title: Live_seq.ASPC.not_treated.9_4.sample759


title: Live_seq.ASPC.DMIR_treated.9_4.sample756

status: Public on May 01 2022

type: SRA

city: Lausanne

first: Wanze

last: Chen

address: SV IBI-SV UPDELA, Station 19

country: Switzerland

institute: EPFL

description: merged data from different sequencing lanes

library_source: transcriptomic

data_processing:
Basecalls performed using bcl2fastq v2.19.1
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR 2.6.1c with parameters "--runMode alignReads --runThreadN 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMultimapNmax 1 --outSAMtype BAM Unsorted SortedByCoordinate"
The bam files were used for generate gene couting matrix using HTSeq with parameters "htseq-count -s no -m union -f"
Assembly: mm10
Supplementary files format and content: A comma-separated values file of read counting for all samples

molecule: polyA RNA

organism: Mus musculus

source_name: ASPC

growth_protocol: All these cells are culture in high-glucose DMEM medium (Life Technologies, Carlsbad, CA)  supplemented with 10% fetal bovine serum (FBS) (Gibco), and 1× penicillin/streptomycin solution (Life Technologies) in a 5% CO2 humidified atmosphere at 37 °C and maintained at less than 80% confluence before passaging

extract_protocol:
Live_seq
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752
Tn5 tagmentation

treatment_protocol:
DMIR_treated
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752

tag: batch


title: Live_seq.ASPC.not_treated.9_4.sample757

treatment_protocol:
not_treated
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: Live_seq.ASPC.not_treated.9_4.sample752


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample755

treatment_protocol:
LPS_treated
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: Live_seq.ASPC.DMIR_treated.9_4.sample751


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample772


title: Live_seq.IBA.not_treated.9_4.sample749

source_name: IBA


title: Live_seq.ASPC.DMIR_treated.9_4.sample750


title: Live_seq.ASPC.DMIR_treated.9_4.sample747


title: Live_seq.ASPC.DMIR_treated.9_4.sample746


title: Live_seq.ASPC.DMIR_treated.9_4.sample753


title: Live_seq.ASPC.not_treated.9_4.sample748


title: Live_seq.ASPC.not_treated.9_4.sample745


title: Live_seq.IBA.not_treated.9_4.sample744


title: Live_seq.ASPC.DMIR_treated.9_4.sample742


title: Live_seq.ASPC.DMIR_treated.9_4.sample743


title: Live_seq.IBA.not_treated.9_4.sample738


title: Live_seq.IBA.not_treated.9_4.sample739


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample740


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample785


title: Live_seq.ASPC.not_treated.9_4.sample735


title: Live_seq.ASPC.not_treated.9_4.sample736


title: Live_seq.ASPC.DMIR_treated.9_4.sample737


title: Live_seq.ASPC.not_treated.9_4.sample741


title: Live_seq.ASPC.not_treated.9_4.sample733


title: Live_seq.ASPC.not_treated.9_4.sample754


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample734


title: scRNA.Raw264.7_G9.not_treated.9_1.sample731

extract_protocol:
scRNA
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752
Tn5 tagmentation


