title: DU16-02S0004902_L2

city: Durham

first: Emily

middle: R.

last: Ko

state: NC

address: 4103 Graceview Way

department: Medicine

institute: Duke University

data_processing:
Batch 1 was sequenced on an Illumina HiSeq 2500, and batch 2 was sequenced on an Illumina NovaSeq 6000.
For batch 1, adapters were removed by EA Genomics prior to receipt of sequences.  For batch 2, adapters were remvoed using Trimmomatic v0.38.
Reads were aligned to the hg38 reference transcriptome using Bowtie2 with "option --very-sensitive-local"
Express version 1.5.1 was used for quantification at the transcript level. For batch 1 the option "strand rf-stranded" was used, and for batch 2 "strand fr-stranded" was used.
Expression data were normalized using the trimmed mean of M-values approach, specifically using the calcNormFactors function in the edgeR package in R.
Supplementary files format and content: The processed data file contains log2-transformed and normalized counts per million.

source_name: whole blood

extract_protocol:
Total RNA was extracted from whole blood collected and stored at -80°C in PAXgene Blood RNA tubes using the PAXgene miRNA Extraction Kit
For batch 1, libraries were constructed using GlobinClear Globin RNA Reduction (Invitrogen) with TruSeq Stranded mRNA Library Kit (Illumina).  For batch 2, libraries were contructed using NuGEN Universal Plus mRNA-Seq Library Prep Kit with AnyDeplete Globin depletion (NuGEN/Tecan).

tag: sequencing batch

tag: gender

value: female

tag: age

tag: site

tag: infection type

value: Viral

tag: pathogen


title: HeLa D7ZF-EGFP ChIP-Seq

status: Public on Dec 19 2023

type: SRA

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

library_source: genomic

data_processing:
Sequencing reads obtained from multiple sequencing runs were pooled and aligned to the human reference genome assembly GRCh38.p13 [PMID: 21750661] using bwa-mem2 aligner [DOI: 10.1109/IPDPS.2019.00041, https://doi.org/10.1109/IPDPS.2019.00041] and samtools [PMID: 19505943], followed by removal of PCR and optical duplicates by the Picard MarkDuplicates tool.
Peak calling was performed with Genrich (https://github.com/jsh58/Genrich), using the ENCODE blacklist (https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz) for filtering out problematic regions and "EGFP ChIP-Seq" sample as a control.
Assembly: hg38
Supplementary files format and content: Putative binding sites are provided in a narrowPeak format, as repored by Genrich (https://github.com/jsh58/Genrich).

molecule: genomic DNA

organism: Homo sapiens

source_name: Hela cells infected with a modified version of the tetracycline inducible LentiX vector carrying D7ZF-EGFP fusion.

growth_protocol: Cells were grown in 10 cm dishes and the expression of D7ZF or EGFP (control) was induced for 24h with 100ng/mL doxycycline.

extract_protocol:
The cell lines were crosslinked with 1% formaldehyde for 10 min at room temperature and further processed following the manufacturer’s protocol for High Cell number using the kit TruChip Chromatin Shearing Kit, Covaris. Chromatin shearing was performed using Covaris M220 sonicator. 1% of the sheared chromatin was separated for qPCR validation (input sample) and the rest was used for immunoprecipitation. Sonicated chromatin was immunoprecipitated using a goat GFP-antibody (MPI-CBG antibody facility) and Protein G sepharose beads (Protein G Sepharose® 4 Fast Flow, GE Healthcare). Eluates were reverse crosslinked followed by RNA and protein digestion.
Sequencing libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® from 17-75 ng of ChIP DNA with 15 PCR amplification cycle and size selection using AMPure XP beads.

tag: cell line

value: HeLa

tag: treatment

value: tetracycline inducible LentiX vector carying RecF8-EGFP fusion

tag: chip antibody

value: Anti-GFP antibody, MPI-CBG


title: M2_3D_P5* [RNAseq]

city: Lyon

first: Thomas

last: Diot

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

library_source: transcriptomic

data_processing:
Trimming of adapter sequences was done with Cutadapt (v.3.4) using -a CTGTCTCTTATACACATCT and -A CTGTCTCTTATACACATCT parameters.
Reads were mapped using STAR (v.2.7.9) to the human reference genome assembly GRCh38.p13 with --seedSearchStartLmax 38 --outFilterMatchNminOverLread 0.66 --outReadsUnmapped Fastx --outSAMmultNmax -1 --outMultimapperOrder Random --outFilterScoreMinOverLread 0.66 --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --twopassMode Basic --limitSjdbInsertNsj 1324910 parameters.
Gene expression data was generated with HTseq-count (v.0.13.5) using --order pos --stranded reverse parameters.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: polyA RNA

growth_protocol: Culture medium was changed twice a week, and RMS_O were split every 2 weeks on average. Finally, culture medium was changed 24 to 48 h before extraction.

extract_protocol:
RNA from both RMS tissues and matched in vitro models cultured in 2D or 3D conditions with DMEM, M3 and M5 media were extracted using the Allprep DNA/RNA/miRNA universal kit (Qiagen, cat. no. 80224) and Arcturus® PicoPure® RNA Isolation Kit (ThermoFisher Scientific, cat. no. KIT0204) only for small tumor pieces, following manufacturer’s instructions.
For RNA‑seq library construction, 100 to 1 000 ng of total RNAs were used. Libraries were prepared with Illumina Stranded mRNA Prep (Illumina, cat. no. 20040534) following recommendations.
ssRNA-seq (stranded RNA-seq)

tag: tissue

value: RMS1 organoid

tag: cell type

value: Rhabdomyosarcoma

tag: age in_years

tag: Sex

value: M

tag: histological subtype

value: Embryonal

tag: disease state

value: Relapse

tag: sample location

value: Parameningeal

tag: primary tumor_location

tag: fresh/cryopreserved

value: cryopreserved

tag: medium

tag: passage number

tag: culture type


title: DMEM_2D_P19 [Exome panel]

data_processing:
Unique Molecular Identifiers (UMIs) were extracted and deduplicated using UMI-tools(v.1.1.2) with default parameters.
Reads from each sequencing lane were mapped separately to thehg38human genome using bwa-mem2 (v.2.2.1) with default parameters.
Optical duplicates were removed using Picard MarkDuplicates(v.2.27.4) with default parameters.
GATK (v.4.3.0.0) BaseRecalibrator and ApplyBQSR were used with default parameters.
GATK (v.4.3.0.0) Mutect2 (with parameter ‘--callable-depth 1’) in multi-sample tumor-only mode (with sample groups as RMS1, RMS2)
Variant filtering with GATK (v.4.3.0.0) LearnReadOrientationModel, GetPileupSummaries, CalculateContamination and FilterMutectCalls, with default parameters.
Germline variants were filtered with vcftools (v.0.1.16) ‘vcf-isec’ (using germline variants from gnomAD and 1000 Genomes VCF files), with default parameters.
vcftools (v.0.1.16) ‘vcf-merge’ was used to merge all samples into a single VCF file, with default parameters.
A custom Python script was used to re-annotate variants whose FILTER value was wrongly modified by vcf-merge.
Variants were annotated using Ensembl Variant Effect Predictor (VEP,v.108.1) with default parameters.
Assembly: hg38
Supplementary files format and content: VCF file includes germline-filtered variants for each Sample

extract_protocol:
genomic DNA (gDNA) from both RMS tissues and matched in vitro models cultured in 2D or 3D conditions with DMEM, M3 and M5 media were extracted using the Allprep DNA/RNA/miRNA universal kit (Qiagen, cat. no. 80224), following manufacturer’s instructions.
For DNA‑seq library construction, a total of 200 ng input gDNA per sample was used for SureSelect XT low input library preparation (Agilent, Santa Clara, CA).

value: RMS2 cell line

value: Relapse/metastatic

value: Lung

value: Ischioanal

value: fresh

value: DMEM


title: DU16-02S0004898_L1

country: USA

molecule: total RNA

tag: sequencing batch

tag: gender

value: female

tag: age

tag: site

tag: infection type

value: Viral

value: Dengue


title: LB1 pA-DamID, d11, recombined, clone 6, replicate 2, dam only

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 25 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Finally, samples were z-scale normalized to account for different in dynamic range between replicates and experiments.
Assembly: mm10
Supplementary files format and content: BigWig files of log2-normalized LaminB1 or H3K9me3 pA-DamID scores for 25 kb genomic bins.

organism: Mus musculus

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) female mouse embryonic stem cells (mESCs) F1 hybrid cell line and derived clones were cultured in 2i+LIF condition, according to the 4D Nucleome guidelines (https://data.4dnucleome.org/biosources/4DNSRMG5APUM/). Briefly, cells were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1), supplemented with N-2 (Gibco), B-27 (Gibco), 0.05% BSA (Gibco), 10 × 4 U leukemia inhibitory factor (LIF; Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress), 1.5 × 10−4 M 1-thioglycerol (Sigma-Aldrich), and 1% penicillin-streptomycin (Gibco, 15070063) on 0.1% gelatin-coated plates. Cells were passaged every 2 days. Cells were seeded and incubated overnight before harvesting. Mycoplasma contamination was ruled out by regular testings (#LT07-318; Lonza).

extract_protocol:
One million cells were collected by centrifugation (500 g, 3 min) and washed sequentially in PBS and digitonin wash buffer (DigWash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 h at 4 °C in 200 μL DigWash with 1:100 LaminB1 antibody (Abcam, ab16048, rabbit) or 1:100 H3K9me3 antibody (Diagenone, C15410193, Rabbit), followed by a wash step with DigWash. This was repeated with a 1:200 pA-Dam solution (~60 NEB Dam units), followed by 2 wash steps. Dam activity was induced by an incubation for 30 min at 37 °C in 100 μL DigWash supplemented with 80 μM SAM. For every condition, another 1 million cells were processed in only DigWash and during Dam activation incubated with 4 units of Dam enzyme (NEB, M0222L). This Dam only control sample serves to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C).

