title: Untreated_UT_rep1

city: Worcester

first: Athma

middle: A

last: pai

state: MA

address: 55 Lake Avenue North

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

description:
Library name: Untreated_UT_rep1
RNA-seq following ASO treatment and transcript-pull down

data_processing:
Amplicon-sequencing: Resulting sequences were then mapped to the hg38 reference genome with ENSEMBL GRCH38.95 reference annotations using STAR (Dobin et al. 2013) with default parameters and cryptic exon usage was confirmed using visualization of read coverage and junction reads across the region.
RNA-seq following ASO treatment: Samples were analyzed as described in (Khokhar et al. 2025). Briefly, samples were PEAR-procssed (Zhang et al. 2014), subsampled to 10.7M single reads with seqtk (Li 2018), and mapped using STAR with parameters specified in (Khokhar et al. 2025). Cryptic splice sites were identified CRYPTID-SS as described in (Khokhar et al. 2025) and cryptic exons were identified with CRYPTID-exon
Targeted-RNA sequencing: Samples were analyzed as described in (Khokhar et al. 2025). Briefly, samples were PEAR-procssed (Zhang et al. 2014), subsampled to 112M single reads with seqtk (Li 2018), mapped using STAR with parameters specified in (Khokhar et al. 2025). Kallisto (Bray et al. 2016) was used to estimate gene expression levels in the target-enriched samples and confirm enrichment relative to whole nuclear RNA. Samples were analyzed with CRYPTID-ss to obtain high-confidence cryptic splice sites and processed with CRYPTID-exon to predict exons associated with the detected cryptic splice sites. Exons from the sites with the highest usage were chosen for downstream experimentation following visual inspection of the region and validation by amplicon sequencing.
Assembly: Grch38
Supplementary files format and content: SJ.out.tab files containing splice junctions detected from STAR

growth_protocol: K562 cells were grown in IMDM supplemented with 10% FBS. KNS60 cells were grown in DMEM supplemented with 5% FBS. All cell lines were maintained at 37°C and 5% CO2 until 70% confluent.

extract_protocol:
Amplicon sequencing: Total RNA was extracted from whole cells; For RNA-seq following ASO treatment and Targeted-RNA sequencing: Nuclear RNA was extracted from KNS60 cells as described in (Khokhar etal., 2025)
Amplicon sequencing: PCR amplification was performed using Phire Hot Start II PCR Master Mix (Thermofisher, F126) with a 55°C annealing temperature, 15 second extension time, and 40 cycles. Completed reactions were run on 1% agarose gel. Selected amplicons were sent to Genewiz from Azenta Life Sciences for Amplicon-EZ Next-Generation Sequencing and sequenced on a MiSeq platform in 500-cycle paired-end format.
For RNA-seq following ASO treatment and Targeted-RNA sequencing:
Reverse transcription of nuclear RNA from KNS60 cells isolated as described in (Khokhar et al. 2025) was performed using the High-Capacity cDNA Reverse Transcription Kit (Thermofisher, 4368814) according to manufacturer specifications. Single-stranded cDNA was treated with alkaline hydrolysis buffer (150mM NaOH, 1mM EDTA) to degrade any remaining RNA template. 10X TE buffer, pH 7.4 treatment for 10 minute incubation at 50°C was used to neutralize the hydrolysis reaction. cDNA was purified and buffer-exchanged into 1X TE buffer using 3K MWCO Amicon cartridges. The purified cDNA was added to 1 Unit of SUPERase IN RNase Inhibitor per 100ng cDNA (Invitrogen, AM2696), 1pmol biotinylated probe mix per 16ng cDNA, and 200uL per 400ng cDNA of hybridization/wash buffer (40mM Tris-HCl, 300mM NaCl, 0.2% Tween 20 (w/v), 1% SDS) and the sample was incubated at 60°C for 20 minutes with regular agitation. 500ug of magnetic streptavidin beads (Pierce, 88816) per 400ng of cDNA were added to the reaction and the reaction was again incubated at 60°C for 20 minutes with regular agitation. Following incubation, the beads were immobilized and washed 3x with hybridization/wash buffer. Alkaline hydrolysis buffer was added to destroy the RNA probes and release the enriched cDNA transcripts. 10X TE buffer was used to neutralize the hydrolysis reaction and samples were buffer exchanged into 1X TE using 3K MWCO Amicon cartridges. Samples were purified using ethanol precipitation (2.67X volumes of 100% EtOH and 0.1X volumes 3M sodium acetate).
Second-strand synthesis and library preparation. DNA Polymerase I (E. coli) was used to generate second-strand cDNA from the enriched, single-stranded cDNA. The following reagents were combined: 10X NEBuffer 2, 25mM dNTPs, 10X random primers, DNA polymerase I (NEB, M0209), and water for a total reaction volume of 50uL. The reaction was incubated at 95°C for 60 seconds, 16°C for 4 hours, and 37°C for 1 hour. Second-strand cDNA was ethanol precipitated (2.67X volumes of 100% EtOH and 0.1X volumes 3M sodium acetate).
For RNA-seq following ASO treatment Libraries were prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina,  inputs <100ng (NEB, E7805) according to manufacturer’s instructions. Libraries were sequenced as 2x100 reads on a NextSeq 2000 using NextSeq 1000/2000 P2 Reagents (200 cycles) v3 (Illumina, 20046812).
For Targeted-RNA sequencing: Library preparation was performed using NEBNext Ultra II FS Library Prep Kit. Libraries were sequenced on a NextSeq2000 using 2x100 reads.

treatment_protocol: Cells for targeted-RNA sequencing and amplicon sequencing were untreated.  RNA-seq following ASO treatment: Single ASO transfections in KNS60 cells were performed with Lipofectamine RNAiMAX (Invitrogen, 13778150) with ASOs against their respective targets at a final concentration of 80nM (from an ASO stock concentration of 20uM). The stock ASO concentration:lipid ratio was 4:3. Reagents were combined in Opti-MEM and introduced to cells 24 hours after plating and incubated at 37°C and 5% CO2 for 24 hours.

value: glioblastoma

value: WT

value: untreated


title: ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep3

status: Public on Feb 26 2026

type: SRA

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

country: China

institute: Tsinghua University

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep3
ATAC-seq sample ZSWIM3_dead_sgrna_rep3

library_source: genomic

data_processing:
ATAC-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For uploaded processed bigWig files, bamCoverage was used with -p 8 --normalizeUsing RPKM --binSize 100.
Assembly: mm10/hg38
Supplementary files format and content: ATAC-seq coverage bigWig

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Cells were collected and washed with ice-cold PBS. Cell pellets were resuspended in ATAC-seq RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 10 minutes. ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL-630 or digitonin) was then added for washing. Nuclei were pelleted in a pre-chilled centrifuge. Nuclei were incubated with Tn5 transposase and tagmentation buffer at 37°C for 30 minutes. Stop buffer and Proteinase K were added, and samples were incubated at 55°C for 30 minutes to terminate tagmentation and remove proteins.
PCR was performed to amplify the ATAC library for 5 cycles using KAPA HiFi PCR kit. To determine additional amplification cycles for each sample, qPCR was performed, and the additional cycle number was determined as the cycle reaching one-third of maximal abundance in the qPCR amplification curve. All samples were then amplified for another N+3 cycles, followed by final extension. Libraries were purified with DNA clean beads and sequenced as paired-end libraries on Illumina platforms.

tag: cell line

tag: batch


title: Untreated_UT_rep2

country: USA

description:
Library name: Untreated_UT_rep2
RNA-seq following ASO treatment and transcript-pull down

library_source: transcriptomic

molecule: nuclear RNA

tag: cell type

tag: genotype

tag: treatment


title: Cont 0wks, rep1

type: RNA

city: La Jolla

first: Ruth

middle: T

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description:
4903688033_A
Replicate 1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: primary cardiac endothelial cells, control, chow diet

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

value: LDLr-/- mice in C57BL/6 bkg

tag: age

value: 13 wks

tag: tissue

value: heart

value: primary cardiac endothelial cells

value: chow diet


title: Micro-C for pachytene stage (Sample3)

city: Bethesda

first: Florencia

last: Pratto

state: MD

address: 5 Memorial Dr Bg 5 Room 324

department: NIDDK

institute: NIH

description: Library name: PA.hom_BioRep3

library_source: other

data_processing:
Hi-C and Micro-C: Both Hi-C and Micro-C data were processed following the 4DN Hi-C data processing pipeline. Briefly, the pair-end sequenced reads were mapped to mm10 using BWA (version 0.7). The pairs were then filtered by Pairtools (Open2C et al. 2023) to generate valid pairs. Matrices at different resolutions were built and balanced by the Cooler package (Abdennur and Mirny 2020).
Assembly: mm10
Supplementary files format and content: Matrices at different resolutions were built and balanced by the Cooler package (Abdennur and Mirny 2020).

molecule: other

source_name: Testes

extract_protocol:
Mice were euthanized and testes were retrieved. The testes were first fixed with 1% formaldehyde for 10 minutes at room temperature.  Formaldehyde reaction was quenched by 0.125 M glycine. After two times of PBS wash, testes were first fixed with 3mM disuccinimidyl glutarate (DSG) for 45 minutes at room temperature.  DSG was quenched by 0.125 M glycine and testes were homogenized to prepare cell suspension. The cell suspension was filtered by 70 μm cell strainer, washed with 1X PBS (phosphate buffered saline) and then resuspended in nucleus extraction buffer (15 mM Tris-HCl pH 7.4, 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA (Ethylenediaminetetraacetic acid), 0.2 mM EGTA (ethylene glycol tetraacetic acid). Nuclei were extracted using a Dounce homogenizer, 100 strokes with the tight pestle, and repeated once. Nuclei were filtered through a 40-μm cell strainer and resuspended in chilled PBTB buffer (1× PBS with 0.1% Triton X-100, 5% bovine serum albumin, and protease inhibitor). To purify the populations of interest, a combination of intranuclear markers were used (Figure S1). Micro-C was performed as described (Tsung-Han S. Hsieh et al., 2020) with minor modifications.
MicroC libraries were prepared using the KAPA Hyper Prep Kit (Cat. No. KK8502) following the manufacturer's instructions.

value: Testes

value: Sorted nuclei from testes

value: Pachynema


title: RNA-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep2

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep2
RNA-seq sample ZSWIM3_dead_sgrna_rep2