title: Live_seq.ASPC.DMIR_treated.9_4.sample732


title: scRNA.ASPC.not_treated.9_1.sample728


title: scRNA.Raw264.7_G9.not_treated.9_1.sample730


title: scRNA.ASPC.not_treated.9_1.sample729


title: scRNA.Raw264.7_G9.not_treated.9_1.sample727


title: scRNA.ASPC.not_treated.9_1.sample726


title: scRNA.ASPC.DMIR_treated.9_1.sample725


title: scRNA.ASPC.not_treated.9_1.sample724


title: scRNA.ASPC.DMIR_treated.9_1.sample721


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample723


title: scRNA.Raw264.7_G9.not_treated.9_1.sample720


title: scRNA.Raw264.7_G9.not_treated.9_1.sample718


title: scRNA.Raw264.7_G9.not_treated.9_1.sample715


title: scRNA.IBA.not_treated.9_1.sample716


title: scRNA.ASPC.DMIR_treated.9_1.sample714


title: scRNA.ASPC.not_treated.9_1.sample712


title: scRNA.Raw264.7_G9.not_treated.9_1.sample713


title: scRNA.IBA.not_treated.9_1.sample710


title: scRNA.Raw264.7_G9.not_treated.9_1.sample709


title: scRNA.Raw264.7_G9.not_treated.9_1.sample708


title: scRNA.ASPC.DMIR_treated.9_1.sample707


title: scRNA.ASPC.DMIR_treated.9_1.sample706


title: scRNA.ASPC.DMIR_treated.9_1.sample705


title: scRNA.ASPC.not_treated.9_1.sample704


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample702


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample701


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample703


title: scRNA.ASPC.DMIR_treated.9_1.sample722


title: scRNA.Raw264.7_G9.not_treated.9_1.sample700


title: scRNA.ASPC.not_treated.9_1.sample699


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample698


title: scRNA.Raw264.7_G9.not_treated.9_1.sample697


title: scRNA.ASPC.not_treated.9_1.sample694


title: scRNA.ASPC.not_treated.9_1.sample719


title: scRNA.ASPC.DMIR_treated.9_1.sample717


title: scRNA.ASPC.not_treated.9_1.sample695


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample691


title: scRNA.ASPC.not_treated.9_1.sample711


title: scRNA.IBA.not_treated.9_1.sample689


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample688


title: scRNA.ASPC.not_treated.9_1.sample687


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample690


title: scRNA.Raw264.7_G9.not_treated.9_1.sample686


title: scRNA.Raw264.7_G9.not_treated.9_1.sample685


title: scRNA.ASPC.DMIR_treated.9_1.sample684


title: scRNA.ASPC.not_treated.9_1.sample683


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample679


title: scRNA.IBA.not_treated.9_1.sample680


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample682


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample678


title: scRNA.IBA.not_treated.9_1.sample696


title: scRNA.IBA.not_treated.9_1.sample675


title: scRNA.ASPC.not_treated.9_1.sample676


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample674


title: scRNA.IBA.not_treated.9_1.sample671


title: scRNA.ASPC.DMIR_treated.9_1.sample672


title: scRNA.ASPC.not_treated.9_1.sample677


title: scRNA.Raw264.7_G9.not_treated.9_1.sample692


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample673


title: scRNA.ASPC.DMIR_treated.9_1.sample693


title: scRNA.ASPC.not_treated.9_1.sample668


title: scRNA.Raw264.7_G9.not_treated.9_1.sample666


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample667


title: scRNA.IBA.not_treated.9_1.sample669


title: scRNA.ASPC.not_treated.9_1.sample664


title: scRNA.IBA.not_treated.9_1.sample663


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample661


title: scRNA.ASPC.not_treated.9_1.sample662


title: scRNA.IBA.not_treated.9_1.sample659


title: scRNA.ASPC.not_treated.9_1.sample656


title: scRNA.ASPC.DMIR_treated.9_1.sample681


title: scRNA.IBA.not_treated.9_1.sample655


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample654


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample660


title: scRNA.IBA.not_treated.9_1.sample658


title: scRNA.Raw264.7_G9.not_treated.9_1.sample652


title: scRNA.ASPC.DMIR_treated.9_1.sample651


title: scRNA.IBA.not_treated.9_1.sample670


title: scRNA.Raw264.7_G9.not_treated.9_1.sample649


title: scRNA.ASPC.DMIR_treated.9_1.sample665


title: scRNA.Raw264.7_G9.not_treated.9_1.sample648


title: scRNA.Raw264.7_G9.not_treated.9_1.sample647


title: scRNA.IBA.not_treated.9_1.sample645


title: scRNA.ASPC.not_treated.9_1.sample646


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample642


title: scRNA.IBA.not_treated.9_1.sample643


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample641


title: scRNA.IBA.not_treated.9_1.sample644


title: scRNA.IBA.not_treated.9_1.sample657


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample639


title: scRNA.ASPC.not_treated.9_1.sample637


title: scRNA.ASPC.not_treated.9_1.sample640


title: scRNA.ASPC.not_treated.9_1.sample638


title: scRNA.Raw264.7_G9.not_treated.9_1.sample636


title: scRNA.Raw264.7_G9.not_treated.9_1.sample634


title: scRNA.Raw264.7_G9.not_treated.9_1.sample632


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample630


title: scRNA.IBA.not_treated.9_1.sample628


title: scRNA.ASPC.not_treated.9_1.sample629


title: scRNA.ASPC.DMIR_treated.9_1.sample650


title: scRNA.ASPC.DMIR_treated.9_1.sample627


title: scRNA.IBA.not_treated.9_1.sample626


title: scRNA.ASPC.not_treated.9_1.sample625


title: scRNA.IBA.not_treated.9_1.sample631


title: scRNA.IBA.not_treated.9_1.sample623


title: scRNA.Raw264.7_G9.not_treated.9_1.sample622


title: scRNA.ASPC.not_treated.9_1.sample621


title: scRNA.IBA.not_treated.9_1.sample624


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample619


title: scRNA.ASPC.DMIR_treated.9_1.sample618


title: scRNA.Raw264.7_G9.not_treated.9_1.sample620


title: scRNA.ASPC.DMIR_treated.9_1.sample617


title: scRNA.ASPC.not_treated.9_1.sample613


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample635


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample612


title: scRNA.Raw264.7_G9.not_treated.9_1.sample614


title: scRNA.Raw264.7_G9.not_treated.9_1.sample608


title: scRNA.IBA.not_treated.9_1.sample611


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample633


title: scRNA.ASPC.DMIR_treated.9_1.sample606


title: scRNA.Raw264.7_G9.not_treated.9_1.sample610


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample653


title: scRNA.Raw264.7_G9.not_treated.9_1.sample607


title: scRNA.ASPC.not_treated.9_1.sample616


title: scRNA.ASPC.not_treated.9_1.sample605


title: scRNA.ASPC.DMIR_treated.9_1.sample602


title: scRNA.ASPC.DMIR_treated.9_1.sample603


title: scRNA.Raw264.7_G9.not_treated.9_1.sample601


title: scRNA.IBA.not_treated.9_1.sample615


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample599


title: scRNA.Raw264.7_G9.not_treated.9_1.sample598


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample597


title: scRNA.ASPC.DMIR_treated.9_1.sample596


title: scRNA.Raw264.7_G9.not_treated.9_1.sample594


title: scRNA.Raw264.7_G9.not_treated.9_1.sample600


title: scRNA.Raw264.7_G9.not_treated.9_1.sample593


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample595


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample590


title: scRNA.Raw264.7_G9.not_treated.9_1.sample591


title: scRNA.ASPC.DMIR_treated.9_1.sample609


title: scRNA.Raw264.7_G9.not_treated.9_1.sample587


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample588


title: scRNA.ASPC.not_treated.9_1.sample589


title: scRNA.IBA.not_treated.9_1.sample585


title: scRNA.IBA.not_treated.9_1.sample583


title: scRNA.IBA.not_treated.9_1.sample604


title: scRNA.IBA.not_treated.9_1.sample581


title: scRNA.ASPC.DMIR_treated.9_1.sample586


title: scRNA.IBA.not_treated.9_1.sample584


title: scRNA.IBA.not_treated.9_1.sample576


title: scRNA.Raw264.7_G9.not_treated.9_1.sample582


title: scRNA.ASPC.not_treated.9_1.sample580


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample575


title: scRNA.ASPC.not_treated.9_1.sample573


title: scRNA.IBA.not_treated.9_1.sample571


title: scRNA.ASPC.DMIR_treated.9_1.sample572


title: scRNA.Raw264.7_G9.not_treated.9_1.sample570


title: scRNA.ASPC.not_treated.9_1.sample592


title: scRNA.ASPC.not_treated.9_1.sample568


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample567


title: scRNA.Raw264.7_G9.not_treated.9_1.sample565


title: scRNA.ASPC.DMIR_treated.9_1.sample566


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample564


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample562


title: scRNA.ASPC.DMIR_treated.9_1.sample579


title: scRNA.Raw264.7_G9.not_treated.9_1.sample569


title: scRNA.IBA.not_treated.9_1.sample561


title: scRNA.ASPC.DMIR_treated.9_1.sample560


title: scRNA.IBA.not_treated.9_1.sample578


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample559


title: scRNA.Raw264.7_G9.not_treated.9_1.sample558


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample577


title: scRNA.ASPC.not_treated.9_1.sample574


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample554


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample556


title: scRNA.ASPC.DMIR_treated.9_1.sample553


title: scRNA.ASPC.DMIR_treated.9_1.sample557


title: scRNA.IBA.not_treated.9_1.sample555


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample550


title: scRNA.ASPC.not_treated.9_1.sample552


title: scRNA.IBA.not_treated.9_1.sample547


title: scRNA.IBA.not_treated.9_1.sample549


title: scRNA.IBA.not_treated.9_1.sample548


title: scRNA.ASPC.DMIR_treated.9_1.sample546


title: scRNA.ASPC.not_treated.9_1.sample563


title: scRNA.Raw264.7_G9.not_treated.9_1.sample544


title: scRNA.IBA.not_treated.9_1.sample542


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample543


title: scRNA.IBA.not_treated.9_1.sample539


title: scRNA.ASPC.DMIR_treated.9_1.sample538


title: scRNA.IBA.not_treated.9_1.sample541


title: scRNA.IBA.not_treated.9_1.sample540


title: scRNA.ASPC.not_treated.9_1.sample536


title: scRNA.ASPC.not_treated.9_1.sample537


title: scRNA.IBA.not_treated.9_1.sample551


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample531


title: scRNA.ASPC.not_treated.9_1.sample530


title: scRNA.ASPC.DMIR_treated.9_1.sample533


title: scRNA.IBA.not_treated.9_1.sample532


title: scRNA.ASPC.not_treated.9_1.sample534


title: scRNA.Raw264.7_G9.not_treated.9_1.sample535


title: scRNA.Raw264.7_G9.not_treated.9_1.sample529


title: scRNA.IBA.not_treated.9_1.sample528


title: scRNA.Raw264.7_G9.not_treated.9_1.sample525


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample523


title: scRNA.ASPC.DMIR_treated.9_1.sample545


title: scRNA.Raw264.7_G9.not_treated.9_1.sample522


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample526


title: scRNA.ASPC.not_treated.9_1.sample527


title: scRNA.IBA.not_treated.9_1.sample521


title: scRNA.ASPC.not_treated.9_1.sample519


title: scRNA.ASPC.DMIR_treated.9_1.sample518


title: scRNA.ASPC.not_treated.9_1.sample517


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample516


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample514


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample515


title: scRNA.ASPC.not_treated.8_8.sample513


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample512


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample511


title: Live_seq.ASPC.not_treated.8_8.sample510


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample509


title: scRNA.ASPC.not_treated.8_8.sample508


title: scRNA.Raw264.7_G9.not_treated.8_8.sample507


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample503


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample506


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample505


title: scRNA.Raw264.7_G9.not_treated.9_1.sample524


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample502


title: Live_seq.IBA.not_treated.8_8.sample500


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample498


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample499


title: scRNA.Raw264.7_G9.LPS_treated.9_1.sample520


title: scRNA.ASPC.not_treated.8_8.sample501


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample495


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample496


title: Live_seq.IBA.not_treated.8_8.sample497


title: Live_seq.IBA.not_treated.8_8.sample494


title: Live_seq.ASPC.not_treated.8_8.sample492


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample486


title: Live_seq.ASPC.not_treated.8_8.sample487


title: scRNA.Raw264.7_G9.not_treated.8_8.sample490


title: scRNA.ASPC.not_treated.8_8.sample489


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample491


title: Live_seq.IBA.not_treated.8_8.sample504


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample484


title: scRNA.ASPC.not_treated.8_8.sample485


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample493


title: scRNA.IBA.not_treated.8_8.sample483


title: Live_seq.ASPC.not_treated.8_8.sample482


title: Live_seq.ASPC.not_treated.8_8.sample481


title: scRNA.ASPC.not_treated.8_8.sample479


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample478


title: scRNA.ASPC.not_treated.8_8.sample476


title: scRNA.ASPC.not_treated.8_8.sample480


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample471


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample468


title: Live_seq.IBA.not_treated.8_8.sample472


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample469


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample464


title: scRNA.IBA.not_treated.8_8.sample470


title: scRNA.Raw264.7_G9.not_treated.8_8.sample474


title: Live_seq.ASPC.not_treated.8_8.sample473


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample467


title: Live_seq.ASPC.not_treated.8_8.sample461


title: Live_seq.ASPC.not_treated.8_8.sample475


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample460


title: Live_seq.IBA.not_treated.8_8.sample451


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample459


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample466


title: scRNA.IBA.not_treated.8_8.sample458


title: scRNA.IBA.not_treated.8_8.sample455


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample457


title: scRNA.Raw264.7_G9.not_treated.8_8.sample465


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample477


title: scRNA.IBA.not_treated.8_8.sample463


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample462


title: scRNA.IBA.not_treated.8_8.sample456


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample452


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample454


title: Live_seq.ASPC.not_treated.8_8.sample450


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample447


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample449


title: scRNA.Raw264.7_G9.not_treated.8_8.sample448


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample488


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample439


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample446


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample445


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample440


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample444


title: scRNA.ASPC.not_treated.8_8.sample438


title: scRNA.ASPC.not_treated.8_8.sample442


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample430


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample441


title: scRNA.IBA.not_treated.8_8.sample434


title: scRNA.IBA.not_treated.8_8.sample436


title: Live_seq.IBA.not_treated.8_8.sample443


title: Live_seq.IBA.not_treated.8_8.sample453


title: Live_seq.ASPC.not_treated.8_8.sample437


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample426


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample431


title: scRNA.Raw264.7_G9.not_treated.8_8.sample435


title: Live_seq.ASPC.not_treated.8_8.sample432


title: Live_seq.ASPC.not_treated.8_8.sample429


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample423


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample420


title: scRNA.Raw264.7_G9.not_treated.8_8.sample419


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample421


title: Live_seq.IBA.not_treated.8_8.sample418


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample428


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample416


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample417


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample415


title: scRNA.Raw264.7_G9.not_treated.8_8.sample422


title: Live_seq.IBA.not_treated.8_8.sample414


title: scRNA.ASPC.not_treated.8_8.sample425


title: scRNA.ASPC.not_treated.8_8.sample424


title: scRNA.ASPC.not_treated.8_8.sample433


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample413


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample412


title: Live_seq.ASPC.not_treated.8_8.sample408


title: scRNA.Raw264.7_G9.not_treated.8_8.sample407


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample427


title: scRNA.ASPC.not_treated.8_8.sample406


title: Live_seq.IBA.not_treated.8_8.sample411


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample409


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample410


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample405


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample402


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample404


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample403


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample399


title: Live_seq.ASPC.not_treated.8_8.sample401


title: scRNA.ASPC.not_treated.8_8.sample400


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample397


title: scRNA.IBA.not_treated.8_8.sample395


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample396


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample393


title: scRNA.Raw264.7_G9.not_treated.8_8.sample392


title: scRNA.Raw264.7_G9.not_treated.8_8.sample394


title: scRNA.IBA.not_treated.8_8.sample391


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample390


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample389


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample386


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample388


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample385


title: Live_seq.ASPC.not_treated.8_8.sample387


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample379


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample378


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample381


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample380


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample376


title: scRNA.ASPC.not_treated.8_8.sample374


title: scRNA.IBA.not_treated.8_8.sample373


title: scRNA.IBA.not_treated.8_8.sample398


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample372


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample369


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample370


title: scRNA.IBA.not_treated.8_8.sample375


title: Live_seq.IBA.not_treated.8_8.sample366


title: scRNA.Raw264.7_G9.not_treated.8_8.sample377


title: scRNA.Raw264.7_G9.LPS_treated.8_8.sample360


title: Live_seq.ASPC.not_treated.8_8.sample365


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample363


title: scRNA.Raw264.7_G9.not_treated.8_8.sample362


title: scRNA.Raw264.7_G9.not_treated.8_8.sample357


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample364


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample368


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample383


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample361


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample384


title: Live_seq.Raw264.7_G9.LPS_treated.8_8.sample353


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample382


title: Live_seq.IBA.not_treated.8_8.sample359


title: Live_seq.ASPC.not_treated.8_8.sample350


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample349

value: scRNA


title: scRNA.IBA.not_treated.8_8.sample371


title: Live_seq.ASPC.not_treated.8_8.sample351


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample367


title: Live_seq.Raw264.7_G9.not_treated.8_8.sample358


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample348


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample346


title: Live_seq.IBA.not_treated.8_8.sample356


title: scRNA.Raw264.7_G9.not_treated.8_8.sample355


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample345


title: scRNA.IBA.not_treated.scRNA.sample342


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample344


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample343


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample338


title: Live_seq.Raw264.7_G9.not_treated.7.sample334