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: genotype

value: recombined

tag: antibody


title: RMS1_O_P17 [Exome panel]

tag: tissue

value: RMS1 organoid

tag: cell type

value: Rhabdomyosarcoma

tag: age in_years

tag: Sex

value: M


title: DU16-02S0004893_L1

value: male

tag: pathogen


title: DMEM_2D_P16 [Exome panel]

tag: histological subtype

value: Embryonal

tag: disease state

tag: sample location

tag: primary tumor_location

tag: fresh/cryopreserved


title: RMS1_T [Exome panel]

source_name: RMS1 tissue

value: RMS1 tissue

value: Relapse

value: Parameningeal

tag: medium

tag: passage number

tag: culture type


title: DU16-02S0004892_L1

tag: sequencing batch

tag: gender

tag: age

tag: site

tag: infection type


title: DU16-02S0004890_L7

value: Bacterial

value: Leptospira


title: LB1 pA-DamID, d11, parental, replicate 2, dam only

tag: cell line

tag: cell type

tag: genotype

value: control

tag: antibody


title: LB1 pA-DamID, d11, recombined, clone 21, replicate 2, dam only


title: RMS1_O_P23* [Exome panel]

tag: tissue

tag: age in_years

tag: Sex

tag: histological subtype

value: cryopreserved


title: DU16-02S0004882_L6

value: Viral

tag: pathogen


title: DU16-02S0004883_L7

value: female

value: Dengue


title: DU16-02S0004879_L4


title: DU16-02S0004880_L4


title: LB1 pA-DamID, i9, recombined, clone 14, replicate 1, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: DU16-02S0004878_L4


title: RMS1_O_P6* [Exome panel]

value: RMS1 organoid

tag: disease state

tag: sample location

tag: primary tumor_location

tag: fresh/cryopreserved

tag: medium


title: DU16-02S0004877_L4

tag: sequencing batch

tag: gender

tag: age


title: LB1 pA-DamID, i9, recombined, clone 12, replicate 1, dam-LB1

tag: cell line

value: recombined


title: DU16-02S0004876_L4

tag: site

tag: infection type


title: LB1 pA-DamID, i9, parental, replicate 1, dam-LB1

tag: cell type

tag: genotype

tag: antibody


title: DU16-02S0004875_L3


title: DU16-02S0004869_L1


title: RMS1_O_P13 [Exome panel]

tag: tissue

value: Rhabdomyosarcoma

tag: age in_years

tag: Sex

value: M

value: fresh

tag: passage number

tag: culture type


title: RMS2_O_P7 [Exome panel]

value: RMS2 organoid

tag: histological subtype

value: Embryonal

tag: disease state

value: Relapse/metastatic

tag: sample location

value: Lung

tag: primary tumor_location

value: Ischioanal


title: DU16-02S0004873_L1

tag: sequencing batch

tag: gender

value: male

value: Bacterial

tag: pathogen

value: Leptospira


title: DU16-02S0004874_L2

tag: age

tag: site


title: LB1 pA-DamID, i7, recombined, clone 7, replicate 1, dam-LB1

tag: cell line

tag: cell type


title: LB1 pA-DamID, i7, recombined, clone 12, replicate 1, dam-LB1

tag: genotype

tag: antibody


title: RMS2_O_P6 [Exome panel]

tag: tissue

tag: age in_years

tag: fresh/cryopreserved

tag: medium


title: DU16-02S0004864_L1

value: female

tag: infection type

value: Rickettsia


title: RMS1_O_P22* [Exome panel]

tag: Sex

tag: histological subtype

tag: disease state

value: Relapse

value: Parameningeal

value: cryopreserved

tag: passage number

tag: culture type


title: DU16-02S0004862_L8

tag: sequencing batch

tag: gender

tag: pathogen


title: DU16-02S0004863_L1

tag: age

tag: site


title: DU16-02S0004861_L8


title: LB1 pA-DamID, d11, recombined, clone 21, replicate 1, dam-LB1

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

value: mESC

tag: genotype

value: recombined


title: RMS2_O_P7* [Exome panel]

tag: tissue

value: Rhabdomyosarcoma

tag: age in_years

value: M

tag: sample location

tag: primary tumor_location


title: DU16-02S0004868_L1

tag: infection type

value: Viral

value: Dengue


title: DU16-02S0004867_L1


title: RMS2_O_P29* [Exome panel]

value: RMS2 organoid

tag: Sex

tag: histological subtype

value: Embryonal

value: Relapse/metastatic

value: Lung

tag: fresh/cryopreserved

tag: medium


title: DU16-02S0004859_L8

tag: sequencing batch


title: LB1 pA-DamID, i7, parental, replicate 1, dam-LB1

value: control

tag: antibody


title: LB1 pA-DamID, d11, parental, replicate 1, dam-LB1


title: DU16-02S0004860_L8

tag: gender

value: female

value: Bacterial

tag: pathogen


title: RMS2_T [Exome panel]

source_name: RMS2 tissue

value: RMS2 tissue

tag: disease state

value: Ischioanal

tag: passage number

tag: culture type


title: DU16-02S0004857_L1

tag: age

tag: site


title: DU16-02S0004858_L8

value: male


title: LB1 pA-DamID, d11, recombined, clone 6, replicate 1, dam-LB1

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

tag: genotype


title: RMS2_O_P28* [Exome panel]

tag: tissue

tag: age in_years

tag: sample location

tag: primary tumor_location

value: cryopreserved


title: DU16-02S0004856_L7

tag: infection type


title: DU16-02S0004853_L6

tag: sequencing batch

value: Rickettsia


title: RMS2_O_P8* [Exome panel]

value: Rhabdomyosarcoma

tag: Sex

tag: histological subtype

tag: fresh/cryopreserved

tag: medium


title: DU16-02S0004852_L1

tag: gender

tag: pathogen

value: Leptospira


title: DU16-02S0004851_L6

tag: age


title: LB1 pA-DamID, i9, parental, replicate 1, dam only

value: mESC

tag: antibody


title: DU16-02S0004850_L6

tag: site


title: LB1 pA-DamID, i7, recombined, clone 12, replicate 1, dam only

tag: cell line

tag: cell type

value: recombined


title: DU16-02S0004846_L5

value: Viral

value: Dengue


title: LB1 pA-DamID, i7, recombined, clone 7, replicate 1, dam only

tag: genotype


title: Tonsil_Multiome_2, Chromium Single Cell Multiome ATAC, Sorting Strategy 2

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

description: Tonsil cells sorted as in Strategy 2

library_source: transcriptomic single cell

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
Paired scRNAseq/scATACseq data produced from Chromium Single Cell Multiome ATAC + Gene Expression was processed using the cellranger-arc count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix folder contents produced by the CellRanger pipelines, containing three files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz. For the multiome samples, we also have deposited atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi files.

source_name: Tonsil

extract_protocol:
Using the Chromium Single Cell 3′ Reagent Kit v2 or v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

tag: tissue

value: Tonsil

value: Sorting Strategy 2 (Described in Extended Data Fig. 5)

tag: treatment


title: DU16-02S0004845_L1


title: DU16-02S0004844_L3


title: CD34_BM_Culture, IL7/Flt3L/SCF

description: CD34+ progenitors from BM cultured with IL7, SCF and Flt3L for 15 days

source_name: Bone Marrow

value: Bone Marrow

value: Live, CD45+ cells

value: IL-7, FLT3-L, SCF


title: DU16-02S0004843_L3

value: Bacterial


title: Tonsil_Multiome_2, Chromium Single Cell Multiome Gene Expression, Sorting Strategy 2

description: Tonsil cells sorted as in Strategy 2


title: DU16-02S0004842_L3


title: Tonsil_Multiome_1B, Chromium Single Cell Multiome Gene Expression, Sorting Strategy 1

description: Tonsil cells sorted as in Strategy 1

value: Sorting Strategy 1 (Described in Extended Data Fig. 5)


title: LB1 pA-DamID, i9, recombined, clone 14, replicate 1, dam only


title: LB1 pA-DamID, i7, parental, replicate 1, dam only

value: control


title: LB1 pA-DamID, i9, recombined, clone 12, replicate 1, dam only

value: F1 hybrid 129/Sv:CAST/EiJ


title: LB1 pA-DamID, d11, recombined, clone 21, replicate 1, dam only


title: DU16-02S0004840_L2

value: female


title: CD34_Blood_Culture, GM-CSF/Flt3L/SCF

description: CD34+ progenitors from blood cultured with GM-CSF, SCF and Flt3L for 15 days

source_name: Blood

value: Blood

value: GM-CSF, Flt3-L, SCF


title: Tonsil_Multiome_1B, Chromium Single Cell Multiome ATAC, Sorting Strategy 1

description: Tonsil cells sorted as in Strategy 1


title: DU16-02S0004839_L2


title: DU16-02S0004838_L2

value: male


title: DU16-02S0004836_L8

value: Leptospira


title: DU16-02S0004835_L8

value: Rickettsia


title: DU16-02S0004847_L5

value: Viral


title: Tonsil_Multiome_1A, Chromium Single Cell Multiome Gene Expression, Sorting Strategy 1

description: Tonsil cells sorted as in Strategy 1


title: LB1 pA-DamID, d11, recombined, clone 6, replicate 1, dam only

value: mESC

value: recombined


title: LB1 pA-DamID, d11, parental, replicate 1, dam only


title: Tonsil_Multiome_1A, Chromium Single Cell Multiome ATAC_Sorting Strategy 1

description: Tonsil cells sorted as in Strategy 1

value: Tonsil


title: DU16-02S0004834_L8


title: LB1 pA-DamID, i10, recombined, clone 33, replicate 2, dam-LB1


title: Lin-NCR-BDCA2-CD34-CD1c-CD4-CD161-DR+ cells sorted from tonsil, 3 TotalSeqB antibodies

description: Cultured tonsil cells (Figure 4). 3 different samples were hash-tagged with TotalSeqB antibodies. Hashtag_B0251 (rdcPrimary_TotalSeqB, sequence GTCAACTCTTTAGCG), Hashtag_B0252 (rdcCulture1_TotalSeqB, sequence TGATGGCCTATTGGG), Hashtag_B0253 (rdcCulture2_TotalSeqB, sequence TTCCGCCTCTCTTTG).

value: Lin- NCR- BDCA2- CD34- CD1c- CD4- CD161- DR+ cells sorted from tonsil

value: GM-CSF, Flt3L, SCF


title: DU16-02S0004832_L7

value: Dengue


title: DU16-02S0004830_L7


title: LB1 pA-DamID, i10, recombined, clone 18, replicate 2, dam-LB1


title: DU16-02S0004841_L2

value: Bacterial


title: N-1425-4, Healthy Control, Patient 3

description: Lamina Propria extracted as described in the manuscript.

source_name: Terminal ileum

value: Terminal ileum

value: CD45+CD3-CD19- cells sorted from lamina propria of terminal ileum


title: LB1 pA-DamID, i12, recombined, clone 10, replicate 2, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ


title: DU16-02S0004826_L5

value: female


title: DU16-02S0004825_L5


title: DU16-02S0004824_L5


title: LB1 pA-DamID, i12, recombined, clone 2, replicate 2, dam-LB1


title: LB1 pA-DamID, i10, parental, replicate 2, dam-LB1

value: control


title: CD-1818-6, Chron's Disease, Patient 2 (non-inflammed)


title: CD-1818-4, Chron's Disease, Patient 2 (inflamed)


title: DU16-02S0004822_L5


title: LB1 pA-DamID, i12, parental, replicate 2, dam-LB1


title: H3K9me2; TetR-SET; Suv39x; ChIP-seq (B)

city: BOSTON

first: Andy

last: Yuan

state: MA

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

data_processing:
ChIP-seq reads were mapped to the S288C reference genome R64.3.1 using Bowtie with default settings
Data was normalized to counts per million using the bamCoverage module of deepTools 3.5.2
Data was visualized in IGV 2.16.0.

organism: Saccharomyces cerevisiae

growth_protocol: 50-100 ml cultures of S. cerevisiae cells were grown in YPAD medium to an OD600 of 1 to 2.

extract_protocol:
Cells were fixed in the presence of 1% formaldehyde for 15 minutes at room temperature with gentle mixing on a moving platform.  For FLAG3X-Suv39x and Sir3-FLAG3X-SET immunoprecipitations, cells were fixed in the presence of 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) for 30 minutes at room temperature and then fixed in the presence of 1% formaldehyde for 30 minutes at room temperature.  Crosslinking reactions were quenched in the presence of 125 mM glycine.  Crosslinked cells were pelleted, washed twice in cold tris-buffered saline (TBS), once in cold water, and stored at -80oC.  Samples were sonicated in a cold room using a tip sonicator (Sonics VCX 500; set at 30% amplitude) for a total of 80 seconds, with five-minute incubations on ice after every 20 seconds of sonication.  Samples were further sheared by sonication using a Q800R3 sonicator (Qsonica; set at 20% amplitude).  Samples were sonicated for a total of 15 minutes, with 15-second incubations without sonication following every 15 seconds of sonication.
Libraries were prepared by ligating Y-adapters encoding unique barcode sequences (Wong, Jin, and Moqtaderi, 2013) to immunoprecipitated DNA.  Libraries were amplified by PCR for 18 cycles.  Amplified DNA 150-500 bp in length was purified using a gel extraction kit (Omega Bio-tek) and SPRIselect beads (Beckman Coulter).

