: bigwig of pileup graph

organism: Neurospora crassa

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC

extract_protocol:
Lysates were cleared by centrifugation and 1/20th input was saved. H3K27me2/3 antibody was added (Active Motif, 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl wash buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the Qiagen MinElute PCR purification kit and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions. AMPure XP beads (Beckman Coulter A63881) were used for size selection of ~200-800 bp fragments. Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 3x 10 min with a cycle of 30 sec on followed by 30 sec off, at high power.

tag: sample type

value: nuclei


title: R_S7109

description: PBMC Young CD4_BulkNaive

tag: cell type


title: R_S7105

description: PBMC Young CD4_BulkNaive


title: R_S7104

description: PBMC Young CD4_Treg


title: R_S7102

description: PBMC Young CD4_BulkNonNaive


title: H3K36me3_acf1_N8016

tag: antibody


title: H3K36me3_acf1_N8017


title: H3K36me2_iswi_N6171


title: R_S7131

description: PBMC Young CD4_Tfh


title: R_S7101

description: PBMC Young CD4_BulkNaive


title: H3K36me2_iswi_N6170


title: R_S7100

description: PBMC Young CD8_PD1+CD39+


title: R_S7099

description: PBMC Young CD8_SCM-R3-


title: H3K36me2_acf1_N8017


title: R_S7098

description: PBMC Young CD8_SCM-R3+


title: H3K36me2_acf1_N8016


title: R_S7097

description: PBMC Young CD8_Naive


title: MNaseSeq_ash1_N6877

growth_protocol: A 50 ml culture of Vogel’s solution plus 1.5% sucrose was inoculated with 2.5E7 cells, harvested from freshly grown conidia, and grown at 32oC with shaking for ~3.5 hours, until at least 70% of conidia have germinated as determined by microscopy

extract_protocol:
Cells were treated with 2 mg of zymolyase (100T) in a 1 ml solution of spheroplast buffer (1M sorbitol, 50mM Tris pH 7.5, 10mM BME) for 15 minutes while rotating at room temperature. Cells were pelleted at full speed and resuspended in 100 ul MNase digestion buffer (1M sorbitol, 50mM NaCl, 10mM Tris pH 7.5, 5mM MgCl2, 1mM CaCl2, 0.075% (v/v) IGEPAL (Sigma), 0.5mM spermidine and 1mM BME). Exonuclease III (NEB) (30 units) and micrococcal nuclease (Takara) were added to samples and rapidly mixed. Digestion proceeded for 10 minutes at 37oC and was quenched with final concentration of 5mM EGTA and 5mM EDTA (from 50mM/50mM stock). MNase concentration was optimized for each strain to yield ~80-90% mononucleosomes (20 units for N3752, N3753, N7966, N8018, N7990, N7992, N7988, N7989; 60 units for N4718; and 80 units for N4730, N6170, N6171, N8016, N8017). RNase (40 ug) treatment was for 1.5 hours at 42C and proteinase K (200 ug) treatment was for 1 hour at 65 C.
10 ug of gel-purified (minelute, Qiagen) mononucleosome DNA was prepared for high-throughput sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: Cells were crosslinked by addition of fresh formaldehyde for a final concentration of 1%, then shaken at room temperature for 10 minutes. The crosslinking reaction was quenched by the addition of 6.8 ml of 1M Tris-HCl pH 8 to a final concentration of 125mM for 10 minutes, shaking at room temperature. Conidia were then harvested by centrifugation.


title: R_S7096

description: PBMC Young CD8_CM


title: MNaseSeq_ash1_N6876


title: K18_M3

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description:
K18 hACE2
3313_S3

data_processing:
FASTQ data were generated by Illumina Basespace.
FASTQ data quality assessment and trimming, read mapping, and expression analyses were done by Banana Slug Analytics Platform.

organism: Mus musculus

source_name: Lung

growth_protocol: All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks.