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample335


title: Live_seq.Raw264.7_G9.not_treated.7.sample339


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample337


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample333


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample331


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample332


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample340


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample330


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample347


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample328


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample325


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample324


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample327


title: scRNA.IBA.not_treated.scRNA.sample326


title: scRNA.IBA.not_treated.scRNA.sample323


title: Live_seq.Raw264.7_G9.not_treated.7.sample322


title: scRNA.IBA.not_treated.scRNA.sample320


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample321


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample319


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample341


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample318


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample336


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample317


title: scRNA.IBA.not_treated.scRNA.sample314


title: scRNA.IBA.not_treated.scRNA.sample329


title: Live_seq.IBA.not_treated.7.sample313


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample315


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample316


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample310


title: scRNA.IBA.not_treated.scRNA.sample311


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample308


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample307


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample312


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample306


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample299


title: Live_seq.Raw264.7_G9.not_treated.7.sample300


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample304


title: scRNA.IBA.not_treated.scRNA.sample301


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample303


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample305


title: scRNA.IBA.not_treated.scRNA.sample298


title: scRNA.IBA.not_treated.scRNA.sample297


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample295


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample296


title: scRNA.IBA.not_treated.scRNA.sample294


title: Live_seq.Raw264.7_G9.not_treated.7.sample293


title: scRNA.IBA.not_treated.scRNA.sample292


title: scRNA.IBA.not_treated.scRNA.sample309


title: scRNA.IBA.not_treated.scRNA.sample291


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample289


title: scRNA.IBA.not_treated.scRNA.sample284


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample288


title: scRNA.IBA.not_treated.scRNA.sample285


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample287


title: scRNA.IBA.not_treated.scRNA.sample283


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample302


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample279


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample286


title: scRNA.IBA.not_treated.scRNA.sample282


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample281


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample280


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample278


title: scRNA.IBA.not_treated.scRNA.sample276


title: Live_seq.Raw264.7_G9.not_treated.7.sample277


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample275


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample272


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample271


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample273


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample270


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample269


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample268


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample266


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample290


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample267


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample265


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample264


title: Live_seq.IBA.not_treated.7.sample259


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample260


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample258


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample256


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample263


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample261


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample262


title: Live_seq.IBA.not_treated.7.sample274


title: scRNA.IBA.not_treated.scRNA.sample257


title: Live_seq.IBA.not_treated.7.sample250


title: scRNA.IBA.not_treated.scRNA.sample248


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample249


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample253


title: scRNA.IBA.not_treated.scRNA.sample251


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample245


title: scRNA.IBA.not_treated.scRNA.sample246


title: scRNA.IBA.not_treated.scRNA.sample242


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample243


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample238


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample240


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample255


title: scRNA.IBA.not_treated.scRNA.sample254


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample239


title: scRNA.IBA.not_treated.scRNA.sample235


title: scRNA.IBA.not_treated.scRNA.sample237


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample236


title: scRNA.IBA.not_treated.scRNA.sample252


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample233


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample247


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample231


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample230


title: scRNA.IBA.not_treated.scRNA.sample229


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample228


title: scRNA.IBA.not_treated.scRNA.sample224


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample227


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample225


title: scRNA.IBA.not_treated.scRNA.sample223


title: scRNA.IBA.not_treated.scRNA.sample226


title: scRNA.IBA.not_treated.scRNA.sample222


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample221


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample220


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample241


title: scRNA.IBA.not_treated.scRNA.sample244


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample219


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample218


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample216


title: scRNA.IBA.not_treated.scRNA.sample234


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample232


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample217


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample215


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample213


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample214


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample212


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample209


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample208


title: scRNA.IBA.not_treated.scRNA.sample207


title: scRNA.Raw264.7_G9.not_treated.8_8.sample352


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample210


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample211


title: scRNA.IBA.not_treated.8_8.sample354


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample204


title: scRNA.IBA.not_treated.scRNA.sample205


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample203


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample202


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample199


title: scRNA.IBA.not_treated.scRNA.sample198


title: scRNA.IBA.not_treated.scRNA.sample200


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample206


title: Live_seq.IBA.not_treated.7.sample197


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample193


title: Live_seq.IBA.not_treated.7.sample194


title: scRNA.IBA.not_treated.scRNA.sample195


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample196


title: scRNA.IBA.not_treated.scRNA.sample192


title: scRNA.IBA.not_treated.scRNA.sample191


title: scRNA.IBA.not_treated.scRNA.sample188


title: scRNA.IBA.not_treated.scRNA.sample189


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample190


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample187


title: scRNA.IBA.not_treated.scRNA.sample186


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample185


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample184


title: Live_seq.Raw264.7_G9.not_treated.7.sample183


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample181


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample201


title: scRNA.IBA.not_treated.scRNA.sample180


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample178


title: scRNA.IBA.not_treated.scRNA.sample182


title: Live_seq.Raw264.7_G9.not_treated.7.sample177


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample175


title: scRNA.IBA.not_treated.scRNA.sample179


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample174


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample172


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample169


title: scRNA.IBA.not_treated.scRNA.sample173


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample171


title: scRNA.IBA.not_treated.scRNA.sample176


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample168


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample170


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample167


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample165


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample166


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample164


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample163


title: scRNA.IBA.not_treated.scRNA.sample162


title: scRNA.IBA.not_treated.scRNA.sample161


title: scRNA.IBA.not_treated.scRNA.sample160


title: scRNA.IBA.not_treated.scRNA.sample158


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample159


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample157


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample156


title: scRNA.IBA.not_treated.scRNA.sample155


title: Live_seq.Raw264.7_G9.not_treated.7.sample153


title: scRNA.IBA.not_treated.scRNA.sample151


title: Live_seq.IBA.not_treated.7.sample150


title: Live_seq.IBA.not_treated.7.sample152


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample149


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample148


title: scRNA.IBA.not_treated.scRNA.sample146


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample147


title: Live_seq.Raw264.7_G9.not_treated.7.sample144


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample145


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample142


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample141


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample140


title: scRNA.IBA.not_treated.scRNA.sample139


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample138


title: scRNA.IBA.not_treated.scRNA.sample143


title: Live_seq.IBA.not_treated.7.sample136


title: Live_seq.IBA.not_treated.7.sample137


title: scRNA.IBA.not_treated.scRNA.sample135


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample134


title: scRNA.IBA.not_treated.scRNA.sample133


title: Live_seq.Raw264.7_G9.not_treated.7.sample132


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample131


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample129


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample130


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample128


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample126


title: Live_seq.Raw264.7_G9.not_treated.7.sample122


title: Live_seq.IBA.not_treated.7.sample124


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample125


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample118


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample121


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample120


title: scRNA.IBA.not_treated.scRNA.sample117


title: Live_seq.Raw264.7_G9.not_treated.7.sample115


title: Live_seq.Raw264.7_G9.not_treated.7.sample114


title: scRNA.IBA.not_treated.scRNA.sample112


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample116


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample123


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title: scRNA.IBA.not_treated.scRNA.sample110


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample119


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample108


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample111


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title: scRNA.IBA.not_treated.scRNA.sample107


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title: scRNA.Raw264.7_G9.not_treated.scRNA.sample104


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample102


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample105


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title: scRNA.IBA.not_treated.scRNA.sample99


title: scRNA.IBA.not_treated.scRNA.sample101


title: scRNA.IBA.not_treated.scRNA.sample127


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample100


title: scRNA.IBA.not_treated.scRNA.sample109


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample92


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample95


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample96


title: scRNA.IBA.not_treated.scRNA.sample93


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample94


title: scRNA.IBA.not_treated.scRNA.sample91


title: Live_seq.Raw264.7_G9.not_treated.7.sample97


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample90


title: Live_seq.Raw264.7_G9.not_treated.7.sample84


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample87


title: scRNA.IBA.not_treated.scRNA.sample85


title: scRNA.IBA.not_treated.scRNA.sample86


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample89


title: scRNA.IBA.not_treated.scRNA.sample80


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample83


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample88


title: scRNA.IBA.not_treated.scRNA.sample79


title: scRNA.IBA.not_treated.scRNA.sample77


title: scRNA.IBA.not_treated.scRNA.sample82


title: Live_seq.Raw264.7_G9.not_treated.7.sample78


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample74


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample72


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample73


title: scRNA.IBA.not_treated.scRNA.sample71


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample75


title: scRNA.IBA.not_treated.scRNA.sample68


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample70


title: Live_seq.IBA.not_treated.7.sample67


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample66


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample69


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample81


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample65


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample64


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample76


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample63


title: scRNA.IBA.not_treated.scRNA.sample57


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample55


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample56


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample54


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample48


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample47


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample46


title: Live_seq.Raw264.7_G9.not_treated.7.sample51


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample49


title: Live_seq.Raw264.7_G9.LPS_treated.7.sample53


title: Live_seq.IBA.not_treated.7.sample61


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample62


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample45


title: scRNA.IBA.not_treated.scRNA.sample42


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample43


title: Live_seq.Raw264.7_G9.not_treated.7.sample39


title: scRNA.IBA.not_treated.scRNA.sample36


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample40


title: scRNA.IBA.not_treated.scRNA.sample37


title: scRNA.IBA.not_treated.scRNA.sample38


title: scRNA.IBA.not_treated.scRNA.sample34


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample58


title: scRNA.IBA.not_treated.scRNA.sample52


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample59


title: scRNA.IBA.not_treated.scRNA.sample33


title: Live_seq.Raw264.7_G9.not_treated.7.sample35


title: scRNA.IBA.not_treated.scRNA.sample60


title: scRNA.IBA.not_treated.scRNA.sample32


title: scRNA.IBA.not_treated.scRNA.sample50


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample44


title: scRNA.IBA.not_treated.scRNA.sample26


title: scRNA.Raw264.7_G9.not_treated.scRNA.sample25


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample41


title: Live_seq.Raw264.7_G9.not_treated.6.sample24


title: Live_seq.Raw264.7.not_treated.5Reseq.sample23


title: scRNA.IBA.not_treated.scRNA.sample27


title: Live_seq.Raw264.7_G9.LPS_treated.6.sample22


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample28


title: Live_seq.Raw264.7_G9.LPS_treated.6.sample20


title: Live_seq.Raw264.7_G9.not_treated.6.sample21


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample19


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample15


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample14


title: Live_seq.Raw264.7_G9.LPS_treated.6.sample17


title: Live_seq.Raw264.7_G9.not_treated.6.sample13


title: Live_seq.Raw264.7_G9.not_treated.6.sample12


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample31


title: Live_seq.Raw264.7_G9.not_treated.6.sample10


title: Live_seq.Raw264.7_G9.LPS_treated.6.sample8


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample11


title: Live_seq.Raw264.7_G9.not_treated.6.sample6


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample9


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample30


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample5


title: scRNA.Raw264.7_G9.LPS_treated.scRNA.sample29


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample7


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample4


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample18


title: Live_seq.Raw264.7_G9.not_treated.6.sample2


title: RNA_4.3_4

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa

description: differentially expressed genes, Processed_counts_star

data_processing:
Paired-end FastQ files were downloaded from the sequencing facility’s website and processed through FastQC  (Galaxy Version 0.72+galaxy1) for quality control
Reads were trimmed to remove adaptor sequences using Trim Galore (Galaxy Version 0.6.3)
Bowtie2 (Galaxy Version 2.3.4.3+ galaxy 0) was used to map the reads against the hg19 genome assembly. The --very-sensitive-local parameter was applied. Any reads not considered the primary alignment or without mapped mate were excluded by using samtools (version 1.3.1).
For generation of BogWig files the deepTools package (version 3.3.0) was used. With the help of the ‘bamCompare’ command the controls IgG and were subtracted from the CUT&RUN tracks. The resulting BigWig files were normalised using the RPKM option. Other options applied were ‘--binSize 50’  and ‘--centerReads’ for highest possible resolution and sharper signals.
Assembly: Hg19
Supplementary files format and content: BigWig files representing anti-TFAP2A, anti-MITF, anti-H3K27Ac, anti-H3K4Me3 and anti-H3K27Me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing and ATAC-Sequening SkMel28 WT and TFAP2A;TFAP2C mutant cells lines

molecule: total RNA

organism: Homo sapiens

growth_protocol: SK-MEL-28 cell lines were cultured in RPMI media contaning 10% FBS and 1% PS. Cells were maintained in log-phase growth (approximately 80% confluent) and media changed every 24 hour.

