title: gDNA from diagnosic pediatric AML 700

description:
pediatric AML
PAWXSX_Dx

source_name: pediatric AML sample 700


title: gDNA from diagnosic pediatric AML 695

status: Public on Dec 15 2021

type: genomic

city: Seattle

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
pediatric AML
PAWXCK_Dx

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours. Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode

data_processing:
DNA methylation profiling was performed at Arkansas Children’s Research Institute  on the Illumina Infinium HumanMethylationEPIC platform, using recommended manufacturer protocols. The resulting data were processed as recommended to match LAML, TARGET AML, and TARGET AML-IF HumanMethylation450 array results, then corrected for artifacts resulting from copy number alterations and differences in cellularity where estimates were available.  Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
Processed data file includes normalized (SeSAMe) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: pediatric AML sample 695

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA)

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow or Peripheral Blood, cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

tag: trial protocol

tag: batch

tag: Sex

value: Female

tag: age (years)

tag: timepoint

value: Diagnosis

tag: fusion


title: gDNA from diagnosic pediatric AML 693

description:
pediatric AML
PAWWYV_Dx

source_name: pediatric AML sample 693


title: gDNA from diagnosic pediatric AML 694

description:
pediatric AML
PAWWXU_Dx

source_name: pediatric AML sample 694

value: Male


title: gDNA from diagnosic pediatric AML 679

description:
pediatric AML
PAWWFF_Dx

source_name: pediatric AML sample 679


title: gDNA from diagnosic pediatric AML 692

description:
pediatric AML
PAWWWU_Dx

source_name: pediatric AML sample 692


title: gDNA from diagnosic pediatric AML 680

description:
pediatric AML
PAWWID_Dx

source_name: pediatric AML sample 680


title: gDNA from diagnosic pediatric AML 683

description:
pediatric AML
PAWWMJ_Dx

source_name: pediatric AML sample 683


title: gDNA from diagnosic pediatric AML 678

description:
pediatric AML
PAWWCW_Dx

source_name: pediatric AML sample 678


title: gDNA from diagnosic pediatric AML 690

description:
pediatric AML
PAWWWM_Dx

source_name: pediatric AML sample 690


title: gDNA from diagnosic pediatric AML 691

description:
pediatric AML
PAWWWE_Dx

source_name: pediatric AML sample 691


title: gDNA from diagnosic pediatric AML 676

description:
pediatric AML
PAWVVJ_Dx

source_name: pediatric AML sample 676


title: gDNA from diagnosic pediatric AML 689

description:
pediatric AML
PAWWWL_Dx

source_name: pediatric AML sample 689


title: gDNA from diagnosic pediatric AML 675

description:
pediatric AML
PAWVVR_Dx

source_name: pediatric AML sample 675


title: gDNA from diagnosic pediatric AML 687

description:
pediatric AML
PAWWTP_Dx

source_name: pediatric AML sample 687


title: gDNA from diagnosic pediatric AML 686

description:
pediatric AML
PAWWRG_Dx

source_name: pediatric AML sample 686


title: gDNA from diagnosic pediatric AML 685

description:
pediatric AML
PAWWLI_Dx

source_name: pediatric AML sample 685


title: gDNA from diagnosic pediatric AML 684

description:
pediatric AML
PAWWPA_Dx

source_name: pediatric AML sample 684


title: gDNA from diagnosic pediatric AML 668

description:
pediatric AML
PAWVGN_Dx

source_name: pediatric AML sample 668


title: gDNA from diagnosic pediatric AML 666

description:
pediatric AML
PAWVBV_Dx

source_name: pediatric AML sample 666


title: gDNA from diagnosic pediatric AML 667

description:
pediatric AML
PAWVGF_Dx

source_name: pediatric AML sample 667


title: gDNA from diagnosic pediatric AML 682

description:
pediatric AML
PAWWJN_Dx

source_name: pediatric AML sample 682


title: gDNA from diagnosic pediatric AML 681

description:
pediatric AML
PAWWEI_Dx

source_name: pediatric AML sample 681


title: gDNA from diagnosic pediatric AML 715

description:
pediatric AML
PAWYTW_Dx

source_name: pediatric AML sample 715


title: gDNA from diagnosic pediatric AML 688

description:
pediatric AML
PAWWUN_Dx

source_name: pediatric AML sample 688


title: gDNA from diagnosic pediatric AML 677

description:
pediatric AML
PAWWEE_Dx

source_name: pediatric AML sample 677


title: gDNA from diagnosic pediatric AML 665

description:
pediatric AML
PAWVCG_Dx

source_name: pediatric AML sample 665


title: gDNA from diagnosic pediatric AML 674

description:
pediatric AML
PAWVUX_Dx

source_name: pediatric AML sample 674


title: gDNA from diagnosic pediatric AML 663

description:
pediatric AML
PAWUUY_Dx

source_name: pediatric AML sample 663


title: gDNA from diagnosic pediatric AML 664

description:
pediatric AML
PAWUWJ_Dx

source_name: pediatric AML sample 664


title: gDNA from diagnosic pediatric AML 673

description:
pediatric AML
PAWVUA_Dx

source_name: pediatric AML sample 673


title: gDNA from diagnosic pediatric AML 672

description:
pediatric AML
PAWVPZ_Dx

source_name: pediatric AML sample 672


title: gDNA from diagnosic pediatric AML 670

description:
pediatric AML
PAWVNP_Dx

source_name: pediatric AML sample 670


title: gDNA from diagnosic pediatric AML 671

description:
pediatric AML
PAWVNC_Dx

source_name: pediatric AML sample 671


title: gDNA from diagnosic pediatric AML 669

description:
pediatric AML
PAWVLI_Dx

source_name: pediatric AML sample 669


title: gDNA from diagnosic pediatric AML 655

description:
pediatric AML
PAWUEW_Dx

source_name: pediatric AML sample 655


title: gDNA from diagnosic pediatric AML 662

description:
pediatric AML
PAWUUE_Dx

source_name: pediatric AML sample 662


title: gDNA from diagnosic pediatric AML 661

description:
pediatric AML
PAWUTL_Dx

source_name: pediatric AML sample 661


title: gDNA from diagnosic pediatric AML 652

description:
pediatric AML
PAWUBZ_Dx

source_name: pediatric AML sample 652


title: gDNA from diagnosic pediatric AML 659

description:
pediatric AML
PAWUNI_Dx

source_name: pediatric AML sample 659


title: gDNA from diagnosic pediatric AML 657

description:
pediatric AML
PAWUKE_Dx

source_name: pediatric AML sample 657


title: gDNA from diagnosic pediatric AML 656

description:
pediatric AML
PAWUEX_Dx

source_name: pediatric AML sample 656


title: gDNA from diagnosic pediatric AML 658

description:
pediatric AML
PAWUMM_Dx

source_name: pediatric AML sample 658


title: gDNA from diagnosic pediatric AML 653

description:
pediatric AML
PAWUCF_Dx

source_name: pediatric AML sample 653


title: gDNA from diagnosic pediatric AML 654

description:
pediatric AML
PAWUCG_Dx

source_name: pediatric AML sample 654


title: gDNA from diagnosic pediatric AML 660

description:
pediatric AML
PAWURP_Dx

source_name: pediatric AML sample 660


title: gDNA from diagnosic pediatric AML 645

description:
pediatric AML
PAWTSM_Dx

source_name: pediatric AML sample 645


title: gDNA from diagnosic pediatric AML 644

description:
pediatric AML
PAWTRR_Dx

source_name: pediatric AML sample 644


title: gDNA from diagnosic pediatric AML 651

description:
pediatric AML
PAWTYT_Dx

source_name: pediatric AML sample 651


title: gDNA from diagnosic pediatric AML 650

description:
pediatric AML
PAWUAE_Dx

source_name: pediatric AML sample 650


title: gDNA from diagnosic pediatric AML 641

description:
pediatric AML
PAWTLZ_Dx

source_name: pediatric AML sample 641


title: gDNA from diagnosic pediatric AML 649

description:
pediatric AML
PAWTYD_Dx

source_name: pediatric AML sample 649


title: gDNA from diagnosic pediatric AML 648

description:
pediatric AML
PAWTWW_Dx

source_name: pediatric AML sample 648


title: gDNA from diagnosic pediatric AML 647

description:
pediatric AML
PAWTTI_Dx

source_name: pediatric AML sample 647


title: gDNA from diagnosic pediatric AML 646

description:
pediatric AML
PAWTSD_Dx

source_name: pediatric AML sample 646


title: gDNA from diagnosic pediatric AML 643

description:
pediatric AML
PAWTPD_Dx

source_name: pediatric AML sample 643


title: gDNA from diagnosic pediatric AML 642

description:
pediatric AML
PAWTNN_Dx

source_name: pediatric AML sample 642


title: gap-GR18-3_12.5nM_4

type: RNA

city: Kawasaki

first: Takao

last: Inoue

state: Kanagawa

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome U133 Plus 2.0 Array　using the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The scanned data were processed for signal values using Microarray Suite 5.0 software  .

label: biotin

molecule: total RNA

source_name: The Huh-7 cells transfected with gap-GR18-3 at 12.5 nM using Lipofectamine 2000 for 24hr.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: The Huh-7 cells were maintained at 37 °C and 5% CO2 in Dulbecco’s Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The Huh-7 cells transfected with the gapmer ASOs using Lipofectamine 2000 (Invitrogen, Gaithersburg, MD, USA) according to the manufacturer’s protocol. The cells treated with transfection reagent in the absence of ASO were used as a control.

tag: tissue

value: Liver


title: gap-GR18-3_12.5nM_3


title: gDNA from diagnosic pediatric AML 636

description:
pediatric AML
PAWTEB_Dx

source_name: pediatric AML sample 636


title: gDNA from diagnosic pediatric AML 637

description:
pediatric AML
PAWTDZ_Dx

source_name: pediatric AML sample 637


title: gap-GR18-3_12.5nM_1


title: gap-GR18-2_40nM_2

source_name: The Huh-7 cells transfected with gap-GR18-2 at 40 nM using Lipofectamine 2000 for 24hr.


title: gDNA from diagnosic pediatric AML 640

description:
pediatric AML
PAWTKY_Dx

source_name: pediatric AML sample 640


title: gDNA from diagnosic pediatric AML 639

description:
pediatric AML
PAWTJU_Dx

source_name: pediatric AML sample 639


title: gDNA from diagnosic pediatric AML 638

description:
pediatric AML
PAWTGF_Dx

source_name: pediatric AML sample 638


title: gap-GR18-2_40nM_3


title: gDNA from diagnosic pediatric AML 634

description:
pediatric AML
PAWTBX_Dx

source_name: pediatric AML sample 634


title: gap-GR18-3_12.5nM_2


title: gDNA from diagnosic pediatric AML 635

description:
pediatric AML
PAWTEI_Dx

source_name: pediatric AML sample 635


title: gap-GR18-2_40nM_4


title: gap-GR18-2_40nM_1


title: gap-GR18-2_45nM_1

source_name: The Huh-7 cells transfected with gap-GR18-2 at 45 nM using Lipofectamine 2000 for 24hr.


title: Control_4

source_name: The Huh-7 cells treated with transfection reagent in the absence of ASO.