extract_protocol:
Total RNA was extracted from lung tissue according to RNeasy Plus Mini Kit protocol from QIAGEN.
Library construction was performed according to TruSeq totalRNA protocol from Illumina

tag: strain

value: K18 hACE2 transgenic mice

tag: time point of infection

value: SARS-CoV2_6 days post infection

tag: tissue

value: lung

value: male


title: R_S7091

description: PBMC Young CD8_BulkNaive

value: Male


title: R_S7092

description: PBMC Young CD8_BulkNonNaive


title: R_S7115

description: PBMC Young CD4_Tfh


title: K18_M1

description:
K18 hACE2
3311_S1


title: WT_M3

description:
wt
3189_S9

value: C57BL/6J mice


title: R_S7113

description: PBMC Young CD4_BulkNaive

value: Female


title: K18_M2

description:
K18 hACE2
3312_S2


title: R_S7087

description: PBMC Young CD8_Naive

value: Indeterminate


title: WT_M1

description:
wt
3183_S7


title: R_S7086

description: PBMC Young CD8_CM


title: H3K36me3_iswi_N6170


title: R_S7106

description: PBMC Young CD4_BulkNonNaive


title: HC14

data_processing:
RNA-seq data were de-multiplexed, aligned to the GRCh38 reference genome, and converted into gene counts matrices using CellRanger 3.1.0.
Downstream analysis was performed using the Seurat 3.0 package.
Cells with fewer than 800 detected genes, more than 3000 detected genes or more than 10% mitochondrial genes were discarded.
CD8+ T cells (expressing CD8A and CD8B but not TRDC transcripts) from each individual were selected for further analysis.
To make counts comparable among cells, gene counts were normalized to 10,000 reads per cell, then log-transformed.
We identified highly-variable genes for each individual, then integrated gene expression data from all individuals using Seurat’s integration anchor discovery algorithm
We performed PCA dimensionality reduction on the integrated data, then clustered cells with the Louvain algorithm and visualized the data using UMAP.
We identified canonical cell type marker genes that were conserved across conditions using the Wilcoxon rank-sum test implemented in the Seurat package’s ‘FindConservedMarkers’ function.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files of each healthy subject or MS patient
Supplementary_files_format_and_content: h5ad file for CD8 T cells from 25 COVID-19 patients

molecule: polyA RNA

extract_protocol:
Single cell suspension, barcoded Gel Beads and partitioning oil were loaded to Chromium Chip G to generate single-cell gel bead-in-emulsion (GEM). The poly-adenylated transcripts were reverse-transcribed later.
The downstream library constructions were performed using the Chromium Single Cell 5’ library construction kit according to the manufacturer’s protocol (10x Genomics).

value: PBMC

value: pan T cells

tag: disease state

value: healthy control


title: R_S7085

description: PBMC Young CD8_EM1


title: HC13


title: R_S7083

description: PBMC Young CD8_EMRA


title: HC12


title: R_S7084

description: PBMC Young CD8_EM2


title: HC11


title: R_S7081

description: PBMC Young CD8_BulkNaive


title: R_S7082

description: PBMC Young CD8_BulkNonNaive


title: R_S7077

description: PBMC Young CD8_Naive


title: R_S7080

description: PBMC Young CD8_PD1+CD39+


title: R_S7076

description: PBMC Young CD8_CM


title: MS11132018

value: multiple sclerosis


title: R_S7075

description: PBMC Young CD8_EM1

value: UPenn


title: MS01092019


title: R_S7074

description: PBMC Young CD8_EM2

value: Negative


title: HC0806_KIR3DL1-lo

data_processing:
We aligned the reads to the human reference genome (NCBI GRCh38) using STAR v2.7.0e.
Gene counts were quantified and normalized (TPM) with Salmon.
Differential gene expression analysis was determined via the DESeq function in the DESeq2 R package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

extract_protocol:
Live KIR+ or KIR- CD8+ T cells were bulk sorted directly into 350 μL TRIzol (Qiagen) by FACSAria Fusion flow cytometer (BD).  Total RNA was extracted from TRIzol samples using chloroform separation and isopropanol precipitation and then RNAeasy Plus Mini kit (Qiagen) for clean-up.
After analysis on the 2100 Bioanalyzer, the sequencing libraries were prepared using the RiboGone Mammalian rRNA Depletion Kit (Clontech) and the SMARTer Stranded RNA-seq Kit (Clontech). The resulting library was sequenced on the HiSeq 4000 platform (Illumina) in Stanford Functional Genomics Facility. For each sample in the bulk RNA sequencing library, 75-base-pair paired-end reads were acquired from the sequencer.