extract_protocol:
We performed anti-TFAP2A, anti-MITF, anti-H3K27Ac, anti-H3K4Me3 and anti-H3K27Me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing and ATAC-Sequening in wild-type and TFAP2A; TFAP2C double mutant SK-MEL-28 cell lines essentially as described (Skene and Henikoff 2017).
CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit (Roche). Quality control post-library amplification was conducted using the 2100 Bioanalyzer for fragment analysis. Libraries were pooled to equimolar concentrations and sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 instrument.
ATAC-seq was performed according to (Buenrostro et al., 2015; Liu et al., 2020) with minor alterations. Briefly, 70,000 TFAP2-KO cells (clone 2.12 and clone 4.3, four replicates each) and WT cells (four replicates) were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed directly on nuclei using 25 µl tagmentation reaction mix (Tagment DNA Buffer #15027866, Tagment DNA Enzyme #15027865 from Illumina Tagment DNA kit #20034210). Tagged DNA was subjected to PCR amplification and library indexing, using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs #M0451S) with Nextera DNA CD Indexes (Illumina #20015882), according to the following program: 72 ̊C for 5 minutes; 98 ̊C for 30 seconds; 12 cycles of 98 ̊C for 10 seconds, 63 ̊C for 30 seconds, and 72 ̊C for 1 minute. The PCR product was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter #A63881). Library quality was assessed using a BioAnalyzer 2100 High Sensitivity DNA Chip (Agilent Technologies). All DNA libraries that exhibited a nucleosome pattern were pooled and processed for 150bp paired-end sequencing.
RNA-seq was performed on four replicate RNA-seq experiments were performed on TFAP2-KO cells (clone 2.12 and clone 4.3) and WT cells. Total RNA was extracted by direct cell lysis using the RNeasy Plus Mini Kit with QiaShredder (Qiagen #47134). RNA samples with an RNA integrity number (RIN) above nine were used for library generation and 150 bp paired-end sequencing on the Illumina HiSeq2500 platform (Novogene, Sacramento, CA). FASTQ sequence files were processed using FastQC (Babraham Bioinformatics) for quality control, and reads were trimmed using Trim Galore Version 0.6.3 (Developed by Felix Krueger at the Babraham Institute) and subsequently aligned to human genome assembly hg19 (GRCh37) using STAR. The output of the --quantMode GeneCounts function of STAR was used for the calculation of differential transcript expression using DESeq2 [1].The rlog function was used to generate log2-transformed normalized counts. Adjusted p-value < 0.05 was used as the threshold for statistically significant differences.

tag: type

value: Melanoma cell line

tag: cell line background

value: SkMel28 cell line

tag: genotype


title: RNA_4.3_3


title: RNA_4.3_2


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample16


title: RNA_Clone2.12_4


title: RNA_Clone2.12_3


title: RNA_WT3

value: WT


title: RNA_Clone2.12_1


title: RNA_4.3_1


title: RNA_WT1


title: RNA_Clone2.12_2


title: RNA_WT4


title: RNA_WT2


title: Vegt stage 9 ChIP-seq

status: Public on Apr 29 2022

city: Irvine

first: Kitt

middle: D.

last: Paraiso

state: CA

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

library_source: genomic

data_processing:
ChIP-seq peak calling and IDR: Reads were aligned to the X. tropicalis genome v9.0 (Mitros et al., 2019; Karimi et al., 2018) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called using Macs v2.0.10 (Zhang et al., 2008) with default options.
Assembly: Xenopus tropicalis v9.0
Supplementary files format and content: Peak calls

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: Whole embryos

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Vegt. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).

tag: tissue type

value: whole embryos at N&F stage 9

tag: strain

value: Nigerian strain


title: Ventx2 stage 11 ChIP-seq

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Ventx2. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).

value: whole embryos at N&F stage 11


title: Smad1 stage 10 ChIP-seq

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Smad1. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).

value: whole embryos at N&F stage 10


title: Sox7 stage 8 ChIP-seq

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Sox7. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).

value: whole embryos at N&F stage 8


title: Vegt stage 10 ChIP-seq


title: Sia1 stage 10 ChIP-seq

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Sia1. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).


title: YTHDF3_RIP_rep2

status: Public on Apr 26 2022

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

description:
RIP_seq.featureCounts.output.txt
DF3_RIP_DESeq.txt

data_processing:
Unique Molecular Identifiers (UMIs) were extracted from read2 using UMI-tools (v1.1.1) with the option: --bc-pattern=NNNNNNN
Adapters were trimmed Cutadapt (v3.4), removing the first 6 nucleotides of read2 and the adapter sequences with using the options: -j 4 -U 6 -m 18
Reads were mapped to mouse genome (mm10) and duplicates marked using STAR v2.7.7a and the following options: ' --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterMismatchNmax 25 outFilterMatchNminOverLread 0.33 outSAMattributes All , followed sorting with STAR with the following options: '--runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdentical'
Duplicate reads were removed from the bam files using UMI-tools dedup in paired-end mode
Raw gene counts were calculated using featureCounts v2.0.1 with the following options: "-s 2 -p -t exon -g gene_id -O -M". Neurite enrichment was calculated with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Result of DESeq2 analysis for enrichment in each YTHDF RIP samples

source_name: Hippocampal Neurons

growth_protocol: Primary hippocampal neurons isolated from neonate mouse were plated on poly-D-lysine coated plates and maintained in growth media (Neurobasal A, B27, 0.6mM Glutamax) for 14 days.

extract_protocol:
For each replicate, approximately 1.5x106 cultured neurons growing in a 6 well plates were used. Cells lysates (25mM Tris-Cl pH7.4; 150mM NaCl; 2.5mM EDTA, 0.5mM DTT; 0.5% NP-50) were used for RIP using antibodies targeting the endogenous YTHDF1, YTHDF2 or YTHDF3 antibody. Total RNA was extracted from a fraction of the cell lysate (Input samples) or eluted from antibody coupled beads using 1mL of TRIZOL reagent (Thermo) and the RNA was extracts according to the manufacturer’s protocol. RNA was resuspended in Nuclease-Free water.
9ng of total RNA was used for library preparation with the SMARTer Stranded Total RNA-Seq Kit V3 (Takara).

tag: rip antibody


title: Mix1 stage 10 ChIP-seq

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Mix1. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).


title: D3_OSKM (scRNA-seq)

status: Public on Apr 28 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: OSKM reprogrammed stem cells

library_source: transcriptomic single cell

data_processing:
SC-RNA-seq libraries were generated from each time point using the 10X Genomics. The cellranger-3.0.2, https://github.com/10XGenomics/cellranger was used for mapping of the 10x single cell RNA-seq data. Read1 data of pooled cells were split into single-cell data using the barcode sequences contained in the first 16 bps. The next 10 bps were recorded as unique molecular identifiers (UMIs). Read2 with 75 bp were aligned to the mm9 reference genome
We used Seurat (V 3.1.4) to pre-processing the data and perform clustering. The function 'FindAllMarkers' to identify the marker genes for each of the clusters in the UMAP representation
Assembly: mm9
Supplementary files format and content: feature, matrix and barcode tables

source_name: embryonic stem cells

extract_protocol:
Single cell RNA libraries were prepared using Chromium Single Cell 3' Library Kit v2 (10X genomics, 120234) and the generated libraries were sequenced using Illumina NextSeq 500 platform.
Reprogrammable cells at day 3 were prepared as instructed in the 10X Genomics cell preparation guidelines. Briefly, cells were trypsinized and centrifuged at 1000 RPM for 3 minutes, then were washed twice with PBSx1 containing 0.04% BSA and cleaned from cell debris and large clumps by filtering throw mesh paper. Next, resuspended cells were subjected to dead cell removal kit (MACS, 130-090-101) to remove any non-viable cells. Cell viability were estimated using trypan blue staining. Cells were then resuspended in PBSx1 with 0.04% BSA at the concentration 1000 cells/µl and 4000 cells from each condition were subjected to 10x Genomics.

tag: cell type

value: embryonic stem cells

tag: days from treatment

tag: reprogramming factors

value: OSKM


title: YTHDF3_RIP_rep3


title: YTHDF3_RIP_rep1


title: YTHDF1_RIP_rep3

description:
RIP_seq.featureCounts.output.txt
DF1_RIP_DESeq.txt


title: Live_seq.Raw264.7_G9.not_treated.6.sample1


title: Input_rep1


title: Live_seq.Raw264.7.LPS_treated.5Reseq.sample3


title: Input_rep2


title: YTHDF2_RIP_rep2

description:
RIP_seq.featureCounts.output.txt
DF2_RIP_DESeq.txt


title: YTHDF1_RIP_rep2


title: YTHDF2_RIP_rep3


title: YTHDF1_RIP_rep1


title: WT_Soma_KCl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed

data_processing:
Adapters were trimmed from the 3' end of reads using Flexbar with the following options: --adapter-trim-end LEFT --adapter-revcomp ON --adapter-revcomp-end RIGHT --htrim-left GT --htrim-right CA --htrim-min-length 3 --htrim-max-length 5 --htrim-max-first  --htrim-adapter --min-read-length 2
Reads were mapped to mouse genome (mm10) and duplicates marked using STAR v2.7.7a and the following options: ' --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterMismatchNmax 30 --outSAMattributes All --outFilterScoreMinOverLread 0.25 --outFilterMatchNminOverLread 0.25', followed by running STAR with the following options: '--runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdentical'
For RNAseq analysis, raw gene counts were calculated using featureCounts v2.0.1 with the following options: "-M -p -t exon -g gene_id". Neurite enrichment was calculated with DESeq2.
For DART-seq, bam files were parsed to build a matrix of coverage at each position in the transcriptome for each library. C-to-U mutations in WT cells were compared to background editing in Mettl3-/- libraries. m6A sites were called as those found in a RAC motif, with a at least 3 mutations, 50 covering reads, 1-95% C-to-U editing, more than 1.5-fold editing and foun in at least 2 biological replicates.
To compare editing levels across compartments in DART-seq experiments, the cummulative editing rates in each transcript was fitted in a binomial generalized linear model to obtain log2FoldChange and P-values (Wald-test).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Result of DESeq2 analysis for enrichment in neurites over soma for under untreated or KCl-treated conditions.
Supplementary_files_format_and_content: For DART-seq: bed files with position of m6A sites identified under each condition.
Supplementary_files_format_and_content: For DART-seq: Tab separated table containing the differential editing analysis in Soma and neurites for all transcript with mapped m6A sites.

growth_protocol: Primary hippocampal neurons isolated from neonate mouse were plated on PET microporous membranes (Millipore) coated with poly-D-lysine and laminin and maintained in growth media (Neurobasal A, B27, 0.6mM Glutamax) for 15 days.

extract_protocol:
Soma and neurites fractions were respectively isolated from the top and bottom of the microporous membrane using a cell scraper. RNA extraction was performed with the Qiagen RNeasy Mini plus kit.
For all samples, 50ng of total RNA was used for library preparation with the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina. For DART-seq samples, 50ng of total RNA was incubated with 250ng of recombinant APOBEC1-YTH protein for 6 h at 37C prior to library preparation.