value: anti-H3K9me2 (Abcam ab1220)


title: DU16-02S0004820_L4

value: male


title: LB1 pA-DamID, i10, recombined, clone 33, replicate 2, dam only


title: DU16-02S0004819_L4


title: DU16-02S0004818_L4


title: DU16-02S0004831_L7


title: DU16-02S0004814_L2


title: CD-1813-7, Chron's Disease, Patient 1 (non-inflammed)


title: CD-1813-5, Chron's Disease, Patient 1 (inflammed)


title: DU16-02S0004813_L2


title: DU16-02S0004828_L6


title: LB1 pA-DamID, i10, recombined, clone 18, replicate 2, dam only


title: N-7420-3, Healthy Control, Patient 4


title: DU16-02S0004827_L6

value: Leptospira


title: LB1 pA-DamID, i12, recombined, clone 10, replicate 2, dam only


title: DU16-02S0004823_L5


title: DU16-02S0004810_L1


title: DU16-02S0004807_L7

value: Rickettsia


title: LB1 pA-DamID, i12, recombined, clone 2, replicate 2, dam only


title: DU16-02S0004806_L7


title: LB1 pA-DamID, i10, parental, replicate 2, dam only


title: DU16-02S0004805_L7


title: RNA-Seq - suboptimal donor EX28-3

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

data_processing:
For each bulk ATAC-seq sample, the pair-end reads from fastq files were aligned to the human genome (GRCh38) using bwa mem mode with duplicated reads removed. The 5' end of ATAC-seq reads were shifted to the actual cut-site of the Transposase using alignmentSieve module implemented in DeepTools (4). The peaks were called using Macs2 (5) with using the pair-end read information.
Gene expression was quantified with RSEM (v1.3.3) (rsem-calculate-expression --strandedness reverse --no-bam-output --paired-end --bowtie2) using the bowtie2  (v2.4.2) as the aligner and hg19 transcriptome as the reference. TPM values from RSEM were log 2 transformed (log2(TPM+1)) and the top five thousand variably expressed genes were used to perform PCA and visualize clustering of the samples.  The peak sets from multiple samples were identified as the overlap ones among samples using bUseSummarizeOverlaps function in DiffBind. We then calculated the TF activity
Assembly: GRCh38

source_name: suboptimal donor EX28-3

extract_protocol:
By applying RNA  and ATAC sequencing, we want to investigate the transcriptomics and epigenetic factors that contributing for difference between optimal and suboptimcal  in NK cells
scATAC-Seq: Single‐nucleus libraries were generated using the 10X Genomics Chromium Next GEM ATAC Capture and Library (V1.1), following the manufacturer’s protocol. Nine samples were pooled to give a final concentration of 10 nM. Pooled samples underwent further qPCR prior to sequencing with the NovaSeq 6000 sequencer using the S1, 100 cycles flow cell and sequenced with read 1 for 50 cycles, i7 8 cycles, i5 index 16 cycles, and read 2 for 49 cycles.
ATAC-Seq: Libraries were sequenced  2 x 100 bp on an Illumina NovaSeq6000 to obtain at least 50 million high quality mapping reads per sample.
RNA-Seq: Libraries were prepared using Illumina next generation RNA sequencing .

value: CBNK

value: suboptimal

tag: strain


title: DU16-02S0004804_L7

tag: infection type


title: RNA-Seq - Replicate2 of optimal donor EX28-1

source_name: Replicate2 of optimal donor EX28-1

value: optimal


title: DU16-02S0004803_L6

tag: sequencing batch


title: RNA-Seq - Replicate1 of optimal donor EX28-1

source_name: Replicate1 of optimal donor EX28-1


title: DU16-02S0004802_L6


title: LB1 pA-DamID, i12, parental, replicate 2, dam only

value: mESC


title: LB1 pA-DamID, i10, recombined, clone 33, replicate 1, dam-LB1

value: recombined


title: DU16-02S0004801_L6


title: DU16-02S0004812_L1


title: RNA-Seq - Replicate2 of optimal donor EX27-4

source_name: Replicate2 of optimal donor EX27-4


title: RNA-Seq - suboptimal donor EX29-4

source_name: suboptimal donor EX29-4


title: DU16-02S0004799_L6


title: DU16-02S0004795_L5

value: Viral


title: DU16-02S0004796_L5


title: RNA-Seq - Replicate2 of optimal donor EX29-2

source_name: Replicate2 of optimal donor EX29-2


title: LB1 pA-DamID, i12, recombined, clone 10, replicate 1, dam-LB1


title: RNA-Seq - Replicate1 of optimal donor EX27-4

source_name: Replicate1 of optimal donor EX27-4


title: DU16-02S0004798_L6


title: RNA-Seq - Replicate3 of optimal donor EX29-2

source_name: Replicate3 of optimal donor EX29-2


title: DU16-02S0004793_L5

source_name: whole blood

value: Dengue


title: DU16-02S0004808_L1


title: LB1 pA-DamID, i12, recombined, clone 2, replicate 1, dam-LB1


title: LB1 pA-DamID, i10, recombined, clone 18, replicate 1, dam-LB1


title: DU16-02S0004792_L1


title: DU16-02S0004794_L5


title: DU16-02S0004790_L1

value: Bacterial


title: RNA-Seq - Replicate2 of optimal donor EX29-1

source_name: Replicate2 of optimal donor EX29-1


title: LB1 pA-DamID, i10, parental, replicate 1, dam-LB1

source_name: F1 hybrid 129/Sv:CAST/EiJ


title: RNA-Seq - Replicate1 of optimal donor EX29-1

source_name: Replicate1 of optimal donor EX29-1


title: DU16-02S0004788_L1


title: DU16-02S0004787_L1


title: DU16-02S0004786_L1


title: RNA-Seq - Replicate1 of optimal donor EX47-15

source_name: Replicate1 of optimal donor EX47-15


title: heart tissue, WT genotype, HFHS diet, Carnosine treatment rep 4

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

description:
library name: 24
transcript_tpms_all_samples.tsv column 26

data_processing:
Reads were aligned using Kallisto version 0.43.1, to Ensemble transcriptome release 98 (119215 transcript targets), run using default settings, with specific input parameters of 100 bootstraps and 16 threads.
Differential gene expression was quantified using Sleuth version 0.30.0, aggregating abundance on Ensemble genes, with a two-step Likelihood Ratio Test and Wald Test
Gene ontology analyses were performed by inputting the indicated gene sets into the using ToppFun web-server tool, ToppGene Suiteand using default settings. Results were exported and up to the top 50 enriched terms in each “Category” were tabulated in Supplement Tables
Assembly: ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary files format and content: TSV; transcript abundance table,  "Transcript Per Million"  TPM sample matrix per transcript with ensembl transcript annotation.

source_name: heart

extract_protocol:
Total RNA was extracted from left ventricular tissues (~10 mg), using the RNeasy Fibrous Tissue Kit (QIAGEN, Germantown, Maryland)
Illumina TruSeq® Stranded mRNA Library Prep kits (Illumina) were used to prepare sequencing libraries from mRNA, followed by reverse transcription to cDNA, fragment purification and ligation to indexed (barcoded) adaptors. Indexed libraries were pooled for multiplex sequencing and run on an SP flow cell on the Illumina NovaSeq 6000 sequencer for 300 cycles with 150-base paired-end reads.

value: heart

value: wt

value: hfhs/carn


title: DU16-02S0004785_L1

value: female


title: DU16-02S0004784_L1


title: RNA-Seq - Replicate3 of optimal donor EX47-17

source_name: Replicate3 of optimal donor EX47-17


title: LB1 pA-DamID, i12, parental, replicate 1, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ

value: control


title: LB1 pA-DamID, i10, recombined, clone 18, replicate 1, dam only


title: DU16-02S0004783_L8


title: LB1 pA-DamID, i12, recombined, clone 10, replicate 1, dam only


title: LB1 pA-DamID, i10, recombined, clone 33, replicate 1, dam only


title: DU16-02S0004782_L8

value: male


title: RNA-Seq - Replicate2 of optimal donor EX47-17

source_name: Replicate2 of optimal donor EX47-17


title: DU16-02S0004780_L8


title: DU16-02S0004781_L8


title: LB1 pA-DamID, i12, recombined, clone 2, replicate 1, dam only


title: DU16-02S0004777_L5


title: RNA-Seq - Replicate1 of optimal donor EX29-2

source_name: Replicate1 of optimal donor EX29-2


title: RNA-Seq - Replicate1 of optimal donor EX47-17

source_name: Replicate1 of optimal donor EX47-17


title: LB1 pA-DamID, i10, parental, replicate 1, dam only


title: DU16-02S0004789_L1


title: DU16-02S0004776_L5


title: LB1 pA-DamID, i12, parental, replicate 1, dam only


title: DU16-02S0004774_L5

value: Leptospira


title: DU16-02S0004775_L5


title: RNA-Seq - Replicate2 of optimal donor EX47-16

source_name: Replicate2 of optimal donor EX47-16


title: LB1 pA-DamID, d1, recombined, clone 29, replicate 2, dam-LB1


title: DU16-02S0004773_L5


title: RNA-Seq - Replicate1 of optimal donor EX47-16

source_name: Replicate1 of optimal donor EX47-16


title: DU16-02S0004771_L4

value: Rickettsia


title: LB1 pA-DamID, d1, recombined, clone 29, replicate 2, dam only


title: DU16-02S0004770_L4


title: RNA-Seq - Replicate3 of optimal donor EX47-15

source_name: Replicate3 of optimal donor EX47-15

value: CBNK


title: DU16-02S0004769_L4


title: LB1 pA-DamID, d1, recombined, clone 28, replicate 2, dam-LB1


title: RNA-Seq - Replicate2 of optimal donor EX47-15

source_name: Replicate2 of optimal donor EX47-15


title: DU16-02S0004766_L3


title: DU16-02S0004768_L4


title: LB1 pA-DamID, d1, recombined, clone 28, replicate 2, dam only


title: RNA-Seq - Replicate2 of suboptimal donor EX47-14

source_name: Replicate2 of suboptimal donor EX47-14

value: suboptimal


title: DU16-02S0004765_L3


title: RNA-Seq - Replicate3 of optimal donor EX47-16

source_name: Replicate3 of optimal donor EX47-16

value: optimal


title: LB1 pA-DamID, d4, recombined, clone 6, replicate 2, dam-LB1

value: mESC


title: RNA-Seq - Replicate1 of suboptimal donor EX47-14

source_name: Replicate1 of suboptimal donor EX47-14


title: LB1 pA-DamID, d4, recombined, clone 6, replicate 2, dam only

value: recombined


title: RNA-Seq - Replicate3 of suboptimal donor EX47-11

source_name: Replicate3 of suboptimal donor EX47-11


title: DU16-02S0004772_L4

source_name: whole blood


title: DU14-03S0000018_L5

tag: race

value: White

value: Staphylococcus


title: DU14-03S0000019_L8

value: Viral


title: DU14-03S0000020_L2

value: Bacterial

value: Enterobacter


title: RNA-Seq - Replicate2 of suboptimal donor EX47-11

source_name: Replicate2 of suboptimal donor EX47-11


title: LB1 pA-DamID, d4, recombined, clone 1, replicate 2, dam only

source_name: F1 hybrid 129/Sv:CAST/EiJ


title: DU14-03S0000021_L8


title: DU14-03S0000017_L5

value: Noninfection


title: DU14-03S0000015_L3


title: RNA-Seq - Replicate1 of suboptimal donor EX47-11

source_name: Replicate1 of suboptimal donor EX47-11


title: LB1 pA-DamID, d3, recombined, clone 21, replicate 2, dam-LB1


title: DU14-03S0000014_L3


title: DU14-03S0000013_L2


title: DU14-03S0000012_L2

value: female


title: RNA-Seq - Replicate3 of suboptimal donor EX47-7

source_name: Replicate3 of suboptimal donor EX47-7


title: LB1 pA-DamID, d3, recombined, clone 21, replicate 2, dam only

value: F1 hybrid 129/Sv:CAST/EiJ


title: DU16-02S0004767_L3

value: Dengue


title: DU14-03S0000010_L1


title: LB1 pA-DamID, d3, recombined, clone 12, replicate 2, dam-LB1


title: DU14-03S0000007_L7

value: male


title: DU14-03S0000008_L1


title: LB1 pA-DamID, d3, recombined, clone 12, replicate 2, dam only


title: DU14-03S0000011_L2

value: Asian


title: RNA-Seq - Replicate3 of suboptimal donor EX47-13

source_name: Replicate3 of suboptimal donor EX47-13


title: RNA-Seq - Replicate2 of suboptimal donor EX47-7

source_name: Replicate2 of suboptimal donor EX47-7


title: LB1 pA-DamID, d4, recombined, clone 1, replicate 2, dam-LB1


title: DU14-03S0000006_L1

value: Streptococcus


title: RNA-Seq - Replicate2 of suboptimal donor EX47-13

source_name: Replicate2 of suboptimal donor EX47-13

value: CBNK


title: DU14-03S0000005_L6


title: DU14-03S0000016_L5


title: RNA-Seq - Replicate1 of suboptimal donor EX47-13

source_name: Replicate1 of suboptimal donor EX47-13

value: suboptimal


title: DU14-03S0000003_L3


title: DU14-03S0000001_L8


title: LB1 pA-DamID, d2, recombined, clone 14, replicate 2, dam-LB1


title: RNA-Seq - Replicate1 of suboptimal donor EX47-7

source_name: Replicate1 of suboptimal donor EX47-7


title: LB1 pA-DamID, d2, recombined, clone 14, replicate 2, dam only


title: LB1 pA-DamID, d2, recombined, clone 3, replicate 2, dam-LB1


title: DU14-03S0000002_L8


title: DU10-01S0000031_L3


title: RNA-Seq - Replicate3 of suboptimal donor EX47-14

source_name: Replicate3 of suboptimal donor EX47-14


title: DU10-01S0000029_L3


title: LB1 pA-DamID, d2, recombined, clone 3, replicate 2, dam only


title: DU10-01S0000026_L8


title: DU10-01S0000028_L1


title: DU10-01S0000025_L6


title: optimal donor EX29-1

source_name: optimal donor EX29-1

value: optimal


title: DU10-01S0000022_L6


title: LB1 pA-DamID, d5, recombined, clone 11, replicate 2, dam-LB1

value: mESC


title: DU10-01S0000024_L6


title: LB1 pA-DamID, d5, recombined, clone 11, replicate 2, dam only

value: recombined


title: Replicate1 of suboptimal donor EX28-4

source_name: Replicate1 of suboptimal donor EX28-4


title: DU10-01S0000020_L5


title: LB1 pA-DamID, d5, recombined, clone 2, replicate 2, dam-LB1


title: Replicate2 of suboptimal donor EX28-4

source_name: Replicate2 of suboptimal donor EX28-4


title: DU10-01S0000023_L6


title: DU14-03S0000004_L3


title: LB1 pA-DamID, d5, recombined, clone 2, replicate 2, dam only


title: DU10-01S0000019_L3

value: White


title: Replicate1 of suboptimal donor EX28-3

source_name: Replicate1 of suboptimal donor EX28-3


title: DU10-01S0000018_L1

value: Staphylococcus


title: Replicate2 of suboptimal donor EX28-3

source_name: Replicate2 of suboptimal donor EX28-3


title: DU10-01S0000015_L7

value: Viral


title: LB1 pA-DamID, d6, recombined, clone 16, replicate 2, dam-LB1


title: suboptimal donor EX29-4

source_name: suboptimal donor EX29-4


title: DU10-01S0000027_L8

source_name: whole blood


title: DU10-01S0000016_L7


title: LB1 pA-DamID, d6, recombined, clone 16, replicate 2, dam only


title: DU10-01S0000014_L1


title: DU10-01S0000013_L5

value: Bacterial


title: DU10-01S0000011_L4


title: Replicate4 of optimal donor EX27-4

source_name: Replicate4 of optimal donor EX27-4


title: LB1 pA-DamID, d6, recombined, clone 8, replicate 2, dam-LB1

source_name: F1 hybrid 129/Sv:CAST/EiJ


title: DU10-01S0000010_L4

value: Enterobacter


title: LB1 pA-DamID, d6, recombined, clone 8, replicate 2, dam only


title: Replicate3 of optimal donor EX27-4

source_name: Replicate3 of optimal donor EX27-4


title: DU10-01S0000009_L4

value: Noninfection


title: DU10-01S0000008_L4


title: LB1 pA-DamID, d1, parental, replicate 2, dam only

value: control


title: DU10-01S0000007_L2


title: Replicate1 of optimal donor EX27-4

source_name: Replicate1 of optimal donor EX27-4


title: Replicate2 of optimal donor EX27-4

source_name: Replicate2 of optimal donor EX27-4


title: LB1 pA-DamID, d1, parental, replicate 2, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ


title: DU10-01S0000004_L8

value: female


title: DU10-01S0000005_L4


title: DU10-01S0000006_L1


title: DU10-01S0000003_L8


title: LB1 pA-DamID, d4, parental, replicate 2, dam-LB1


title: Replicate2 of optimal donor EX27-2

source_name: Replicate2 of optimal donor EX27-2


title: optimal donor EX28-1

source_name: optimal donor EX28-1


title: DU10-01S0000001_L4


title: LB1 pA-DamID, d3, parental, replicate 2, dam-LB1


title: LB1 pA-DamID, d4, parental, replicate 2, dam only


title: DU09-03S0000039_L2


title: DU09-03S0000038_L1

value: male


title: DU09-03S0000040_L3


title: LB1 pA-DamID, d3, parental, replicate 2, dam only


title: DU09-03S0000036_L3


title: Replicate3 of suboptimal donor EX27-1

source_name: Replicate3 of suboptimal donor EX27-1


title: DU09-03S0000035_L3


title: DU09-03S0000037_L4


title: DU09-03S0000032_L1


title: Replicate2 of suboptimal donor EX27-1

source_name: Replicate2 of suboptimal donor EX27-1


title: Replicate1 of suboptimal donor EX27-1

source_name: Replicate1 of suboptimal donor EX27-1


title: LB1 pA-DamID, d2, parental, replicate 2, dam only


title: DU09-03S0000034_L1


title: DU09-03S0000031_L1


title: DU09-03S0000030_L8


title: LB1 pA-DamID, d5, parental, replicate 2, dam-LB1


title: DU09-03S0000028_L7


title: LB1 pA-DamID, d5, parental, replicate 2, dam only


title: DU09-03S0000027_L6


title: DU09-030000029_L1


title: sub optimal donor EX27-3

source_name: sub optimal donor EX27-3


title: DU09-03S0000026_L3


title: LB1 pA-DamID, d6, parental, replicate 2, dam-LB1


title: Replicate1 of optimal donor EX27-2

source_name: Replicate1 of optimal donor EX27-2


title: DU09-03S0000020_L4


title: DU09-03S0000024_L3


title: LB1 pA-DamID, d1, recombined, clone 29, replicate 1, dam-LB1


title: DU09-03S0000025_L3


title: DU09-03S0000022_L1


title: DU09-03S0000019_L4


title: DU09-03S0000023_L8


title: DU09-03S0000021_L7


title: LB1 pA-DamID, d2, parental, replicate 2, dam-LB1


title: LB1 pA-DamID, d1, recombined, clone 29, replicate 1, dam only


title: LB1 pA-DamID, d6, parental, replicate 2, dam only


title: DU09-03S0000018_L4


title: LB1 pA-DamID, d1, recombined, clone 28, replicate 1, dam-LB1


title: DU09-03S0000016_L3


title: DU09-03S0000017_L3


title: DU09-03S0000014_L3


title: LB1 pA-DamID, d4, recombined, clone 6, replicate 1, dam-LB1


title: DU09-03S0000012_L1


title: DU09-03S0000015_L3


title: LB1 pA-DamID, d4, recombined, clone 6, replicate 1, dam only


title: LB1 pA-DamID, d1, recombined, clone 28, replicate 1, dam only


title: DU09-03S0000013_L3


title: DU09-03S0000011_L1


title: COH5 EXPT3 human CD34+ cells treated (IDASANUTLIN + NILOTINIB)

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

description: 10X Genomics

data_processing:
Single cell RNA-seq data were pre-processed using the 10X Genomics Cell Ranger (3.1.0) suite of analysis pipelines.  Demultiplexing of raw base call (BCL) files produced by the Illumina Hiseq4000 platform and conversion to FASTQ file formats was performed using the cellranger mkfastq pipeline. Alignment of sequencing reads (FASTQ) to the GRCh38 (GENCODE v32/Ensembl 98) human genome assembly was performed using the cellranger count pipeline.
Assembly: human GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: xenograft from murine bone marrow

growth_protocol: CML CD34+ cells were cultured overnight at 37oC in serum free media (20% BIT, 100 μM β-mercaptoethanol, 0.04 mg/mL low density lipoprotein, 2 mM L-glutamine and 1% penicillin-streptomycin in IMDM) containing physiological levels of growth factors (SCF 0.2ng/mL, G-CSF 1ng/mL, GM-CSF 0.2ng/mL, IL-6 1ng/mL, LIF 0.05ng/mL, MIP-α 0.2ng/mL, StemCell Technologies)before being transplanted (1×106 cells per mouse) via tail vein injection into female 8-12-week-old sub-lethally irradiated immune-compromised mice (200 cGy). Mouse model used was NRG- W41/W41 -SGM3 (NOD.Cg-Rag1tm1Mom KitW-41J Il2rgtm1Wjl Tg(CMV-IL3,CSF2,KITLG)1Eav/J) (derived in house from mice obtained from the Jackson laboratory and the Eaves Lab, Vancouver). Eight to 12 weeks post-transplant, human cell engraftment was determined by measuring human CD45+ cells in the blood of transplanted mice by flow cytometry.

extract_protocol:
At the end of treatment, or after an additional 28 day treatment-free period, all mice were euthanised and the BM harvested from the two hind legs (ilia, femurs, and tibias) of each mouse by crushing in a mortar and pestle. BM was filtered and stained with mouse CD45-APC-Cy7, huCD45-PE, huCD34-APC and huCD38-Pe-Cy7 (all BD Biosciences) and the immunophenotypes of engrafted human cells determined by flow cytometry. For isolation of human cells from PDX model (huCD45+ and huCD45+34+) for scRNA-seq mouse BM cells were co-stained with muCD45 APC-Cy7 and huCD45 PE to distinguish mouse and human cells, together with huCD34 APC where appropriate, before being subject to FACS using the FACSAriaTM Fusion cell sorter (BD Biosciences) to isolate the specified human populations.
Library was performed according to the manufacter’s instructions (single cell 5’ v1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: Those mice showing evidence of huCD45+ cell engraftment were randomized and treated with vehicle(s), nilotinib (LC Laboratories) or nilotinib + idasanutlin according to the schedules described in the main text. Nilotinib was administered once daily by oral gavage at a dose of 50 mg/kg in its vehicle (10% NMP in PEG300).  Idasanutlin was administered twice daily by oral gavage at a dose of 150 mg/kg in its vehicle (GTX014903; 2% Klucel LF, 0.10% Tween 80, 0.09% methylparaben, 0.01% propylparaben in water pH 6.46).