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)

molecule: polyA RNA

extract_protocol:
Dynabeads M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) were diluted 1:10 in 1× PBS (Invitrogen, AM9624), magnetically washed, and incubated with Nesprin1 antibody (abcam, ab192234) at room temperature for 30 minutes. Antibody-coupled beads were washed and resuspended in cell lysis buffer containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1 mM DTT (ThermoFisher, 707265ML), 0.5% Triton X-100 (Sigma, 93443), and 2 U recombinant RNase inhibitor (Takara, 2313A). A population of 500 GFP-positive cells per sample was sorted into 10 µL lysis buffer in 96-well plates, centrifuged at 700 g for 1 minute, and incubated at 4°C with shaking (300 rpm) for 30 minutes. After magnetic separation, the supernatant was transferred to a new plate for RNA-seq workflow, while nuclei were retained for ATAC-side tagmentation workflow in AR-seq. RNA in the supernatant was purified using 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) and reverse-transcribed using SMART-seq2.
RNA-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual. Libraries were generated from SMART-seq2-derived cDNA and sequenced in paired-end mode on short-read sequencing platforms.


title: RNA-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep3

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep3
RNA-seq sample ZSWIM3_dead_sgrna_rep3


title: NTC_NTC_rep2

description:
Library name: NTC_NTC_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NTC_NTC


title: NTC_NTC_rep1

description:
Library name: NTC_NTC_rep1
RNA-seq following ASO treatment and transcript-pull down


title: ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep1

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep1
ATAC-seq sample ZSWIM3_dead_sgrna_rep1


title: ATAC-seq 20200928_hek293t_cas9_empty_vector_rep1

description:
Library name: 20200928_hek293t_cas9_empty_vector_rep1
ATAC-seq sample empty_vector_rep1


title: ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep2

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep2
ATAC-seq sample ZSWIM3_dead_sgrna_rep2


title: RNA-seq 20201013_nih3t3_cas9_TYR_rep3

description:
Library name: 20201013_nih3t3_cas9_TYR_rep3
RNA-seq sample TYR_rep3


title: Micro-C for diplotene stage (Sample1)

description: Library name: DI.hom_BioRep1

value: Diplonema


title: Micro-C for pachytene stage (Sample2)

description: Library name: PA.hom_BioRep2


title: RNA-seq 20201013_nih3t3_cas9_TYR_rep2

description:
Library name: 20201013_nih3t3_cas9_TYR_rep2
RNA-seq sample TYR_rep2


title: ATAC-seq 20200928_hek293t_cas9_TYR_rep3

description:
Library name: 20200928_hek293t_cas9_TYR_rep3
ATAC-seq sample TYR_rep3


title: Cont 0wks, rep2

description:
4903688033_B
Replicate 2.


title: NF1_20_rep2

description:
Library name: NF1_20_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_20


title: targetedKNS60

description:
Library name: targetedKNS60
RNA-seq following combined transcript pulldown against 13 genes in nuclear RNA from KNS60 cells


title: RNA-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep1

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep1
RNA-seq sample ZSWIM3_dead_sgrna_rep1


title: ATAC-seq 20200928_hek293t_cas9_TYR_rep2

description:
Library name: 20200928_hek293t_cas9_TYR_rep2
ATAC-seq sample TYR_rep2


title: RNA-seq 20201013_nih3t3_cas9_TYR_rep1

description:
Library name: 20201013_nih3t3_cas9_TYR_rep1
RNA-seq sample TYR_rep1


title: NF1_19_rep2

description:
Library name: NF1_19_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_19


title: Micro-C for zygotene stage (Sample1)

description: Library name: ZY.hom_BioRep1

value: Zygonema


title: Micro-C for pachytene stage (Sample1)

description: Library name: PA.hom_BioRep1


title: RNA-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep3

description:
Library name: 20201013_nih3t3_cas9_TYR_dead_sgrna_rep3
RNA-seq sample TYR_dead_sgrna_rep3


title: ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep3

description:
Library name: 20200928_hek293t_cas9_TYR_dead_sgrna_rep3
ATAC-seq sample TYR_dead_sgrna_rep3


title: ATAC-seq 20200928_hek293t_cas9_TYR_rep1

description:
Library name: 20200928_hek293t_cas9_TYR_rep1
ATAC-seq sample TYR_rep1


title: NF1_20_rep1

description:
Library name: NF1_20_rep1
RNA-seq following ASO treatment and transcript-pull down


title: Micro-C for zygotene stage (Sample2)

description: Library name: ZY.hom_BioRep2


title: Micro-C for leptotene stage (Sample2)

description: Library name: LE.hom_BioRep2

value: Leptonema


title: Micro-C for leptotene stage (Sample1)

description: Library name: LE.hom_BioRep1


title: NF1_19_rep1

description:
Library name: NF1_19_rep1
RNA-seq following ASO treatment and transcript-pull down

value: glioblastoma


title: ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep2

description:
Library name: 20200928_hek293t_cas9_TYR_dead_sgrna_rep2
ATAC-seq sample TYR_dead_sgrna_rep2


title: RNA-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep2

description:
Library name: 20201013_nih3t3_cas9_TYR_dead_sgrna_rep2
RNA-seq sample TYR_dead_sgrna_rep2


title: RNA-seq 20201013_nih3t3_cas9_EMX1_rep3

description:
Library name: 20201013_nih3t3_cas9_EMX1_rep3
RNA-seq sample EMX1_rep3


title: Micro-C for Meiotic-S stage (Sample2)

description: Library name: PL.hom_BioRep2

value: Meiotic S-phase


title: NF1_18_rep1

description:
Library name: NF1_18_rep1
RNA-seq following ASO treatment and transcript-pull down

value: WT

value: treated with ASO with Oligo_ID:NF1_18


title: RNA-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep1

description:
Library name: 20201013_nih3t3_cas9_TYR_dead_sgrna_rep1
RNA-seq sample TYR_dead_sgrna_rep1


title: ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep1

description:
Library name: 20200928_hek293t_cas9_TYR_dead_sgrna_rep1
ATAC-seq sample TYR_dead_sgrna_rep1


title: Hi-C for diplotene stage (Sample 2)

description: Library name: DI_HiC_BxC.hom_BioRep2


title: Micro-C for Meiotic-S stage (Sample1)

description: Library name: PL.hom_BioRep1


title: ATAC-seq 20200928_hek293t_cas9_EMX1_rep1

description:
Library name: 20200928_hek293t_cas9_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: RNA-seq 20201013_nih3t3_cas9_EMX1_rep1

description:
Library name: 20201013_nih3t3_cas9_EMX1_rep1
RNA-seq sample EMX1_rep1


title: ATAC-seq 20200928_hek293t_cas9_EMX1_rep2

description:
Library name: 20200928_hek293t_cas9_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: NF1_16_rep2

description:
Library name: NF1_16_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_16


title: Hi-C for  diplotene stage (Sample 1)

description: Library name: DI_HiC_BxC.hom_BioRep1


title: ATAC-seq 20200928_hek293t_cas9_EMX1_rep3

description:
Library name: 20200928_hek293t_cas9_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: RNA-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep3

description:
Library name: 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep3
RNA-seq sample EMX1_dead_sgrna_rep3


title: NF1_16_rep1

description:
Library name: NF1_16_rep1
RNA-seq following ASO treatment and transcript-pull down


title: NF1_14_rep2

description:
Library name: NF1_14_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_14


title: ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep3

description:
Library name: 20200928_hek293t_cas9_EMX1_dead_sgrna_rep3
ATAC-seq sample EMX1_dead_sgrna_rep3


title: RNA-seq 20201013_nih3t3_cas9_EMX1_rep2

description:
Library name: 20201013_nih3t3_cas9_EMX1_rep2
RNA-seq sample EMX1_rep2


title: NF1_18_rep2

description:
Library name: NF1_18_rep2
RNA-seq following ASO treatment and transcript-pull down


title: RNA-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep1

description:
Library name: 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep1
RNA-seq sample EMX1_dead_sgrna_rep1


title: Hi-C for pachytene stage (Sample 2)

description: Library name: PA_HiC_BxC.hom_BioRep2


title: RNA-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep2

description:
Library name: 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep2
RNA-seq sample EMX1_dead_sgrna_rep2


title: ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep2

description:
Library name: 20200928_hek293t_cas9_EMX1_dead_sgrna_rep2
ATAC-seq sample EMX1_dead_sgrna_rep2


title: Hi-C for  pachytene stage (Sample 1)

description: Library name: PA_HiC_BxC.hom_BioRep1


title: NF1_14_rep1

description:
Library name: NF1_14_rep1
RNA-seq following ASO treatment and transcript-pull down


title: NF1_11_rep2

description:
Library name: NF1_11_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_11


title: NF1_11_rep1

description:
Library name: NF1_11_rep1
RNA-seq following ASO treatment and transcript-pull down


title: RNA-seq 20230725_hek293t_pe_SMPDL3B_PE2_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B_PE2_rep3
RNA-seq sample SMPDL3B_PE2_rep3


title: KDM5b Hom8

city: Exeter

first: Michiel

middle: Albert

last: Basson

address: Hatherly Labs, Prince of Wales Road

country: United Kingdom

institute: University of Exeter

description:
Library name: H8
Parse

library_source: transcriptomic single cell

data_processing:
Demultiplexing with Parse Biosciences python code fastq_sep_groups_v0.5.py
Parse Biosciences Trailmaker
Assembly: Mouse GRCm38/mm10
Supplementary files format and content: .csv and .h5ad
Supplementary files format and content: The .csv file contains a counts matrix generated using Parse Trailmaker. The .h5ad object for further analysis was generated using the code available at  https://doi.org/10.5281/zenodo.17466762 .

source_name: neocortex

extract_protocol:
Tissue was homogenised and nuclei extracted as described in dx.doi.org/10.17504/protocols.io.36wgq4965vk5/v2. Nuclei were fixed using the Parse Biosciences Evercode Fixation kit as per manufacturers instructions.
Libraries were prepared using the Parse Biosciences Evercode WT kit (chemistry V3)

value: neocortex

value: Homozygous deltaARID


title: NF1_08_rep2

description:
Library name: NF1_08_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_08


title: ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep1

description:
Library name: 20200928_hek293t_cas9_EMX1_dead_sgrna_rep1
ATAC-seq sample EMX1_dead_sgrna_rep1


title: Hi-C for  zygotene stage (Sample 1)

description: Library name: ZY_HiC_BxC.hom_BioRep1

value: Testes

value: Sorted nuclei from testes


title: Hi-C for zygotene stage (Sample 2)

description: Library name: ZY_HiC_BxC.hom_BioRep2


title: KDM5b Hom7

description:
Library name: H7
Parse


title: NF1_08_rep1

description:
Library name: NF1_08_rep1
RNA-seq following ASO treatment and transcript-pull down