title: gap-GR18-2_45nM_2


title: gap-GR18-2_45nM_4


title: gDNA from diagnosic pediatric AML 632

description:
pediatric AML
PAWSWR_Dx

source_name: pediatric AML sample 632


title: gap-GR18-2_45nM_3


title: gDNA from diagnosic pediatric AML 633

description:
pediatric AML
PAWSZL_Dx

source_name: pediatric AML sample 633


title: gDNA from diagnosic pediatric AML 722

description:
pediatric AML
PAWZHY_Dx

source_name: pediatric AML sample 722


title: gDNA from diagnosic pediatric AML 631

description:
pediatric AML
PAWSWU_Dx

source_name: pediatric AML sample 631


title: Control_2


title: Control_1


title: gDNA from diagnosic pediatric AML 630

description:
pediatric AML
PAWSTK_Dx

source_name: pediatric AML sample 630


title: gDNA from diagnosic pediatric AML 712

description:
pediatric AML
PAWYNR_Dx

source_name: pediatric AML sample 712


title: gDNA from diagnosic pediatric AML 629

description:
pediatric AML
PAWSKR_Dx

source_name: pediatric AML sample 629


title: gDNA from diagnosic pediatric AML 627

description:
pediatric AML
PAWSJC_Dx

source_name: pediatric AML sample 627


title: gDNA from diagnosic pediatric AML 624

description:
pediatric AML
PAWSED_Dx

source_name: pediatric AML sample 624


title: gDNA from diagnosic pediatric AML 617

description:
pediatric AML
PAWRSP_Dx

source_name: pediatric AML sample 617


title: gDNA from diagnosic pediatric AML 620

description:
pediatric AML
PAWRVC_Dx

source_name: pediatric AML sample 620


title: gDNA from diagnosic pediatric AML 628

description:
pediatric AML
PAWSRG_Dx

source_name: pediatric AML sample 628


title: gDNA from diagnosic pediatric AML 613

description:
pediatric AML
PAWRPD_Dx

source_name: pediatric AML sample 613


title: gDNA from diagnosic pediatric AML 625

description:
pediatric AML
PAWSHR_Dx

source_name: pediatric AML sample 625


title: gDNA from diagnosic pediatric AML 622

description:
pediatric AML
PAWSBW_Dx

source_name: pediatric AML sample 622


title: gDNA from diagnosic pediatric AML 623

description:
pediatric AML
PAWSCV_Dx

source_name: pediatric AML sample 623


title: gDNA from diagnosic pediatric AML 621

description:
pediatric AML
PAWRYC_Dx

source_name: pediatric AML sample 621


title: gDNA from diagnosic pediatric AML 610

description:
pediatric AML
PAWRIY_Dx

source_name: pediatric AML sample 610


title: gap-GR14_40nM_3

source_name: The Huh-7 cells transfected with gap-GR14 at 40 nM using Lipofectamine 2000 for 24hr.


title: gap-GR18-1_60nM_2

source_name: The Huh-7 cells transfected with gap-GR18-1 at 60 nM using Lipofectamine 2000 for 24hr.


title: gDNA from diagnosic pediatric AML 619

description:
pediatric AML
PAWRUX_Dx

source_name: pediatric AML sample 619


title: gDNA from diagnosic pediatric AML 618

description:
pediatric AML
PAWRUK_Dx

source_name: pediatric AML sample 618


title: gap-GR14_40nM_1


title: Control_3

source_name: The Huh-7 cells treated with transfection reagent in the absence of ASO.


title: gap-GR14_40nM_4


title: gap-GR18-1_60nM_4


title: gDNA from diagnosic pediatric AML 626

description:
pediatric AML
PAWSJZ_Dx

source_name: pediatric AML sample 626


title: gap-GR14_45nM_4

source_name: The Huh-7 cells transfected with gap-GR14 at 45 nM using Lipofectamine 2000 for 24hr.


title: gDNA from diagnosic pediatric AML 616

description:
pediatric AML
PAWRSI_Dx

source_name: pediatric AML sample 616


title: gDNA from diagnosic pediatric AML 615

description:
pediatric AML
PAWRSU_Dx

source_name: pediatric AML sample 615


title: gDNA from diagnosic pediatric AML 614

description:
pediatric AML
PAWRPX_Dx

source_name: pediatric AML sample 614


title: gap-GR18-1_60nM_3


title: gap-GR18-1_60nM_1


title: gDNA from diagnosic pediatric AML 612

description:
pediatric AML
PAWRNZ_Dx

source_name: pediatric AML sample 612

value: FUS-ERG


title: gap-GR14_45nM_2


title: gDNA from diagnosic pediatric AML 611

description:
pediatric AML
PAWRKX_Dx

source_name: pediatric AML sample 611


title: gDNA from diagnosic pediatric AML 604

description:
pediatric AML
PAWPLE_Dx

source_name: pediatric AML sample 604


title: gap-GR14_40nM_2


title: gDNA from diagnosic pediatric AML 608

description:
pediatric AML
PAWRGN_Dx

source_name: pediatric AML sample 608


title: Mak1_S

type: SRA

city: Beijing

first: Xianyun

last: Sun

email: xysun3@163.com, sunxy@im.ac.cn

state: China

address: No.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Neurospora crassa OR74A.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files include FRKM values for each Sample.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: To obtain RNA at vegetative growth stage, strains were cultured in liquid Vogel’s medium at 28 °C for 22 hours with orbital shaking, and the mycelia were harvested by vacuum filtration. To obtain RNA in the initial stage of protoperithecium formation, strains were inoculated on solid synthetic crossing medium with 0.1% sucrose, on which sterilized cellophane was overlaid. Plates were incubated under constant dark at 25 °C for 3.5 days.

extract_protocol:
Mycelia were immediately frozen after harvest and ground into fine powder in liquid nitrogen. Total RNA was extracted according to the standard TRIzol protocol.
RAN libraries were prepared for sequencing using standard Illumina protocols

tag: growth stage

tag: genotype


title: Mak2_A

value: vegetative growth stage


title: gDNA from diagnosic pediatric AML 609

description:
pediatric AML
PAWRGZ_Dx

source_name: pediatric AML sample 609


title: gDNA from diagnosic pediatric AML 601

description:
pediatric AML
PAWPET_Dx

source_name: pediatric AML sample 601


title: Mak1_A


title: gDNA from diagnosic pediatric AML 600

description:
pediatric AML
PAWPBT_Dx

source_name: pediatric AML sample 600


title: gDNA from diagnosic pediatric AML 599

description:
pediatric AML
PAWPDC_Dx

source_name: pediatric AML sample 599


title: gDNA from diagnosic pediatric AML 598

description:
pediatric AML
PAWPCN_Dx

source_name: pediatric AML sample 598


title: gap-GR14_45nM_1


title: gDNA from diagnosic pediatric AML 597

description:
pediatric AML
PAWNZJ_Dx

source_name: pediatric AML sample 597


title: gap-GR14_45nM_3


title: gDNA from diagnosic pediatric AML 607

description:
pediatric AML
PAWREX_Dx

source_name: pediatric AML sample 607


title: gDNA from diagnosic pediatric AML 606

description:
pediatric AML
PAWPVX_Dx

source_name: pediatric AML sample 606


title: Mak2_S

value: the initial stage of protoperithecium formation


title: gDNA from diagnosic pediatric AML 594

description:
pediatric AML
PAWNWV_Dx

source_name: pediatric AML sample 594


title: gDNA from diagnosic pediatric AML 602

description:
pediatric AML
PAWPGW_Dx

source_name: pediatric AML sample 602


title: gDNA from diagnosic pediatric AML 605

description:
pediatric AML
PAWPVR_Dx

source_name: pediatric AML sample 605


title: wt 30 min replicate 2

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

description: wild type

data_processing:
Basecalling with Illumina Cassava 1.8
FASTX Toolkit v0.0.13 was used to remove the linker sequences, to retain the first 25 nt from the 5' end and to filter with a minimum threshold quality of Q30 in 50% of the remaining bases.
Cleaned reads were mapped on TAIR10 reference genome with Bowtie v1.1.2 with the parameters -t best -strata -v -k 10 -y -p 6 -phred33-quals -chunksmbs 512 -e 120 -q -un.
The 5'-end of the CAGE tags were counted at each genomic position to obtain a set of CAGE transcription start sites (CTSSs).
CTSS coordinates were offset by 1 bp to account for the G-bias trimming.
CAGE tags were clustered into tag clusters (TCs) using CAGEfightR bioconductor package
CAGE TCs were quantified and further normalized into TPM (tags per million), with CAGEfightR.
Gene-level expression was obtained by aggregating (sum) CAGE TCs belonging to the same gene.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files, one per strand, host the number of CAGE tags 5'-end per bp (raw count CTSSs)
Supplementary_files_format_and_content: matrices in text format, tab-delimited

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Following 12 days of growth in MS 1% under sterile conditions at room temperature and long-days luminosity, seedlings were transferred to liquid MS media 1% and allowed to acclimate 48 hours at 130 rpm prior to treatment.

extract_protocol:
A pool of 10 intact whole seedlings was flash frozen and total RNA was extracted using TRI-Reagent. Polysaccharide precipitation was carried out using the double sodium acetate method.
CAGE libraries were prepared as in (Takahashi et al., 2012) with a starting material of 5ug of total RNA. Phi-X spike-ins were added (30%) to each sequencing lane to account for low complexity of the 5' ends of the CAGE libraries

treatment_protocol: flg22 peptide dissolved in DMSO (1 mg/mL) was added to the liquid MS for a final concentration of 3.3 uM. Treatment was conducted for two timepoints: 10 and 30 minutes.