treatment_protocol: Cells were transduced with AAV particles expressing Cre-P2A-dTomato at DIV7 (50,000 vg/cell). Cells were treated with 1 µM tetrodotoxin and 50 µM D-AP5 for 16 hours at DIV14. For treated cells, KCl was added to a final concentration of 55 mM for 2 hours prior to RNA extraction.

tag: compartment

value: Soma

tag: treatment

value: Treated with KCl for 2 h.

tag: library type

value: DART-seq


title: Input_rep3


title: WT_Neurite_KCl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed

value: Neurite


title: Mettl3_KO_Soma_KCl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed


title: WT_Soma_Ctrl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed

value: untreated


title: YTHDF2_RIP_rep1


title: Mettl3_KO_Neurite_Ctrl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Neurite_KCl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Soma_KCl_rep2

description:
featureCounts.output.txt
DESeq2_KCl_treated_neurite_enrichment.txt

value: RNAseq


title: WT_Neurite_KCl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Neurite_Ctrl_rep2

description:
featureCounts.output.txt
DESeq2_untreated_neurite_enrichment.txt


title: Mettl3_KO_Soma_Ctrl_rep2


title: WT_Soma_KCl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: WT_Soma_KCl_rep2


title: WT_Neurite_Ctrl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed


title: WT_Soma_Ctrl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed


title: WT_Soma_Ctrl_rep2


title: WT_Neurite_Ctrl_rep1


title: Mettl3_KO_Soma_KCl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Neurite_Ctrl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Neurite_KCl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Soma_Ctrl_rep1


title: Mettl3_KO_Neurite_Ctrl_rep1


title: Mettl3_KO_Soma_Ctrl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Neurite_KCl_rep2


title: WT_Neurite_KCl_rep1


title: WT_Neurite_KCl_rep2


title: WT_Soma_KCl_rep1


title: WT_Neurite_Ctrl_rep2


title: WT_Soma_Ctrl_rep1


title: WT_Neurite_Ctrl_DART_rep1

description:
DART_analysis_results.txt
m6A_sites.bed


title: Mettl3_KO_Neurite_KCl_rep1


title: WT hap + WTVeh hap multiplexed (hashtags)

status: Public on Apr 21 2022

city: Cambridge

first: Michael

last: Hemann

state: MA

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

description:
HTO
10X Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.
HTO fraction of the reads were assigned to the mRNA reads based on cell barcodes using the DemuxEM algorithm (https://www.nature.com/articles/s41592-020-0905-x, https://github.com/lilab-bcb/demuxEM) to demultiplex samples that were processed within the same 10X run.
Cells were filtered for singlets as well as cells that express at least 200 genes.
Assembly: hg19 concatenated (PDX samples) or GRCh38 (KBM7)
Supplementary files format and content: gene-by-cell matrix (comma-separated values, CSV) of counts mapping to each gene for each demultiplexed cell barcode (PDX samples)
Supplementary files format and content: Metadata file (CSV) containing batch info and sample name for each demultiplexed cell barcode (PDX samples)
Supplementary files format and content: gene-by-cell matrix (MTX format) of counts mapping to each gene for each cell barcode (KBM7 samples)
Supplementary files format and content: List of cell barcodes used in 10X experiments

molecule: other

source_name: multiplexed sample: bone marrow and spleen

extract_protocol:
For patient-derived xenograft (PDX) samples, spleen and bone marrow cells are collected from tumor-bearing mice and filtered through a 70-micron filter to generate single-cell suspensions. For KBM7 cells, fresh cell culture is collected for the desired number of cells, centrifuged to remove medium and cells are resuspended in PBS containing BSA prior to processing using the 10X Genomics scRNA-seq pipeline below.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with SPRI beads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.   For PDX samples, cells were incubated with antibodies conjugated with hashtag oligonucleotides (HTOs) for sample multiplexing prior to 10X Genomics pipelines, and SI-PCR was performed separately on the HTO cDNA fragment after size selection. mRNA and HTO libraries for each sample were mixed at a 0.975:0.025 ratio prior to sequencing.   The PCR primers used in the library construction processes are:  SI-PCR: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC  HTO cDNA PCR additive primer: GTGACTGGAGTTCAGACGTGTGCTC  Illumina TruSeq D701_s primer for amplifying HTO (8 Xs represent sample barcode):: CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGC  Hashtag oligo read 2 (conjugated to TotalSeq-A antibodies for sample multiplexing within the same 10X run):  GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTXXXXXXXXXXXXBAAAAAAAAAAAAAAAAAAAAAAAAAAAA*A*A  where the 12 Xs are hashtag barcodes (see sample sheet above), B is C/G/T (not A), and * denotes phosphorothioate bond.

tag: tissue

value: multiplexed sample:bone marrow and spleen

value: patient-derived xenograft leukemia

value: Multiplexed sample:no treatment and vehicle treatment

tag: totalseq-a antibody_tag

value: TTCCGCCTCTCTTTG (no treatment bone marrow), AGTAAGTTCAGCGTA (no treatment spleen), TGTCTTTCCTGCCAG (vehicle bone marrow), CTCCTCTGCAATTAC (vehicle spleen)


title: Mettl3_KO_Soma_Ctrl_DART_rep2

description:
DART_analysis_results.txt
m6A_sites.bed


title: KBM7 diploid

description:
mRNA
10X Genomics

tag: cell line

value: Chronic Myeloid Leukemia

value: no treament


title: Mettl3_KO_Soma_KCl_rep1


title: KBM7 haploid

description:
mRNA
10X Genomics

value: no treatment


title: WTTX hap (hashtags)

description:
HTO
10X Genomics

value: combination chemotherapy

value: TTCCGCCTCTCTTTG (bone marrow), AGTAAGTTCAGCGTA (spleen)


title: WTTX dip (hashtags)

description:
HTO
10X Genomics

value: AGTAAGTTCAGCGTA (bone marrow), CTCCTCTGCAATTAC (spleen)


title: 02_CO_42_HC_02

status: Public on Apr 13 2022

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

description: This sample was sequenced in two runs to reach enough sequencing depth, which resulted in four raw files.

data_processing:
Raw reads were cleaned by fastp v0.19.4
Mapped by hisat2 v2.2.0 and annotated according to the GENCODE v37
Only expressed genes (mean count across all samples > 10) were included in the count matrix. Counts were normalized by TMM method (for normalized count matrix).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv. The first column, gene_name, is the standard gene symbol (HGNC or MGI-approved gene symbols; if no official gene symbol exists, Havana clone-based name is used). The remaining columns contain the expression level for each sample.

source_name: skin biopsy

extract_protocol:
Total RNA was extracted and processed by Eurofins using the INVIEW Transcriptome service (Aarhus, Denmark)
Paired-end (2x150bp) sequencing (Illumina, CA) resulted in an average sequencing depth of 35M reads per sample.

value: skin

tag: skin type

value: HC

tag: gender

value: female

tag: scorad

tag: easi

value: arm


title: 02_AD_06_NL_02

value: NL


title: 04_AD_12_LS_02

value: LS

value: leg


title: 03_AD_22_NL_02

value: male


title: 03_CO_46_HC_02


title: WTTX hap

description:
mRNA
10X Genomics

value: multiplexed sample:bone marrow and spleen

value: patient-derived xenograft leukemia


title: WTTX dip

description:
mRNA
10X Genomics


title: WT hap + WTVeh hap multiplexed

description:
mRNA
10X Genomics

value: Multiplexed sample:no treatment and vehicle treatment

value: TTCCGCCTCTCTTTG (no treatment bone marrow), AGTAAGTTCAGCGTA (no treatment spleen), TGTCTTTCCTGCCAG (vehicle bone marrow), CTCCTCTGCAATTAC (vehicle spleen)


title: 01_CO_41_HC_01


title: 05_CO_46_HC_01


title: 01_AD_03_LS_02


title: 01_CO_52_HC_02


title: 01_AD_24_NL_01


title: 01_AD_23_LS_01


title: 02_CO_41_HC_02


title: WT dip + WTVeh dip multiplexed

description:
mRNA
10X Genomics

value: TGTCTTTCCTGCCAG (no treatment bone marrow), CTCCTCTGCAATTAC (no treatment spleen), AAGTATCGTTTCGCA (vehicle bone marrow), GGTTGCCAGATGTCA (vehicle spleen)


title: 01_CO_45_HC_01


title: 01_AD_22_LS_01


title: 01_AD_12_NL_02

value: feet


title: 02_CO_46_HC_01


title: 04_AD_12_LS_01


title: 01_AD_16_NL_01


title: 02_AD_02_NL_01


title: WT dip + WTVeh dip multiplexed (hashtags)

description:
HTO
10X Genomics


title: 03_AD_13_NL_01


title: 01_AD_14_NL_01


title: 03_AD_02_LS_01


title: 03_CO_33_HC_02


title: scRNA.IBA.not_treated.scRNA.sample154

tag: batch

value: scRNA


title: 02_AD_17_LS_01


title: 05_AD_22_NL_02


title: 04_AD_15_NL_02


title: 01_AD_13_LS_01


title: 02_AD_12_NL_02


title: 01_AD_19_LS_02

value: hand


title: 01_AD_28_LS_01


title: 01_AD_20_LS_02


title: 01_AD_28_NL_01


title: 05_CO_52_HC_02


title: 05_AD_16_NL_01


title: 01_CO_37_HC_02


title: 05_AD_06_NL_01


title: 05_AD_16_LS_01


title: 04_CO_52_HC_02


title: 05_CO_39_HC_01


title: 05_AD_02_LS_01


title: 01_AD_03_LS_01


title: 04_CO_48_HC_02


title: 05_AD_15_NL_01


title: 04_CO_33_HC_02


title: 05_AD_02_LS_02


title: 04_AD_25_LS_01


title: 04_AD_15_NL_01


title: 04_CO_42_HC_01


title: 04_AD_15_LS_01


title: 04_AD_16_LS_01


title: 04_AD_02_LS_02


title: 03_CO_56_HC_01


title: 04_AD_06_LS_01


title: 04_AD_12_NL_01


title: 03_AD_25_NL_02


title: 03_CO_33_HC_01


title: 04_AD_22_NL_01


title: 03_CO_43_HC_01


title: 03_AD_25_LS_01


title: 03_AD_16_NL_02


title: 03_AD_16_LS_02


title: 03_AD_15_NL_02


title: 03_AD_23_LS_02


title: 03_AD_15_NL_01


title: D3_GETM (scRNA-seq)