value: KIR3DL1-lo CD8 T

value: healthy


title: MS09102018


title: R_S7093

description: PBMC Young CD8_EMRA

value: Young


title: R_S7095

description: PBMC Young CD8_EM1


title: HC0806_KIR3DL1-hi

value: KIR3DL1-hi CD8 T


title: HC2130_KIR3DL1-lo


title: MS08162018


title: R_S7071

description: PBMC Young CD8_BulkNaive


title: HC2129_KIR2DL3-lo

value: KIR2DL3-lo CD8 T


title: HC2183_KIR3DL1-lo


title: WT_M2

description:
wt
3184_S8

value: SARS-CoV2_6 days post infection

value: lung


title: R_S7066

description: PBMC Young CD8_CM

value: Male

value: Positive


title: HC2183_KIR3DL1-hi


title: R_S7063

description: PBMC Young CD8_EMRA


title: HC2130_KIR3DL1-hi


title: R_S7064

description: PBMC Young CD8_EM2


title: R_S7065

description: PBMC Young CD8_EM1


title: R_S7072

description: PBMC Young CD8_BulkNonNaive

value: Female


title: MS9020


title: HC2129_KIR2DL3-hi

value: KIR2DL3-hi CD8 T


title: R_S7067

description: PBMC Young CD8_Naive


title: HC2180_KIR2DL3-hi

value: PBMC


title: R_S7061

description: PBMC Young CD8_BulkNaive


title: HC2175_KIR2DL3-lo


title: R_S7062

description: PBMC Young CD8_BulkNonNaive


title: HC2180_KIR2DL3-lo


title: R_S7058

description: PBMC Young CD8_SCM-R3+


title: HC2175_KIR2DL3-hi


title: MS658

value: pan T cells


title: R_S7057

description: PBMC Young CD8_Naive


title: R_S7056

description: PBMC Young CD8_CM


title: MDS-23.38_RNA

description:
processed data file:
RNA_norm_counts.txt.gz

extract_protocol:
Magnetic-activated cell sorting (MACS) with anti-CD45 MACS cell separation microbeads and reagents (Miltenyi Biotec). RNA was extracted with the Direct-zol RNA purification kit (Zymo R2061).
Sequencing libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina 20020594) from 500ng input RNA. Samples were barcoded and run on a Hi-seq 4000 in a 100bp/100bp paired-end run, using the Hi-seq 3000/4000 SBS kit (Illumina).