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep3
RNA-seq sample SMPDL3B-sgpair3_PE3_rep3


title: Hi-C for leptotene stage (Sample 2)

description: Library name: LE_HiC_BxC.hom_BioRep2


title: KDM5b Hom6

description:
Library name: H6
Parse


title: RNA-seq 20230725_hek293t_pe_SMPDL3B_PE2_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B_PE2_rep1
RNA-seq sample SMPDL3B_PE2_rep1


title: RNA-seq 20230725_hek293t_pe_SMPDL3B_PE2_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B_PE2_rep2
RNA-seq sample SMPDL3B_PE2_rep2


title: NF1_02_rep2

description:
Library name: NF1_02_rep2
RNA-seq following ASO treatment and transcript-pull down

value: treated with ASO with Oligo_ID:NF1_02


title: NF1_02_rep1

description:
Library name: NF1_02_rep1
RNA-seq following ASO treatment and transcript-pull down


title: KDM5b Hom4

description:
Library name: H4
Parse


title: K562_IDU-4SU_rep2

description: Library name: K562_IDU-4SU_rep2

data_processing:
Adapters were trimmed and removed from reads with trimmomatic v0.32. Adapter removal was verified by running fastqc v0.11.565 on trimmed fastqc files. Overlapping read-mates were merged with PEAR v0.9.1166 and merged overlapping read-mates, non-overlapping read 1 and non-overlapping read 2 for each sample were pooled into a single fastq file per library. Fastq files for cell lines were subsampling to 112.67M reads to match the depth of the library with the lowest sequencing depth  using seqtk v1.3. Fastq files for K562 transcriptional noise experiments were subsampled to 33.1M reads to match the depth of library with the lowest sequencing depth.
Subsampled reads were mapped to GRCH38 genome by STAR v2.7.0e69 using default parameters with the following modifications or additions: --outSAMattributes All --outSJfilterOverhangMin 40 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --alignIntronMin 100 --alignIntronMax 250000 --limitOutSJcollapsed 2000000 --outSJfilterDistToOtherSJmin 20 0 10 10 --alignSJstitchMismatchNmax 2 2 2 2
Assembly: Grch38
Supplementary files format and content: Sj.out.tab  output from STAR

growth_protocol: K562 cells were grown in IMDM supplemented with 10% FBS. KNS60 cells were grown in DMEM supplemented with 5% FBS. AM38 cells were grown in EMEM supplemented with 20% FBS. HepG2 cells were grown in DMEM supplemented with 10% FBS. SH-SY5Y cells were grown in DMEM:F12 supplemented with 10% FBS. All cell lines were maintained at 37°C and 5% CO2 until 70% confluent.

extract_protocol:
Nuclear extraction: Nuclear isolation from total cells was performed following a previously established protocol(Nabbi and Riabowol 2015). Briefly, trypsinized cells were pelleted, washed with ice cold 1X PBS, and resuspended in ice cold Nuclear Isolation Buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.3% NP40, Roche EDTA-free protease inhibitor (Millipore Sigma, 11836153001), Sigma PhosSTOP phosphatase inhibitor (Millipore Sigma, 4906845001). The suspension was briefly centrifuged again to pellet the nuclei. The supernatant was removed (cytoplasmic fraction) and the pellet was resuspended in ice cold Nuclear Isolation Buffer. The suspension was centrifuged at 10,000 RCF and supernatant removed. The nuclear pellet was resuspended in TRIzol (Invitrogen, 15596018) before RNA isolation. Nascent RNA isolation from nuclei: Cells were incubated with 1mM 4-thiouridine (Sigma, T4509), dissolved in wter, for 8 minutes and spun down to pellet cells. The pellet was resuspended in Trizol and flash frozen in liquid nitrogen. After nuclear isolation and RNA isolation and described below, 4sU pulldowns were performed using MTSEA biotin-XX (VWR, 89139-636) 4sU-containing (nascent) transcripts were purified following previously established protocols(Garibaldi et al. 2017; Duffy and Simon 2016).  RNA was extracted from whole cells or nuclear pellets using TRIzol reagent to separate the aqueous RNA phase from the DNA and protein phases. The aqueous RNA phase was carried forward into column purification using a Zymo-25 RNA Clean & Concentrator kit (Zymo, R1018)
Library preparation for polyA RNA, CHX-treated, NMDi14-treated, and DMSO-treated samples was performed using the KAPA Stranded mRNA-Seq Kit for Illumina Platforms (KK8421). Library preparation for the nuclear and 4sU-labeled samples was performed using Kapa Biosystems KAPA RNA HyperPrep Kit with RiboErase (KK8561). Libraries were sequenced commercially at Novogene using an Illumina Novaseq 6000,  Illumina Nextseq 2000. SIRV libraries were made with both KAPA Stranded mRNA-Seq Kit and KAPA RNA HyperPrep Kit and sequenced on Illumina NextSeq 500

treatment_protocol: For 4sU labelleing experiments, K562 and KNS60 cells were labelled with either 500uM  or 1mM 4sU (Sigma, T4509) for 8 mins, whereas AM38, SY5Y and HepG2 cells were labelled with 1mM 4SU for 8 mins. For cychoheximide experiments, K562 or KNS60 cells were treated 50ug/mL cycloheximide (CHX) (Sigma, C7698) resuspended in DMSO for 3 hours (or only DMSO as a control). For NMDi14 experiments, K562 and KNS60 cells were  treated with 50uM NMDi14 (Sigma, SML1538) resuspended in DMSO for 6 hours. For transcriptional noise experiments, K562 cells were treated with 10uM 5-Iodo-2’-deoxyuridine (IdU) resuspended in DMSO for 24 hours and media containing 1mM 4sU (Sigma, T4509) was added during the last 8 minutes for subsequent nuclear isolation and nascent mRNA enrichment, as described below. Control cells were treated with equivalent amounts of DMSO without CHX, NMDi14, or IdU for 3, 6, and 24 hours, respectively. Uridine treatment: Control cells were treated 1mM uridine (ChemGenes, RP-1186) dissolved in water for 8 minutes or with 1mM 4sU for 24 hours. For synthetic SIRV: Synthetic Spike-In RNA Variant (SIRV-Set1; Lexogen 025.03 & SIRV-Set4: Lexogen 141.01) were pooled before library prep

value: chronic myeloid leukemia

value: 10 uM 5-Iodo-2‚Äô-deoxyuridine (IdU), 24 hour; 1 mM 4SU in last 8 min


title: Hi-C for Meiotic-S stage (Sample 2)

description: Library name: PL_HiC_BxC.hom_BioRep2


title: Hi-C for  leptotene stage (Sample 1)

description: Library name: LE_HiC_BxC.hom_BioRep1


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep2
RNA-seq sample SMPDL3B-sgpair3_PE3_rep2


title: KDM5b Hom3

description:
Library name: H3
Parse


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep1
RNA-seq sample SMPDL3B-sgpair3_PE3_rep1


title: KDM5b Hom2

description:
Library name: H2
Parse


title: Hi-C for Meiotic-G1 stage (Sample 3)

description: Library name: MM3_HiC_BxC.hom_BioRep3

value: Meiotic G1


title: K562_IDU-4SU_rep1

description: Library name: K562_IDU-4SU_rep1


title: KDM5b Hom1

description:
Library name: H1
Parse


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep2
RNA-seq sample SMPDL3B-sgpair2_PE3_rep2


title: K562_IDU_rep1

description: Library name: K562_IDU_rep1

value: 10 uM 5-Iodo-2‚Äô-deoxyuridine (IdU), 24 hour


title: Hi-C for Meiotic-G1 stage (Sample 2)

description: Library name: MM3_HiC_BxC.hom_BioRep2


title: Hi-C for  Meiotic-G1 stage (Sample 1)

description: Library name: MM3_HiC_BxC.hom_BioRep1


title: Hi-C for transition II stage (Sample 3)

description: Library name: MM2_HiC_BxC.hom_BioRep3

value: Transition II


title: KDM5b Hom5

description:
Library name: H5
Parse


title: KDM5b WT8

description:
Library name: WT8
Parse


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep3
RNA-seq sample SMPDL3B-sgpair1_PE3_rep3


title: KDM5b WT7

description:
Library name: WT7
Parse


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep1
RNA-seq sample SMPDL3B-sgpair2_PE3_rep1


title: K562_control_rep2

description: Library name: K562_control_rep2

value: DMSO, 24 hour


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep2
RNA-seq sample SMPDL3B-sgpair1_PE3_rep2


title: K562_4SU_rep2

description: Library name: K562_4SU_rep2

value: WT

value: DMSO, 24 hour; 1 mM 4SU in last 8 min


title: Hi-C for transition II stage (Sample 2)

description: Library name: MM2_HiC_BxC.hom_BioRep2


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep1
RNA-seq sample SMPDL3B-sgpair1_PE3_rep1


title: KDM5b WT6

description:
Library name: WT6
Parse


title: Hi-C for transition II stage (Sample 1)

description: Library name: MM2_HiC_BxC.hom_BioRep1


title: Hi-C for  Meiotic-S stage (Sample 1)

description: Library name: PL_HiC_BxC.hom_BioRep1

value: Meiotic S-phase


title: Hi-C for transition I stage (Sample 3)

description: Library name: MM1_HiC_BxC.hom_BioRep3

value: Transition I


title: K562_4SU_rep1

description: Library name: K562_4SU_rep1


title: K562_control_rep1

description: Library name: K562_control_rep1


title: HD10

city: Frankfurt am Main

first: Marius

last: Külp

address: Theodor-Stern-Kai 7

department: Department of Medicine II, Hematology/Oncology

country: Germany

institute: Goethe University Hospital Frankfurt

description:
Library name: healthy_ctrl_10-SMALLRNA_A-tRNA_Seq
tpm_HD10

data_processing:
Sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt (4.6) with the arguments "-e 0.1 -O 3 -q 20 -m 20 -n 8". Additional sequencing artifacts were removed from the reads with the arguments "-m 20 -u 4 -a 'A{300}X' -a 'A{10};o=10'".
Further processing steps were performed using the public server at usegalaxy.org. An artificial tRNA isotranscript genome was created based on the Homo sapiens hg38 high confidence tRNA dataset from GtRNAdb using the Collapse sequences tool (Galaxy Version 1.0.1) to merge identical tRNA isotranscripts.
Adapter-trimmed FASTQ files are mapped against the artificial tRNA isotranscript genome using Bowtie2 with the arguments “-N 1 -L 10 -i S,1,0.5 --local --score-min G,1,8 --np 0”.
The resulting mapped reads were filtered using BAM filter to remove reads outside the 11 bp anticodon loop region with the arguments “-mapped YES -includebed [GFF filtering file]”.
FeatureCounts was used to count reads assigned to tRNA isotranscripts with the arguments “-t tRNA -g transcript_id -M -O --fraction YES --minOverlap 30”.
Reads were normalized to transcripts per million (tpm).
Assembly: hg38 GtRNAdb high confidence dataset
Supplementary files format and content: tab-delimited text file includes raw counts and tpm values for each sample

source_name: Peripheral Blood Cells

extract_protocol:
Total RNA was extracted and purified using the PAXgene Blood RNA Kit (Qiagen, 762174) according to the manufacturer’s protocol
tRNA-sequencing libraries were generated using the TrueQuant SmallRNA Seq Kit (GenXPro) according to the manufacturer’s protocol.