description: GETM reprogrammed stem cells

value: embryonic stem cells

value: GETM


title: 05_AD_13_LS_02

value: skin


title: 02_CO_56_HC_02

value: HC


title: 02_AD_14_LS_01

value: female


title: 02_AD_02_NL_02

value: NL

value: arm


title: 02_CO_33_HC_02

value: elbow


title: 01_CO_46_HC_02


title: 01_CO_54_HC_02


title: 01_CO_58_HC_02

value: male


title: 02_AD_23_LS_02

value: LS


title: 01_CO_52_HC_01


title: 01_CO_50_HC_01


title: 02_AD_09_NL_02


title: 02_AD_13_LS_02


title: 01_CO_59_HC_01


title: 01_CO_56_HC_01


title: 02_AD_14_NL_01


title: 02_AD_16_LS_01


title: 02_AD_13_LS_01


title: 01_CO_51_HC_02


title: 02_CO_46_HC_02


title: 01_CO_35_HC_01


title: 02_AD_06_LS_02


title: 01_CO_47_HC_01


title: 02_AD_22_NL_02

value: leg


title: 02_CO_52_HC_02


title: 01_CO_31_HC_01


title: 01_AD_30_NL_02


title: 01_AD_28_NL_02


title: 01_AD_26_LS_02


title: 01_AD_29_NL_02


title: 02_AD_13_NL_01


title: 01_AD_25_LS_01


title: 01_AD_23_NL_02


title: 01_AD_14_LS_02


title: 01_AD_06_LS_02


title: 01_AD_02_LS_02


title: 05_CO_48_HC_02


title: 01_AD_08_NL_02


title: 05_AD_06_NL_02


title: 04_CO_46_HC_02


title: 04_AD_16_NL_02


title: 01_AD_11_NL_02


title: 01_AD_02_NL_01


title: 01_AD_08_LS_01


title: 01_AD_14_LS_01


title: 05_AD_12_LS_02


title: 05_CO_33_HC_02


title: 04_AD_16_LS_02


title: 05_AD_12_NL_02


title: 05_AD_16_NL_02


title: 01_AD_07_LS_01


title: 05_AD_13_NL_02


title: 05_CO_33_HC_01


title: 04_AD_13_LS_02


title: 03_CO_54_HC_02


title: 04_AD_13_NL_02


title: 03_CO_46_HC_01


title: 03_CO_48_HC_01


title: 04_AD_25_NL_01


title: 04_AD_16_NL_01


title: 03_CO_52_HC_01


title: 04_AD_06_NL_02


title: 03_CO_42_HC_01


title: 03_AD_23_NL_02


title: 03_AD_13_LS_01


title: 03_AD_16_NL_01


title: 03_AD_22_NL_01


title: 03_AD_12_LS_02


title: 03_AD_02_NL_01


title: 02_CO_54_HC_02


title: 02_CO_52_HC_01


title: 02_CO_45_HC_01


title: 02_AD_23_LS_01


title: 02_AD_23_NL_01


title: 02_AD_17_LS_02


title: 02_CO_33_HC_01


title: 01_CO_59_HC_02


title: 02_AD_12_LS_01


title: 02_AD_06_LS_01


title: 02_AD_15_LS_01


title: 02_AD_11_LS_02


title: 01_CO_33_HC_01


title: 02_AD_02_LS_02


title: 01_CO_40_HC_01


title: 01_CO_55_HC_01


title: 02_AD_06_NL_01


title: 02_AD_17_NL_01


title: 01_AD_25_NL_01


title: 01_CO_45_HC_02


title: 01_CO_48_HC_01


title: 01_AD_25_LS_02


title: 01_AD_18_NL_02

value: wrist


title: 01_AD_19_LS_01


title: 01_AD_18_NL_01


title: 01_AD_15_NL_02


title: 01_AD_18_LS_02


title: 01_AD_15_LS_01


title: 03_AD_06_NL_01


title: 01_CO_31_HC_02


title: 01_AD_26_LS_01


title: 01_AD_12_LS_02


title: 01_AD_07_NL_01


title: 01_AD_06_LS_01


title: 01_AD_03_NL_01


title: 01_AD_09_NL_02


title: 01_AD_01_NL_02


title: 01_AD_11_LS_02


title: 01_AD_02_NL_02


title: 05_CO_46_HC_02


title: 05_CO_45_HC_01


title: 01_AD_11_NL_01


title: 01_AD_06_NL_01


title: 01_AD_24_NL_02


title: 05_CO_56_HC_01


title: 01_AD_12_NL_01


title: 05_CO_52_HC_01


title: 01_AD_03_NL_02


title: 05_CO_42_HC_01


title: 05_AD_22_NL_01


title: 05_CO_43_HC_02


title: 05_AD_22_LS_01


title: 05_AD_23_LS_02


title: 05_AD_12_NL_01


title: 04_CO_48_HC_01


title: 04_CO_45_HC_02


title: 04_CO_52_HC_01


title: 01_AD_05_NL_02


title: 04_CO_42_HC_02


title: 05_CO_42_HC_02


title: 04_CO_39_HC_02


title: 04_AD_25_NL_02


title: 04_CO_39_HC_01


title: 04_AD_13_LS_01


title: 04_AD_06_NL_01


title: 03_CO_42_HC_02


title: 03_CO_39_HC_02


title: 03_AD_15_LS_01


title: 05_AD_25_LS_02


title: 04_AD_12_NL_02


title: 03_AD_22_LS_01


title: 03_AD_13_NL_02


title: 03_AD_16_LS_01


title: 03_AD_25_LS_02


title: 02_CO_43_HC_02


title: 02_CO_48_HC_01


title: 03_AD_06_LS_02


title: 02_AD_23_NL_02


title: 05_AD_15_LS_01


title: 02_AD_22_LS_02


title: 02_AD_16_NL_02


title: 02_AD_16_NL_01


title: 02_AD_15_NL_02


title: 04_AD_02_NL_02


title: 02_AD_09_LS_01


title: 02_AD_15_NL_01


title: 02_AD_13_NL_02


title: 01_CO_49_HC_01


title: 01_CO_51_HC_01


title: 04_AD_25_LS_02


title: 01_CO_43_HC_01


title: 03_AD_02_LS_02


title: 01_CO_43_HC_02


title: 04_AD_22_NL_02


title: 01_CO_39_HC_01


title: 01_CO_37_HC_01


title: 01_CO_41_HC_02


title: 01_CO_44_HC_01


title: 01_AD_30_LS_01


title: 01_CO_48_HC_02


title: 02_AD_25_NL_01


title: 01_CO_38_HC_02


title: 01_CO_35_HC_02


title: 01_AD_29_NL_01


title: 01_AD_27_LS_02


title: 01_CO_36_HC_01


title: 01_AD_27_NL_01


title: 01_AD_26_NL_02


title: 01_AD_24_LS_01


title: 01_AD_23_NL_01


title: 01_AD_20_NL_02


title: 01_AD_20_NL_01


title: 01_AD_19_NL_01


title: 01_AD_17_NL_02


title: 01_CO_46_HC_01


title: 01_AD_17_NL_01


title: 01_AD_17_LS_02


title: 01_AD_16_NL_02


title: 01_AD_13_NL_02


title: 01_AD_12_LS_01


title: 01_AD_16_LS_02


title: 01_AD_29_LS_02


title: 01_AD_10_NL_01


title: 01_AD_13_NL_01


title: 05_CO_48_HC_01


title: 01_AD_09_LS_02


title: 01_AD_08_NL_01


title: 05_CO_45_HC_02


title: 01_AD_04_LS_02


title: 05_AD_13_LS_01


title: 05_AD_25_LS_01


title: 05_AD_13_NL_01


title: 05_AD_16_LS_02


title: 01_AD_09_LS_01


title: 05_AD_15_NL_02


title: 05_AD_12_LS_01


title: 01_AD_10_LS_01


title: 01_AD_18_LS_01


title: 05_AD_02_NL_01


title: 04_CO_46_HC_01


title: 04_CO_33_HC_01


title: 04_CO_45_HC_01


title: 01_AD_11_LS_01


title: 04_AD_06_LS_02


title: 04_AD_02_LS_01


title: 03_CO_52_HC_02


title: 03_CO_54_HC_01


title: 03_CO_45_HC_02


title: 05_CO_43_HC_01


title: 03_CO_43_HC_02


title: 03_CO_48_HC_02


title: 03_AD_06_LS_01


title: 02_CO_43_HC_01


title: 02_CO_42_HC_01


title: 02_AD_25_LS_02


title: 02_AD_25_NL_02


title: 02_AD_25_LS_01


title: 02_CO_54_HC_01


title: 03_AD_06_NL_02


title: 02_AD_14_NL_02


title: 02_AD_14_LS_02


title: 02_AD_16_LS_02


title: 04_CO_54_HC_01


title: 02_AD_09_NL_01


title: 05_AD_06_LS_02


title: 02_AD_12_NL_01


title: 02_AD_09_LS_02


title: 02_AD_02_LS_01


title: 01_CO_60_HC_02


title: 01_CO_60_HC_01


title: 01_CO_55_HC_02


title: 01_CO_50_HC_02


title: 03_AD_25_NL_01


title: 01_CO_47_HC_02


title: 03_AD_12_NL_02


title: 01_CO_40_HC_02


title: 01_CO_49_HC_02


title: 01_CO_39_HC_02


title: 01_CO_34_HC_01


title: 02_AD_22_NL_01


title: 01_CO_32_HC_01


title: 01_AD_30_LS_02


title: 01_CO_32_HC_02


title: 01_AD_25_NL_02


title: 01_AD_30_NL_01


title: 01_AD_27_NL_02


title: 01_AD_20_LS_01


title: 01_AD_19_NL_02


title: 01_AD_13_LS_02


title: 01_AD_10_LS_02


title: 01_AD_15_NL_01


title: 01_AD_09_NL_01


title: 01_AD_14_NL_02


title: 01_AD_06_NL_02


title: 01_AD_07_LS_02


title: 01_AD_05_LS_01


title: 01_AD_05_LS_02


title: 01_AD_04_NL_02


title: 01_AD_04_LS_01


title: 01_CO_38_HC_01


title: hif1_05_3

status: Public on Mar 16 2022

city: Vancouver

first: Stefan

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

country: Canada

institute: UBC

data_processing:
Sequenced reads were trimmed for low-quality sequences using Trimmomatic version 0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, then aligned to aligned to the NCBI reference genome WBcel235 WS277 using Salmon version 0.9.1 61 with parameters -l A -p 8 --gcBias.
Transcript-level read counts were imported into R and summed into gene-level read counts using tximport. Genes not expressed at a level greater than 1 count per million (CPM) reads in at least three of the samples were excluded from further analysis.
The filtered gene-level read counts were then normalized using the trimmed mean of M‐values (TMM) in edgeR to adjust samples for differences in library size.
Genome_build: WBcel235
Supplementary_files_format_and_content: Tab-delimited text files include TMM values for each Sample
Supplementary_files_format_and_content: Comma-delimited matrix table with raw read counts for every gene and every sample
Supplementary_files_format_and_content: Comma-delimited matrix table with TMM normalized counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: whole worm RNA

growth_protocol: Synchronized L1 wild-type, nhr-49(nr2041), and hif-1(ia4) worms were allowed to grow on OP50 plates for 48 hr to L4 stage, then either kept in 21% O2 or transferred to 0.5% O2 for 3 hr.

extract_protocol:
RNA was extracted from whole worms using Trizol and RNeasy Mini Kit (Qiagen #74106) according to the manufacturer’s protocol
Construction of strand-specific mRNA sequencing libraries and sequencing (75bp PET) was performed on an Illumina HiSeq 2500 machine

treatment_protocol: L4 worms were either kept in 21% O2 or transferred to 0.5% O2 for 3 hr. Hypoxic conditions were maintained using continuous flow chambers. Compressed gas tanks (5000 ppm O2 balanced with N2) were certified as standard to within 2% of indicated concentration from Praxair Canada (Delta, BC). Oxygen flow was regulated using Aalborg rotameters (Aalborg Instruments and Controls, Inc., Orangeburg, NY, USA). Hypoxic chambers (and room air controls) were maintained in a 20°C incubator for the duration of the experiments.