tag: cell genotype

value: SF3B1 K700E

tag: patient id

value: iPS-derived hematopoietic stem/progenitor cells


title: MDS-23.24_RNA


title: MDS-23.6_RNA


title: R_S7054

description: PBMC Young CD8_EM2

tag: donor id

tag: Sex

value: UPenn


title: N-23.28_RNA

value: wild type


title: N-23.13_RNA


title: R_S7073

description: PBMC Young CD8_EMRA

tag: age

value: Negative


title: R_S7053

description: PBMC Young CD8_EMRA

tag: library preparation group


title: R_S7055

description: PBMC Young CD8_EM1

tag: donor type


title: N-23.5_RNA


title: MDS-22.44_RNA


title: R_S7052

description: PBMC Young CD8_BulkNonNaive

tag: cmv serostatus


title: N-22.45_RNA


title: R_S7051

description: PBMC Young CD8_BulkNaive

tag: cell subset


title: R_S7050

description: PBMC Young CD8_PD1+CD39+

tag: sample acquisition location


title: N-22.22_RNA


title: N-22.27_RNA


title: R_S7049

description: PBMC Young CD8_SCM-R3-


title: R_S7048

description: PBMC Young CD8_SCM-R3+


title: MDS-21.31_RNA


title: R_S7047

description: PBMC Young CD8_Naive


title: MDS-21.16_RNA


title: R_S7045

description: PBMC Young CD8_EM1


title: R_S7046

description: PBMC Young CD8_CM


title: N-21.14_RNA


title: R_S7044

description: PBMC Young CD8_EM2


title: N-21.6_RNA


title: N-21.1_RNA


title: R_S7043

description: PBMC Young CD8_EMRA


title: R_S7042

description: PBMC Young CD8_BulkNonNaive


title: R_S7060

description: PBMC Young CD8_PD1+CD39+


title: R_S7041

description: PBMC Young CD8_BulkNaive


title: cc14 STS BLOCK CM-48h-2

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
The FASTQ files were mapped to human genome hg38 using STAR aligner (STAR_2.5.2b) and gencode gtf annotation (gencode.v25.GRCh38.gtf)
The differential expression analyses were performed using DESeq2 software (DESeq2_1.20.0). Significant differnetially expressed genes were filtered using the criterion adjusted p.value (padj) < 0.05
Genome_build: hg38

source_name: cc14 colon cancer cells primary culture

growth_protocol: Cells were cultured with DMEM/F12 medium with 5%FBS and 1% Pennicilin/Streptomycin

extract_protocol:
Total RNA extraction using TRIzol
Illumina TruSeq protocol

treatment_protocol: Cells were treated withconditionned medium (CM) of cells treated 5 days before with Staurosporine (1μM)or DMSO for 6 hours, washed with PBS and treated for 5 days with DIDS(100μM) and Q-VD-Oph (10μM). The medium has been conditionned from day5 to day 7 post STS treatment. Cells treated with CM for 48h were harvested for RNA extraction.

value: colon cancer

tag: cell line

tag: Stage

tag: agent

value: STS


title: cc14 STS BLOCK CM-48h-1


title: R_S7040

description: PBMC Young CD8_PD1+CD39+

value: Young

tag: cell type


title: R_S7037

description: PBMC Young CD8_Naive


title: cc14 control CM-48h-3

value: DMSO


title: R_S7036

description: PBMC Young CD8_CM


title: R_S7035

description: PBMC Young CD8_EM1


title: cc14 control CM-48h-2


title: cc14 control CM-48h-1


title: R_S7034

description: PBMC Young CD8_EM2


title: cc14 STS-BLOCK-7D-2

data_processing:
The FASTQ files were mapped to human genome hg38 using STAR aligner (STAR_2.5.2b) and gencode gtf annotation (gencode.v25.GRCh38.gtf)
The differential expression analyses were performed using DESeq2 software (DESeq2_1.20.0). Significant differnetially expressed genes were filtered using the criterion adjusted p.value (padj) < 0.05
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2-counts data

treatment_protocol: Cells were treated with Staurosporine (1μM)or DMSO for 6 hours, washed withPBS and treated for 5 days with DIDS(100μM) and Q-VD-Oph (10μM). Cells were replated and harvested at 7 days for RNA extraction.