value: Peripheral Blood Cells


title: RNA-seq 20230725_hek293t_pe_MPP4_PE2_rep3

description:
Library name: 20230725_hek293t_pe_MPP4_PE2_rep3
RNA-seq sample MPP4_PE2_rep3


title: Hi-C for transition I stage (Sample 2)

description: Library name: MM1_HiC_BxC.hom_BioRep2


title: KDM5b WT5

description:
Library name: WT5
Parse

value: neocortex


title: HD9

description:
Library name: healthy_ctrl_9-SMALLRNA_A-tRNA_Seq
tpm_HD9


title: KDM5b WT3

description:
Library name: WT3
Parse


title: Hi-C for transition I stage (Sample 1)

description: Library name: MM1_HiC_BxC.hom_BioRep1


title: RNA-seq 20230725_hek293t_pe_MPP4_PE2_rep1

description:
Library name: 20230725_hek293t_pe_MPP4_PE2_rep1
RNA-seq sample MPP4_PE2_rep1


title: KDM5b WT4

description:
Library name: WT4
Parse


title: KDM5b WT1

description:
Library name: WT1
Parse


title: HD8

description:
Library name: healthy_ctrl_8-SMALLRNA_A-tRNA_Seq
tpm_HD8


title: KDM5b WT2

description:
Library name: WT2
Parse


title: Hi-C for differentiating spermatogonia (Sample 2)

description: Library name: SD2_HiC_BxC.hom_BioRep2

value: Differentiating Spermatogonia


title: HD7

description:
Library name: healthy_ctrl_7-SMALLRNA_A-tRNA_Seq
tpm_HD7


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep2

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep2
RNA-seq sample MPP4-sgpair3_PE3_rep2


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep3

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep3
RNA-seq sample MPP4-sgpair3_PE3_rep3


title: Hi-C for undifferentiated spermatogonia (Sample 4)

description: Library name: SGA_HiC_BxC.hom_BioRep4


title: sorted colonic lamina propria iNKT mouse ctrl

city: St. Louis

first: Rodney

middle: D

last: Newberry

address: 660 S. Euclid Ave

department: Medicine

description:
Library name: M_HS-EGFRi
10X Genomics

data_processing:
The demultiplexed human fastq files were processed with the PIPseeker 3.0.5 software (Fluent Biosciences) to determine UMI for each cell for each sample.
The demultiplexed mouse fastq files were processed with the cellranger-6.0.1 software (10X Genomics) against mouse genome mm10 to determine UMI for each cell for each mouse sample.
Assembly: Mouse mm 10 2020
Assembly: Human  GRCh38-2022.04
Supplementary files format and content: Tab separated values and matrix file

source_name: colon lamina propria

extract_protocol:
Human colonic resections were stored in MACS storage solution prior to processing. For lamina propria isolation, white fatty muscularis layer was removed and tissues washed with 40ml Hank’s Balanced Salt solution (HBSS) containing 5mM of EDTA for 30 mins for 2 times at37°C in a shaking incubator.  Remaining tissues were cut into pieces and digested with Dispase (50U/ml stock) and Type VIII Collagenase Collagenase (10,000 U/ml) at 37°C under shaking conditions for 90 mins in R5 media. The digested tissues were filtered through 100-µm cell strainer and centrifuged at 1,500 rpm for 5 mins. The cells were and resuspended in PBS before performing the cell staining for flow cytometry staining. Cells were stained with CD45, TCRb, CD3, loaded CD1d tetramer and viability dye and sorted on a FACS Aria II.
For mouse lamina propria isolation, white fatty muscularis layer was removed and tissues washed with 20ml Hank’s Balanced Salt solution (HBSS) containing 5mM of EDTA for 15 mins for 3 times at 37°C in a shaking incubator. Remaining tissues were cut into pieces and digested with Dispase (50U/ml stock) and Type VIII Collagenase Collagenase (10,000 U/ml) at 37°C under shaking conditions for 90 mins in R5 media. The digested tissues were filtered through 100-µm cell strainer and centrifuged at 1,500 rpm for 5 mins. The cells were and resuspended in PBS before performing the cell staining for flow cytometry staining. Cells were stained with CD45, TCRb, CD3, loaded CD1d tetramer and viability dye before being sorted on a FACS Aria II.
Sorted human  iNKT cells were processed with the T2 PIPseq kit following manufacturer instructions prior to sequencing on Illumina NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol at the Genome Technology Access Center at Washington University School of Medicine in St. Louis
Sorted mouse iNKT cells were counted and 10,000 cells were loaded onto a 10X Genomics Chromium controller for 3’v3.1 library preparation as per the manufacturer’s recommendations.  The concentration of each library was determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library. Library preparation and sequencing was performed at the Genome Technology Access Center at Washington University in Saint Louis School of Medicine.

treatment_protocol: Mice were treated i.p. with 6.6ug of EGFRi for 4 days or vehicle control prior to LP isolation. Human samples were from healthy surgical resections.

value: colon lamina propria

tag: Sex

value: F

value: iNKT

value: EGFRi

value: 8 weeks

tag: resection

value: Colon


title: RNA-seq 20230725_hek293t_pe_MPP4_PE2_rep2

description:
Library name: 20230725_hek293t_pe_MPP4_PE2_rep2
RNA-seq sample MPP4_PE2_rep2


title: HD6

description:
Library name: healthy_ctrl_6-SMALLRNA_A-tRNA_Seq
tpm_HD6


title: HD5

description:
Library name: healthy_ctrl_5-SMALLRNA_A-tRNA_Seq
tpm_HD5


title: K562_IDU_rep2

description: Library name: K562_IDU_rep2

value: chronic myeloid leukemia


title: sorted colonic lamina propria iNKT mouse EGFri

institute: Washington University School of Medicine

description:
Library name: M_HS-Control
10X Genomics

value: Ctrl


title: Spherule, Exosome, RiboMarker, 3

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

description: Library name: Spherule_Exosome_RiboMarker_3

data_processing:
Sequencing reads were trimmed of adapter sequence using cutadapt version 4.6 [--nextseq-trim=15 -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15] (31). Reads were then aligned to ncRNA transcripts identified using RFAM, with the addition of the high-confidence set of tRNA isodecoders containing -CCA tails identified using tRNAScan-SE (32),  and then to theC. posadasii strain Silveira (GCA_000170175.2) genome. ShortStack v4.1.0 (33) with the parameters [-pad 3 –mincov 0.5rpm] was used to identify potential novel sRNA transcripts. Reads overlapping with known annotations were summed and the corresponding read counts were used for downstream differential analysis.
Assembly: GCA_000170175.2 (Silveria 2011)
Supplementary files format and content: csv files contain raw read counts for each sample

organism: Coccidioides posadasii

source_name: exosomes

growth_protocol: C. posadasii (strain Δcts2/Δard1/Δcts3, NR-166; BEI Resources) arthroconidia were harvested from 6-week-old plates as previously described (29). The spores were inoculated at 1 × 106 arthroconidia into a 250 mL baffled Erlenmeyer flask containing 100 mL of 2xGYE at 150 rpm at 30 °C for 48 hours. Conditioned medium was harvested by collecting conditioned media with cells into centrifuge tubes and spun at 12,000 × g for 8 min to pellet the cells. The supernatant was pooled and filtered with a 0.22-µm syringe filter before being stored at −80°C.  To generate samples for the time course, in which arthroconidia transition to mycelia, 1 × 106 of harvested arthroconidia were incubated in 250 mL flat-bottom Erlenmeyer flasks (Corning, Corning, NY, USA) in 100 mL of 2x GYE media at 150 rpm at 30 °C. After 48 hours, the conditioned medium with cells was placed in into centrifuge tubes and spun at 12,000 × g for 8 min to pellet the cells. Half of the filtered fungal cells were kept for RNA isolation, while the condition media was spun down and supernatant was removed for extracellular RNA isolation. The remaining cells were reinoculated in fresh 2X GYE for 48 hours at 150 rpm at 30 °C. At 72 hrs post-media change, the fungal cells were separated from the growth media by filtering with a sterile 40 µm nylon mesh cell strainer.  Half of the filtered fungal cells were kept for RNA isolation, while the condition media was filtered with a 0.22-µm syringe filter before being stored at −80°C for extracellular RNA isolation. The remaining half of the filtered fungal cells were reintroduced again into fresh 2X GYE for 24 hours at 150 rpm at 30 °C.  This sample processing was performed again at 96 hrs for a total of 3 replicates of fungal cell samples and filtered conditioned media. C. posadasii spherules were propagated and harvested from 6-week-old plates as previously described (29). For spherule samples, 50 mL of Converse medium (30) was inoculated to a final concentration of 106 arthroconidia/mL. Cultures are then incubated at 39°C in a 10% CO2 shaking incubator at 150 rpm for ~ 3 days. Spherules are harvested by filtering culture through a nested filter into a 50 mL conical tube and then centrifuged at 9000 x g for 8 mins to pellet. Pellets were washed with 1x PBS twice, pelleted, then snap frozen for storage at -80°C until use.

extract_protocol:
C. posadasii mycelium, arthroconidia, and young (no endosporulation) spherule samples were stored in RNA Shield (Zymo Research) at −80°C until processing using the Quick-RNA™ Fungal
For small RNA-seq, libraries were prepared from total RNA using the RealSeq®-Biofluids library preparation kit (RealSeq Biosciences) according to the manufacturer’s instructions. Libraries for each ecotype, as well as cell-free and exosome samples, were generated separately and then pooled for the analysis. In some cases, triplicate libraries for each sample type and condition were not met, and thus, only duplicates were used in downstream analyses to avoid batch effects in the data. Finally, prepared libraries were pooled and subjected to single-end 75 cycles of sequencing using the F3 50 cycle sequencing kit (Note: reagents for 50 additional cycles above what is represented were included to account for index sequencing needs) on the Singular G4 system according to the manufacturer’s instructions (Singular Genomics).

treatment_protocol: For treatment of RNA with the Ribomarker® platform, 10 uL of RNA sample was incubated in a 15 μl reaction mixture containing 1.5 μl Ribomarker® Buffer 1, 1.5 uL of Ribomarker® Enzyme 1, and 2 uL of RNase-Free H2O at 37 °C for 10 min, followed by 80 °C for 2 min. Then, to this mixture was added 2 uL of Ribomarker® Buffer 2 and 2 uL of Ribomarker® Enzyme 2, which was then incubated at 37 °C for 60 min. Finally, 1 uL of Buffer 3 was added to the reaction and incubated at 37 °C for 60 min. The treated RNA was then isolated using an RNA Clean and Concentrator-5 kit for downstream use in library preparation.