tag: genotype

tag: oxygen exposure


title: hif1_05_2


title: 01_AD_02_LS_01


title: hif1_21_3


title: 01_AD_22_LS_02


title: 01_AD_16_LS_01


title: hif1_21_1


title: nhr49_05_2


title: nhr49_05_1


title: nhr49_21_3


title: nhr49_21_2


title: 01_AD_08_LS_02


title: WT_05_3


title: hif1_21_2


title: nhr49_21_1


title: 01_CO_33_HC_02


title: WT_05_2


title: WT_21_3


title: 01_AD_05_NL_01


title: WT_21_1


title: WT_05_1


title: WT_21_2


title: nhr49_05_3


title: CDC1 donor A

status: Public on Mar 05 2022

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description:
hef_all_counts.txt.gz
hef_idc_cdc1_counts.txt.gz
hdf_idc_cdc1_counts.txt.gz

data_processing:
The Cell Ranger v2.2.0 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a hg38 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-26bp.
Scater R library was used for QC
The resulting expression matrix was used as input to the Seurat library v3
Genome_build: hg38
Supplementary_files_format_and_content: 10x Digital Gene Expression matrix.  Each  column is named in the following way: Sample name,  underscore, cellular barcode.

source_name: Dendritic cell type 1

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v2 Reagent Kit from 10x Genomics.

treatment_protocol: Cells were sorted by FACS.

value: Dendritic cell type 1

tag: sorted cells

value: wildtype

tag: transduction

tag: time

tag: presence or absence of cytokines


title: hif1_05_1


title: hiDC d9 CD45+HLA-DR+ donor A rep1

source_name: human embryonic fibroblast

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

value: HEF

tag: cell type

value: human embryonic fibroblast

value: 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.

value: Cells were collected 9 days after viral transduction

value: Absence


title: CDC2 donor A

source_name: Dendritic cell type 2

value: Dendritic cell type 2


title: PDC donor A

source_name: Plasmacytoid dendritic cell

value: PDC

value: Plasmacytoid dendritic cell


title: hiDC d9 CD45+HLA-DR- donor C

description:
CD45+HLA-DR-
hef_all_counts.txt.gz

data_processing:
The Cell Ranger v2.2.0 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a hg38 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-28bp.
Scater R library was used for QC
The resulting expression matrix was used as input to the Seurat library v4
Genome_build: hg38
Supplementary_files_format_and_content: 10x Digital Gene Expression matrix

tag: presence of absence of cytokines


title: hiDC d3 donor A rep1

value: Cells were collected 3 days after viral transduction


title: hiDC d6 donor C

description:
CD45+
hef_all_counts.txt.gz

value: Cells were collected 6 days after viral transduction


title: hiDC d3 donor C

description:
CD45+
hef_all_counts.txt.gz


title: HEF donor A rep1

description:
hef_all_counts.txt.gz
hef_idc_cdc1_counts.txt.gz

value: unsorted cells


title: hiDC d9 CD45+HLA-DR+ donor C

description:
CD45+HLA-DR+
hef_all_counts.txt.gz


title: HEF donor C

description:
unsorted cells
hef_all_counts.txt.gz


title: hiDC d9 CD45+HLA-DR+ donor B

description:
CD45+HLA-DR+
hef_all_counts.txt.gz


title: hiDC d6 donor B

description:
CD45+
hef_all_counts.txt.gz


title: hiDC d3 donor B

description:
CD45+
hef_all_counts.txt.gz


title: hiDC d9 CD45+HLA-DR- donor B

description:
CD45+HLA-DR-
hef_all_counts.txt.gz


title: HEF donor B

description:
unsorted cells
hef_all_counts.txt.gz


title: hiDC d9 CD45+HLA-DR- donor A

description:
CD45+HLA-DR-
hef_all_counts.txt.gz


title: hiDC d9 CD45+HLA-DR+CD226+ donor A


title: hiDC d9 CD45+HLA-DR+ donor A rep2

description:
CD45+HLA-DR+
hef_all_counts.txt.gz


title: hiDC d3 donor A rep2

description:
CD45+
hef_all_counts.txt.gz


title: HEF donor A rep2

description:
unsorted cells
hef_all_counts.txt.gz


title: hiDC d6 donor A

description:
CD45+
hef_all_counts.txt.gz


title: PDC donor C

description:
HLA-DR+CD11C-CD123+
hef_all_counts.txt.gz


title: CDC2 donor C

description:
HLA-DR+CD11C+CD141-CD1C+
hef_all_counts.txt.gz


title: CDC2 donor B


title: CDC1 donor B

description:
HLA-DR+CD11C+CD141+
hef_all_counts.txt.gz
hef_idc_cdc1_counts.txt.gz
hdf_idc_cdc1_counts.txt.gz


title: CDC1 donor C


title: PDC donor B


title: hiDC d9_SFFV-PIB+cyt (HDF)

source_name: human dermal fibroblast

value: HDF

value: human dermal fibroblast

value: Presence


title: hiDC d9_SFFV-PIB (HDF)


title: HDF


title: hiDC d9_tetO-PIB+cyt


title: hiDC d9_SFFV-PIB


title: hiDC d9_SFFV-PIB+cyt


title: OT3

status: Public on Mar 01 2022

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Genome_build: http://ftp.ensembl.org/pub/release-104/fasta/tetraodon_nigroviridis/dna/Tetraodon_nigroviridis.TETRAODON8.dna.toplevel.fa.gz
Supplementary_files_format_and_content: excel files containing read count, fpkm, log2 fold change, p-value

organism: Dichotomyctere nigroviridis

source_name: green-spotted puffer

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number (RIN) ≥ 7 were used for RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencng was performed by Novogene.

value: ovary

tag: treatment

value: PNX-treated


title: OT5

tag: tissue


title: OT4


title: OT2


title: OC6

value: Control


title: OC5


title: OC2


title: HT5

value: hypothalamus


title: OC1


title: HT3


title: HT2


title: HT6


title: HC5


title: OC3


title: HC4


title: HT1


title: HC2


title: OT6


title: HC1


title: HC3


title: HC6


title: GBS_infected_human_placental_macs, hpm_E_C4H11

status: Public on Feb 18 2022

city: New York

first: Itai

last: Yanai

state: NY

address: 435 East. 30th St.

institute: NYU Langone Health

data_processing:
Basecalls was done using cellranger mkfastq V3.0.0
alignment, filtering, counting and umi counting was doe using cellranger count V3.0.0
Genome_build: human GRCh38
Supplementary_files_format_and_content: expression matrix of umi counts
Supplementary_files_format_and_content: h5

source_name: human placental macrophages

growth_protocol: human placental cells were dissociated into suspension, macrophages were selected by CD14 expression and cultured overnight

extract_protocol:
human placental macrophages were isolated by selection of CD14+ expression by magnetic beads from single cell suspension
10x single cell RAN seq V3

treatment_protocol: macrophages were infected with GBS or PBS control. After 1 hour excess GBS was washed away and cells were incubated for an additional 3 hours.

value: placental

value: macrophage

tag: agent

value: GBS


title: AITL_b3_3823_scADT

status: Public on Feb 25 2022

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

data_processing:
Pre-processes including debarcoding and unique molecular identifier (UMI) counting were done by Cell Ranger version 3.1.0 (10x Genomics). After we got gene count table, Seurat version 4.1.0 was applied for downstream analyses. Cells with unique feature counts less than 300 or mitochondrial counts greater than 10% were filtered out. The resulting dataset was normalized and scaled using the ‘NormalizeData’ and ‘ScaleData’ functions in Seurat. We applied Principal Component Analysis (PCA) on scale data and used the first 30 PCs as input to do Uniform Manifold Approximation and Projection (UMAP). Cell clustering was done by Louvain algorithm.
Genome_build: hg38
Supplementary_files_format_and_content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count

molecule: protein

source_name: lymph node

extract_protocol:
Minced tissues which were stored in 1ml of  freezing media (10% DMSO in FBS) were quick thawed in 37C water bath for 1-2 mins. Tissues and freezing media were transferred to 15ml falcon tube and topped with 4ml PBS, spun at 240 xg, 3min. Discarded the solution and tissues were dissociated into single cells using Tumor Dissociation Kit human (Miltenyi Biotec, 130-095-929) according to the manufacturer instruction. One to four million (1-4 x106) live cells were used to stain with the following antibodies. Human TruStain FcX were used to block unspecific binding of primary antibodies.
Single cell suspensions were stained with LIVE/DEAD Fixable stain (ThermoFisher) following the manufacturer’s protocol, then with a panel of TotalSeq-C antibodies (BioLegend). Live cells were sorted on a BD Influx fluorescence-activated cell sorter, centrifuged, and resuspended in PBS + 1% BSA to approximately 2000 cells/µL. Cells were counted and 10,000-15,000 cells were loaded for droplet encapsulation with the Chromium Single Cell 5’ Kit v1 or v1.1 (10x Genomics), targeting capture of 5,000-8,000 cells. The manufacturer’s protocols were followed for both kits, with minor adjustments to PCR cycle numbers as needed. The compatible Chromium Single Cell V(D)J Enrichment Kits for Human T cells and 5’ Feature Barcode Library Kits were also utilized to obtain TCR sequences and quantify the surface markers labelled by TotalSeq-C antibodies. After quantification on the Agilent Bioanalyzer, the prepared libraries were pooled for 2 x 151 bp sequencing on the Illumina NovaSeq 6000 S4 platform aiming for 50,000 read-pairs/cell for cDNA libraries, 3,500-7,000 read-pairs/cell for TCR library, and 10,000 read-pairs/cell for Feature Barcode library. The library was sequenced on one lane of HiSeq 4000.

tag: disease

value: AITL

value: male

tag: age


title: AITL_b3_3823_scTCR

tag: gender


title: GBS_infected_human_placental_macs, hpm_E_G4H10


title: AITL_b3_3823_scRNA


title: GBS_infected_human_placental_macs, hpm_E_K4H9


title: hiDC d9_tetO-PIB

tag: cell line

value: HEF

value: human embryonic fibroblast

value: wildtype

value: 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.

value: Cells were collected 9 days after viral transduction

value: Absence


title: D5 CD14 Neg C

status: Public on Feb 07 2022

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

country: United Kingdom

institute: King's College London

data_processing:
Base calling performed using FastQC version 0.11.9
Sequenced reads were trimmed for adaptor sequence using Trim Galore! Version 0.6.5 with the following settings Max trimming error rate: 0.1  Minimum required adapter overlap: 1bp  Minimum read length allowed after trimming: 20bp  All sequences trimmed by 8bp from their 3’ end to avoid problems with invalid paired-end alignments and poor qualities or biases
mapped to human hg38 reference genome release 32 from Gencode using STAR on the following parameters Paired end: yes  Extra SAM attributes to include: standard  All other setting was on the default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human peripheral blood CD14+ monocyte_negative control

growth_protocol: CD14+ monocytes isolated from the peripheral blood of healthy donors cultured at 500,000 cells/ml in a 48 well plate for 24h in RPMI (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% penicillin, streptomycin and L-Glutamine (Life technologies).