value: colon


title: R_S7033

description: PBMC Young CD8_EMRA


title: cc14 STS-BLOCK-7D-3


title: cc14 STS-BLOCK-7D-1


title: R_S7032

description: PBMC Young CD8_BulkNonNaive


title: R_S7029

description: PBMC Young CD8_SCM-R3-


title: cc14 DMSO-BLOCK-7D-3


title: cc14 DMSO-BLOCK-7D-2


title: R_S7031

description: PBMC Young CD8_BulkNaive


title: R_S7027

description: PBMC Young CD8_Naive


title: CeD1_KIR-

source_name: celiac disease_KIR- CD8 T

tag: subject status

value: celiac disease

value: KIR- CD8 T


title: CeD1_KIR+

source_name: celiac disease_KIR+ CD8 T

tag: tissue

value: KIR+ CD8 T


title: R_S7026

description: PBMC Young CD8_CM

value: Female


title: R_S7025

description: PBMC Young CD8_EM1


title: MDS-21.29_RNA


title: SLE4_KIR-

source_name: Systemic Lupus Erythematosus_KIR- CD8 T

value: Systemic Lupus Erythematosus


title: cc14 DMSO-BLOCK-7D-1


title: R_S7024

description: PBMC Young CD8_EM2


title: SLE4_KIR+

source_name: Systemic Lupus Erythematosus_KIR+ CD8 T

value: PBMC


title: cc14 STS BLOCK CM-48h-3


title: SLE3_KIR+


title: R_S7023

description: PBMC Young CD8_EMRA


title: R_S7022

description: PBMC Young CD8_BulkNonNaive


title: SLE3_KIR-


title: R_S7020

description: PBMC Young CD8_PD1+CD39+

value: Male


title: SLE2_KIR-


title: SLE2_KIR+


title: R_S7018

description: PBMC Young CD8_SCM-R3+


title: R_S7019

description: PBMC Young CD8_SCM-R3-


title: R_S7017

description: PBMC Young CD8_Naive


title: SLE1_KIR+


title: R_S7016

description: PBMC Young CD8_CM


title: HC6_KIR-

source_name: healthy_KIR- CD8 T

value: healthy


title: R_S7015

description: PBMC Young CD8_EM1


title: HC6_KIR+

source_name: healthy_KIR+ CD8 T


title: HC5_KIR-


title: R_S7014

description: PBMC Young CD8_EM2


title: R_S7013

description: PBMC Young CD8_EMRA


title: HC5_KIR+


title: R_S7012

description: PBMC Young CD8_BulkNonNaive


title: R_S7011

description: PBMC Young CD8_BulkNaive


title: R_S7030

description: PBMC Young CD8_PD1+CD39+


title: HC4_KIR+


title: HC3_KIR-


title: R_S7006

description: PBMC Young CD8_CM


title: R_S7007

description: PBMC Young CD8_Naive


title: HC2_KIR-


title: R_S7004

description: PBMC Young CD8_EM2


title: R_S7003

description: PBMC Young CD8_EMRA


title: HC2_KIR+


title: HC3_KIR+


title: R_S7005

description: PBMC Young CD8_EM1


title: MS3_KIR-

source_name: multiple sclerosis_KIR- CD8 T

value: multiple sclerosis


title: R_S7002

description: PBMC Young CD8_BulkNonNaive

value: UPenn


title: MS2_KIR-


title: A_S10039

data_processing:
The fastqs were aligned to hg19 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Genome_build: hg19
Supplementary_files_format_and_content: Chromatin accessibility counts at peaks

extract_protocol:
Transposed DNA was prepared with Tn5 (Illumina #FC-121-1031) as described in Buenrostro et al. 2013. Libraries were barcoded with Nextera Index Kit (Illumina # FC-121-1012)
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell

tag: tumor recurrence 1 year


title: MS2_KIR+

source_name: multiple sclerosis_KIR+ CD8 T


title: MS1_KIR-


title: SLE1_KIR-


title: A_S10029

value: No


title: A_S10026


title: A_S10027


title: A_S10019


title: A_S10017


title: A_S10016


title: A_S10009

value: Yes


title: HC4_KIR-


title: A_S10007


title: A_S10006


title: A_S657


title: ATAC-seq_Wt1b Over expression replicate 3

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

institute: University of Bern

data_processing:
All base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20
Quality check of the samples was performed using FASTQC and reports summarized using MultiQC
Adapters from the fastq files were trimmed using trimmomatic software
Reads were aligned using bowtie2 with flags `--very-sensitive`. Paired-end reads were used for downstream analysis.
The files were then converted to bam, downsampled to the lowest counts, indexed and the mitochondrial chromosome was removed using samtools. Duplicates were removed using Picard tools. The samples were processed to select for unique reads using samtools.
The peaks were identified using Genrich in ATACSeq mode and zebrafish genome size. The zebrafish genome size was estimated using faCount script from public utilities from UCSC.
To analyze the differential accessible regions, we used DiffBind using background and DeSeq2 normalization and a cutoff threshold of p<0.05. To annotate the peaks, we used ChIPSeeker. Transcription start site region as +/-1kb for annotation.
The bigwig files to visualize the peaks were made using bamCoverage in deepTools2
Genome_build: Ensembl GRCz11 danRer11 v102
Supplementary_files_format_and_content: BigWig and NarrowPeak Bedgraph files