value: xenograft from murine bone marrow

value: human CML CD34+ cells

value: CML chronic phase at diagnosis

value: idasanutlin plus nilotinib

tag: timepoint

value: end of 28 day treatment-free period


title: DU09-03S0000009_L7


title: LB1 pA-DamID, d3, recombined, clone 21, replicate 1, dam-LB1

value: mESC


title: COH5 EXPT3 human CD34+ cells treated (NILOTINIB)

description: 10X Genomics

value: nilotinib


title: DU09-03S0000010_L8


title: COH5 EXPT3 human CD34+ cells untreated (VEHICLE)

description: 10X Genomics

value: vehicle only (no drug control)


title: DU09-03S0000008_L7

value: White


title: DU09-03S0000004_L6


title: DU09-03S0000006_L7


title: COH4 EXPT3 human CD34+ cells untreated (VEHICLE)

description: 10X Genomics

value: end of 28 day treatment


title: LB1 pA-DamID, d3, recombined, clone 21, replicate 1, dam only

value: recombined


title: DU09-03S0000002_L6


title: DU16-02S0003206_S10

value: Viral


title: LB1 pA-DamID, d3, recombined, clone 12, replicate 1, dam only


title: DU09-03S0000001_L6


title: DU16-02S0003205_S3

value: Dengue


title: LB1 pA-DamID, d3, recombined, clone 12, replicate 1, dam-LB1


title: DU09-03S0000003_L6

value: Noninfection


title: abf1/2/3/4 mutant whole leaf, abscisic acid (4 hours), replicate2

city: La Jolla

first: Charles

middle: Anthony

last: Seller

state: CA

address: 9500 Gilman Dr

department: Cell and Developmental Biology

institute: UC San Diego

data_processing:
Raw fastq files were subjected to adapter trimming and quality control checks were performed using Trim Galore version 0.6.5 (Cutadapt and FastQC).
Reads were aligned to the Arabidopsis thaliana genome (TAIR10) using the Rsubread (version 2.14.0).
Low quality alignments (mapping quality < 2) were removed using the Samtools view function (version 1.17).
RNA- seq reads per transcript were counted to generate count matrices using the Rsubread featureCounts function.
Differential expression analysis was performed using DESeq2 (version 1.26.0). Transcripts were defined as significantly differentially expressed using the following thresholds: P adjusted value < 0.001 and fold change > 2.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: tab-delimited file containing raw counts per sample per AGI locus.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis thaliana plants were grown in soil containing pots incubated in a Conviron growth chamber with the following growth parameters: 12hr-12hr light-dark cycle, 22 C temperature, 65% humidity, ambient CO2, and a light intensity of 100 µmol m-2 s-1.

extract_protocol:
For whole leaf samples, total RNA was extracted from leaf tissue harvested from 5-6 week old plants using the Spectrum Total RNA Isolation Kit following the manufacturer's protocol. For guard cell samples, total RNA was extracted from isolated leaf epidermal fragments using the Qiagen RNeasy mini kit following the manufacturer's protocol.
RNA-Seq libraries were prepared using the TruSeq V2 mRNA-seq library prep kit following the manufacturer's protocol.

treatment_protocol: Rossettes were sprayed with 50 µM abscisic acid or with vehicle control (Ethanol).

value: leaf

value: Abscisic acid


title: LB1 pA-DamID, d2, recombined, clone 14, replicate 1, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ


title: abf1/2/3/4 mutant whole leaf, control, replicate2

value: control


title: abf1/2/3/4 mutant whole leaf, control, replicate1


title: abf1/2/3/4 mutant whole leaf, abscisic acid (4 hours), replicate1


title: DU16-02S0003199_S50

value: male

value: Bacterial

value: Leptospira


title: Whole leaf, abscisic acid (4 hours), replicate1

value: WT


title: LB1 pA-DamID, d2, recombined, clone 14, replicate 1, dam only

value: mESC


title: DU16-02S0003193_S27

value: female


title: LB1 pA-DamID, d2, recombined, clone 3, replicate 1, dam-LB1


title: Whole leaf, control, replicate2


title: Whole leaf, control, replicate1


title: DU16-02S0003200_S51


title: LB1 pA-DamID, d2, recombined, clone 3, replicate 1, dam only


title: Guard cell, abscisic acid (4 hours), replicate2

source_name: Guard cell

value: Guard cell


title: Whole leaf, abscisic acid (4 hours), replicate2


title: LB1 pA-DamID, d5, recombined, clone 2, replicate 1, dam-LB1


title: Guard cell, abscisic acid (4 hours), replicate1


title: Guard cell, control, replicate2


title: LB1 pA-DamID, d5, recombined, clone 2, replicate 1, dam only


title: Guard cell, control, replicate1


title: DU16-02S0003186_S12


title: LB1 pA-DamID, d6, recombined, clone 16, replicate 1, dam-LB1


title: Guard cell, 1000 ppm carbon dioxide 4 hours, ATAC-seq replicate3

data_processing:
Raw ATAC-seq sequence files were subjected to adapter trimming and quality control checks using Trim Galore version 0.6.5 (Cutadapt and FastQC).
Processed reads were aligned to the Arabidopsis thaliana genome (TAIR10) using the Rsubread align function (version 2.14.0).
Low quality alignments (mapping quality < 2) and alignments to the mitochondrial and chloroplast genomes were removed using the Samtools view function (version 1.17).
Alignments in a region of chromosome 2 (3239001 – 3510171) with abnormally high ATAC-seq signal in all samples were removed prior to further processing using BEDtools (version 2.30)
Reads derived from PCR duplicates were marked for exclusion using the Picard tools function Markduplicates (version 1.141).
ATAC-seq peaks were called across all biological replicated using Genrich (9) with the following parameters: -r -d -j -p 0.01 -a 200. For differential accessibility analysis, peaks were merged across all samples using the BEDtools merge function to generate a master list of peaks.
Differential chromatin accessibility analysis was performed using DESeq2 (version 1.26.0). Regions were defined as significantly differentially accessible using the following thresholds: P adjusted value < 0.001 and fold change > 1.5 or 2.
bigwig coverage tracks were generated on merged replicate bam files using the deepTools (version 3.5.0) bamCoverage function (bin size of 1 bp and normalization by RPKM).
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: narrowPeak files containing genomic coordinates of regions of ATAC-seq signal enrichment (peaks) called using Genrich. Genrich calls peaks for multiple replicates collectively, generating a single output peak file.

source_name: Guard Cell

growth_protocol: For experiments on seedlings, Arabidopsis thaliana seeds were germinated on standard 1/2MS media plates solidified with 1% PhytoAgar. For experiments on mature plants, Arabidopsis thaliana plants were grown in soil containing pots incubated in a Conviron growth chamber with the following growth parameters: 12hr-12hr light-dark cycle, 22 C temperature, 65% humidity, ambient CO2, and a light intensity of 100 µmol m-2 s-1.

extract_protocol:
Tagmentation (Tn5-based fragmentation) was performed on FACS isolated nuclei for 30 minutes at 37 C. Tagged DNA fragments were purified using the Qiagen min-Elute PCR purification kit.
ATAC-seq libraries were amplified with Nextera indexed primers for a limited number of cycles (determined by side-qPCR reaction). Amplified libraries were size-selected and purified using SPRI beads.

treatment_protocol: For experiments on seedlings, seedlings were transferred in bulk from standard 1/2MS agar plates to 1/2MS agar plates supplemented with 50 µM abscisic acid or with vehicle control (Ethanol). For experiment on mature plants, rossettes were sprayed with 50 µM abscisic acid or with vehicle control (Ethanol). For CO2 experiments, plants were placed in a Conviron chamber with carbon dioxide concentration set at 100 ppm or 1000 ppm for 4 hours.

value: Guard Cell

value: 1000 ppm carbon dioxide

tag: treatment time

value: 4 hours


title: Guard cell, 1000 ppm carbon dioxide 4 hours, ATAC-seq replicate2


title: DU16-02S0003185_S11

source_name: whole blood

value: Viral


title: LB1 pA-DamID, d6, recombined, clone 16, replicate 1, dam only

value: recombined


title: Guard cell, 100 ppm carbon dioxide 4 hours, ATAC-seq replicate3

value: 100 ppm carbon dioxide


title: DU16-02S0003184_S10

value: Dengue


title: DU16-02S0003192_S26


title: LB1 pA-DamID, d6, recombined, clone 8, replicate 1, dam-LB1


title: LB1 pA-DamID, d6, recombined, clone 8, replicate 1, dam only


title: DU16-02S0003179_S49


title: abf1/2/3/4 mutant Guard cell, ABA 4 hours, ATAC-seq replicate2

value: abscisic acid


title: DU16-02S0003180_S50


title: Guard cell, 100 ppm carbon dioxide 4 hours, ATAC-seq replicate2


title: abf1/2/3/4 mutant Guard cell, ABA 4 hours, ATAC-seq replicate1


title: LB1 pA-DamID, d1, parental, replicate 1, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ


title: DU16-02S0003178_S48


title: abf1/2/3/4 mutant Guard cell, control, ATAC-seq replicate2

value: control


title: abf1/2/3/4 mutant Guard cell, control, ATAC-seq replicate1


title: DU16-02S0003191_S25


title: DU16-02S0003177_S47


title: LB1 pA-DamID, d1, parental, replicate 1, dam only


title: Guard cell, ABA 24 hours, ATAC-seq replicate3

value: 24 hours


title: LB1 pA-DamID, d3, parental, replicate 1, dam-LB1


title: Guard cell, 1000 ppm carbon dioxide 4 hours, ATAC-seq replicate1


title: Guard cell, ABA 24 hours, ATAC-seq replicate2


title: DU16-02S0003173_S29


title: Guard cell, 100 ppm carbon dioxide 4 hours, ATAC-seq replicate1


title: Guard cell, ABA 24 hours, ATAC-seq replicate1


title: Guard cell, ABA 4 hours, ATAC-seq replicate2


title: abf1/2/3/4 mutant Guard cell, ABA 4 hours, ATAC-seq replicate3


title: Guard cell, ABA 4 hours, ATAC-seq replicate3


title: LB1 pA-DamID, d3, parental, replicate 1, dam only


title: LB1 pA-DamID, d2, parental, replicate 1, dam-LB1


title: DU16-02S0003172_S28


title: abf1/2/3/4 mutant Guard cell, control, ATAC-seq replicate3


title: Guard cell, control, ATAC-seq replicate3


title: DU16-02S0003171_S27

value: male


title: Guard cell, control, ATAC-seq replicate2


title: LB1 pA-DamID, d2, parental, replicate 1, dam only


title: LB1 pA-DamID, d5, parental, replicate 1, dam-LB1


title: DU16-02S0003165_S13


title: Mesophyll, ABA 4 hours, ATAC-seq replicate3

source_name: Mesophyll

value: Mesophyll


title: Mesophyll, ABA 4 hours, ATAC-seq replicate2

value: WT


title: Mesophyll, ABA 4 hours, ATAC-seq replicate1


title: DU16-02S0003164_S12


title: LB1 pA-DamID, d5, parental, replicate 1, dam only

source_name: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: LB1 pA-DamID, d6, parental, replicate 1, dam-LB1


title: DU16-02S0003163_S11

value: female


title: Mesophyll, control, ATAC-seq replicate3


title: Mesophyll, control, ATAC-seq replicate2


title: Mesophyll, control, ATAC-seq replicate4


title: Guard cell, ABA 4 hours, ATAC-seq replicate1


title: DU16-02S0003157_S45


title: abf1/2/3/4 mutant root, ABA 2 hours, ATAC-seq replicate2

source_name: seedling root

value: seedling root


title: abf1/2/3/4 mutant root, ABA 2 hours, ATAC-seq replicate3


title: Guard cell, control, ATAC-seq replicate1

value: Guard Cell


title: Mesophyll, ABA 4 hours, ATAC-seq replicate4


title: DU16-02S0003170_S26

value: Bacterial

value: Leptospira


title: DU16-02S0003158_S46

value: Viral


title: abf1/2/3/4 mutant root, ABA 2 hours, ATAC-seq replicate1

value: 4 hours


title: abf1/2/3/4 mutant root, ABA 45 minutes, ATAC-seq replicate1

value: 45 minutes


title: DU16-02S0003150_S15_L001


title: LB1 pA-DamID, d6, parental, replicate 1, dam only


title: DU16-02S0003149_S14_L001

value: Dengue


title: abf1/2/3/4 mutant root, control, ATAC-seq replicate3


title: 1_kPa_rep1_RNA

city: Los Angeles

first: Song

last: Li

state: California

address: 404 Westwood Plaza, Eng VI

institute: UCLA

data_processing:
Raw reads were trimmed with Trim Galore and cutadapt based on quality.
Pair-ended reads were then aligned to mouse reference genome (mm10) with STAR v2.7.10b.
Transcriptome alignments were quantified using featureCount using the gene annotation file from GENCODE.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Ear

extract_protocol:
Upon isolating RNA from the samples, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: A total of 500,000 fibroblasts were cultured on matrices of varying stiffness for 3 days and stored at -80 °C prior to sample processing.