extract_protocol:
RNA extracted using miRNeasy mini kit (Qiagen) according to manufactureres protocol.
Libraries were prepared according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L)

treatment_protocol: Transfected with 20nM negative control or miR-155 mimic

value: female

value: Peripheral blood CD14+ monocyte

value: negative control


title: D4 CD14 miR-155

source_name: Human peripheral blood CD14+ monocyte_miR-155 mimic

value: miR-155 mimic


title: D3 CD14 miR-155


title: D4 CD14 Neg C


title: D5 CD14 miR-155


title: D3 CD14 Neg C


title: HT4

value: PNX-treated


title: D2 CD14 miR-155


title: AITL_b3_3823_scBCR


title: D1 CD14 miR-155


title: WBCs, A00000EEC

status: Public on Feb 01 2022

type: genomic

city: Lebanon

first: Ji-Qing

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

institute: Dartmouth College

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

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

data_processing:
R studio
Matrix_Processed.csv  represents SeSAMe Processed Average Beta values.

label: Cy5 and Cy3

source_name: White blood cell

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: non-muscle-invasive bladder cancer (NMIBC)

tag: ten year-recurrence or death

value: No

value: White blood cell


title: D1 CD14 Neg C


title: D2 CD14 Neg C


title: WBCs, A00000FC5

value: Yes


title: WBCs, 5238DS


title: WBCs, A00000ED9


title: WBCs, 4647DS


title: WBCs, A00000EF6


title: WBCs, A00000EB3


title: WBCs, 5554DS


title: WBCs, 5283DS


title: WBCs, 4236DS


title: WBCs, 5253DS


title: WBCs, A00000EH4


title: WBCs, A00000EDV


title: WBCs, 4822DS


title: WBCs, 3786DS


title: WBCs, 5667DS


title: WBCs, 4099DS


title: WBCs, A00000EGG


title: WBCs, 4009DS


title: WBCs, 5731DS


title: WBCs, 5360DS


title: WBCs, A00000FBI


title: WBCs, 3953DS


title: WBCs, 3846DS


title: WBCs, A00000ECS


title: WBCs, 3684DS


title: WBCs, A00000EDG


title: WBCs, A00000FBT


title: WBCs, 5514DS


title: WBCs, A00000EGD


title: WBCs, A00000FC8


title: WBCs, A00000EAV


title: WBCs, 5309DS


title: WBCs, 5331DS


title: WBCs, 3843DS


title: WBCs, A00000EES


title: WBCs, 5733DS


title: WBCs, 3793DS


title: WBCs, A00000FC6


title: WBCs, 4270DS


title: WBCs, 5456DS


title: WBCs, 4086DS


title: WBCs, A00000EDJ


title: WBCs, 5412DS


title: WBCs, A00000EB9


title: WBCs, 5473DS


title: WBCs, 4877DS


title: WBCs, A00000EFC


title: WBCs, A00000EEJ


title: WBCs, A00000ECX


title: WBCs, A00000ECD


title: WBCs, 5685DS


title: WBCs, 5660DS


title: WBCs, 5585DS


title: WBCs, A00000EGF


title: WBCs, A00000EHA


title: WBCs, 3841DS


title: WBCs, A00000ECY


title: WBCs, A00000ECG


title: WBCs, A00000EEL


title: WBCs, A00000EAX


title: WBCs, 3939DS


title: WBCs, A00000FBJ


title: WBCs, A00000EEM


title: WBCs, A00000EE1


title: WBCs, 3757DS


title: WBCs, 4775DS


title: WBCs, A00000EG7


title: WBCs, A00000EFD


title: WBCs, 5714DS


title: WBCs, 5199DS


title: WBCs, 4022DS


title: WBCs, 5181DS


title: WBCs, 5464DS


title: WBCs, 5616DS


title: WBCs, A00000FBN


title: WBCs, 4748DS


title: WBCs, 5333DS


title: WBCs, A00000FBU


title: WBCs, A00000EAP


title: WBCs, 3703DS


title: WBCs, A00000EC7


title: WBCs, A00000ECI


title: WBCs, 5299DS


title: WBCs, A00000EDA


title: WBCs, 5609DS


title: WBCs, 5485DS


title: WBCs, 5461DS


title: WBCs, A00000EEF


title: WBCs, 4950DS


title: WBCs, A00000EGU


title: WBCs, 3992DS


title: WBCs, 5079DS


title: WBCs, A00000EC6


title: WBCs, A00000FBV


title: WBCs, 4640DS


title: WBCs, 5629DS


title: WBCs, 3880DS


title: WBCs, A00000EEI


title: WBCs, 4053DS


title: WBCs, A00000EFG


title: WBCs, A00000FC2


title: WBCs, A00000EBJ


title: WBCs, 4133DS


title: WBCs, 5425DS


title: WBCs, 5177DS


title: WBCs, 3694DS


title: WBCs, A00000EED


title: WBCs, 4012DS


title: WBCs, 5632DS


title: WBCs, 5626DS


title: WBCs, 5649DS


title: WBCs, A00000ECL


title: WBCs, 3823DS


title: WBCs, A00000EBI


title: WBCs, 3920DS


title: WBCs, 4085DS


title: WBCs, A00000EEV


title: WBCs, 5457DS


title: WBCs, A00000EBS


title: WBCs, A00000FBK


title: WBCs, A00000EC3


title: WBCs, A00000EBU


title: WBCs, A00000EEX


title: WBCs, 5577DS


title: WBCs, 5118DW


title: WBCs, A00000EE7


title: WBCs, A00000EDM


title: WBCs, 3970DS


title: WBCs, A00000EGX


title: WBCs, 4912DS


title: WBCs, A00000ED7


title: WBCs, 4180DS


title: WBCs, 3733DS


title: WBCs, A00000EGS


title: WBCs, 5595DS


title: WBCs, A00000EFM


title: WBCs, A00000EH3


title: WBCs, 5686DS


title: WBCs, 4069DS


title: WBCs, A00000EGI


title: WBCs, 4215DS


title: WBCs, 4939DS


title: WBCs, A00000EBR


title: WBCs, 4639DS


title: WBCs, A00000EDS


title: WBCs, A00000EGC


title: WBCs, 4230DS


title: WBCs, 4825DS


title: WBCs, 5374DS


title: WBCs, 4055DS


title: WBCs, 3925DS


title: WBCs, 5385DS


title: WBCs, A00000EBD


title: WBCs, A00000EB0


title: WBCs, A00000EDR


title: WBCs, A00000EBV


title: WBCs, A00000EFY


title: WBCs, A00000EAR


title: WBCs, A00000EGV


title: WBCs, A00000EG1


title: WBCs, 3700DS


title: WBCs, 4642DS


title: WBCs, 4753DS


title: WBCs, A00000EBC


title: WBCs, 5719DS


title: WBCs, A00000EE0


title: WBCs, A00000EDF


title: WBCs, 4239DS


title: WBCs, 3815DS


title: WBCs, A00000EFL


title: WBCs, 4804DS


title: WBCs, 5375DS


title: WBCs, A00000EDP


title: WBCs, A00000EFI


title: WBCs, 3826DS


title: WBCs, 5444DS


title: WBCs, 5435DS


title: WBCs, A00000EFS


title: WBCs, A00000EGY


title: WBCs, A00000EH7


title: WBCs, A00000EBY


title: WBCs, 5348DS


title: WBCs, 3687DW


title: WBCs, A00000EE3


title: WBCs, 4743DS


title: WBCs, 4836DS


title: WBCs, 5563DS


title: WBCs, A00000FBZ


title: WBCs, A00000ECP


title: WBCs, 5557DS


title: WBCs, A00000EC0


title: WBCs, 5542DS


title: WBCs, 5161DS


title: WBCs, A00000EC4


title: WBCs, A00000EB1


title: WBCs, 4769DS


title: WBCs, A00000EBL


title: WBCs, A00000FBM


title: WBCs, 3995DS


title: WBCs, A00000EBO


title: WBCs, A00000EDX


title: WBCs, 4025DS


title: WBCs, 5081DS


title: WBCs, 5587DS


title: WBCs, A00000EFX


title: WBCs, 5472DS


title: WBCs, A00000EEA


title: WBCs, A00000ECJ


title: WBCs, A00000EC1


title: WBCs, 3858DS


title: WBCs, 4266DS


title: WBCs, A00000FBW


title: WBCs, 5418DS


title: WBCs, A000007AX


title: WBCs, 3983DS


title: WBCs, 3828DS


title: WBCs, A00000EGL


title: WBCs, 3906DS


title: WBCs, A00000EC9


title: WBCs, 4271DS


title: WBCs, 5688DW


title: WBCs, 5224DS


title: WBCs, A00000ED1


title: WBCs, 3718DS


title: WBCs, 5286DS


title: WBCs, 5018DS


title: WBCs, 5295DS


title: WBCs, 5662DS


title: WBCs, 4255DS


title: WBCs, A00000FBP


title: WBCs, 5482DS


title: WBCs, 4125DS


title: WBCs, 5329DS


title: WBCs, 5708DS


title: WBCs, A00000ECA


title: WBCs, 5651DS


title: WBCs, A00000ECU


title: WBCs, A00000EFF


title: WBCs, 4254DS


title: WBCs, A00000FCA


title: WBCs, A00000FBR


title: WBCs, A00000ECR


title: WBCs, A00000EG0


title: WBCs, 5536DS


title: WBCs, A00000FC3


title: WBCs, 4252DS


title: WBCs, 4005DW


title: WBCs, 5668DS


title: WBCs, 3763DS


title: WBCs, 3990DS


title: WBCs, 5570DS


title: WBCs, 4985DS


title: WBCs, 2337DS


title: WBCs, 5606DS


title: WBCs, 3678DS


title: WBCs, 5365DS


title: WBCs, 5779DS


title: WBCs, A00000EH6


title: WBCs, 5583DS


title: WBCs, 4088DW


title: WBCs, A00000EFJ


title: WBCs, 3851DS


title: WBCs, 3753DS


title: WBCs, 3773DS


title: WBCs, 3721DS


title: WBCs, 5200DW


title: WBCs, A00000EF1


title: WBCs, A00000FBF


title: WBCs, 5644DS


title: WBCs, 3708DS


title: WBCs, 5294DS


title: WBCs, 4237DS


title: WBCs, 3912DW


title: WBCs, A00000EF0


title: WBCs, A00000EEO


title: WBCs, A00000EDC


title: WBCs, 3949DW


title: WBCs, 5386DS


title: WBCs, 3936DW


title: WBCs, 5357DS


title: WBCs, 4840DS


title: WBCs, A00000ECM


title: WBCs, A00000EGR


title: WBCs, 4852DS


title: WBCs, 3770DS


title: WBCs, 3927DS


title: WBCs, A00000EDU


title: WBCs, 5217DS


title: WBCs, 3944DS


title: WBCs, 5031DS


title: WBCs, 4114DS


title: WBCs, A00000EH1


title: WBCs, 4260DS


title: WBCs, BDB1P03095


title: WBCs, BDB1P03094


title: WBCs, A00000EB7


title: WBCs, BDB1P03090


title: WBCs, BDB1P03086


title: WBCs, BDB1P03093


title: WBCs, BDB1P03092


title: WBCs, BDB1P03087


title: WBCs, BDB1P03083