value: exosomes


title: Hi-C for undifferentiated spermatogonia (Sample 3)

description: Library name: SGA_HiC_BxC.hom_BioRep3

value: Testes

value: Sorted nuclei from testes

value: Undifferentiating spermatogonia


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep3

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep3
RNA-seq sample MPP4-sgpair2_PE3_rep3


title: Hi-C for differentiating spermatogonia (Sample 1)

description: Library name: SD2_HiC_BxC.hom_BioRep1


title: HD4

description:
Library name: healthy_ctrl_4-SMALLRNA_A-tRNA_Seq
tpm_HD4


title: Spherule, Exosome, RiboMarker, 2

description: Library name: Spherule_Exosome_RiboMarker_2


title: Mycelia, Exosome, RiboMarker, 1

description: Library name: Mycelia_Exosome_RiboMarker_1


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep1

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep1
RNA-seq sample MPP4-sgpair3_PE3_rep1


title: HD3

description:
Library name: healthy_ctrl_3-SMALLRNA_A-tRNA_Seq
tpm_HD3


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep1

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep1
RNA-seq sample MPP4-sgpair2_PE3_rep1


title: Arthrocelia, Exosome, RiboMarker, 3

description: Library name: Arthrocelia_Exosome_RiboMarker_3


title: imput sample from mouse testes rep 1

description:
Library name: input_Chip_BxC.testis_BioRep1
Input sample

data_processing:
Sequencing tags were aligned to the mouse mm10 reference genome using BWA mem 0.7.12.
Assembly: mm10
Supplementary files format and content: Peaks for CTCF ChIP-Seq were called using MACS2 (version 2.2.7) with default parameters and an input DNA sample as a control.

extract_protocol:
Testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. CTCF ChIP was performed as described previously (Kwan-Wood Gabriel Lam et al., 2019) with minor modifications.
Library was constructed using the KAPA Hyperprep Kit following manufacturer's protocol


title: HD1

description:
Library name: healthy_ctrl_1-SMALLRNA_A-tRNA_Seq
tpm_HD1


title: Hi-C for undifferentiated spermatogonia (Sample 2)

description: Library name: SGA_HiC_BxC.hom_BioRep2


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep2

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep2
RNA-seq sample MPP4-sgpair1_PE3_rep2


title: Hi-C for undifferentiated spermatogonia (Sample 1)

description: Library name: SGA_HiC_BxC.hom_BioRep1


title: HD10

description:
Library name: healthy_ctrl_10-MACE_D-MACE_Seq
tpm_healthy_ctrl_10-MACE_Seq

data_processing:
Sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt (4.645) with the arguments "-e 0.1 -O 3 -q 20 -m 20 -n 8". Additional sequencing artifacts were removed from the reads with the arguments "-m 20 -u 4 -a 'A{300}X' -a 'A{10};o=10'"
Processed sequencing reads were mapped to ENSEMBL_dna of hg38 (Homo sapiens) using Bowtie2 with the arguments "--sensitive --local".
Quantification of reads mapped to each gene was performed using HTSeq (2.0.2) with the arguments "-i gene_id -r pos -a 0" and setting strandedness to YES.
Reads were normalized to transcripts per million (tpm).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and tpm values for each sample

extract_protocol:
Total RNA was extracted and purified using the PAXgene Blood RNA Kit (Qiagen, 762174) according to the manufacturer’s protocol
3’-mRNA Massive Analysis of cDNA Ends (MACE) sequencing libraries were generated using the MACE-Seq Kit (GenXPro) according to the manufacturer’s protocol.


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep2

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep2
RNA-seq sample MPP4-sgpair2_PE3_rep2


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep3

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep3
RNA-seq sample MPP4-sgpair1_PE3_rep3


title: imput sample from mouse testes rep 2

description:
Library name: input_Chip_BxC.testis_BioRep2
Input sample


title: Arthrocelia, Exosome, RiboMarker, 1

description: Library name: Arthrocelia_Exosome_RiboMarker_1


title: CTCF ChIP-seq from mouse testes rep 2

description:
Library name: CTCF_Chip_BxC.testis_BioRep2
IP sample


title: HD8

description:
Library name: healthy_ctrl_8-MACE_D-MACE_Seq
tpm_healthy_ctrl_8-MACE_Seq


title: Mycelia, Exosome, RiboMarker, 3

description: Library name: Mycelia_Exosome_RiboMarker_3


title: RNA-seq 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep3
RNA-seq sample SMPDL3B-sgpair2_PE3_rep3


title: Arthrocelia, Exosome, RiboMarker, 2

description: Library name: Arthrocelia_Exosome_RiboMarker_2


title: HD2

description:
Library name: healthy_ctrl_2-SMALLRNA_A-tRNA_Seq
tpm_HD2


title: RNA-seq 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep1

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep1
RNA-seq sample MPP4-sgpair1_PE3_rep1


title: RNA-seq 20230725_hek293t_pe_EMX1_PE2_rep2

description:
Library name: 20230725_hek293t_pe_EMX1_PE2_rep2
RNA-seq sample EMX1_PE2_rep2


title: Arthroconidia, Exosome, RiboMarker, 3

description: Library name: Arthroconidia_Exosome_RiboMarker_3


title: Induced D6XY  gonad

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
Raw paired-end sequence data were converted to FASTQ files and mapped to mouse mm10 genome using Cell Ranger software version 3.0.2(10X Genomics).
Assembly: mm10

source_name: gonad somatic cells

growth_protocol: ESCs were cultured with N2B27 medium containing 12 ng/mL of FGF2 and 20 ng/mL of Activin A for 42 hours. Then, 3 x 106 cells of EpiLCs dissociated with TrypLE were seeded in a 35 mm dish named EZsphere SP (Type 904; IWAKI, Japan) and cultured in GK15 medium (GMEM supplemented with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 1 x Antibiotic-Antibiotic (Gibco), and 2 mM L-glutamine (Invitrogen)) containing 14 μM CHIR99021(CHIR) (BioVision Inc., Cat # 1677-25 and FUJIFILM), 1 ng/ml BMP4 (R & D Systems), and 50 ng/ml EGF (R & D Systems) to form cell aggregations. The next day (D1), cell aggregates were collected and suspended in medium containing 2% FCeM, a cell suspension polymer solution (Nissan Chemical, Japan), and transferred to a low-cell-binding culture dish (Greiner) for continuing cultivation. On D2, the culture medium was changed to GK15 + 2%FCeM containing 3 μM retinoic acid (Sigma), 30 ng/ml Sonic hedgehog (SHH) (R&D Systems), 1 μM PD0325901 (PD) (FUJIFILM), 50 ng/ml EGF and 1 ng/ml BMP4 medium. After 49 hours of culture, on D4, GK15 + 2%FCeM containing 20 ng/ml BMP4, 2 ng/ml FGF9 (PeproTech) and 20 μM IWR1 (FUJIFILM) medium.

extract_protocol:
cells were dissociated enzymatically by papain for 30 mins and then harvested by centrifugation.
Single-cell RNA sequencing libraries were prepared from the freshly isolated female mouse gonad tissues and ES-derived gonad cells by using Chromium Single Cell 3ʹ v2 Reagent Kits (10X Genomics) for in vivo gonad samples and Chromium Next GEM Single Cell 3ʹ v3 Reagent Kits (10X Genomics) for ES cell-derived gonadal somatic cells as previously described (Hashimoto et. al. PNAS, 2019). Briefly, the dissociated cells were mixed with the Single cell Master Mix and generated gel bead-in-emulsions (GEMs). The RNAs in each GEM were revers-transcribed and the resulting cDNAs were amplified by PCR. Illumina sequencer adapted sequencing libraries were constricted from the amplified cDNAs. Single-cell RNA sequencing libraries were sequenced with paired-end reads on the Illumina HiSeq X Ten platform.

tag: strain

value: ES cell-derived gonadal somatic cells

tag: transgenes

value: Nr5a1-hCD27a and Sox9-2A-CGFP


title: RNA-seq 20230725_hek293t_pe_EMX1_PE2_rep1

description:
Library name: 20230725_hek293t_pe_EMX1_PE2_rep1
RNA-seq sample EMX1_PE2_rep1


title: CTCF ChIP-seq from mouse testes rep 1

description:
Library name: CTCF_Chip_BxC.testis_BioRep1
IP sample


title: RNA-seq 20230725_hek293t_pe_EMX1_PE2_rep3

description:
Library name: 20230725_hek293t_pe_EMX1_PE2_rep3
RNA-seq sample EMX1_PE2_rep3


title: E11.5XY gonad

source_name: gonad

value: ICR

value: in vivo gonad


title: E12.5XY gonad


title: HD9

description:
Library name: healthy_ctrl_9-MACE_D-MACE_Seq
tpm_healthy_ctrl_9-MACE_Seq

value: Peripheral Blood Cells


title: Arthroconidia, Exosome, RiboMarker, 1

description: Library name: Arthroconidia_Exosome_RiboMarker_1


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep3

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep3
RNA-seq sample EMX1-sgpair3_PE3_rep3


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep2

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep2
RNA-seq sample EMX1-sgpair3_PE3_rep2


title: HD6

description:
Library name: healthy_ctrl_6-MACE_D-MACE_Seq
tpm_healthy_ctrl_6-MACE_Seq


title: HD4

description:
Library name: healthy_ctrl_4-MACE_D-MACE_Seq
tpm_healthy_ctrl_4-MACE_Seq


title: Arthroconidia, Exosome, RiboMarker, 2

description: Library name: Arthroconidia_Exosome_RiboMarker_2


title: Spherule, CellFree, RiboMarker, 3

description: Library name: Spherule_CellFree_RiboMarker_3

source_name: cell-free media

value: cell-free media


title: E10.5XY gonad


title: HD5

description:
Library name: healthy_ctrl_5-MACE_D-MACE_Seq
tpm_healthy_ctrl_5-MACE_Seq


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, L15

city: San Antonio

first: Bowen

last: Yang

state: TEXAS

address: 7703 Floyd Curl Drive, Mail code 7971

institute: University of Texas Health Science Center at San Antonio

description: Library name: MLLr24_R_T

data_processing:
ChIP-seq reads were aligned to hg19 using Bowtie2 and peaks were called with MACS2 (default parameters), followed by filtering to retain high-confidence peaks reproducibly detected across replicates. RNA-seq reads were aligned to hg19 using STAR; alternative splicing was quantified using rMATS, and skipped exon (SE) events were summarized using PSI values (significance thresholds: |ΔPSI| > 0.1 and FDR < 0.05). H3K79me2 peaks were assigned to SE events based on genomic overlap with exon bodies and flanking intronic regions for integrated chromatin–splicing analyses.
Assembly: hg19
Supplementary files format and content: Tab-separated value files and matrix files from the output of MISO alternative spilicing tool.