value: whole seedlings

tag: ecotype

value: wt

tag: age

value: 14 day-old

value: 30 min

tag: rna population

value: 5' capped RNAs


title: WT_S

value: wild type


title: gDNA from diagnosic pediatric AML 596

description:
pediatric AML
PAWNYX_Dx

source_name: pediatric AML sample 596


title: gDNA from diagnosic pediatric AML 595

description:
pediatric AML
PAWNXH_Dx

source_name: pediatric AML sample 595


title: WT_A


title: wt 10 min replicate 3

description: wild type

value: 10 min


title: wt 30 min replicate 1

description: wild type


title: gDNA from diagnosic pediatric AML 585

description:
pediatric AML
PAWNIK_Dx

source_name: pediatric AML sample 585


title: gDNA from diagnosic pediatric AML 589

description:
pediatric AML
PAWNLU_Dx

source_name: pediatric AML sample 589


title: gDNA from diagnosic pediatric AML 587

description:
pediatric AML
PAWNIX_Dx

source_name: pediatric AML sample 587


title: gDNA from diagnosic pediatric AML 593

description:
pediatric AML
PAWNSL_Dx

source_name: pediatric AML sample 593


title: gDNA from diagnosic pediatric AML 592

description:
pediatric AML
PAWNPG_Dx

source_name: pediatric AML sample 592


title: gDNA from diagnosic pediatric AML 591

description:
pediatric AML
PAWNPU_Dx

source_name: pediatric AML sample 591


title: gDNA from diagnosic pediatric AML 588

description:
pediatric AML
PAWNKT_Dx

source_name: pediatric AML sample 588


title: wt 30 min replicate 3

description: wild type


title: gDNA from diagnosic pediatric AML 586

description:
pediatric AML
PAWNGC_Dx

source_name: pediatric AML sample 586


title: gDNA from diagnosic pediatric AML 582

description:
pediatric AML
PAWNHH_Dx

source_name: pediatric AML sample 582


title: wt 10 min replicate 2

description: wild type


title: gDNA from diagnosic pediatric AML 584

description:
pediatric AML
PAWNHU_Dx

source_name: pediatric AML sample 584


title: gDNA from diagnosic pediatric AML 577

description:
pediatric AML
PAWNAP_Dx

source_name: pediatric AML sample 577


title: gDNA from diagnosic pediatric AML 576

description:
pediatric AML
PAWMRJ_Dx

source_name: pediatric AML sample 576


title: gDNA from diagnosic pediatric AML 583

description:
pediatric AML
PAWNHW_Dx

source_name: pediatric AML sample 583


title: gDNA from diagnosic pediatric AML 581

description:
pediatric AML
PAWRUF_Dx

source_name: pediatric AML sample 581


title: gDNA from diagnosic pediatric AML 580

description:
pediatric AML
PAWNYK_Dx

source_name: pediatric AML sample 580


title: rrp4 30 min replicate 3

description: hypomorphic allele

source_name: whole seedlings


title: hen2 30 min replicate 1

description: T-DNA line


title: gDNA from diagnosic pediatric AML 590

description:
pediatric AML
PAWNMU_Dx

source_name: pediatric AML sample 590


title: rrp4 30 min replicate 2

description: hypomorphic allele


title: wt 10 min replicate 1

description: wild type


title: gDNA from diagnosic pediatric AML 578

description:
pediatric AML
PAWNBB_Dx

source_name: pediatric AML sample 578


title: gDNA from diagnosic pediatric AML 579

description:
pediatric AML
PAWNFJ_Dx

source_name: pediatric AML sample 579


title: hen2 30 min replicate 3

description: T-DNA line


title: rrp4 30 min replicate 1

description: hypomorphic allele


title: gDNA from diagnosic pediatric AML 574

description:
pediatric AML
PAWMNN_Dx

source_name: pediatric AML sample 574


title: gDNA from diagnosic pediatric AML 570

description:
pediatric AML
PAWMLN_Dx

source_name: pediatric AML sample 570


title: gDNA from diagnosic pediatric AML 575

description:
pediatric AML
PAWMPH_Dx

source_name: pediatric AML sample 575


title: hen2 10 min replicate 2

description: T-DNA line


title: gDNA from diagnosic pediatric AML 567

description:
pediatric AML
PAWMKP_Dx

source_name: pediatric AML sample 567


title: gDNA from diagnosic pediatric AML 573

description:
pediatric AML
PAWMKU_Dx

source_name: pediatric AML sample 573


title: hen2 30 min replicate 2

description: T-DNA line


title: gDNA from diagnosic pediatric AML 571

description:
pediatric AML
PAWMLA_Dx

source_name: pediatric AML sample 571


title: gDNA from diagnosic pediatric AML 569

description:
pediatric AML
PAWMLK_Dx

source_name: pediatric AML sample 569


title: hen2 10 min replicate 3

description: T-DNA line


title: hen2 10 min replicate 1

description: T-DNA line


title: gDNA from diagnosic pediatric AML 566

description:
pediatric AML
PAWMIX_Dx

source_name: pediatric AML sample 566


title: gDNA from diagnosic pediatric AML 563

description:
pediatric AML
PAWMHE_Dx

source_name: pediatric AML sample 563


title: gDNA from diagnosic pediatric AML 561

description:
pediatric AML
PAWMFH_Dx

source_name: pediatric AML sample 561


title: gDNA from diagnosic pediatric AML 565

description:
pediatric AML
PAVYVR_Dx

source_name: pediatric AML sample 565


title: gDNA from diagnosic pediatric AML 572

description:
pediatric AML
PAWMFY_Dx

source_name: pediatric AML sample 572


title: gDNA from diagnosic pediatric AML 568

description:
pediatric AML
PAWMKF_Dx

source_name: pediatric AML sample 568


title: gDNA from diagnosic pediatric AML 562

description:
pediatric AML
PAWMGT_Dx

source_name: pediatric AML sample 562


title: Microglia-WT_FKDL210056119

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Chromatin IP against H3K9me3

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2 with the following configurations.
Quality control checks on raw sequence data by FastQC.
Peaks were called using MACS with the following setting: FDR=10%, Enrichment Fold (H2AZ/input), p-value <= 10-5.
Gene Ontology based on top300 peaks (the 300 most enrichments, p-value<=10-5, FDR<=0.1).
Genome_build: mm9
Supplementary_files_format_and_content: fastq files were generated using …; Scores represent …

organism: Mus musculus

source_name: microglia

extract_protocol:
The brain microglia were purified by FACS from E14.5 telencephalon of Arid1afl/fl and Arid1acKO-Cx3cr1 mice. 100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 10μL Concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at RT for 10min. Remove unbound supernatant and resuspended beadbound cells with dig wash buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2mM EDTA) and a 1:50 dilution of primary antibody or IgG control antibody incubated on a roating platform overnight at 4℃. The primary antibody was removed using magnet stand. Sencondary antibody was diluted 1:100 in dig wash buffer and cells were incubated at RT for 60 min. cells were washed using the magnet stand 2-3 times in dig wash buffer . A 1:100dilution of pA-Tn5 adapter complex was prepared in digmed buffer (0.01% Digitonin; 20mM HEPES pH 7.5; 300mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) and incubated with cells at RT for 1h. Cells were washed 2–3× for 5 min in 1 mL Dig-med buffer. Then  cells were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).
ChIP-Seq (CUT&Tag)

tag: strain

tag: development stage

tag: chip antibody


title: Microglia-WT-IgG_FKDL210056121

description: Chromatin IP against IgG

value: IgG


title: gDNA from diagnosic pediatric AML 564

description:
pediatric AML
PAWMII_Dx

source_name: pediatric AML sample 564


title: gDNA from diagnosic pediatric AML 553

description:
pediatric AML
PAWLUX_Dx

source_name: pediatric AML sample 553


title: gDNA from diagnosic pediatric AML 554

description:
pediatric AML
PAWLUE_Dx

source_name: pediatric AML sample 554


title: Microglia-KO-IgG_FKDL210056122

description: Chromatin IP against IgG


title: gDNA from diagnosic pediatric AML 552

description:
pediatric AML
PAWLTL_Dx

source_name: pediatric AML sample 552


title: gDNA from diagnosic pediatric AML 550

description:
pediatric AML
PAWLKP_Dx

source_name: pediatric AML sample 550


title: gDNA from diagnosic pediatric AML 555

description:
pediatric AML
PAWLTG_Dx

source_name: pediatric AML sample 555


title: gDNA from diagnosic pediatric AML 558

description:
pediatric AML
PAWMDY_Dx

source_name: pediatric AML sample 558


title: gDNA from diagnosic pediatric AML 559

description:
pediatric AML
PAWMEZ_Dx

source_name: pediatric AML sample 559


title: WH4

city: Houston

first: Cullen

last: Taniguchi

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The raw sequencing data was downloaded from the core server and low-quality reads were removed and Q20 and GC contents were calculated. Transcript abundance was quantified using the RSEM software package (RRID:SCR_013027)  Differential expression analysis was performed using EBSeq software package (RRID:SCR_003526)
Genome_build: GRC38
Supplementary_files_format_and_content: expected_count, TPM,    FPKM

source_name: Doudenal organoids

growth_protocol: Duodenal crypts were isolated from C57BL/6 mice, R26-LSL-hHIF2adPA mice, and Wnt5afl/fl mice and grown matrigel doem to make 3D oragnoids using L-WRN conditioned media

extract_protocol:
RNA was purified using an RNeasy mini kit
Library preparation and sequencing were performed in the Sequencing and Microarray Facility at MD Anderson Cancer Center.

treatment_protocol: Duodenal organoids were transduced Ad-GFP, Ad-hHIF1, or Ad-hHIF2 viral vectors

tag: transduced with

value: Intestine

tag: treatment

value: Adeno treated

value: Wild type


title: Control group

city: Wuhan

first: Xuan

last: Yu

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were preprocessed by cellranger software (v.1.3.0). Sequencing data of each sample was analyzed using the count function of cellranger, and the sequencing data of different samples were identified by their barcodes.The sequencing data were aligned to reference genome sequence by mm10_premrna, and the expression levels of genes in every nucleus were obtained.
The batch effects between samples were eliminated by the aggr function of cellranger software (v.1.3.0).
Seurat software (v. 3.1.4) was used for initial quality control and mitochondrial gene elimination.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

molecule: polyA RNA

source_name: brain PFC

extract_protocol:
Iodixanol gradient centrifugation was used for single nucleus isolation. A proper amount of single nuclei (~8,000) was added to the reverse transcription mixture, single cell 3' gel beads (combined with 10x barcode), and partitioning oil in the 10x Genomics Chromium™ Single Cell Controller before starting the GEM (Gel Bead-In-EMulsions) generation program. GEM generation, reverse transcription, cDNA amplification, and library construction were performed followed by the standard protocols of 10x genomics.
The library sequencing was performed in the Illumina Hiseq platform (Illumina, San Diego, CA, USA) under the 2 × 150-bp double-ended sequencing pattern to generate FastQ data.

treatment_protocol: Animals included in current study were all 2-month-old male C57BL/6 mice. All animals were socially housed on a 12-h light/dark cycle with water and food ad libitum. Mice were treated with 5 mg/kg METH or saline (intraperitoneal) for 14 days in the METH and control groups, respectively. Then all mice were deeply anesthetized with chloral hydrate and sacrificed, and the PFCs of three mice per group were rapidly removed and prepared for single nucleus isolation on ice.

value: 5 mg/kg saline (intraperitoneal) for 14 days

value: 2 month


title: METH group

value: 5 mg/kg METH (intraperitoneal) for 14 days


title: gDNA from diagnosic pediatric AML 557

description:
pediatric AML
PAWMAV_Dx

source_name: pediatric AML sample 557

tag: trial protocol

value: Male

value: Diagnosis


title: gDNA from diagnosic pediatric AML 551

description:
pediatric AML
PAWLRX_Dx

source_name: pediatric AML sample 551

tag: batch


title: gDNA from diagnosic pediatric AML 556

description:
pediatric AML
PAWLYM_Dx

source_name: pediatric AML sample 556

tag: Sex

value: Female


title: gDNA from diagnosic pediatric AML 560

description:
pediatric AML
PAWMGH_Dx

source_name: pediatric AML sample 560

tag: age (years)


title: Microglia-KO_FKDL210056120

description: Chromatin IP against H3K9me3


title: gDNA from diagnosic pediatric AML 547

description:
pediatric AML
PAWLHJ_Dx

source_name: pediatric AML sample 547

tag: timepoint


title: gDNA from diagnosic pediatric AML 545

description:
pediatric AML
PAWLEB_Dx

source_name: pediatric AML sample 545

tag: fusion


title: gDNA from diagnosic pediatric AML 543

description:
pediatric AML
PAWLER_Dx

source_name: pediatric AML sample 543


title: gDNA from diagnosic pediatric AML 548

description:
pediatric AML
PAWLII_Dx

source_name: pediatric AML sample 548


title: gDNA from diagnosic pediatric AML 549

description:
pediatric AML
PAWLKE_Dx

source_name: pediatric AML sample 549


title: WEP1

tag: tissue


title: WH3


title: WH1


title: gDNA from diagnosic pediatric AML 546

description:
pediatric AML
PAWLGJ_Dx

source_name: pediatric AML sample 546


title: gDNA from diagnosic pediatric AML 544

description:
pediatric AML
PAWLFB_Dx

source_name: pediatric AML sample 544


title: WEP4


title: gDNA from diagnosic pediatric AML 541

description:
pediatric AML
PAWLAJ_Dx

source_name: pediatric AML sample 541


title: WG4

value: Adeno-GFP


title: WG1


title: Nkx2.9-ko-3

city: Amsterdam

first: Marten P.

middle: Piet

last: Smidt

address: Sciencepark 904

department: SILS

country: Netherlands

institute: UvA

data_processing:
fastqc control
aligments (Hisat2)
mRNAseq readcounting (featurecounts)
differential expression analysis
Deseq2
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: txt file, DESeq regulated genes

source_name: Midbrain dissected material E14.5

extract_protocol:
Dissected midbrain material from E14.5 mouse embryo’s, total RNA extraction (trizol)
RNAseq library construction from Total RNA samples (1-9) (Illumina “preparing samples for sequencing of mRNA” Rev. A ,September 2008)