value: Ear

value: Fibroblast


title: Mesophyll, control, ATAC-seq replicate1

value: control


title: 20_kPa_rep2_RNA


title: 1_kPa_rep2_RNA


title: Glass_rep2_RNA

value: Glass


title: 20_kPa_rep1_RNA


title: Glass_rep1_RNA


title: DU16-02S0003143_S18

value: male


title: DU16-02S0003142_S9

value: Rickettsia


title: DU16-02S0003144_S19


title: abf1/2/3/4 mutant root, control, ATAC-seq replicate1


title: LIDAR, total + RiboCOP depletion, mES_serum.b3

city: Philadelphia

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For LIDAR, LIDAR3, NEB, and TAKARA samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
LIDAR samples with UMI: UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed). TAKARA samples with UMI: UMIs were extracted using umi_tools v1.1.2 with the parameters "--extract-method=string --bc-pattern=X --bc-pattern2=NNNNNNNN", then the remainder of the linker was trimmed with cutadapt with the parameter "-u 6".
Reads were mapped sequentially with STAR to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP with SNP database provided, then to GRCm39 genome with all of the sequences above masked and provided as extra scaffolds using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

source_name: cells

extract_protocol:
For ESC and NPC, cell pellets were resuspended in 1ml of TriPure and RNA was extracted following standard protocol. DNA was digested with Turbo DNase-I at 37°C for 30min, RNA was re-purified using TriPure, and resuspend in 10mM Bis/Tris pH=6.7, 0.1mM EDTA. For mouse sperm, sperm were resuspended in 120 ul of water and 66 μl of Sperm_lysis_buffer were added [120mM Tris-HCl (pH=8), 6.4M Guanidine-HCl, 5% Tween-20, 5% Triton-X-100, 120mM EDTA]. Proteins were digested by adding 6.6 μl of 20 mg/ml proteinase K and 6.6 μl of 1M DTT, followed by incubation at 60°C for 15 min under 600 rpm constant shaking. Volume was adjusted with water to 400 μl and 400 μl of TriPure were added. RNA was extracted by adding 120 μl of BCP Phase Separation Reagent and precipitated with isopropanol. DNA was digested with Turbo DNase-I at 37°C for 30min, RNA was re-purified using TriPure, and resuspend in modBTE buffer (10mM Bis/Tris pH=6.7, 0.1mM EDTA). For enrichment of <200nt RNAs, the Zymo RNA Clean and Concentrator-5 kit was used, starting from 1ug of total RNA. For enrichment of <50nt RNAs, 18ug of total RNA were run on a denaturing 12% polyacrylamide-urea gel, and bands between 10nt and 50nt were excised. Gel pieces were shredded trough pierced 0.5ml tubes, and RNA was elute from the gel by overnight incubation in 400μl RNA elution buffer (10mM Bis/Tris pH=6.7, 300mM NaCl, 10mM EDTA) at 4°C with constant rotation. Eluate was filtered though 5μm PVDF spin filters, and RNA was precipitated by adding 1μl of Glycoblue, 40μl of 3M NaOAc pH=5.2, and 1.1ml of ice-cold 100% EtOH, followed by incubation at -80°C for 1h. RNA was pelleted at 20000g for 30min (4°C), washed once with 1ml of 70% EtOH, once with 1ml of 80% EtOH, air-dried for 5 min, and resuspended in modBTE buffer.
LIDAR and LIDAR-3 library preparation The desired amount of total and fractionated RNAs was diluted to 1μl and mixed with 0.4μl of 10μM LIDAR_RT_primer (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNND). To anneal the LIDAR_RT_primer to the template RNA, samples were heated to 65°C for 5 min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix [25mM Tris-HCl pH=8.3, 20mM NaCl, 2.5mM MgCl2, 8mM DTT, 5% PEG-8000, 0.5mM dNTPs, 1mM GTP, 0.5 U/μl Murine RNase inhibitor, and 2U/μl Maxima H-minus Reverse Transcriptase – concentrations refer to a final volume of 8 μl] were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix (equimolar ratio of the following oligos: /5Biosg/CGTCAGATGTGTATAAGAGACAGtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhmtgNNcgNNagNNrGrGrG) were added, and samples were incubated at 42°C for 80 min, followed by 10 cycles at 50°C for 2 min and 42°C for 2 min, then at 85°C for 5 min. To pre-amplify and add adapters to cDNA, 12μl of KAPA_mix [1X KAPA HiFi HotStart buffer Ready Mix, 0.5μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.1μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl]  were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 18 cycles of amplification (98°C for 20s, 70°C for 30s, 72°C for 30s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 0.5μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase (Cat. No M0491, New England Biolabs) – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 18 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 2 min). Indexed libraries were purified using 2.3X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA). For LIDAR-3, the LIDAR-3_RT_oligo was generated by mixing equimolar amounts of LIDAR-3_RT_sense (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNNN) and LIDAR-3_RT_antisense (CdUGdUCdUCdUdUAdUACACAdUCdUCCGAG/3ddC/), followed by heating at 95°C for 5 min, and a slow cool down to 25°C (0.1°C/s). To prepare LIDARsp libraries, 1μl of input RNA was first denatured at 70°C for 2 min, then temperature was lowered to 50°C and 0.4μl of 1μM LIDAR-3_RT_oligo were added. Samples were incubated at 50°C for further 2min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix were added, and samples were incubated at 50°C for 80 min, followed by 10 cycles at 55°C for 2 min and 50°C for 2 min, then at 85°C for 5 min. LIDAR-3_RT_antisense was digested by adding 1ul of USER II enzyme and incubating at 37°C for 30 min. USER II was heat inactivated by incubation at 65°C for 10 min. To pre-amplify and add adapters to cDNA, 12μl of KAPAsp_mix [1X KAPA HiFi HotStart buffer Ready Mix, 2μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.5μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl] were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 6 cycles of 3-step amplification (98°C for 20s, 63°C for 30s, 72°C for 30s), 12 cycles of 2-step amplification (98°C for 20s, 72°C for 50s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 1μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5sp_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 7 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 5 min). Indexed libraries were purified using 2.4X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).  Small RNA-seq and mRNA-seq library preparation Small RNA libraries were prepared using the NEBnext Small RNA Library Prep Set for Illumina (Cat. No E7330S, New England Biolabs), following the standard protocol with the following parameters: 1) 1:2 dilution of 3’SR Adaptor, SR RT Primer, and 5’SR Adaptor 2) 15 indexing PCR cycles 3) cleanup of final libraries with QIAgen MinElute PCR purification kit, followed by a second cleanup with 2X SPRI. Libraries were analyzed on a 6% non-denaturing polyacrylamide gel. For mRNA-seq libraries, polyA RNA was enriched from 2 μg total RNA using Dynabeads Oligo(dT)25. Poly-A-enriched fraction was used for library construction using the NEBnext Ultra II Directional Library Prep Kit for Illumina (Cat. No. E7760L, New England Biolabs), following the standard protocol but using half the reaction volumes recommended. Libraries were analyzed on a 2% agarose gel. Both small RNA-seq and mRNA-seq libraries were quantified using NEBNext Library Quant Kit for Illumina (Cat. No E7630L, New England Biolabs). Libraries were sequenced on an Illumina NextSeq500 instrument.

treatment_protocol: C57BL/6 mouse embryonic stem cells (ESC) were purchased from ATCC (SCRC-1002) and maintained onto 1% gelatin-coated dishes in DMEM knockout medium supplemented with 15% ES-grade Fetal Bovine Serum, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin solution, 110μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. Cells were passaged through trypsinization (0.05%) every 2–3 days. Prior to neuronal progenitor cells (NPC) differentiation, embryonic stem cells that were maintained in N2B27 serum-free medium consisting of 1:1 mix of Neurobasal medium and DMEM/F12, supplemented with 1X N2, 1X B27, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin, 55μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. For NPC differentiation differentiation, Epiblast-like cells (EpiLC) were induced from ESC in N2B27 serum-free medium (without 2i and LIF) supplemented with 40μg/ml of BSA, and 10ng/ml bFGF for 72h. EpiLC were treated with 500nM SAG in N2B27 serum-free medium (without 2i and LIF) for 48h to generate NPC.

value: cells

value: ESC serum

tag: input amount_(ng)


title: NEB, <50nt, mES_serum-free, b2

value: ESC serum-free


title: LIDAR, total + RiboCOP depletion, mES_serum.b2


title: 20_kPa_rep1_ATAC

data_processing:
FASTQ files were trimmed with Trim Galore and cutadapt. Pair-ended reads were then aligned to the mouse reference genome (mm10) with Bowtie2.
Mitochondrial reads and PCR duplicates were removed using SAMtools and Picard, respectively.
Peaks were called over input using MACS3, and only peaks outside the ENCODE blacklist region were kept.
Assembly: mm10
Supplementary files format and content: bigwig file includes peak profiles of each sample

extract_protocol:
100,000 cells were added to ATAC lysis buffer after thawing and centrifuged at 500 g in a pre-chilled centrifuge for 5 minutes. Supernatant was removed and the nuclei were resuspended in 50 µL of tagmentation reaction mix by pipetting up and down. The reactions were incubated at 37 °C for 30 minutes in a thermomixer with shaking at 1,000 rpm, and then cleaned up using the MiniElute reaction clean up kit (Qiagen).
Tagmented DNA was amplified with barcoded primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher), Tapestation High Sensitivity D1000 Assay (Agilent Technologies), and QuantStudio ® 5 System (Applied Biosystems). Equimolar pooling of libraries was performed based on QC values.

treatment_protocol: A total of 1,000,000 fibroblasts were cultured on matrices of varying stiffness for 3 days and stored at -80 °C prior to sample processing.