source_name: Peripheral Blood

extract_protocol:
ChIP DNA: Primary tissue samples were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. Nuclei were isolated, chromatin was sheared to ~200–500 bp using a Covaris E220, and immunoprecipitation was performed overnight at 4°C with anti-H3K79me2 (Abcam, ab3594). DNA was purified using the MinElute PCR Purification Kit (Qiagen). RNA: Total RNA was extracted using TRIzol (Invitrogen) followed by DNase I treatment. RNA integrity was assessed by Agilent 2100 Bioanalyzer and samples with RIN ≥ 7 were used.
ChIP-Seq Library: ChIP DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) and sequenced on an Illumina NextSeq 3000. RNA-Seq Library: Poly(A)+ RNA was enriched using oligo(dT) magnetic beads. Strand-specific libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on an Illumina NextSeq 3000 (~50M reads per sample).

treatment_protocol: For DOT1L inhibition, Mixed Lineage Leukemia rearrangement samples were treated with EPZ5676 (pinometostat) prior to RNA-seq and H3K79me2 ChIP-seq.

value: Peripheral Blood

value: EPZ-5676 Treatment


title: Spherule, CellFree, RiboMarker, 1

description: Library name: Spherule_CellFree_RiboMarker_1


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep1

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep1
RNA-seq sample EMX1-sgpair3_PE3_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, L13

description: Library name: MLLr23_R_T


title: HD3

description:
Library name: healthy_ctrl_3-MACE_D-MACE_Seq
tpm_healthy_ctrl_3-MACE_Seq


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep3

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep3
RNA-seq sample EMX1-sgpair2_PE3_rep3


title: HD2

description:
Library name: healthy_ctrl_2-MACE_D-MACE_Seq
tpm_healthy_ctrl_2-MACE_Seq


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep2

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep2
RNA-seq sample EMX1-sgpair2_PE3_rep2


title: Spherule, CellFree, RiboMarker, 2

description: Library name: Spherule_CellFree_RiboMarker_2


title: Mycelia, CellFree, RiboMarker, 2

description: Library name: Mycelia_CellFree_RiboMarker_2


title: Mycelia, CellFree, RiboMarker, 3

description: Library name: Mycelia_CellFree_RiboMarker_3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T3

description: Library name: MLLr21_R_T


title: HD1

description:
Library name: healthy_ctrl_1-MACE_D-MACE_Seq
tpm_healthy_ctrl_1-MACE_Seq


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep1

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep1
RNA-seq sample EMX1-sgpair2_PE3_rep1


title: HD7

description:
Library name: healthy_ctrl_7-MACE_D-MACE_Seq
tpm_healthy_ctrl_7-MACE_Seq


title: Local Patient Derived Organoid 3

city: Calgary

first: Arshad

last: Ayyaz

state: Alberta

address: BI238D, 507 Campus Dr nw

country: Canada

institute: University of Calgary

description:
Library name: CRCc-03
UBC SBME-SEQ

data_processing:
Barcode processing, gene counting, and aggregation for data processing outputs were all done using cellranger version 7.0.1 using recommended parameters.
Assembly: CRCh38 Homo sapien
Supplementary files format and content: Tab-seperated value files and matrix value files

source_name: Local Colorectal Cancer organoids

growth_protocol: Tissues were processed within 12 hours of resection from the patient. Tissue samples were placed in Advanced DMEM (Gibco) containing GlutaMAX (1X, Gibco), 100 U/ml penicillin (Gibco), 100 μg/ml streptomycin (Gibco), and 1X HEPES (Gibco). Samples were subsequently washed 5 times with 1X PBS (Gibco) and mechanically dissected using a razor blade in a 10cm petridish (Falcon). Accumax (innovative cell technologies) was added to the samples for enzymatic digestion for 30 minutes. Following 30 minutes the sample was spun down at 1240 rcf for 5 minutes. The supernatant was removed, and 5 mL of pre-warmed trypsin was added to the tissue for cell dissociation. The sample was incubated for 5 minutes at 37 °C. This process was repeated an additional time and then added with 10% FBS (Gibco) and the sample was spun down at 1240 rcf for 5 minutes.  The supernatant was removed, and the pellet was resuspended with Matrigel (VWR). This mixture was plated on 24 well plates (Corning) and incubated for 15 minutes in an incubator at 37 °C and 5% CO2 to allow time for the Matrigel to settle. Human organoid media was added to each well which comprised of Advanced DMEM (Gibco) containing GlutaMAX (1X, Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco), HEPES (1X Gibco), 1X B27 (invitrogen), 10% FBS (Gibco), 50 ng/mL mouse recombinant EGF (Invitrogen), 100ng/mL beta-EGF (Gibco), 10 µM Y27632 (Sigma), 1 µM NECA (Sigma), and 1 µM SB202190 (Sigma).

extract_protocol:
PDOs were mechanical dissociated using a 12 mL syringe and 16-gauge needle followed by the addition of 5 mL of pre-warmed trypsin and incubated for 5 minutes at 37 °C. The addition of trypsin and incubation at 37 °C was repeated 3 additional times. 10% FBS (Gibco) was added and the sample and spun down at 1240 rcf for 5 minutes. Samples were washed twice with 1X PBS (Gibco) to remove residual trypsin. Cells were then stained with trypan blue (Gibco) and counted on a hemocytometer to access cell quantity and viability.
Samples were run using the 3’ Chromium Single Cell 3’ Reagent Kit (10X genomics) and 10, 000 cell recovery was targeted. Manufactures recommendations and instructions were used in constructing the library.

value: Local Colorectal Cancer organoids


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T4

description: Library name: MLLr20_R_T


title: Mycelia, CellFree, RiboMarker, 1

description: Library name: Mycelia_CellFree_RiboMarker_1


title: Arthrocelia, CellFree, RiboMarker, 3

description: Library name: Arthrocelia_CellFree_RiboMarker_3


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep3

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep3
RNA-seq sample EMX1-sgpair1_PE3_rep3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T2

description: Library name: MLLr22_R_T


title: Local Patient Derived Organoid 1

description:
Library name: CRCc-01
UBC SBME-SEQ


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep2

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep2
RNA-seq sample EMX1-sgpair1_PE3_rep2


title: hPDL-MSCs, miR378a overexpression

city: Tokyo

first: Jingyi

last: Gao

state: Tokyo

address: Yushima, Bunkyo District

department: Periodontology

institute: Institute of Science Tokyo

description:
Library name: miR378a_RNAseq
miR378_RNAseq_count

data_processing:
Low-quality and adaptor sequences were trimmed with fastp (v0.22.0), and the processed paired-end reads were aligned to the human reference genome (GRCh38.p14) using HISAT2 (v2.1.0). Transcript assembly and abundance estimation were conducted using StringTie (v2.1.1).
Differential expression analysis was performed in R using edgeR (v4.0.16) and limma (v3.58.1; voom v1.32.0), applying thresholds of adjusted P < 0.01, FDR < 0.1, and fold change ≥ 1. P values were adjusted for multiple testing using the Benjamini-Hochberg method and converted to q values.
Assembly: GRCh38.p14/Homo_sapiens.GRCh38.112
Supplementary files format and content: CSV files contains count data.

source_name: mesenchymal stem cell

growth_protocol: We used alpha-minimum essential medium (⍺-MEM; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific), 100 U ml−1 penicillin and 100 μg ml−1 streptomycin (P/S; Thermo Fisher Scientific) as the basic medium for hPDL-MSCs, and we changed the medium twice a week. Cell passaging was performed using 0.25% trypsin-EDTA (Thermo Fisher Scientific) to detach the cells.

extract_protocol:
Total RNA was harvested using RNeasy mini kit (Qiagen, 74104) according to the manufacturer's protocol.
Libraries preparation was achieved through poly(A) enrichment of mRNA and sequenced on the NovaSeqX Plus system (Illumina, San Diego, US) using 150 bp paired-end reads.

treatment_protocol: Cells were treated with miR-378a mimic or negative control for 48 hrs via Lipofectamine RNAiMAX (Invitrogen, 13778030). Samples were collected from cells overexpressing either Negative Control mimic or mimic.

value: mesenchymal stem cell

value: hsa-miR-378a-3p mimic transfection


title: Arthrocelia, CellFree, RiboMarker, 2

description: Library name: Arthrocelia_CellFree_RiboMarker_2


title: RNA-seq 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep1

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep1
RNA-seq sample EMX1-sgpair1_PE3_rep1


title: hPDL-MSCs, Control

description:
Library name: CTL_RNAseq
CTL_RNAseq_count

value: NC mimic transfection


title: RNA-seq 20230123_u2os_cas9_ZSWIM3_rep3

description:
Library name: 20230123_u2os_cas9_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3


title: Arthrocelia, CellFree, RiboMarker, 1

description: Library name: Arthrocelia_CellFree_RiboMarker_1


title: PC9, two drugs combined, repeat3

city: Dalian

first: Hai-long

last: Piao

state: Liaoning

address: No.457 Zhongshan Road

institute: Dalian Institute of chemical physics

description:
Library name: P_pa3
column name in mRNA.readcount.xls:P_pa3

data_processing:
After sequences were mapped using HISAT2 (version 2.2.1) against the Homo_sapiens.GRCh38.101.gtf, the reads for each library were converted to counts by HTSeq (https://htseq.readthedocs.io/en/release_0.9.1/)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: xls file includes FPKM for all samples

extract_protocol:
The PC9 or H1975 cell lines treated under control or drug treatments for 24 hours were collected and their RNAs were isolated using TRIzol reagent.
Sequencing libraries were constructed from total RNA using SMART-RNAseq Library Prep Kit (Hangzhou KaiTai, AT4201).