treatment_protocol: WT vs Het vs KO

tag: transcription factor

value: knock out


title: gDNA from diagnosic pediatric AML 540

description:
pediatric AML
PAWKYG_Dx

source_name: pediatric AML sample 540


title: WEP3

tag: genotype


title: gDNA from diagnosic pediatric AML 537

description:
pediatric AML
PAWKPU_Dx

source_name: pediatric AML sample 537


title: gDNA from diagnosic pediatric AML 532

description:
pediatric AML
PAWKIU_Dx

source_name: pediatric AML sample 532


title: gDNA from diagnosic pediatric AML 536

description:
pediatric AML
PAWKRF_Dx

source_name: pediatric AML sample 536


title: gDNA from diagnosic pediatric AML 534

description:
pediatric AML
PAWKLC_Dx

source_name: pediatric AML sample 534


title: WG3

source_name: Doudenal organoids


title: gDNA from diagnosic pediatric AML 535

description:
pediatric AML
PAWKMU_Dx

source_name: pediatric AML sample 535


title: gDNA from diagnosic pediatric AML 533

description:
pediatric AML
PAWKLB_Dx

source_name: pediatric AML sample 533


title: Nkx2.9-ko-2


title: gDNA from diagnosic pediatric AML 531

description:
pediatric AML
PAWKJC_Dx

source_name: pediatric AML sample 531


title: gDNA from diagnosic pediatric AML 530

description:
pediatric AML
PAWKIW_Dx

source_name: pediatric AML sample 530


title: gDNA from diagnosic pediatric AML 542

description:
pediatric AML
PAWLAN_Dx

source_name: pediatric AML sample 542


title: Nkx2.9-ko-1


title: gDNA from diagnosic pediatric AML 529

description:
pediatric AML
PAWKHN_Dx

source_name: pediatric AML sample 529


title: Nkx2.9 het-3

value: het


title: Nkx2.9 het-2


title: gDNA from diagnosic pediatric AML 539

description:
pediatric AML
PAWLAG_Dx

source_name: pediatric AML sample 539


title: gDNA from diagnosic pediatric AML 538

description:
pediatric AML
PAWKUR_Dx

source_name: pediatric AML sample 538


title: Nkx2.9 wt-3


title: gDNA from diagnosic pediatric AML 522

description:
pediatric AML
PAWJGZ_Dx

source_name: pediatric AML sample 522


title: gDNA from diagnosic pediatric AML 603

description:
pediatric AML
PAWPKR_Dx

source_name: pediatric AML sample 603


title: Nkx2.9 wt-1

source_name: Midbrain dissected material E14.5


title: gDNA from diagnosic pediatric AML 524

description:
pediatric AML
PAWJKD_Dx

source_name: pediatric AML sample 524


title: gDNA from diagnosic pediatric AML 525

description:
pediatric AML
PAWJPN_Dx

source_name: pediatric AML sample 525


title: gDNA from diagnosic pediatric AML 527

description:
pediatric AML
PAWKCU_Dx

source_name: pediatric AML sample 527


title: gDNA from diagnosic pediatric AML 528

description:
pediatric AML
PAWKGX_Dx

source_name: pediatric AML sample 528


title: gDNA from diagnosic pediatric AML 515

description:
pediatric AML
PAWIUZ_Dx

source_name: pediatric AML sample 515


title: gDNA from diagnosic pediatric AML 526

description:
pediatric AML
PAWJVZ_Dx

source_name: pediatric AML sample 526


title: gDNA from diagnosic pediatric AML 523

description:
pediatric AML
PAWJIM_Dx

source_name: pediatric AML sample 523


title: Nkx2.9 het-1


title: gDNA from diagnosic pediatric AML 521

description:
pediatric AML
PAWJDM_Dx

source_name: pediatric AML sample 521


title: gDNA from diagnosic pediatric AML 512

description:
pediatric AML
PAWILD_Dx

source_name: pediatric AML sample 512


title: Midbrain tissue-Gpt161f/f;Wnt1-Cre-1

city: Austin

first: Sung Eun

last: Kim

state: TX

address: 1400 Barbara Jordan Blvd

institute: The University of Texas at Austin

data_processing:
Illumina HiSeq 3000 read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into kallisto v0.46.1 for pseudoalignment into tsv files. Pseudoalignment was initially to the transcriptome (mouse genome mm10).
tsv files were imported into the RNA-Seq analysis pipeline of DEseq2 (Bioconductor version: Release (3.13).) in R (4.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: midbrain tissues from E13.5 mouse embryos

extract_protocol:
Midbrain tissues were dissected on ice from the E13.5 mouse embryos of each genotype.  RNA was extracted with Trizol and column (Zymoresearch).
The library was prepared with NEBNext Ultra RNA with Poly-A selection

value: midbrain


title: gDNA from diagnosic pediatric AML 520

description:
pediatric AML
PAWIZG_Dx

source_name: pediatric AML sample 520


title: gDNA from diagnosic pediatric AML 518

description:
pediatric AML
PAWIWJ_Dx

source_name: pediatric AML sample 518


title: gDNA from diagnosic pediatric AML 517

description:
pediatric AML
PAWIUS_Dx

source_name: pediatric AML sample 517


title: gDNA from diagnosic pediatric AML 516

description:
pediatric AML
PAWIVB_Dx

source_name: pediatric AML sample 516


title: Midbrain tissue-Gpr161f/+;Wnt1-Cre-3


title: gDNA from diagnosic pediatric AML 508

description:
pediatric AML
PAWIEJ_Dx

source_name: pediatric AML sample 508


title: gDNA from diagnosic pediatric AML 510

description:
pediatric AML
PAWIIK_Dx

source_name: pediatric AML sample 510


title: Nkx2.9 wt-2

source_name: Midbrain dissected material E14.5


title: gDNA from diagnosic pediatric AML 507

description:
pediatric AML
PAWIDI_Dx

source_name: pediatric AML sample 507


title: gDNA from diagnosic pediatric AML 519

description:
pediatric AML
PAWIXW_Dx

source_name: pediatric AML sample 519


title: Midbrain tissue-Gpr161f/+;Wnt1-Cre-1


title: gDNA from diagnosic pediatric AML 514

description:
pediatric AML
PAWIUT_Dx

source_name: pediatric AML sample 514


title: Midbrain tissue-Gpr161f/f-2


title: Midbrain tissue-Gpr161f/f-3


title: gDNA from diagnosic pediatric AML 501

description:
pediatric AML
PAWHRR_Dx

source_name: pediatric AML sample 501


title: gDNA from diagnosic pediatric AML 513

description:
pediatric AML
PAWITY_Dx

source_name: pediatric AML sample 513


title: Midbrain tissue-Gpt161f/f;Wnt1-Cre-2


title: gDNA from diagnosic pediatric AML 500

description:
pediatric AML
PAWHSM_Dx

source_name: pediatric AML sample 500


title: Midbrain tissue-Gpr161f/+;Wnt1-Cre-2


title: gDNA from diagnosic pediatric AML 499

description:
pediatric AML
PAWHRB_Dx

source_name: pediatric AML sample 499


title: Midbrain tissue-Gpr161f/f-1


title: Midbrain tissue-Gpt161f/f;Wnt1-Cre-3


title: gDNA from diagnosic pediatric AML 505

description:
pediatric AML
PAWIAT_Dx

source_name: pediatric AML sample 505


title: gDNA from diagnosic pediatric AML 509

description:
pediatric AML
PAWIEM_Dx

source_name: pediatric AML sample 509


title: gDNA from diagnosic pediatric AML 498

description:
pediatric AML
PAWHPL_Dx

source_name: pediatric AML sample 498


title: gDNA from diagnosic pediatric AML 494

description:
pediatric AML
PAWHIZ_Dx

source_name: pediatric AML sample 494


title: gDNA from diagnosic pediatric AML 503

description:
pediatric AML
PAWHUX_Dx

source_name: pediatric AML sample 503


title: gDNA from diagnosic pediatric AML 506

description:
pediatric AML
PAWICA_Dx

source_name: pediatric AML sample 506


title: gDNA from diagnosic pediatric AML 502

description:
pediatric AML
PAWHTL_Dx

source_name: pediatric AML sample 502


title: gDNA from diagnosic pediatric AML 504

description:
pediatric AML
PAWHZX_Dx

source_name: pediatric AML sample 504


title: gDNA from diagnosic pediatric AML 492

description:
pediatric AML
PAWHFV_Dx

source_name: pediatric AML sample 492


title: gDNA from diagnosic pediatric AML 511

description:
pediatric AML
PAWIHN_Dx

source_name: pediatric AML sample 511


title: gDNA from diagnosic pediatric AML 491

description:
pediatric AML
PAWHFW_Dx

source_name: pediatric AML sample 491


title: mice treated with didymin rep2

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

data_processing:
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Genome_build: mm9

source_name: ALI stage liver

growth_protocol: mice in model group  were injected with LPS (50 μg/kg) and D-Gal (800 mg/kg) to induce ALI, and normal group were given same dose normal saline

extract_protocol:
Total RNA was extracted from liver tissues with Trizol reagent
NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）,AMPure XP system

value: liver

tag: disease state

value: acute liver injury

value: male


title: gDNA from diagnosic pediatric AML 490

description:
pediatric AML
PAWHCT_Dx

source_name: pediatric AML sample 490


title: gDNA from diagnosic pediatric AML 497

description:
pediatric AML
PAWHKK_Dx

source_name: pediatric AML sample 497


title: gDNA from diagnosic pediatric AML 488

description:
pediatric AML
PAWGYA_Dx

source_name: pediatric AML sample 488


title: mice model rep1


title: gDNA from diagnosic pediatric AML 495

description:
pediatric AML
PAWHJP_Dx

source_name: pediatric AML sample 495


title: gDNA from diagnosic pediatric AML 496

description:
pediatric AML
PAWHJI_Dx

source_name: pediatric AML sample 496


title: mice treated with didymin rep3


title: gDNA from diagnosic pediatric AML 486

description:
pediatric AML
PAWGVW_Dx

source_name: pediatric AML sample 486


title: gDNA from diagnosic pediatric AML 487

description:
pediatric AML
PAWHAB_Dx

source_name: pediatric AML sample 487


title: gDNA from diagnosic pediatric AML 484

description:
pediatric AML
PAWGRP_Dx

source_name: pediatric AML sample 484


title: gDNA from diagnosic pediatric AML 493

description:
pediatric AML
PAWHAX_Dx

source_name: pediatric AML sample 493


title: gDNA from diagnosic pediatric AML 483

description:
pediatric AML
PAWGSX_Dx

source_name: pediatric AML sample 483


title: gDNA from diagnosic pediatric AML 481

description:
pediatric AML
PAWGKS_Dx

source_name: pediatric AML sample 481


title: mice model rep3


title: Patient 27

city: Manchester

first: Philip

last: Murray

address: Oxford Road

country: United Kingdom

institute: University of Manchester

data_processing:
Across all cells, genes with fewer than 15 total counts were removed; the minimum count per cell for a feature to be considered expressed is 10.
The large group size was set at 10 samples and genes had to be expressed in 70% of cells of smaller groups to pass filtering
Gene level normalisation was performed using TMM (trimmed mean of M values).
A block design in EdgeR was used to control for the impact of confounding factors (age and gender)
The EdgeR package for R 4.0.0 (23, 24) was used
Genome_build: GCA_000001405.15 GRCh38 from NCBI

source_name: Peripheral blood mononuclea cells

extract_protocol:
Blood collected into PAX Gene tubes and extarcted with PAXGene Blood RNA kit (Cat No./ID: 762174)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: M

tag: age

tag: sex steroid priming

value: No

tag: peakgh mcg/l

tag: test

value: Arginine

tag: ghd

value: Yes


title: mice model rep2

tag: strain


title: gDNA from diagnosic pediatric AML 489

description:
pediatric AML
PAWGYG_Dx

source_name: pediatric AML sample 489

tag: trial protocol


title: mice treated with didymin rep1


title: gDNA from diagnosic pediatric AML 474

description:
pediatric AML
PAWGAZ_Dx

source_name: pediatric AML sample 474

tag: batch


title: Patient 24

description: peroxisomal disorder

value: F


title: gDNA from diagnosic pediatric AML 475

description:
pediatric AML
PAWGCN_Dx

source_name: pediatric AML sample 475

tag: Sex


title: mice wt rep3

source_name: normal control liver

value: normal


title: gDNA from diagnosic pediatric AML 472

description:
pediatric AML
PAWFVC_Dx

source_name: pediatric AML sample 472

tag: age (years)