organism: Danio rerio

source_name: cardiomyocytes

extract_protocol:
FAC sorted GFP+ cells were gently centrifuged and Hank’s solution was replaced by lysis buffer (10mM tris-HCL, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630). Cells were immediately centrifuged at 500 g for 10minutes at 4oC. The supernatant was discarded and replaced with the transposition reaction mix (Tn5 in TD buffer) for tagmentation, and incubated at 37oC for 30min. Afterwards, 500mM of EDTA was used for quenching. The solution was incubated for 30 minutes at 50oC. MgCl2 was added to a final concentration of 45mM. Samples were stored at 4oC before proceeding with PCR amplification
PCR amplification we used 1.25µl IDT® for Illumina Nextera DNA Unique Dual Indexes Set C, which contains two indexes premixed and 25 µL of Bioline MyFi Mix. This is in the place of the NEB Next HiFi PCR mix in your protocol. We performed the PCR as outlined. For PCR amplification 15 cycles were used due to the reduced amount of material. The amplified library was purified using the Qiagen PCR purification MinElute kit. This was followed by a 1 x volume AMPure XP bead-based clean-up according to manufacturer’s guidelines. The resulting libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit, respectively. The ATAC-Seq libraries were further quantified by qPCR using a Bioline JetSeq library Quantification Lo-ROX kit according to their guidelines. The libraries were pooled equimolar and further cleaned using AMPure XP beads as described above. The library pool was then again assessed for quantity and quality using fluorometry and capillary electrophoresis as described above.

value: cardiomyocytes

tag: strain

value: AB

tag: genotype

value: 5 dpf


title: A_S656

tag: donor id


title: ATAC-seq_Wt1b Over expression replicate 1


title: A_S655

tag: Sex


title: A_S654

tag: age


title: 48h_EtOH

type: RNA

city: Hirosaki

first: Kayo

last: Horie

address: 66-1 Hon-cho

country: Japan

institute: Hirosaki university

description: Gene expression ER transfect cell

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

source_name: ER transfect cell_EtOH_48h

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: The human endometrial cancer cell lines Ishikawa and HEC-50B were kindly provided by Dr. Kuramoto and Dr. Nishida. Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin (Thermo Fisher Scientific) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Medium were replaced in phenol-red free DMEM medium with 10% charcoal-treated FBS and 1% penicillin-streptomycin. The cells were treated with 1X10-7M E2 or ethano in 24h,48h,72h incubation period then collected.

value: Endometrial cancer cell

value: Ishikawa

tag: treatment

value: EtOH

tag: time point


title: 72h_EtOH

description: Gene expression ER transfect cell

source_name: ER transfect cell_EtOH_72h


title: HEC50B_Oh

description: Gene expression left untreated cell

source_name: HEC50B 0h

value: untreated

value: Ohr


title: 24h_EtOH

description: Gene expression ER transfect cell

source_name: ER transfect cell_EtOH_24h


title: 24h_E2

description: Gene expression ER transfect cell

source_name: ER transfect cell_E2_24h


title: ATAC-seq_Control replicate 3


title: 72h_E2

description: Gene expression ER transfect cell

source_name: ER transfect cell_E2_72h


title: A_S10037

source_name: PBMC

tag: library preparation group


title: ATAC-seq_Control replicate 1


title: ATAC-seq_Control replicate 2


title: Ishikawa_Oh

description: Gene expression left untreated cell

source_name: ishikawa 0h


title: A_S651


title: MS3_KIR+

value: KIR+ CD8 T


title: R_S7001

description: PBMC Young CD8_BulkNaive

tag: donor type

value: Young

value: Female

tag: cmv serostatus

value: Negative

tag: cell subset


title: A_S652

value: Male


title: CD-D-RNA

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
peak
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited txt files; data show differential peak and expression between the two groups

source_name: Liver tissue

extract_protocol: ChIP-seq, RNA-seq, ATAC-seq

treatment_protocol: mouse fed a high fat diet (60% kcal fat) or a control diet (18% kcal fat) for 10 weeks

value: mouse fed a control diet (18% fat)


title: A_S642


title: CD-C-RNA


title: A_S641


title: A_S640


title: CD-B-RNA


title: CD-A-RNA


title: A_S639


title: A_S395

source_name: Tumor


title: HFD-B-RNA

value: mouse fed a high fat diet (60% fat)


title: A_S394

value: No


title: HFD-C-RNA


title: ATAC-seq_Wt1b Over expression replicate 2


title: A_S392

value: Yes


title: A_S393


title: HFD-A-RNA


title: 48h_E2

description: Gene expression ER transfect cell

source_name: ER transfect cell_E2_48h

tag: cell line


title: Run4_G1

city: Irvine

first: Lupe

last: Gutierrez

address: 825 Health Sciences Rd D288

institute: University of California, Irvine

data_processing:
FASTQ files were trimmed using Trimmomatic version 0.35
The sequenced where aligned to the mm10 genome and counted using STAR version 2.5.2a
Genome_build: mm10

source_name: Mouse mammary gland

growth_protocol: All mouse lines were maintained and bred following the procedures that conform with and have been approved by the UC Irvine Institutional Animal Care and Use Committee (IACUC).