value: two drugs combined


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T1

description: Library name: MLLr17_R_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T6

description: Library name: MLLr16_R_T


title: RNA-seq 20230123_u2os_cas9_ZSWIM3_rep2

description:
Library name: 20230123_u2os_cas9_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T11

description: Library name: MLLr18_R_T


title: PC9, two drugs combined, repeat2

description:
Library name: P_pa2
column name in mRNA.readcount.xls:P_pa2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T10

description: Library name: MLLr19_R_T


title: Arthroconidia, CellFree, RiboMarker, 3

description: Library name: Arthroconidia_CellFree_RiboMarker_3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T12

description: Library name: MLLr15_R_T


title: Arthroconidia, CellFree, RiboMarker, 2

description: Library name: Arthroconidia_CellFree_RiboMarker_2


title: RNA-seq 20230123_u2os_cas9_ZSWIM3_rep1

description:
Library name: 20230123_u2os_cas9_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: Arthroconidia, CellFree, RiboMarker, 1

description: Library name: Arthroconidia_CellFree_RiboMarker_1


title: PC9, paclitaxel, repeat3

description:
Library name: P_p3
column name in mRNA.readcount.xls:P_p3

value: paclitaxel


title: RNA-seq 20230123_u2os_cas9_TYR_rep3

description:
Library name: 20230123_u2os_cas9_TYR_rep3
RNA-seq sample TYR_rep3


title: RNA-seq 20230123_u2os_cas9_TYR_rep2

description:
Library name: 20230123_u2os_cas9_TYR_rep2
RNA-seq sample TYR_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T9

description: Library name: MLLr14_R_T


title: PC9, paclitaxel, repeat2

description:
Library name: P_p2
column name in mRNA.readcount.xls:P_p2


title: PC9, two drugs combined, repeat1

description:
Library name: P_pa1
column name in mRNA.readcount.xls:P_pa1


title: Spherule, RiboMarker, 2

description: Library name: Spherule_RiboMarker_2

source_name: culture

value: culture


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T8

description: Library name: MLLr13_R_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T5

description: Library name: MLLr12_R_T


title: RNA-seq 20230123_u2os_cas9_TYR_rep1

description:
Library name: 20230123_u2os_cas9_TYR_rep1
RNA-seq sample TYR_rep1


title: PC9, paclitaxel, repeat1

description:
Library name: P_p1
column name in mRNA.readcount.xls:P_p1


title: PC9, control, repeat3

description:
Library name: P_c3
column name in mRNA.readcount.xls:P_c3

value: control


title: RNA-seq 20230123_u2os_cas9_EMX1_rep3

description:
Library name: 20230123_u2os_cas9_EMX1_rep3
RNA-seq sample EMX1_rep3


title: RNA-seq 20210930_k562_cas9_ZSWIM3_rep2

description:
Library name: 20210930_k562_cas9_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR7

description: Library name: MLLr7_R_T


title: PC9, almonertinib,repeat2

description:
Library name: P_a2
column name in mRNA.readcount.xls:P_a2

value: almonertinib


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR10

description: Library name: MLLr10_R_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, T7

description: Library name: MLLr11_R_T


title: Arthrocelia, RiboMarker, 3

description: Library name: Arthrocelia_RiboMarker_3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR9

description: Library name: MLLr9_R_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR8

description: Library name: MLLr8_R_T


title: RNA-seq 20230123_u2os_cas9_EMX1_rep1

description:
Library name: 20230123_u2os_cas9_EMX1_rep1
RNA-seq sample EMX1_rep1


title: PC9, control, repeat1

description:
Library name: P_c1
column name in mRNA.readcount.xls:P_c1


title: Mycelia, RiboMarker, 1

description: Library name: Mycelia_RiboMarker_1


title: RNA-seq 20230123_u2os_cas9_EMX1_rep2

description:
Library name: 20230123_u2os_cas9_EMX1_rep2
RNA-seq sample EMX1_rep2


title: Arthrocelia, RiboMarker, 2

description: Library name: Arthrocelia_RiboMarker_2


title: PC9, almonertinib,repeat3

description:
Library name: P_a3
column name in mRNA.readcount.xls:P_a3


title: Arthrocelia, RiboMarker, 1

description: Library name: Arthrocelia_RiboMarker_1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR5

description: Library name: MLLr5_R_T


title: PC9, almonertinib,repeat1

description:
Library name: P_a1
column name in mRNA.readcount.xls:P_a1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR6

description: Library name: MLLr6_R_T


title: RNA-seq 20210930_k562_cas9_ZSWIM3-L_rep3

description:
Library name: 20210930_k562_cas9_ZSWIM3-L_rep3
RNA-seq sample ZSWIM3-L_rep3


title: Arthroconidia, RiboMarker, 3

description: Library name: Arthroconidia_RiboMarker_3


title: H1975,two drugs combined,repreat3

description:
Library name: H_pa3
column name in mRNA.readcount.xls:H_pa3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR4

description: Library name: MLLr4_R_T


title: Arthroconidia, RiboMarker, 2

description: Library name: Arthroconidia_RiboMarker_2


title: Arthroconidia, RiboMarker, 1

description: Library name: Arthroconidia_RiboMarker_1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR3

description: Library name: MLLr3_R_T


title: Spherule, Exosome, 3

description: Library name: Spherule_Exosome_3


title: H1975,paclitaxel,repeat3

description:
Library name: H_p3
column name in mRNA.readcount.xls:H_p3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR2

description: Library name: MLLr2_R_T


title: H1975,two drugs combined,repreat2

description:
Library name: H_pa2
column name in mRNA.readcount.xls:H_pa2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TMR1

description: Library name: MLLr1_R_T


title: RNA-seq 20210930_k562_cas9_TYR_rep3

description:
Library name: 20210930_k562_cas9_TYR_rep3
RNA-seq sample TYR_rep3


title: H1975,two drugs combined,repreat1

description:
Library name: H_pa1
column name in mRNA.readcount.xls:H_pa1


title: RNA-seq 20210930_k562_cas9_ZSWIM3_rep1

description:
Library name: 20210930_k562_cas9_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: RNA-seq 20210930_k562_cas9_TYR_rep2

description:
Library name: 20210930_k562_cas9_TYR_rep2
RNA-seq sample TYR_rep2


title: Spherule, RiboMarker, 1

description: Library name: Spherule_RiboMarker_1


title: RNA-seq 20210930_k562_cas9_ZSWIM3-L_rep1

description:
Library name: 20210930_k562_cas9_ZSWIM3-L_rep1
RNA-seq sample ZSWIM3-L_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, L14

description: Library name: MLLr24_R


title: RNA-seq 20210930_k562_cas9_ZSWIM3-L_rep2

description:
Library name: 20210930_k562_cas9_ZSWIM3-L_rep2
RNA-seq sample ZSWIM3-L_rep2


title: H1975,paclitaxel,repeat2

description:
Library name: H_p2
column name in mRNA.readcount.xls:H_p2


title: Spherule, Exosome, 2

description: Library name: Spherule_Exosome_2

value: exosomes


title: Spherule, Exosome, 1

description: Library name: Spherule_Exosome_1


title: Mycelia, Exosome, 3

description: Library name: Mycelia_Exosome_3


title: H1975,control,repreat3

description:
Library name: H_c3
column name in mRNA.readcount.xls:H_c3


title: RNA-seq 20210930_k562_cas9_TYR_rep1

description:
Library name: 20210930_k562_cas9_TYR_rep1
RNA-seq sample TYR_rep1


title: Mycelia, Exosome, 2

description: Library name: Mycelia_Exosome_2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q18

description: Library name: MLLr22_R


title: PC9, control, repeat2

description:
Library name: P_c2
column name in mRNA.readcount.xls:P_c2


title: RNA-seq 20210930_k562_cas9_MPP4-L_rep2

description:
Library name: 20210930_k562_cas9_MPP4-L_rep2
RNA-seq sample MPP4-L_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, L12

description: Library name: MLLr23_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q16

description: Library name: MLLr20_R


title: Arthrocelia, Exosome, 3

description: Library name: Arthrocelia_Exosome_3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q17

description: Library name: MLLr21_R


title: H1975,control,repreat1

description:
Library name: H_c1
column name in mRNA.readcount.xls:H_c1


title: H1975,paclitaxel,repeat1

description:
Library name: H_p1
column name in mRNA.readcount.xls:H_p1


title: H1975,almonertinib,repeat3

description:
Library name: H_a3
column name in mRNA.readcount.xls:H_a3


title: RNA-seq 20210930_k562_cas9_EMX1_rep3

description:
Library name: 20210930_k562_cas9_EMX1_rep3
RNA-seq sample EMX1_rep3


title: H1975,almonertinib,repeat2

description:
Library name: H_a2
column name in mRNA.readcount.xls:H_a2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q14

description: Library name: MLLr18_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q15

description: Library name: MLLr19_R


title: H1975,control,repreat2

description:
Library name: H_c2
column name in mRNA.readcount.xls:H_c2


title: Spherule, RiboMarker, 3

description: Library name: Spherule_RiboMarker_3


title: Arthrocelia, Exosome, 2

description: Library name: Arthrocelia_Exosome_2


title: Mycelia, Exosome, 1

description: Library name: Mycelia_Exosome_1


title: Arthrocelia, Exosome, 1

description: Library name: Arthrocelia_Exosome_1


title: RNA-seq 20210930_k562_cas9_EMX1_rep1

description:
Library name: 20210930_k562_cas9_EMX1_rep1
RNA-seq sample EMX1_rep1


title: RNA-seq 20210930_k562_cas9_MPP4-L_rep1

description:
Library name: 20210930_k562_cas9_MPP4-L_rep1
RNA-seq sample MPP4-L_rep1


title: RNA-seq 20210930_k562_cas9_MPP4-L_rep3

description:
Library name: 20210930_k562_cas9_MPP4-L_rep3
RNA-seq sample MPP4-L_rep3


title: RNA-seq 20210930_k562_cas9_EMX1_rep2

description:
Library name: 20210930_k562_cas9_EMX1_rep2
RNA-seq sample EMX1_rep2


title: RNA-seq 20210930_k562_cas9_EMX1-H_rep3

description:
Library name: 20210930_k562_cas9_EMX1-H_rep3
RNA-seq sample EMX1-H_rep3


title: Arthroconidia, Exosome, 3

description: Library name: Arthroconidia_Exosome_3


title: Mycelia, RiboMarker, 3

description: Library name: Mycelia_RiboMarker_3


title: RNA-seq 20210930_k562_cas9_ZSWIM3_rep3

description:
Library name: 20210930_k562_cas9_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q12

description: Library name: MLLr16_R


title: H1975,almonertinib,repeat1

description:
Library name: H_a1
column name in mRNA.readcount.xls: H_a1


title: NBSD_Input

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

description:
Library name: NBSD_Input
Input

data_processing:
Quality control tests for unmapped sequenced were performed using FASTQC software and aligned to the human GRCh38/hg38 genome with bowtie2 (v2.5.3) aligner. PCR duplicates were removed with Picard. Mapped reads were normalized to reads per kilobase per million (RPKM) and tracks for RPKM were created using bamCoverage tool as part of DeepTools (v3.5.3). Peak calling was performed against the input control using MACS2 (v2.2.9) software and the significance cut-offf of FDR ≤0.01.  Quantification of ChIP-seq signal under the curve (AUC) for peak regions was calculated by converting BigWig to bedGraph files using the UCSC utility bigWigToBedGraph (v3.7.7) . These files were then intersected with merged peak regions using bedtools v2.27.1, producing files that included overlapping signal segments for each peak. The intersected files were loaded into python as data frames, and each entry’s contribution to the AUC was calculated by multiplying the length of peak (i.e., end - start) with its associated signal intensity value. These values were then aggregated across all intervals corresponding to the same peak, resulting in peak-wise AUC.  MACS2-detected peaks for which log2(AUC+1) was ≤ 12, irrespective of the sample conditions, or overlapping with the ENCODE black-listed regions for hg38 were filtered. Peaks were annotated with the nearest hg38 gene using the annotatePeak function in ChIPseeker (v1.42.1) in R with promoters identified as within 3kb of the transcription start site. Log2 fold-change in AUC between conditions were determined Motif analysis was performed using HOMER (v5.1) platform with a P value cut-off of ≤0.01 and ChIP-seq binding peaks were visualized using Integrative Genomic Viewer (IGV) v2.9.0.
Heatmaps for global H2AK119Ub ChIP-seq tracks were created using computeMatrix and plotHeatmap tools available in deepTools. For consensus analysis in Figure 5G, rows were rank ordered according to highest to lowest changes in gene transcription with PCGF1 knockout RNA-sequencing in NB-SD. Metaplots on RPKM normalized enrichment were created using plotProfile in deepTools.
Assembly: Hg38
Supplementary files format and content: RPKM normalized bigwig signal files

source_name: NBSD

growth_protocol: Neuroblastoma cell lines KELLY, NB1, NB-SD, NGP, and SK-N-AS were kindly provided by the Stegmaier laboratory at the Dana-Farber Cancer Institute (DFCI).  KELLY, NB1, and NB-SD were grown in RPMI-1640 (Corning, 10040CV) and NGP and SK-N-AS were grown in Dulbecco's Modified Eagle Medium (DMEM)(Corning, 10013CV) supplemented with 10% FBS (Corning, 35015CV) and 1x penicillin-streptomycin-glutamine (Gibco, 10378016).