title: gDNA from diagnosic pediatric AML 473

description:
pediatric AML
PAWFZT_Dx

source_name: pediatric AML sample 473

tag: timepoint


title: gDNA from diagnosic pediatric AML 485

description:
pediatric AML
PAWGTG_Dx

source_name: pediatric AML sample 485

tag: fusion


title: Patient 22

description: Chromosomal abnormality 21q deletion


title: gDNA from diagnosic pediatric AML 467

description:
pediatric AML
PAWFBA_Dx

source_name: pediatric AML sample 467


title: Patient 20

description: small ap thin stalk multiple sclerosis

value: Glucagon


title: gDNA from diagnosic pediatric AML 466

description:
pediatric AML
PAWEYY_Dx

source_name: pediatric AML sample 466


title: gDNA from diagnosic pediatric AML 482

description:
pediatric AML
PAWGPM_Dx

source_name: pediatric AML sample 482

value: Male


title: gDNA from diagnosic pediatric AML 478

description:
pediatric AML
PAWGFC_Dx

source_name: pediatric AML sample 478

value: Diagnosis


title: mice wt rep1

tag: tissue


title: mice wt rep2


title: Patient 21


title: Patient 26

description: small ap


title: gDNA from diagnosic pediatric AML 477

description:
pediatric AML
PAWGEW_Dx

source_name: pediatric AML sample 477


title: gDNA from diagnosic pediatric AML 480

description:
pediatric AML
PAWGEG_Dx

source_name: pediatric AML sample 480

value: Female


title: gDNA from diagnosic pediatric AML 471

description:
pediatric AML
PAWFTV_Dx

source_name: pediatric AML sample 471


title: Patient 17


title: gDNA from diagnosic pediatric AML 476

description:
pediatric AML
PAWGCP_Dx

source_name: pediatric AML sample 476


title: gDNA from diagnosic pediatric AML 470

description:
pediatric AML
PAWFIZ_Dx

source_name: pediatric AML sample 470


title: gDNA from diagnosic pediatric AML 460

description:
pediatric AML
PAWEKU_Dx

source_name: pediatric AML sample 460


title: gDNA from diagnosic pediatric AML 469

description:
pediatric AML
PAWFFJ_Dx

source_name: pediatric AML sample 469


title: Patient 23

description: right middle cranial fossa arachnoid cyst, smll ap

source_name: Peripheral blood mononuclea cells


title: gDNA from diagnosic pediatric AML 468

description:
pediatric AML
PAWFEM_Dx

source_name: pediatric AML sample 468


title: gDNA from diagnosic pediatric AML 457

description:
pediatric AML
PAWEFF_Dx

source_name: pediatric AML sample 457


title: gDNA from diagnosic pediatric AML 456

description:
pediatric AML
PAWECG_Dx

source_name: pediatric AML sample 456


title: Patient 14


title: gDNA from diagnosic pediatric AML 453

description:
pediatric AML
PAWEBC_Dx

source_name: pediatric AML sample 453


title: gDNA from diagnosic pediatric AML 455

description:
pediatric AML
PAWEEB_Dx

source_name: pediatric AML sample 455


title: Patient 19

description: small AP


title: gDNA from diagnosic pediatric AML 464

description:
pediatric AML
PAWESF_Dx

source_name: pediatric AML sample 464


title: Patient 18

description: MR pituitary normal


title: gDNA from diagnosic pediatric AML 479

description:
pediatric AML
PAWGEM_Dx

source_name: pediatric AML sample 479


title: gDNA from diagnosic pediatric AML 463

description:
pediatric AML
PAWERN_Dx

source_name: pediatric AML sample 463


title: gDNA from diagnosic pediatric AML 461

description:
pediatric AML
PAWEKW_Dx

source_name: pediatric AML sample 461


title: Patient 16


title: gDNA from diagnosic pediatric AML 450

description:
pediatric AML
PAWDYG_Dx

source_name: pediatric AML sample 450


title: gDNA from diagnosic pediatric AML 462

description:
pediatric AML
PAWENM_Dx

source_name: pediatric AML sample 462


title: gDNA from diagnosic pediatric AML 459

description:
pediatric AML
PAWEKL_Dx

source_name: pediatric AML sample 459


title: Patient 12

description: small pit MR, arachnoid cyst


title: gDNA from diagnosic pediatric AML 458

description:
pediatric AML
PAWEFT_Dx

source_name: pediatric AML sample 458


title: Patient 11


title: gDNA from diagnosic pediatric AML 447

description:
pediatric AML
PAWDTX_Dx

source_name: pediatric AML sample 447


title: gDNA from diagnosic pediatric AML 449

description:
pediatric AML
PAWDWA_Dx

source_name: pediatric AML sample 449


title: gDNA from diagnosic pediatric AML 448

description:
pediatric AML
PAWDVC_Dx

source_name: pediatric AML sample 448


title: gDNA from diagnosic pediatric AML 445

description:
pediatric AML
PAWDKU_Dx

source_name: pediatric AML sample 445


title: gDNA from diagnosic pediatric AML 454

description:
pediatric AML
PAWEBG_Dx

source_name: pediatric AML sample 454


title: Patient 13

source_name: Peripheral blood mononuclea cells


title: Patient 15

description: Normal MR pituitary


title: gDNA from diagnosic pediatric AML 452

description:
pediatric AML
PAWEAN_Dx

source_name: pediatric AML sample 452


title: gDNA from diagnosic pediatric AML 443

description:
pediatric AML
PAWDEG_Dx

source_name: pediatric AML sample 443


title: gDNA from diagnosic pediatric AML 451

description:
pediatric AML
PAWEAD_Dx

source_name: pediatric AML sample 451


title: gDNA from diagnosic pediatric AML 442

description:
pediatric AML
PAVZFT_Dx

source_name: pediatric AML sample 442


title: gDNA from diagnosic pediatric AML 465

description:
pediatric AML
PAWEVC_Dx

source_name: pediatric AML sample 465


title: gDNA from diagnosic pediatric AML 446

description:
pediatric AML
PAWDNF_Dx

source_name: pediatric AML sample 446


title: Patient 10

description: small AP


title: gDNA from diagnosic pediatric AML 444

description:
pediatric AML
PAWDHA_Dx

source_name: pediatric AML sample 444


title: gDNA from diagnosic pediatric AML 441

description:
pediatric AML
PAWDBB_Dx

source_name: pediatric AML sample 441


title: Patient 8

description: Prader-willi


title: gDNA from diagnosic pediatric AML 437

description:
pediatric AML
PAWCXR_Dx

source_name: pediatric AML sample 437


title: Patient 7

description: Wiedemann steiner syndrome


title: Patient 6


title: Patient 3

description: Normal pituitary Mri, incidental finding arachnoid cyst


title: gDNA from diagnosic pediatric AML 440

description:
pediatric AML
PAWDDC_Dx

source_name: pediatric AML sample 440


title: Patient 5


title: gDNA from diagnosic pediatric AML 438

description:
pediatric AML
PAWDCZ_Dx

source_name: pediatric AML sample 438


title: gDNA from diagnosic pediatric AML 439

description:
pediatric AML
PAWDBS_Dx

source_name: pediatric AML sample 439


title: gDNA from diagnosic pediatric AML 433

description:
pediatric AML
PAWCII_Dx

source_name: pediatric AML sample 433


title: gDNA from diagnosic pediatric AML 436

description:
pediatric AML
PAWCLC_Dx

source_name: pediatric AML sample 436


title: gDNA from diagnosic pediatric AML 435

description:
pediatric AML
PAWCIL_Dx

source_name: pediatric AML sample 435


title: Patient 4

description: Normal pituitary Mri


title: gDNA from diagnosic pediatric AML 434

description:
pediatric AML
PAWCKH_Dx

source_name: pediatric AML sample 434


title: gDNA from diagnosic pediatric AML 429

description:
pediatric AML
PAWCCR_Dx

source_name: pediatric AML sample 429


title: gDNA from diagnosic pediatric AML 430

description:
pediatric AML
PAWCBJ_Dx

source_name: pediatric AML sample 430


title: Patient 9

source_name: Peripheral blood mononuclea cells


title: gDNA from diagnosic pediatric AML 428

description:
pediatric AML
PAWCBZ_Dx

source_name: pediatric AML sample 428


title: gDNA from diagnosic pediatric AML 423

description:
pediatric AML
PAWBVL_Dx

source_name: pediatric AML sample 423


title: gDNA from diagnosic pediatric AML 427

description:
pediatric AML
PAWCAW_Dx

source_name: pediatric AML sample 427


title: 175IT_RV_14dpi

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCh38 genome build
Gene counts were obtained using featureCounts on GENCODE v27 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts

source_name: Human nasal epithelial cells (HNEC)

growth_protocol: Human nasal epithelial stem/progenitor cells (hNESPCs) were derived from tissue biopsies

extract_protocol:
Total RNA was extracted using a double extraction protocol: RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction (TRIzol; Thermo Fisher Scientific), followed by RNeasy Micro clean-up (Qiagen, Hilden, Germany). All human RNA was analyzed on an Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA) for quality assessment by RNA integrity number (range 5.8-9.1; median 7.3).
The cDNA libraries were prepared with 2 ng total RNA input and 1 μL of a 1:50000 dilution of ERCC RNA Spike-in Controls (Thermo Fisher Scientific) using the SMARTSeq version 2 protocol with the following modifications: (1) 20 μM template switch oligonucleotides and (2) 250 pg of cDNA with one-fifth of a reaction of a Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on a Labchip GX system (Perkin Elmer, Waltham, MA, USA).
All samples were subjected to an indexed paired-end sequencing run of 2×151 cycles on a HiSeq 4000 platform (Illumina) (30 samples per lane).

treatment_protocol: HRV16 (ATCC VR-283) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The apical secretion, basolateral medium and hNEC lysates of both HRV-infected and mock-infected hNECs were collected at 3, 6, 10 and 14 dpi for the relevant assays. Detailed protocols can be found in the Supplementary Materials.

tag: treatment

tag: time point


title: 175IT_mock_14d

value: mock


title: 175IT_RV_3dpi


title: gDNA from diagnosic pediatric AML 425

description:
pediatric AML
PAWBSE_Dx

source_name: pediatric AML sample 425


title: gDNA from diagnosic pediatric AML 422

description:
pediatric AML
PAWBUN_Dx

source_name: pediatric AML sample 422


title: 175IT_mock_3d


title: gDNA from diagnosic pediatric AML 432

description:
pediatric AML
PAWCJK_Dx

source_name: pediatric AML sample 432


title: 127IT_RV_14dpi


title: gDNA from diagnosic pediatric AML 421

description:
pediatric AML
PAWBRP_Dx

source_name: pediatric AML sample 421


title: gDNA from diagnosic pediatric AML 418

description:
pediatric AML
PAWBSF_Dx

source_name: pediatric AML sample 418


title: 127IT_mock_14d


title: gDNA from diagnosic pediatric AML 420

description:
pediatric AML
PAWBTJ_Dx

source_name: pediatric AML sample 420


title: 127IT_RV_3dpi


title: 133IT_R14


title: gDNA from diagnosic pediatric AML 417

description:
pediatric AML
PAWBDK_Dx

source_name: pediatric AML sample 417


title: gDNA from diagnosic pediatric AML 416

description:
pediatric AML
PAWBAS_Dx

source_name: pediatric AML sample 416


title: gDNA from diagnosic pediatric AML 419

description:
pediatric AML
PAWBSJ_Dx

source_name: pediatric AML sample 419


title: gDNA from diagnosic pediatric AML 431

description:
pediatric AML
PAWCGM_Dx

source_name: pediatric AML sample 431


title: 133IT_R3


title: gDNA from diagnosic pediatric AML 415

description:
pediatric AML
PAWAWL_Dx

source_name: pediatric AML sample 415


title: gDNA from diagnosic pediatric AML 407

description:
pediatric AML
PAWAFE_Dx

source_name: pediatric AML sample 407


title: gDNA from diagnosic pediatric AML 426

description:
pediatric AML
PAWBYK_Dx

source_name: pediatric AML sample 426


title: gDNA from diagnosic pediatric AML 408

description:
pediatric AML
PAWAFT_Dx

source_name: pediatric AML sample 408


title: 132IT_R14


title: gDNA from diagnosic pediatric AML 413

description:
pediatric AML
PAWAMF_Dx

source_name: pediatric AML sample 413


title: 127IT mock 3d


title: gDNA from diagnosic pediatric AML 412

description:
pediatric AML
PAWAMM_Dx

source_name: pediatric AML sample 412


title: 132IT_R3

source_name: Human nasal epithelial cells (HNEC)