title: NEB, <50nt, mES_serum-free, b3


title: Root, ABA 4 hours, ATAC-seq replicate2

value: seedling root

value: WT

value: abscisic acid


title: DU16-02S0003136_S56

tag: gender


title: DU16-02S0003141_S8

tag: pathogen


title: Root, ABA 4 hours, ATAC-seq replicate3


title: abf1/2/3/4 mutant root, ABA 45 minutes, ATAC-seq replicate2


title: LIDAR, total + RiboCOP depletion, mES_serum.b1


title: Takara, total, mES_serum, b3


title: Root, ABA 4 hours, ATAC-seq replicate1


title: DU16-02S0003134_S54

value: female

tag: age


title: abf1/2/3/4 mutant root, control, ATAC-seq replicate2


title: Takara, total, mES_serum, b2


title: Root, ABA 2 hours, ATAC-seq replicate3

value: 2 hours


title: 1_kPa_rep1_ATAC


title: Takara, total, mES_serum, b1


title: DU16-02S0003129_cat

value: Viral


title: Glass_rep2_ATAC


title: Root, ABA 2 hours, ATAC-seq replicate2


title: DU16-02S0003127_S32


title: Glass_rep1_ATAC


title: DU16-02S0003128_S40

value: Bacterial

value: Leptospira


title: Root, ABA 2 hours, ATAC-seq replicate1


title: 1_kPa_rep2_ATAC

value: Ear


title: N2a_mito_ActD_2h

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

country: China

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
For ng-circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 were mapped to the reference genome by bwa-mem. circRNA candidates were predicted by CIRI2 (v 2.0.6).
For smallRNA-seq analysis, the raw data were trimmed by cutadapt (v 1.15) to remove adaptor sequences to get clean data. The clean data were mapped to the mitochondrial genome with bowtie, and the forward or reverse mapping reads were extracted by samtools (v 1.10). The distribution of peaks was generated with an integrative genomics viewer (IGV) (v 2.11.0).
Assembly: hg38, mm10, ce11
Supplementary files format and content: comma-separated value files include count values for each Sample
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: bigwig

extract_protocol:
The isolated mitochondria, total cells were lysed in TRizol reagent (Life Technologies). RNA from  mitochondia, whole cell, mitochondrial fractions and RNA-IP were extracted by using TRizol reagent according to the manufacturer’s instructions.
For small RNA seq, the small RNA bands in fractions 2–4 and the input were excised from the gel and RNAs were purified. Small RNA libraries were constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina following the manufacturer’s protocol. For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.
For TRAP1 RIP and ATP5B RIP, sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations.
For other RIP-seq, NEB Next Ultra RNA Library Prep Kit (NEB) was used for library construction of immunoprecipitated RNA. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

tag: library type

value: RNA-seq


title: 20_kPa_rep2_ATAC

value: Fibroblast


title: DU16-02S0003122_cat

tag: site


title: Root, ABA 45 minutes, ATAC-seq replicate2

value: 45 minutes


title: N2a_mito_ActD_0h

institute: University of Science and Technology of China

tag: cell line


title: Root, ABA 45 minutes, ATAC-seq replicate3


title: DU16-02S0003120_S17

value: male

value: Dengue


title: DU16-02S0003121_S18


title: Root, ABA 45 minutes, ATAC-seq replicate1


title: sciMETcap on PBMCs, standard blockers

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
Raw reads were demultiplexed using unidex
Reads were trimemd using a wrapper for Trim Galore
Trimmed reads were aligned using BSBolt and then duplicate removed
Methylation calls on a per cell basis were then extracted
Methylation calls were used to generate window matrixes used for dimensionality reduction, clustering and visualization
Assembly: hg38
Supplementary files format and content: gzipped tar archives that contain bed files of methylation calls split by chromosome
Supplementary files format and content: gzipped tar archives that contain tab delimited text files for processed matrixes and other analytics
Library strategy: sciMET-cap

source_name: PBMCs

extract_protocol:
Nuclei were extracted using nuclei isolation buffer according to protocols detailed in Nichols et al 2022
Nuclei were isolated and processed using the sciMETv2.SL protocol described in Nichols et al 2022 followed by target capture using the Twist methylome panel

value: PBMCs

tag: cell type


title: N2a_total_ActD_2h

tag: genotype


title: sciMETcap on PBMCs, custom blockers

tag: tissue


title: sciMETcap on PBMCs, no capture control


title: Root, control, ATAC-seq replicate3

tag: treatment

value: control

value: 4 hours


title: DU16-02S0003115_cat

data_processing:
Batch 1 was sequenced on an Illumina HiSeq 2500, and batch 2 was sequenced on an Illumina NovaSeq 6000.
For batch 1, adapters were removed by EA Genomics prior to receipt of sequences.  For batch 2, adapters were remvoed using Trimmomatic v0.38.
Reads were aligned to the hg38 reference transcriptome using Bowtie2 with "option --very-sensitive-local"
Express version 1.5.1 was used for quantification at the transcript level. For batch 1 the option "strand rf-stranded" was used, and for batch 2 "strand fr-stranded" was used.
Expression data were normalized using the trimmed mean of M-values approach, specifically using the calcNormFactors function in the edgeR package in R.
Supplementary files format and content: The processed data file contains log2-transformed and normalized counts per million.

extract_protocol:
Total RNA was extracted from whole blood collected and stored at -80°C in PAXgene Blood RNA tubes using the PAXgene miRNA Extraction Kit
For batch 1, libraries were constructed using GlobinClear Globin RNA Reduction (Invitrogen) with TruSeq Stranded mRNA Library Kit (Illumina).  For batch 2, libraries were contructed using NuGEN Universal Plus mRNA-Seq Library Prep Kit with AnyDeplete Globin depletion (NuGEN/Tecan).


title: DU16-02S0003113_S2


title: DU16-02S0003114_S3


title: sciMETcap on PBMCs, wash temperature increased to 67C


title: Whole seedling, ABA, ATAC-seq replicate2

source_name: whole seedling

tag: strain

value: whole seedling


title: Root, control, ATAC-seq replicate1

value: seedling root

value: WT


title: Whole seedling, ABA, ATAC-seq replicate1

value: abscisic acid


title: DU14-03S0035227_S14

value: female

tag: infection type

value: Noninfection


title: DU16-02S0003112_S1

tag: sequencing batch

value: Viral


title: roots, BPF, rep1

city: Taiyuan

first: Huifeng

last: Yue

state: Shanxi

address: Nanzhonghuandong Street

institute: Shanxi University

data_processing:
The sequenced reads were aligned to the reference genome (TAIR10.28) using spliced mapping of Hisat2 (version: 2.0.4). Then, the uniquely mapped fragments of genes were counted using Stringtie (version: 1.3.0) followed by TMM (trimmed mean of M values) normalization. Finally, gene expression was determined by normalized fragments per kilobase of exon model per million mapped reads (FPKM). The edgeR was used to analyze the differentially expressed genes (DEGs) among samples. After p-value is obtained, multiple hypothesis tests are conducted to correct it. The threshold of p-value is determined by controlling FDR (False Discovery Rate). The corrected p-value is called q-value. At the same time, we calculate the differential expression multiple, namely, fold change (FC), according to the FPKM value. Gene Ontology (GO) enrichment analysis of the DEGs was further conducted based on the Database for Annotation, Visualization and Integrated Discovery (DAVID).
Assembly: TAIR10.28
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: roots

growth_protocol: In all groups, the treatment solutions of BPs were prepared by dissolving the required amount of BPs in 1/2 MS medium supplemented with 10 g/L sucrose and 9 g/L agar (pH 5.8). Seeds were pre-sterilized successively by 1 mL 70% ethanol followed by 1 mL sterilized and deionized water (S&D-water, 2 times), and 3% sodium hypochlorite.

extract_protocol:
Total RNA from the roots (3 replicates for each groups) were extracted and collected using TransZol Up Plus RNA Kit (Cat#ER501-01, Trans) according to the manufacturer’s instructions.
The quality and integrity of extracted RNA were evaluated using a Qubit Fluorometer and an Agilent 2100 Bioanalyzer, with 280/260 nm ratios of approximately 2.0, RIN values of no less than 7.0 and 28S/18S ratios of no less than 0.7. Strand-specific libraries were prepared using the VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (NR604-02, Vazyme) before sequencing on the Illumina HiSeq 2500 system. Library construction and sequencing were performed at the Shanghai Biotechnology Corp.

treatment_protocol: Then, the seeds were washed and resuspended with 1 mL S&D-water (3 times), and sown on agar plates containing different doses of BPA or its analogs (1, 3, and 10 mg/L). For control, none of the BPA or its analogs was added, but DMSO (< 0.01% v/v) was used. Plates were sealed and placed at 4 °C for 48 h for stratification. After that, plants grown in a fully automatic light incubator for 2 weeks (environmentally controlled at 23 °C, 16 h Light/8 h Dark cycle, white light with 100-120 μmol·m−2·s−1 photon flux).

value: roots

value: BPF

tag: time

value: 14 days


title: roots, BPF, rep2


title: roots, BPS, rep1

value: BPS


title: DU14-03S0035226_S13

tag: race


title: roots, BPS, rep3


title: roots, BPS, rep2


title: DU14-03S0035225_S12


title: Whole seedling, control, ATAC-seq replicate1

tag: treatment time


title: roots, BPF, rep3


title: DU14-03S0035224_S53

value: White


title: N2a_total_ActD_0h

value: RNA-seq


title: roots, BPE, rep2

value: BPE


title: roots, BPE, rep3


title: DU14-03S0035222_S31

value: male


title: roots, BPE, rep1


title: DU14-03S0035221_S30


title: Root, control, ATAC-seq replicate2

value: control


title: roots, BPB, rep3

value: BPB


title: DU14-03S0035220_S14


title: BMS-202-SSL_2

type: RNA

city: Tucson

first: Georg

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

institute: University of Arizona

description: Total RNA analyzed for gene expression of 254 transcripts by Mouse nCounter Inflammation V2 panel

hyb_protocol: All samples were run targeting 100 ng of total RNA (19 h at 65°C) prior to being processed on the nCouner FLEX Analysis System.

scan_protocol: Samples were run on the nCounter Prep Station with high sensitivity settings followed by imaging on the Digital Analyzer with FOV (Field of View) data resolution set to 555.

data_processing: Raw data files were uploaded (RCC files) to the NanoString nSolver Analysis 4.0 software.

label: reporter probe: fluorescent barcode; capture probe: biotin

source_name: skin

label_protocol: NanoString nCounter gene expression assay protocol was followed (https://www.nanostring.com/wp-content/uploads/2021/03/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf).

growth_protocol: All SKH-1 mice were housed and treated in accordance with The University of Arizona Animal Care and Use Committee standards under an approved protocol (#08-153).

extract_protocol: Total RNA was extracted from murine full tickness skin tissues using Qiagen RNeasy Mini kit according to manufacturer instructions.

treatment_protocol: SKH-1 mouse skin  (3 mice per treatment group) was treated topically (with 200µl) on their backs either with vehicle (acetone) or 8 mM BMS-202 [all 3 times: 24 hr pre, 1 hr pre, and immediately post acute SSL (solar simulated UV light) treatment] and harvested 24 hr after acute SSL. SSL irradiation of SKH-1 mice was performed at a dose of 90 kJ/m2 UVA/ 6 kJ/m2 UVB.