extract_protocol: G0 and G1 cells were sorted into RNA lysis buffer (R1050, Zymo Research), and RNAs were isolated and purified using Quick-RNA Microprep (R1050, Zymo Research) per manufacturer's protocol. RNAs were quantified using the NanoDrop ND-1000 spectrophotometer (ThermoFisher) and quality checked using the Agilent Bioanalyzer 2100 (Agilent). Library construction was performed according to the Illumina TruSeq® Stranded mRNA Sample Preparation Guide. One μg of total RNA was used and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented for 3 min, followed by reverse transcription to make cDNA. The resulting cDNA was cleaned using AMPure XP beads, end repaired, and the 3' ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter-ligated fragments were enriched by 9 PCR cycles. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA High Sensitivity Chip. The barcoded cDNA libraries were multiplexed on the Illumina HiSeq 4000 platform to yield 100-bp paired-end reads.

treatment_protocol: No treatment

tag: cell cycle phase


title: A_S391

tag: cell type


title: Run4_G0


title: A_S389


title: Run3_G1


title: Run3_G0


title: Run2_G1


title: A_S388


title: A_S653


title: A_S387


title: Run1_G1


title: A_S386


title: A_S385


title: Run1_G0


title: A_S384


title: A_S364


title: CD4_SDHB3_RNA

city: columbus

first: Ruoning

last: Wang

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

description: RNA seq of activated SDHB KO CD4 T cell

data_processing:
Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I.
RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Ribosomal RNA (rRNA) was removed using target-specific oligos combined with rRNA removal beads.
mRNA was fragmented and converted into ds cDNA. The adaptor-ligated cDNA was amplified by limit-cycle PCR. Quality of libraries was determined via Agilent 4200 Tapestation
sample was aligned to the GRCm38.p3 assembly of the Mus musculus reference from NCBI using version 2.6.0c of the RNA-seq aligner STAR
Genome_build: mm10

source_name: RNA seq of activated SDHB KO CD4 T cell

growth_protocol: Total CD4+ T cells isolated from mice were activated with IL-2 as well as plate-bound anti-mCD3/CD28 antibodies for 30hrs.

extract_protocol:
Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols at the nationwidechildrens hospital.

value: CD4 T cell

value: SDHB KO

value: activated


title: A_S361


title: CD4_SDHB1_RNA

description: RNA seq of activated SDHB KO CD4 T cell


title: A_S293


title: CD4_WT3_RNA

description: RNA seq of activated WT CD4 T cell

source_name: RNA seq of activated WT CD4 T cell

value: Wild Type


title: A_S295


title: HFD-D-RNA


title: CD4_WT2_RNA

description: RNA seq of activated WT CD4 T cell


title: A_S291


title: A_S289


title: CD4_WT1_RNA

description: RNA seq of activated WT CD4 T cell


title: CD4_SDHB_Active3_ATAC

description: ATAC seq of activated SDHB KO CD4 T cell

data_processing:
Cells were suspended in  tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components
ATAC-seq libraries were amplified with barcoded Nextera primers for 14 cycles, and excess primers were removed by size selection with AMPure XP beads.
reads are scanned for adaptor sequences and trimmed with cutadapt (version 2.3). Reads are then mapped to mm10 with bowtie2 (version 2.3.4.3). Properly aligned, non-mitochondrial read pairs were retained for peak calling with MACS2 (version 2.2.4).
Genome_build: mm10

growth_protocol: CD4+ T cells isolated from mice as naïve or activated for 30hrs.