title: 132IT_M14


title: gDNA from diagnosic pediatric AML 414

description:
pediatric AML
PAWANV_Dx

source_name: pediatric AML sample 414


title: gDNA from diagnosic pediatric AML 402

description:
pediatric AML
PAVZYI_Dx

source_name: pediatric AML sample 402


title: gDNA from diagnosic pediatric AML 405

description:
pediatric AML
PAWABG_Dx

source_name: pediatric AML sample 405


title: gDNA from diagnosic pediatric AML 406

description:
pediatric AML
PAWACC_Dx

source_name: pediatric AML sample 406


title: gDNA from diagnosic pediatric AML 424

description:
pediatric AML
PAWBVW_Dx

source_name: pediatric AML sample 424


title: gDNA from diagnosic pediatric AML 410

description:
pediatric AML
PAWAKF_Dx

source_name: pediatric AML sample 410


title: gDNA from diagnosic pediatric AML 411

description:
pediatric AML
PAWAMB_Dx

source_name: pediatric AML sample 411


title: 133IT_M14


title: 133IT_M3


title: gDNA from diagnosic pediatric AML 409

description:
pediatric AML
PAWAIG_Dx

source_name: pediatric AML sample 409


title: gDNA from diagnosic pediatric AML 401

description:
pediatric AML
PAVZTJ_Dx

source_name: pediatric AML sample 401


title: gDNA from diagnosic pediatric AML 400

description:
pediatric AML
PAVZNG_Dx

source_name: pediatric AML sample 400


title: 135IT_R14


title: 132IT_M3


title: 135IT_M3


title: gDNA from diagnosic pediatric AML 394

description:
pediatric AML
PAVZCR_Dx

source_name: pediatric AML sample 394


title: gDNA from diagnosic pediatric AML 404

description:
pediatric AML
PAWAAX_Dx

source_name: pediatric AML sample 404


title: gDNA from diagnosic pediatric AML 398

description:
pediatric AML
PAVZJX_Dx

source_name: pediatric AML sample 398


title: 135IT_R3


title: gDNA from diagnosic pediatric AML 399

description:
pediatric AML
PAVZJM_Dx

source_name: pediatric AML sample 399


title: 135IT_M14


title: gDNA from diagnosic pediatric AML 397

description:
pediatric AML
PAVZIF_Dx

source_name: pediatric AML sample 397


title: gDNA from diagnosic pediatric AML 396

description:
pediatric AML
PAVZHF_Dx

source_name: pediatric AML sample 396


title: gDNA from diagnosic pediatric AML 391

description:
pediatric AML
PAVZBA_Dx

source_name: pediatric AML sample 391


title: gDNA from diagnosic pediatric AML 390

description:
pediatric AML
PAVYYR_Dx

source_name: pediatric AML sample 390


title: gDNA from diagnosic pediatric AML 403

description:
pediatric AML
PAVZZC_Dx

source_name: pediatric AML sample 403


title: gDNA from diagnosic pediatric AML 389

description:
pediatric AML
PAVYVH_Dx

source_name: pediatric AML sample 389


title: gDNA from diagnosic pediatric AML 388

description:
pediatric AML
PAVYUD_Dx

source_name: pediatric AML sample 388


title: gDNA from diagnosic pediatric AML 395

description:
pediatric AML
PAVZEC_Dx

source_name: pediatric AML sample 395


title: gDNA from diagnosic pediatric AML 393

description:
pediatric AML
PAVZBG_Dx

source_name: pediatric AML sample 393


title: gDNA from diagnosic pediatric AML 385

description:
pediatric AML
PAVYNF_Dx

source_name: pediatric AML sample 385


title: gDNA from diagnosic pediatric AML 392

description:
pediatric AML
PAVZBM_Dx

source_name: pediatric AML sample 392


title: Non N-ERD, R8367

data_processing:
FASTQ files were mapped using STAR to GRCh38 genome build
Gene counts were obtained using featureCounts on GENCODE v27 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts

source_name: Nasal Polyp tissue

growth_protocol: Not Applicable

extract_protocol:
Total RNA was extracted following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). All human tissue RNAs were analyzed on Agilent Bioanalyser for quality assessment with RNA Integrity Number (RIN) range from 6.2 to 8.6 and median of RIN 6.8.
cDNA libraries were prepared using 2 ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific) using the SMARTSeq v2 protocol2 with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA).
All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina) (25 samples/lane).

treatment_protocol: Not Applicable

value: Nasal Polyp tissue

tag: disease state

value: Chronic rhinosinusitis with nasal polyps (CRSwNP)

tag: phenotype

value: Non N-ERD


title: Non N-ERD, R8364


title: Non N-ERD, R8366


title: gDNA from diagnosic pediatric AML 387

description:
pediatric AML
PAVYKS_Dx

source_name: pediatric AML sample 387


title: gDNA from diagnosic pediatric AML 386

description:
pediatric AML
PAVYTI_Dx

source_name: pediatric AML sample 386


title: Non N-ERD, R8363


title: gDNA from diagnosic pediatric AML 383

description:
pediatric AML
PAVYFM_Dx

source_name: pediatric AML sample 383


title: gDNA from diagnosic pediatric AML 381

description:
pediatric AML
PAVXZS_Dx

source_name: pediatric AML sample 381


title: gDNA from diagnosic pediatric AML 384

description:
pediatric AML
PAVYLW_Dx

source_name: pediatric AML sample 384


title: gDNA from diagnosic pediatric AML 382

description:
pediatric AML
PAVXZL_Dx

source_name: pediatric AML sample 382


title: gDNA from diagnosic pediatric AML 379

description:
pediatric AML
PAVXUR_Dx

source_name: pediatric AML sample 379


title: Non N-ERD, R8365


title: Non N-ERD, R8361


title: gDNA from diagnosic pediatric AML 378

description:
pediatric AML
PAVXUC_Dx

source_name: pediatric AML sample 378


title: Non N-ERD, R8362


title: gDNA from diagnosic pediatric AML 380

description:
pediatric AML
PAVXZH_Dx

source_name: pediatric AML sample 380


title: Non N-ERD, R8360


title: gDNA from diagnosic pediatric AML 375

description:
pediatric AML
PAVXNZ_Dx

source_name: pediatric AML sample 375


title: gDNA from diagnosic pediatric AML 374

description:
pediatric AML
PAVXFA_Dx

source_name: pediatric AML sample 374


title: gDNA from diagnosic pediatric AML 370

description:
pediatric AML
PAVXCF_Dx

source_name: pediatric AML sample 370


title: Non N-ERD, R8358


title: gDNA from diagnosic pediatric AML 369

description:
pediatric AML
PAVWZV_Dx

source_name: pediatric AML sample 369


title: gDNA from diagnosic pediatric AML 377

description:
pediatric AML
PAVXSH_Dx

source_name: pediatric AML sample 377


title: gDNA from diagnosic pediatric AML 376

description:
pediatric AML
PAVXRM_Dx

source_name: pediatric AML sample 376


title: gDNA from diagnosic pediatric AML 367

description:
pediatric AML
PAVWVT_Dx

source_name: pediatric AML sample 367


title: gDNA from diagnosic pediatric AML 368

description:
pediatric AML
PAVWXI_Dx

source_name: pediatric AML sample 368


title: gDNA from diagnosic pediatric AML 366

description:
pediatric AML
PAVWUU_Dx

source_name: pediatric AML sample 366


title: gDNA from diagnosic pediatric AML 372

description:
pediatric AML
PAVXDS_Dx

source_name: pediatric AML sample 372


title: gDNA from diagnosic pediatric AML 371

description:
pediatric AML
PAVXEB_Dx

source_name: pediatric AML sample 371


title: gDNA from diagnosic pediatric AML 373

description:
pediatric AML
PAVXEL_Dx

source_name: pediatric AML sample 373


title: Non N-ERD, R8359

source_name: Nasal Polyp tissue


title: gDNA from diagnosic pediatric AML 362

description:
pediatric AML
PAVWPW_Dx

source_name: pediatric AML sample 362


title: Non N-ERD, R8357


title: gDNA from diagnosic pediatric AML 361

description:
pediatric AML
PAVWNG_Dx

source_name: pediatric AML sample 361


title: gDNA from diagnosic pediatric AML 356

description:
pediatric AML
PAVWEA_Dx

source_name: pediatric AML sample 356


title: gDNA from diagnosic pediatric AML 357

description:
pediatric AML
PAVWFA_Dx

source_name: pediatric AML sample 357


title: Non N-ERD, R8356


title: Non N-ERD, R8355


title: N-ERD, R8345

value: N-ERD


title: N-ERD, R8347


title: N-ERD, R8348


title: N-ERD, R8349


title: gDNA from diagnosic pediatric AML 363

description:
pediatric AML
PAVWRR_Dx

source_name: pediatric AML sample 363


title: gDNA from diagnosic pediatric AML 365

description:
pediatric AML
PAVWRI_Dx

source_name: pediatric AML sample 365


title: gDNA from diagnosic pediatric AML 354

description:
pediatric AML
PAVVUT_Dx

source_name: pediatric AML sample 354


title: gDNA from diagnosic pediatric AML 353

description:
pediatric AML
PAVVKU_Dx

source_name: pediatric AML sample 353


title: gDNA from diagnosic pediatric AML 359

description:
pediatric AML
PAVWJK_Dx

source_name: pediatric AML sample 359


title: N-ERD, R8343


title: gDNA from diagnosic pediatric AML 351

description:
pediatric AML
PAVVCS_Dx

source_name: pediatric AML sample 351


title: gDNA from diagnosic pediatric AML 360

description:
pediatric AML
PAVWJY_Dx

source_name: pediatric AML sample 360


title: gDNA from diagnosic pediatric AML 364

description:
pediatric AML
PAVWRN_Dx

source_name: pediatric AML sample 364


title: N-ERD, R8344


title: gDNA from diagnosic pediatric AML 358

description:
pediatric AML
PAVWJV_Dx

source_name: pediatric AML sample 358


title: N-ERD, R8346


title: gDNA from diagnosic pediatric AML 355

description:
pediatric AML
PAVWBB_Dx

source_name: pediatric AML sample 355


title: gDNA from diagnosic pediatric AML 352

description:
pediatric AML
PAVVTF_Dx

source_name: pediatric AML sample 352


title: gDNA from diagnosic pediatric AML 350

description:
pediatric AML
PAVVAT_Dx

source_name: pediatric AML sample 350


title: gDNA from diagnosic pediatric AML 349

description:
pediatric AML
PAVVAB_Dx

source_name: pediatric AML sample 349


title: N-ERD, R8341

source_name: Nasal Polyp tissue


title: gDNA from diagnosic pediatric AML 348

description:
pediatric AML
PAVUVD_Dx

source_name: pediatric AML sample 348


title: gDNA from diagnosic pediatric AML 346

description:
pediatric AML
PAVUVI_Dx

source_name: pediatric AML sample 346


title: gDNA from diagnosic pediatric AML 347

description:
pediatric AML
PAVUZN_Dx

source_name: pediatric AML sample 347


title: gDNA from diagnosic pediatric AML 344

description:
pediatric AML
PAVUPS_Dx

source_name: pediatric AML sample 344


title: N-ERD, R8339


title: N-ERD, R8340


title: gDNA from diagnosic pediatric AML 345

description:
pediatric AML
PAVUUU_Dx

source_name: pediatric AML sample 345


title: gDNA from diagnosic pediatric AML 343

description:
pediatric AML
PAVUPX_Dx

source_name: pediatric AML sample 343


title: N-ERD, R8337


title: gDNA from diagnosic pediatric AML 342

description:
pediatric AML
PAVULK_Dx

source_name: pediatric AML sample 342


title: N-ERD, R8338


title: gDNA from diagnosic pediatric AML 341

description:
pediatric AML
PAVUHF_Dx

source_name: pediatric AML sample 341


title: gDNA from diagnosic pediatric AML 340

description:
pediatric AML
PAVUGM_Dx

source_name: pediatric AML sample 340


title: N-ERD, R8342


title: gDNA from diagnosic pediatric AML 338

description:
pediatric AML
PAVUBN_Dx

source_name: pediatric AML sample 338


title: gDNA from diagnosic pediatric AML 339

description:
pediatric AML
PAVUEF_Dx

source_name: pediatric AML sample 339


title: gDNA from diagnosic pediatric AML 337

description:
pediatric AML
PAVUAD_Dx

source_name: pediatric AML sample 337


title: gDNA from diagnosic pediatric AML 335

description:
pediatric AML
PAVTXM_Dx

source_name: pediatric AML sample 335


title: gDNA from diagnosic pediatric AML 336

description:
pediatric AML
PAVTWM_Dx

source_name: pediatric AML sample 336


title: GBM Patient [ndGBM-09]

city: Farmington

first: Parveen

last: Kumar

state: Connecticut

address: 10 Farmington Drive

institute: Application Computational Scientist

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12.
For Patient rGBM-01 and ndGBM-01, the sequencing was performed on Illumina for 150 cycles with sequencing recommended condition (Read1: 26nt, Read2: 98nt and Index1: 8 nt). For the remaining patients, the sequencing was performed on Illumina for 300 cycles with sequencing recommended condition (Read1: 151nt, Read2: 151nt and Index1: 8 nt).
Raw FASTQ reads from Illumina were aligned to GRCh38 (human) using CellRanger V5 software from 10X Genomics with default parameters. As an output, Cellranger also generates a bam for each sample
Genome_build: GRCh38 (human)
Supplementary_files_format_and_content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated genes.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

source_name: Human Tumor Tissue

growth_protocol: fresh tumors tissues were obtained from patients

extract_protocol:
Fresh tumor tissues were dissociated and captured using 10X Genomics Chromium system following the 10X Genomics 3' Transcriptomics kit V1
Following 10X Genomics 3' Transcriptomics kit V1, Sequenced at BGI using DNBseq.