value: UV plus BMS-202


title: BMS-202-SSL_3


title: DU14-03S0035218_S54


title: Whole seedling, control, ATAC-seq replicate2

value: whole seedling

value: 4 hours


title: roots, BPB, rep2

value: WT


title: roots, BPB, rep1


title: BMS-202-SSL_1


title: WT-SSL_2

value: UV


title: WT-SSL_3


title: DU14-03S0035217_S53

value: female

value: Noninfection


title: WT-SSL_1


title: DU14-03S0035216_S52

value: Bacterial

value: Streptococcus


title: COH4 EXPT2 human CD34+ cells treated (NILOTINIB)

description: 10X Genomics

value: xenograft from murine bone marrow

value: human CML CD34+ cells

value: CML chronic phase at diagnosis

value: nilotinib

tag: timepoint

value: end of 28 day treatment


title: DU14-03S0035214_S39

tag: gender


title: DU14-03S0035213_S38

value: male

value: White

tag: pathogen


title: roots, BPA, rep1

value: roots

value: BPA

value: 14 days


title: roots, BPA, rep2


title: roots, BPA, rep3


title: roots, control, rep2


title: COH4 EXPT1 human CD45+ cells treated (IDASANUTLIN + NILOTINIB)

description: 10X Genomics

value: human CML CD45+ cells

value: idasanutlin plus nilotinib


title: COH4 EXPT1 human CD45+ cells untreated (VEHICLE)

description: 10X Genomics

value: vehicle only (no drug control)


title: roots, control, rep3

value: WT


title: roots, control, rep1


title: Normal sample E scRNAseq

description: 10X Genomics

data_processing:
Single cell RNA-seq data were pre-processed using the 10X Genomics Cell Ranger (3.1.0) suite of analysis pipelines.  Demultiplexing of raw base call (BCL) files produced by the Illumina Hiseq4000 platform and conversion to FASTQ file formats was performed using the cellranger mkfastq pipeline. Alignment of sequencing reads (FASTQ) to the GRCh38 (GENCODE v32/Ensembl 98) human genome assembly was performed using the cellranger count pipeline.
Assembly: human GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

growth_protocol: CML CD34+ cells were cultured overnight at 37oC in serum free media (20% BIT, 100 μM β-mercaptoethanol, 0.04 mg/mL low density lipoprotein, 2 mM L-glutamine and 1% penicillin-streptomycin in IMDM) containing physiological levels of growth factors (SCF 0.2ng/mL, G-CSF 1ng/mL, GM-CSF 0.2ng/mL, IL-6 1ng/mL, LIF 0.05ng/mL, MIP-α 0.2ng/mL, StemCell Technologies). Control, normal CD34+ cells were cultured overnight at 37oC in in serum free medium in high growth factors (SCF 100 ng/mL, G-CSF 20 ng/mL, IL-3 20 ng/mL, IL-6 20 ng/mL, Flt3 100 ng/mL).

extract_protocol:
For isolation of stem cells (CD34+CD38-), CD34+ cell samples were stained with anti-human (hu) CD34-APC, CD38-V450 or CD38-Pe-Cy7 antibodies (BD Biosciences), before being subjected to fluorescence activated cell sorting (FACS) to obtain the stem cell populations using a FACSAriaTM Fusion cell sorter (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

value: peripheral blood

tag: individual

value: Normal E

value: CD34+CD38- HSC

tag: disease state

tag: age

tag: Sex

value: F


title: DU14-03S0035212_S18

tag: site

value: Noninfection


title: DU14-03S0035211_S17


title: DU14-03S0035210_S16

value: female


title: Normal sample D scRNAseq

description: 10X Genomics

value: Normal D

tag: cell type


title: Normal sample C scRNAseq

description: 10X Genomics

tag: tissue

value: Normal C


title: DU14-03S0035209_S15

value: male

value: Viral


title: DU14-03S0035208_S49

value: White

value: Bacterial

value: Enterobacter


title: Normal sample B scRNAseq

description: 10X Genomics

value: Normal B

value: M


title: COH4 EXPT2 human CD34+ cells treated (IDASANUTLIN + NILOTINIB)

description: 10X Genomics

value: xenograft from murine bone marrow

value: human CML CD34+ cells

tag: genotype

value: CML chronic phase at diagnosis

tag: treatment

value: idasanutlin plus nilotinib

value: end of 28 day treatment


title: DU14-03S0035215_S51

tag: infection type


title: WT+XBP1+Asc_rep4

city: Cambridge

first: Matthew

middle: D

last: Shoulders

address: 77 Massachusetts Avenue

department: Chemistry

institute: Massachusetts Institute of Technology

description: Data were sequenced as paired-end but are submitted as single-end data. The first read only contains read and sample barcodes. Before any analysis is performed, the sequence from read 1 is concatenated with the header of read#2  and the fastq files are handled as SE RNA-Seq data.

data_processing:
Post-sequencing, quality-control on each of the libraries was performed to assess coverage depth, enrichment for messenger RNA (exon/intron and exon/intergenic density ratios), fraction of rRNA reads and number of detected genes using bespoke scripts.
Read pairs were combined into a single fastq with well/UMI information concatenated with the second read name, reads sharing sequence and UMI information were collapsed into single exemplars. Sequences were aligned against the human genome GRCh38/hg38 ENSEMBL 89 using STAR, with parameters --runThreadN 8 --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM, pointing to a Suffix Array assembly containing exon-exon junctions for 75 nucleotide reads.
Gene expression was estimated based on reads mapping near the 3' end of transcripts using ESAT [Derr2016] with the following parameters -task score3p -alignments $sample_list   -wLen 50 -wExt 5000 -wOlap 0 -sigTest 0.01 -multimap ignore, poiting to a refseq-based gene annotation (hg38, as downloaded from the UCSC Genome Browser) and gene-level data were used for downstream analyses.
Genome_build: GRCh38/hg38 ENSEMBL 89
Supplementary_files_format_and_content: ESAT gene by sample count matrices

growth_protocol: 1.0×10^5 cells were plated in a 6-well plate.

extract_protocol:
Cells were harvested by trypsinization, washed with PBS, and total RNA was extracted using the Omega RNA Purification Kit.
RNA samples were quantified and quality assessed using an Advanced Analytical Fragment Analyzer. The initial steps were performed on a Tecan EVO150.10ng of totalRNA was used for library. 3’DGE-custom primers were added to a final concentration of 1 uM.   Maxima H Minus RT was then added per manufacturer’s recommendations with Template-Switching oligo5V6NEXT followed by incubation at 42C for 90’ and inactivation at 80C for 10’. cDNA from 12 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 17 ul of water followed by digestion with Exonuclease I at 37C for 30 minutes, inactivation at 80C for 20 minutes.  Second strand synthesis and PCR amplification was done by adding the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (10 pmol) directly to the exonuclease reaction. 15 cycles of PCR were performed followed by clean up using regular SPRI beads at 0.6X, and eluted with 20ul of EB. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries are then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer in place of the normal N500 primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500 in paired-end mode (20/50 nt reads).

treatment_protocol: 24 h after the cells were plated, the media was replaced and supplemented with adenoviral supernatant. After 24 h of incubation with virus, the media was replaced with fresh media. 48 h post media change, media was replaced with 1 mL of media supplemented with 200 uM sodium ascorbate. 24 h later, cells were harvested for totalRNA isolation.

value: adult derived primary fibroblast cells

value: healthy donor

value: XBP1s Adenovirus ; 24 h 200 uM sodium ascorbate


title: 425S+GFP+Asc_rep4

value: patient donor

value: GFP Adenovirus ; 24 h 200 uM sodium ascorbate


title: COH4 EXPT2 human CD34+ cells untreated (VEHICLE)

description: 10X Genomics

value: vehicle only (no drug control)


title: WT+GFP+Asc_rep4


title: 425S+XBP1+Asc_rep4


title: Normal sample A scRNAseq

description: 10X Genomics

value: peripheral blood

value: Normal A

value: CD34+CD38- HSC


title: 425S+XBP1+Asc_rep3


title: DU14-03S0035206_S47

city: Durham

last: Ko

address: 4103 Graceview Way

institute: Duke University

tag: sequencing batch

value: male

value: Noninfection


title: DU14-03S0035205_S35

value: female


title: CML patient sample D scRNAseq

description: 10X Genomics

value: CML patient D

value: CD34+CD38- LSC

value: CML chronic phase diagnosis

value: F


title: WT+XBP1+Asc_rep3


title: CML patient sample B scRNAseq

description: 10X Genomics

value: CML patient B


title: DU14-03S0035204_S34

value: Viral


title: WT+GFP+Asc_rep3

value: adult derived primary fibroblast cells

value: healthy donor


title: 425S+XBP1+Asc_rep2

value: patient donor

value: XBP1s Adenovirus ; 24 h 200 uM sodium ascorbate


title: CML patient sample E scRNAseq

description: 10X Genomics

value: CML patient E

value: M


title: DU14-03S0035201_cat

value: White


title: CML patient sample A scRNAseq

description: 10X Genomics

value: peripheral blood

value: CML patient A


title: CML 3 NIL+IDASA 72 HRS

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow Galaxy server (https://www.polyomics.gla.ac.uk/galaxy.html) for which quality control was performed by FastQC (0.72) and the reads were trimmed by Trim Galore! (0.4.3.1). Trimmed reads were aligned to human reference genome hg38 using HISAT2 (2.1.0) and assigned by the feature counting tool featureCount (1.6.0.3). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.32.0) in R.
Assembly: human reference genome GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

growth_protocol: CML CD34+ cells were cultured for up to 72 hrs at 37oC in serum free media (20% BIT, 100 μM β-mercaptoethanol, 0.04 mg/mL low density lipoprotein, 2 mM L-glutamine and 1% penicillin-streptomycin in IMDM) containing physiological levels of growth factors (SCF 0.2ng/mL, G-CSF 1ng/mL, GM-CSF 0.2ng/mL, IL-6 1ng/mL, LIF 0.05ng/mL, MIP-α 0.2ng/mL, StemCell Technologies).

extract_protocol:
The cells were pelleted by centrifugation in culture media, washed and then pelleted again in phosphate buffered saline pH 7.4, and total cellular RNA extracted from a minimum of 1 x106 cells in TRIzoLTM Reagent (ThermoFisher). The concentration of the RNA was measured using the Nanodrop 2000, and the quality and RIN value was determined using the Agilent Bioanalyser RNA Nano kit (Agilent).
RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: Primary CD34+ CML cells were treated with nilotinib (3 µM), idasanutlin (166 nM), or a combination for 24 hr or 72 hr.

value: CD34+ stem/progenitor cells

value: nilotinib + idasanutlin

tag: time

value: 72 hrs


title: WT+XBP1+Asc_rep2


title: 425S+GFP+Asc_rep2

value: GFP Adenovirus ; 24 h 200 uM sodium ascorbate


title: DU14-03S0035200_S21

value: male

tag: race

value: Bacterial

value: Streptococcus


title: CML 3 NIL 72 HRS

value: CML chronic phase diagnosis

value: nilotinib


title: DU14-03S0035207_S48

value: female

value: Noninfection


title: WT+GFP+Asc_rep2

value: adult derived primary fibroblast cells

value: healthy donor


title: DU14-03S0000948_S59


title: CML 3 IDASA 72 HRS

value: idasanutlin

value: M


title: 425S+XBP1+Asc_rep1

value: patient donor

value: XBP1s Adenovirus ; 24 h 200 uM sodium ascorbate


title: DU14-03S0000947_S58

value: White


title: DU14-03S0000946_S57

value: Viral


title: CML 3 NDC 72 HRS

value: peripheral blood

value: CD34+ stem/progenitor cells

value: no drug treatment

value: 72 hrs


title: CML patient sample C scRNAseq

description: 10X Genomics

value: CML patient C

value: CD34+CD38- LSC

value: F


title: 425S+GFP+Asc_rep1

value: GFP Adenovirus ; 24 h 200 uM sodium ascorbate


title: 425S+GFP+Asc_rep3


title: DU14-03S0000945_S46

value: female

value: Bacterial

value: Enterobacter


title: WT+XBP1+Asc_rep1

value: adult derived primary fibroblast cells

value: healthy donor


title: DU14-03S0000943_S44


title: DU14-03S0035202_S23

value: Unknown

value: Noninfection