extract_protocol:
Cells were suspended in  tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components
RNA libraries were prepared for sequencing using standard protocols at the nationwidechildrens hospital.
ATAC-seq libraries were amplified with barcoded Nextera primers for 14 cycles, and excess primers were removed by size selection with AMPure XP beads.


title: A_S290


title: A_S287


title: A_S288


title: CD4_SDHB_Active2_ATAC

source_name: ATAC seq of activated SDHB KO CD4 T cell


title: CD4_SDHB_Active1_ATAC


title: CD4_WT_Active3_ATAC

description: ATAC seq of activated WT CD4 T cell

source_name: ATAC seq of activated WT CD4 T cell


title: A_S285


title: CD4_WT_Active2_ATAC

description: ATAC seq of activated WT CD4 T cell


title: A_S284


title: A_S283


title: CD4_WT_Active1_ATAC

description: ATAC seq of activated WT CD4 T cell


title: A_S390


title: CD4_SDHB_Naive3_ATAC

description: ATAC seq of naive SDHB KO CD4 T cell

source_name: ATAC seq of naive SDHB KO CD4 T cell

value: naive


title: A_S281


title: CD4_SDHB_Naive2_ATAC

description: ATAC seq of naive SDHB KO CD4 T cell


title: A_S282


title: Run2_G0


title: MS1_KIR+

source_name: multiple sclerosis_KIR+ CD8 T

tag: subject status

value: multiple sclerosis

value: PBMC


title: A_S266


title: CD4_SDHB_Naive1_ATAC

description: ATAC seq of naive SDHB KO CD4 T cell


title: A_S265


title: CD4_SDHB2_RNA

description: RNA seq of activated SDHB KO CD4 T cell


title: CD4_WT_Naive2_ATAC

description: ATAC seq of naive WT CD4 T cell

source_name: ATAC seq of naive WT CD4 T cell


title: A_S264


title: A_S263


title: CD4_WT_Naive1_ATAC

description: ATAC seq of naive WT CD4 T cell


title: CKO3_S6_L008

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
. Raw reads were trimmed and filtered using sickle (v0.7)
remaining reads aligned to the mm10 reference genome with the subjunc aligner from the subread package (v2.0)
Resulting BAM files were used for gene counts against the ENSEMBL GRCm38 v95 annotation with the featureCounts tool also from the subread package
Differential Expression was performed with DESeq2 (v1.3). Enrichment analysis was performed with the clusterProfiler package (v3.16). All downstream analysis of differentially expressed genes were filtered by an adjusted p-value <= 0.05.

source_name: sciatic nerve

extract_protocol:
RNA was extracted from sciatic nerves using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen, 74106) with on-column DNase treatment. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA-sequencing, approximately 150 ng of total RNA per sample was used for library construction and sequenced using the Illumina HiSeq 4000 instrument.

value: C57 Bl

value: CnpCre Actl6afl/fl

value: postnatal day 3


title: A_S262

value: Female


title: CKO1_S4_L008


title: WT3_S3_L008

value: WT


title: A_S261


title: A_S8260

data_processing:
The fastqs were aligned to hg19 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.001. Peaks present in at least 2 samples were iincluded
Normalization and differential accessibility analysis was done with DESeq2.
Batch correction was performed using combat for library preparation group and sample location.
Genome_build: hg19
Supplementary_files_format_and_content: chromatin accessbility counts file

extract_protocol:
Transposed DNA was prepared with Tn5 (Illumina #FC-121-1031) as described in Buenrostro et al. 2013 using 0.1% Tween 20 instead of IGEPAL CA-630.Libraries were barcoded with Nextera Index Kit (Illumina # FC-121-1012)
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell

value: Older

tag: sample acquisition location

value: NIA


title: A_S8230

value: Male


title: WT2_S2_L008


title: A_S8212


title: A_S8211


title: Zeb1MSKO_9WK

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 2.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across all the libraries for the control and MSKO experiments.
Genome_build: mm10

extract_protocol: FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell

tag: tissue

value: Mouse mammary gland

tag: cell barcode suffix for aggr file


title: A_S8210


title: Control_9WK

tag: strain


title: A_S8209

tag: donor id


title: WT1_S1_L008

tag: genotype


title: A_S8207

tag: age

tag: Sex


title: Control_8WK


title: A_S8202