tag: subject status

value: GBM Patient

tag: tumor grade

value: IV


title: GBM Patient [LGG-03]

value: II


title: GBM Patient [ndGBM-08]


title: gDNA from diagnosic pediatric AML 332

description:
pediatric AML
PAVTLN_Dx

source_name: pediatric AML sample 332


title: gDNA from diagnosic pediatric AML 333

description:
pediatric AML
PAVTRM_Dx

source_name: pediatric AML sample 333


title: GBM Patient [ndGBM-07]


title: GBM Patient [ndGBM-06]


title: gDNA from diagnosic pediatric AML 330

description:
pediatric AML
PAVTDU_Dx

source_name: pediatric AML sample 330


title: gDNA from diagnosic pediatric AML 331

description:
pediatric AML
PAVTIP_Dx

source_name: pediatric AML sample 331


title: GBM Patient [ndGBM-05]


title: gDNA from diagnosic pediatric AML 329

description:
pediatric AML
PAVTFI_Dx

source_name: pediatric AML sample 329


title: gDNA from diagnosic pediatric AML 328

description:
pediatric AML
PAVTDW_Dx

source_name: pediatric AML sample 328


title: gDNA from diagnosic pediatric AML 327

description:
pediatric AML
PAVTBA_Dx

source_name: pediatric AML sample 327


title: gDNA from diagnosic pediatric AML 326

description:
pediatric AML
PAVSYK_Dx

source_name: pediatric AML sample 326

value: FUS-ERG


title: gDNA from diagnosic pediatric AML 323

description:
pediatric AML
PAVSSE_Dx

source_name: pediatric AML sample 323


title: gDNA from diagnosic pediatric AML 324

description:
pediatric AML
PAVSVU_Dx

source_name: pediatric AML sample 324


title: GBM Patient [LGG-04-3]


title: gDNA from diagnosic pediatric AML 322

description:
pediatric AML
PAVSNL_Dx

source_name: pediatric AML sample 322


title: gDNA from diagnosic pediatric AML 321

description:
pediatric AML
PAVSJN_Dx

source_name: pediatric AML sample 321


title: gDNA from diagnosic pediatric AML 320

description:
pediatric AML
PAVSIX_Dx

source_name: pediatric AML sample 320


title: GBM Patient [LGG-04-2]


title: gDNA from diagnosic pediatric AML 325

description:
pediatric AML
PAVSWX_Dx

source_name: pediatric AML sample 325


title: gDNA from diagnosic pediatric AML 319

description:
pediatric AML
PAVSIZ_Dx

source_name: pediatric AML sample 319


title: GBM Patient [LGG-04-1]


title: gDNA from diagnosic pediatric AML 318

description:
pediatric AML
PAVSHX_Dx

source_name: pediatric AML sample 318


title: gDNA from diagnosic pediatric AML 334

description:
pediatric AML
PAVTRU_Dx

source_name: pediatric AML sample 334


title: gDNA from diagnosic pediatric AML 316

description:
pediatric AML
PAVSFB_Dx

source_name: pediatric AML sample 316


title: GBM Patient [ndGBM-10]

source_name: Human Tumor Tissue

value: III


title: GBM Patient [ndGBM-04]


title: GBM Patient [rGBM-05-3]


title: gDNA from diagnosic pediatric AML 315

description:
pediatric AML
PAVSAN_Dx

source_name: pediatric AML sample 315


title: gDNA from diagnosic pediatric AML 314

description:
pediatric AML
PAVSEJ_Dx

source_name: pediatric AML sample 314


title: gDNA from diagnosic pediatric AML 317

description:
pediatric AML
PAVSCL_Dx

source_name: pediatric AML sample 317


title: GBM Patient [rGBM-05-1]


title: gDNA from diagnosic pediatric AML 311

description:
pediatric AML
PAVRTN_Dx

source_name: pediatric AML sample 311


title: GBM Patient [rGBM-05-2]


title: gDNA from diagnosic pediatric AML 310

description:
pediatric AML
PAVRJP_Dx

source_name: pediatric AML sample 310


title: GBM Patient [ndGBM-03-3]


title: GBM Patient [ndGBM-03-2]


title: gDNA from diagnosic pediatric AML 307

description:
pediatric AML
PAVRCS_Dx

source_name: pediatric AML sample 307


title: gDNA from diagnosic pediatric AML 305

description:
pediatric AML
PAVRAT_Dx

source_name: pediatric AML sample 305


title: GBM Patient [rGBM-04-3]


title: gDNA from diagnosic pediatric AML 308

description:
pediatric AML
PAVRGN_Dx

source_name: pediatric AML sample 308


title: gDNA from diagnosic pediatric AML 302

description:
pediatric AML
PAVPXS_Dx

source_name: pediatric AML sample 302


title: gDNA from diagnosic pediatric AML 304

description:
pediatric AML
PAVPWB_Dx

source_name: pediatric AML sample 304


title: GBM Patient [ndGBM-03-1]


title: gDNA from diagnosic pediatric AML 296

description:
pediatric AML
PAVPLM_Dx

source_name: pediatric AML sample 296


title: gDNA from diagnosic pediatric AML 299

description:
pediatric AML
PAVPIU_Dx

source_name: pediatric AML sample 299


title: GBM Patient [rGBM-04-2]


title: gDNA from diagnosic pediatric AML 300

description:
pediatric AML
PAVPUY_Dx

source_name: pediatric AML sample 300


title: GBM Patient [rGBM-04-1]


title: gDNA from diagnosic pediatric AML 312

description:
pediatric AML
PAVRUZ_Dx

source_name: pediatric AML sample 312


title: gDNA from diagnosic pediatric AML 313

description:
pediatric AML
PAVRWU_Dx

source_name: pediatric AML sample 313


title: gDNA from diagnosic pediatric AML 297

description:
pediatric AML
PAVPMJ_Dx

source_name: pediatric AML sample 297


title: GBM Patient [rGBM-03-3]

source_name: Human Tumor Tissue


title: gDNA from diagnosic pediatric AML 294

description:
pediatric AML
PAVPLI_Dx

source_name: pediatric AML sample 294


title: gDNA from diagnosic pediatric AML 293

description:
pediatric AML
PAVPJM_Dx

source_name: pediatric AML sample 293


title: gDNA from diagnosic pediatric AML 292

description:
pediatric AML
PAVPKA_Dx

source_name: pediatric AML sample 292


title: gDNA from diagnosic pediatric AML 309

description:
pediatric AML
PAVRHS_Dx

source_name: pediatric AML sample 309


title: gDNA from diagnosic pediatric AML 295

description:
pediatric AML
PAVPLL_Dx

source_name: pediatric AML sample 295


title: GBM Patient [rGBM-02-5]


title: gDNA from diagnosic pediatric AML 306

description:
pediatric AML
PAVRBA_Dx

source_name: pediatric AML sample 306


title: GBM Patient [rGBM-04-4]


title: gDNA from diagnosic pediatric AML 303

description:
pediatric AML
PAVPZJ_Dx

source_name: pediatric AML sample 303


title: gDNA from diagnosic pediatric AML 289

description:
pediatric AML
PAVPED_Dx

source_name: pediatric AML sample 289


title: GBM Patient [rGBM-02-4]


title: gDNA from diagnosic pediatric AML 288

description:
pediatric AML
PAVPCA_Dx

source_name: pediatric AML sample 288


title: gDNA from diagnosic pediatric AML 301

description:
pediatric AML
PAVPVK_Dx

source_name: pediatric AML sample 301


title: gDNA from diagnosic pediatric AML 286

description:
pediatric AML
PAVNZU_Dx

source_name: pediatric AML sample 286


title: gDNA from diagnosic pediatric AML 287

description:
pediatric AML
PAVPBC_Dx

source_name: pediatric AML sample 287


title: gDNA from diagnosic pediatric AML 285

description:
pediatric AML
PAVNZB_Dx

source_name: pediatric AML sample 285


title: GBM Patient [rGBM-02-2]


title: gDNA from diagnosic pediatric AML 284

description:
pediatric AML
PAVNYE_Dx

source_name: pediatric AML sample 284


title: gDNA from diagnosic pediatric AML 283

description:
pediatric AML
PAVNXC_Dx

source_name: pediatric AML sample 283


title: gDNA from diagnosic pediatric AML 282

description:
pediatric AML
PAVNWF_Dx

source_name: pediatric AML sample 282


title: GBM Patient [ndGBM-01-F]

source_name: Human Tumor Tissue


title: gDNA from diagnosic pediatric AML 280

description:
pediatric AML
PAVNVA_Dx

source_name: pediatric AML sample 280


title: gDNA from diagnosic pediatric AML 281

description:
pediatric AML
PAVNVF_Dx

source_name: pediatric AML sample 281


title: GBM Patient [ndGBM-01-D]


title: gDNA from diagnosic pediatric AML 279

description:
pediatric AML
PAVNUJ_Dx

source_name: pediatric AML sample 279


title: gDNA from diagnosic pediatric AML 291

description:
pediatric AML
PAVPFR_Dx

source_name: pediatric AML sample 291


title: gDNA from diagnosic pediatric AML 277

description:
pediatric AML
PAVNNA_Dx

source_name: pediatric AML sample 277


title: GBM Patient [ndGBM-01-A]


title: gDNA from diagnosic pediatric AML 276

description:
pediatric AML
PAVNPN_Dx

source_name: pediatric AML sample 276


title: GBM Patient [ndGBM-01-C]


title: gDNA from diagnosic pediatric AML 278

description:
pediatric AML
PAVNUW_Dx

source_name: pediatric AML sample 278


title: GBM Patient [rGBM-01-D]


title: gDNA from diagnosic pediatric AML 274

description:
pediatric AML
PAVNIX_Dx

source_name: pediatric AML sample 274


title: gDNA from diagnosic pediatric AML 275

description:
pediatric AML
PAVNKI_Dx

source_name: pediatric AML sample 275


title: gDNA from diagnosic pediatric AML 272

description:
pediatric AML
PAVNHN_Dx

source_name: pediatric AML sample 272


title: gDNA from diagnosic pediatric AML 273

description:
pediatric AML
PAVNHD_Dx

source_name: pediatric AML sample 273


title: GBM Patient [rGBM-02-3]


title: GBM Patient [rGBM-01-C]


title: gDNA from diagnosic pediatric AML 270

description:
pediatric AML
PAVNFA_Dx

source_name: pediatric AML sample 270


title: gDNA from diagnosic pediatric AML 271

description:
pediatric AML
PAVNGY_Dx

source_name: pediatric AML sample 271


title: GBM Patient [rGBM-01-B]


title: gDNA from diagnosic pediatric AML 268

description:
pediatric AML
PAVMWJ_Dx

source_name: pediatric AML sample 268


title: gDNA from diagnosic pediatric AML 267

description:
pediatric AML
PAVNAZ_Dx

source_name: pediatric AML sample 267


title: gDNA from diagnosic pediatric AML 269

description:
pediatric AML
PAVNBL_Dx

source_name: pediatric AML sample 269


title: GBM Patient [rGBM-01-A]

source_name: Human Tumor Tissue


title: gDNA from diagnosic pediatric AML 266

description:
pediatric AML
PAVNAN_Dx

source_name: pediatric AML sample 266


title: gDNA from diagnosic pediatric AML 261

description:
pediatric AML
PAVMIY_Dx

source_name: pediatric AML sample 261


title: A5

city: Shanghai

first: Jibo

last: Zhou

state: Shanghai

address: 639 Zhizaoju Road, Shanghai, 200011, China

department: Department of Ophthalmology, Shanghai Ninth People's Hospital

institute: Shanghai Jiao Tong University School of Medicine

description: volume: 300 μL (100μL from each eye)

data_processing:
Basecalls were performed using CASAVA version 1.8
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs
The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch
The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change. Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value.
Genome_build: hg38
Supplementary_files_format_and_content: .xlsx files include tag reads, and normalized data (TPM), etc.

source_name: aqueous humor

extract_protocol:
aqueous humor was collected at the onset of surgeries, and RNA was extracted using Trizol reagent
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: aqueous humor

tag: eye disorder

value: age-related cataract

tag: mean age (years)


title: A4

description: volume: 300 μL (100μL from each eye)


title: gDNA from diagnosic pediatric AML 263

description:
pediatric AML
PAVMPA_Dx

source_name: pediatric AML sample 263


title: gDNA from diagnosic pediatric AML 259

description:
pediatric AML
PAVMED_Dx

source_name: pediatric AML sample 259


title: NP1400

city: Stanford

first: Tsuguhisa

last: Nakayama

state: CA

address: 801 Welch Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Stanford University

data_processing:
The sequence data were processed with CellRanger software v3.1.0 for demultiplexing, read alignment, filtering,  and transcript counting.
Integration of the two datasets (Stuart, Butler et al, 2019), normalization, dimension reduction, and gene expression analysis were performed using Suerat v3.2.2 in R v4.0.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat v3 RDS files, barcode files, feature files, matrix files

source_name: Nasal polyp

extract_protocol:
Single-cell suspensions were prepared from nasal polyp tissues which were minced into small pieces and placed into a C tube (Miltenyi Biotec) within a solution of RPMI 1640 (Gibco) containing 10% fetal bovine serum (FBS), 0.02 mg/ml DNase I (Millipore Sigma), and 4 mg/ml collagenase type IV (Thermo Fisher Scientific). The mixture was homogenized using the gentleMACS Dissociator (Miltenyi Biotec) and incubated with MACSmix Tube Rotator.
The single cell suspension was loaded onto the Chromium Controller (10x Genomics) using the Chromium single cell 3' Reagent Kit v3 (10x Genomics), and scRNA-seq libraries generated. Sequencing was performed on a Illimina HiSeq 4000 with 75bp pair end reads.

value: Chronic rhinosinusitis with nasal polyp


title: gDNA from diagnosic pediatric AML 262

description:
pediatric AML
PAVMNA_Dx

source_name: pediatric AML sample 262


title: gDNA from diagnosic pediatric AML 256

description:
pediatric AML
PAVMES_Dx

source_name: pediatric AML sample 256


title: A2

description: volume: 300 μL (100μL from each eye)


title: gDNA from diagnosic pediatric AML 264

description:
pediatric AML
PAVMNK_Dx

source_name: pediatric AML sample 264


title: gDNA from diagnosic pediatric AML 257

description:
pediatric AML
PAVMEH_Dx

source_name: pediatric AML sample 257


title: NP1327


title: A1

description: volume: 300 μL (100μL from each eye)


title: gDNA from diagnosic pediatric AML 255

description:
pediatric AML
PAVMBH_Dx

source_name: pediatric AML sample 255


title: A3

description: volume: 300 μL (100μL from each eye)


title: gDNA from diagnosic pediatric AML 254

description:
pediatric AML
PAVLYV_Dx

source_name: pediatric AML sample 254


title: gDNA from diagnosic pediatric AML 253

description:
pediatric AML
PAVLWV_Dx

source_name: pediatric AML sample 253


title: gDNA from diagnosic pediatric AML 258

description:
pediatric AML
PAVMFT_Dx

source_name: pediatric AML sample 258


title: gDNA from diagnosic pediatric AML 265

description:
pediatric AML
PAVMZL_Dx

source_name: pediatric AML sample 265


title: gDNA from diagnosic pediatric AML 251

description:
pediatric AML
PAVLTF_Dx

source_name: pediatric AML sample 251


title: gDNA from diagnosic pediatric AML 252

description:
pediatric AML
PAVLWY_Dx

source_name: pediatric AML sample 252


title: gDNA from diagnosic pediatric AML 250

description:
pediatric AML
PAVLSY_Dx

source_name: pediatric AML sample 250


title: C4

description: volume: 300 μL (100μL from each eye)

value: high myopia


title: gDNA from diagnosic pediatric AML 260

description:
pediatric AML
PAVMGM_Dx

source_name: pediatric AML sample 260


title: gDNA from diagnosic pediatric AML 248

description:
pediatric AML
PAVLJH_Dx

source_name: pediatric AML sample 248


title: gDNA from diagnosic pediatric AML 249

description:
pediatric AML
PAVLPL_Dx

source_name: pediatric AML sample 249


title: C3

description: volume: 300 μL (100μL from each eye)

source_name: aqueous humor


title: gDNA from diagnosic pediatric AML 247

description:
pediatric AML
PAVLLR_Dx

source_name: pediatric AML sample 247

value: Male


title: gDNA from diagnosic pediatric AML 246

description:
pediatric AML
PAVLKG_Dx

source_name: pediatric AML sample 246

value: Diagnosis


title: C2

description: volume: 300 μL (100μL from each eye)


title: C1

description: volume: 300 μL (100μL from each eye)


title: gDNA from diagnosic pediatric AML 245

description:
pediatric AML
PAVLKB_Dx

source_name: pediatric AML sample 245

value: Female


title: gDNA from diagnosic pediatric AML 243

description:
pediatric AML
PAVLGZ_Dx

source_name: pediatric AML sample 243


title: gDNA from diagnosic pediatric AML 242

description:
pediatric AML
PAVLDU_Dx

source_name: pediatric AML sample 242


title: gDNA from diagnosic pediatric AML 241

description:
pediatric AML
PAVLBB_Dx

source_name: pediatric AML sample 241


title: C5

description: volume: 300 μL (100μL from each eye)


title: gDNA from diagnosic pediatric AML 239

description:
pediatric AML
PAVKZH_Dx

source_name: pediatric AML sample 239


title: gDNA from diagnosic pediatric AML 240

description:
pediatric AML
PAVLAE_Dx

source_name: pediatric AML sample 240


title: gDNA from diagnosic pediatric AML 237

description:
pediatric AML
PAVKVT_Dx

source_name: pediatric AML sample 237


title: gDNA from diagnosic pediatric AML 244

description:
pediatric AML
PAVLEG_Dx

source_name: pediatric AML sample 244


title: gDNA from diagnosic pediatric AML 236

description:
pediatric AML
PAVKNA_Dx

source_name: pediatric AML sample 236


title: gDNA from diagnosic pediatric AML 235

description:
pediatric AML
PAVKKI_Dx

source_name: pediatric AML sample 235


title: gDNA from diagnosic pediatric AML 234

description:
pediatric AML
PAVKJV_Dx

source_name: pediatric AML sample 234


title: MM patient 18

city: Barcelona

first: Ester

last: Lozano

state: Barcelona

address: Rosselló, 153

department: Hemato-Oncology

country: Spain

institute: IDIBAPS

hyb_protocol: A minimum of 100 ng of total RNA per sample was loaded and run on the HuV1_Cancer Immu_v1_1_Nanostring for analysis of the NanoString PanCancer Immune Profiling Panel

scan_protocol: The sample cartridge was scanned by an nCounter Digital Analyse (NanoString Technologies) at 555 fields of view.

data_processing: The raw data were re-scaled to account for the differences in raw code counts. This was performed using nSolver Analysis Software (NanoString Technologies), incorporating positive, negative and 'normalisation' gene target counts.

source_name: RNA - CD138-depleted bone marrow cells

label_protocol: Capture probes and reporter probes (NanoString Technologies) were added to the extracted 100ng of mRNA according to manufacturer guidelines.

extract_protocol: CD138-depleted BM cell fraction was isolated with anti-CD138 mAb-coated immunomagnetic beads using an AutoMacs cell sorter (Milteny Biotec, Bergisch Gladbach, Germany). Total RNA from the CD138neg BM cell fraction was extracted using the TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s instructions.

tag: disease

value: MM


title: MM patient 17


title: MM patient 21


title: MM patient 20


title: MM patient 22


title: gDNA from diagnosic pediatric AML 233

description:
pediatric AML
PAVKJD_Dx

data_processing:
DNA methylation profiling was performed at Arkansas Children’s Research Institute  on the Illumina Infinium HumanMethylationEPIC platform, using recommended manufacturer protocols. The resulting data were processed as recommended to match LAML, TARGET AML, and TARGET AML-IF HumanMethylation450 array results, then corrected for artifacts resulting from copy number alterations and differences in cellularity where estimates were available.  Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
Processed data file includes normalized (SeSAMe) Average Beta

source_name: pediatric AML sample 233

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow or Peripheral Blood, cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.


title: MM patient 16


title: gDNA from diagnosic pediatric AML 232

description:
pediatric AML
PAVKEM_Dx

source_name: pediatric AML sample 232


title: gDNA from diagnosic pediatric AML 230

description:
pediatric AML
PAVKFD_Dx

source_name: pediatric AML sample 230


title: MM patient 15


title: gDNA from diagnosic pediatric AML 231

description:
pediatric AML
PAVKEX_Dx

source_name: pediatric AML sample 231


title: gDNA from diagnosic pediatric AML 229

description:
pediatric AML
PAVKEY_Dx

source_name: pediatric AML sample 229


title: gDNA from diagnosic pediatric AML 228

description:
pediatric AML
PAVKBW_Dx

source_name: pediatric AML sample 228


title: MM patient 19


title: gDNA from diagnosic pediatric AML 238

description:
pediatric AML
PAVKXE_Dx

source_name: pediatric AML sample 238


title: MM patient 14


title: gDNA from diagnosic pediatric AML 226

description:
pediatric AML
PAVJXG_Dx

source_name: pediatric AML sample 226


title: gDNA from diagnosic pediatric AML 225

description:
pediatric AML
PAVKAH_Dx

source_name: pediatric AML sample 225


title: MM patient 13


title: gDNA from diagnosic pediatric AML 223

description:
pediatric AML
PAVJRF_Dx

source_name: pediatric AML sample 223


title: MM patient 12


title: gDNA from diagnosic pediatric AML 224

description:
pediatric AML
PAVJVS_Dx

source_name: pediatric AML sample 224


title: gDNA from diagnosic pediatric AML 222

description:
pediatric AML
PAVJPL_Dx

source_name: pediatric AML sample 222


title: MM patient 11


title: gDNA from diagnosic pediatric AML 298

description:
pediatric AML
PAVPMH_Dx

source_name: pediatric AML sample 298


title: gDNA from diagnosic pediatric AML 221

description:
pediatric AML
PAVJIT_Dx

source_name: pediatric AML sample 221


title: MM patient 9


title: MM patient 10


title: gDNA from diagnosic pediatric AML 219

description:
pediatric AML
PAVIYH_Dx

source_name: pediatric AML sample 219


title: gDNA from diagnosic pediatric AML 214

description:
pediatric AML
PAVIDK_Dx

source_name: pediatric AML sample 214


title: gDNA from diagnosic pediatric AML 215

description:
pediatric AML
PAVHWZ_Dx

source_name: pediatric AML sample 215


title: GBM Patient [rGBM-03-1]

source_name: Human Tumor Tissue


title: gDNA from diagnosic pediatric AML 218

description:
pediatric AML
PAVIZK_Dx

source_name: pediatric AML sample 218


title: gDNA from diagnosic pediatric AML 216

description:
pediatric AML
PAVIGB_Dx

source_name: pediatric AML sample 216