extract_protocol:
ChIP sequencing and CUT&RUN sequencing
Histone ChIP-sequencing was performed as previously described17,24. 2 x 107 cells per sample were crosslinked in 1% formaldehyde for 10 minutes and quenched in 0.20M glycine for 5 minutes. Cells were lysed using an SDS buffer (100 mM NaCl, 50 mM Tris-Cl (pH 8.0), 5 mM EDTA (pH 8.0), 0.2% NaN3, 10% SDS) with 1X HALT protease inhibitor (Thermo cat#78429) and incubated at room temperature with gentle inversion for 2 minutes. Following centrifugation at 15,000 rpm nuclei were resuspended in IP buffer (two parts SDS buffer to one part triton dilution buffer (100 mM Tris-Cl (pH 8.0), 100 mM NaCl, 5 mM EDTA (pH 8.0) 0.2% NaN3, 5.0% Triton X-100)), and sheared for 15 minutes on a Covaris E220 ultrasonicator (5% duty cycle, peak power 140 W, cycles per burst 200) at 4 °C. Immunoprecipitation was performed with prepared antibody protein A magnetic beads conjugated overnight at 4°C with rotation. 10µg of antibody H2AK119ub (Cell Signaling Technology, 8240S) and 2 µL of the spike-in drosophila antibody (Active Motif, 61686) for normalization were added to each sample and rotated at 4°C overnight. The next day, chromatin were sequentially washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), twice with LiCl wash buffer (0.25 M LiCl, 1% IGPAL-CH 630, 1% deoxycholic acid, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA), once with ice cold Tris-EDTA (TE), and then eluted in fresh elution buffer. IP samples were decrosslinked with 2.5 M NaCl, proteinase K, and RNAse A and then incubated at 65°C for 18 hours. DNA for all samples was isolated by incubating with AMPure beads (Beckman Coulter, A63880) for 20 minutes at room temperature, washing twice with 80% ethanol, and eluting in 1x TE. CUT&RUN sequencing was performed with the EpiCypher CUTANA ChIC/CUT&RUN (v5.0 #14-1048)  Kit according to manufacturer instructions. Briefly, ~1 x 10^6 cells were adsorbed to activated ConA beads and washed. 0.5 µg of the following antibodies were incubated into specified reaction tubes at 4°C overnight: RING1B (CST #5694), PCGF1 (Invitrogen #49390), PCGF1 (Abcam #259943), EZH2 (CST #5246), and isotype control supplemented with 0.01%  digitonin. The next morning cells were washed with cell permeabilization buffer and manufacturer recommended volume of pAG-MNase and calcium chloride added to each reaction. Chromatin was digested for 2 hours at 4°C before quenching. DNA was purified with AMPure XP beads prior to library preparation using the CUTANA CUT&RUN library Prep Kit (14-1001) according to manufacturer instructions.

value: NBSD

value: Neuroblastoma


title: RNA-seq 20210930_k562_cas9_EMX1-H_rep2

description:
Library name: 20210930_k562_cas9_EMX1-H_rep2
RNA-seq sample EMX1-H_rep2


title: NBSD_Ig

description:
Library name: NBSD_Ig
Ig

data_processing:
Quality control tests for unmapped sequenced were performed using FASTQC software and aligned to the human GRCh38/hg38 genome with bowtie2 (v2.5.3) aligner. PCR duplicates were removed with Picard. Mapped reads were normalized to reads per kilobase per million (RPKM) and tracks for RPKM were created using bamCoverage tool as part of DeepTools (v3.5.3). Peak calling was performed against the input control using MACS2 (v2.2.9) software and the significance cut-offf of FDR ≤0.01.  Quantification of ChIP-seq signal under the curve (AUC) for peak regions was calculated by converting BigWig to bedGraph files using the UCSC utility bigWigToBedGraph (v3.7.7) . These files were then intersected with merged peak regions using bedtools v2.27.1, producing files that included overlapping signal segments for each peak. The intersected files were loaded into python as data frames, and each entry’s contribution to the AUC was calculated by multiplying the length of peak (i.e., end - start) with its associated signal intensity value. These values were then aggregated across all intervals corresponding to the same peak, resulting in peak-wise AUC.  MACS2-detected peaks for which log2(AUC+1) was ≤ 12, irrespective of the sample conditions, or overlapping with the ENCODE black-listed regions for hg38 were filtered. Peaks were annotated with the nearest hg38 gene using the annotatePeak function in ChIPseeker (v1.42.1) in R with promoters identified as within 3kb of the transcription start site. Log2 fold-change in AUC between conditions were determined Motif analysis was performed using HOMER (v5.1) platform with a P value cut-off of ≤0.01 and ChIP-seq binding peaks were visualized using Integrative Genomic Viewer (IGV) v2.9.0.
Heatmaps for global H2AK119Ub ChIP-seq tracks were created using computeMatrix and plotHeatmap tools available in deepTools. For consensus analysis in Figure 5G, rows were rank ordered according to highest to lowest changes in gene transcription with PCGF1 knockout RNA-sequencing in NB-SD. Metaplots on RPKM normalized enrichment were created using plotProfile in deepTools.
Assembly: Hg38
Supplementary files format and content: RPKM normalized bigwig signal files
Library strategy: CUT&Run


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q11

description: Library name: MLLr15_R


title: Arthroconidia, Exosome, 1

description: Library name: Arthroconidia_Exosome_1


title: NBSD_H2AK119Ub

description:
Library name: NBSD_H2AK119Ub
H2AK119Ub


title: RNA-seq 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep3

description:
Library name: 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep3
RNA-seq sample pft-a_cas9_only_vector_rep3


title: NBSD_EZH2

description:
Library name: NBSD_EZH2
EZH2


title: Spherule, CellFree, 3

description: Library name: Spherule_CellFree_3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q13

description: Library name: MLLr17_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q10

description: Library name: MLLr14_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q6

description: Library name: MLLr12_R


title: RNA-seq 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep2

description:
Library name: 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep2
RNA-seq sample pft-a_cas9_only_vector_rep2


title: Spherule, CellFree, 2

description: Library name: Spherule_CellFree_2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q9

description: Library name: MLLr13_R


title: RNA-seq 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep1

description:
Library name: 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep1
RNA-seq sample pft-a_cas9_only_vector_rep1


title: Spherule, CellFree, 1

description: Library name: Spherule_CellFree_1


title: Arthroconidia, Exosome, 2

description: Library name: Arthroconidia_Exosome_2


title: NBSD_RING1B

description:
Library name: NBSD_RING1B
RING1B


title: Mycelia, CellFree, 3

description: Library name: Mycelia_CellFree_3


title: NBSD_PCGF1_Invitrogen

description:
Library name: NBSD_PCGF1_Invitrogen
PCGF1_Invitrogen


title: RNA-seq 20210930_k562_cas9_EMX1-H_rep1

description:
Library name: 20210930_k562_cas9_EMX1-H_rep1
RNA-seq sample EMX1-H_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR10

description: Library name: MLLr10_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, Q5

description: Library name: MLLr11_R


title: RNA-seq 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep2
RNA-seq sample ZSWIM3_pft-a_editing_rep2


title: RNA-seq 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep3
RNA-seq sample ZSWIM3_pft-a_editing_rep3


title: NBSD_PCGF1_Abcam

description:
Library name: NBSD_PCGF1_Abcam
PCGF1_Abcam


title: Mycelia, CellFree, 2

description: Library name: Mycelia_CellFree_2


title: NBSD_PCGF1_G1_Input

description:
Library name: NBSD_PCGF1_G1_Input
ChIP-seq input

data_processing:
Quality control tests for unmapped sequenced were performed using FASTQC software and aligned to the human GRCh38/hg38 genome with bowtie2 (v2.5.3) aligner. PCR duplicates were removed with Picard. Mapped reads were normalized to reads per kilobase per million (RPKM) and tracks for RPKM were created using bamCoverage tool as part of DeepTools (v3.5.3). Peak calling was performed against the input control using MACS2 (v2.2.9) software and the significance cut-offf of FDR ≤0.01.  Quantification of ChIP-seq signal under the curve (AUC) for peak regions was calculated by converting BigWig to bedGraph files using the UCSC utility bigWigToBedGraph (v3.7.7) . These files were then intersected with merged peak regions using bedtools v2.27.1, producing files that included overlapping signal segments for each peak. The intersected files were loaded into python as data frames, and each entry’s contribution to the AUC was calculated by multiplying the length of peak (i.e., end - start) with its associated signal intensity value. These values were then aggregated across all intervals corresponding to the same peak, resulting in peak-wise AUC.  MACS2-detected peaks for which log2(AUC+1) was ≤ 12, irrespective of the sample conditions, or overlapping with the ENCODE black-listed regions for hg38 were filtered. Peaks were annotated with the nearest hg38 gene using the annotatePeak function in ChIPseeker (v1.42.1) in R with promoters identified as within 3kb of the transcription start site. Log2 fold-change in AUC between conditions were determined Motif analysis was performed using HOMER (v5.1) platform with a P value cut-off of ≤0.01 and ChIP-seq binding peaks were visualized using Integrative Genomic Viewer (IGV) v2.9.0.
Heatmaps for global PCGF1, RING1B, and H2AK119Ub ChIP-seq tracks were created using computeMatrix and plotHeatmap tools available in deepTools. For consensus analysis in Figure 5G, rows were rank ordered according to highest to lowest changes in gene transcription with PCGF1 knockout RNA-sequencing in NB-SD. Metaplots on RPKM normalized enrichment were created using plotProfile in deepTools.
Assembly: Hg38
Supplementary files format and content: RPKM normalized bigwig signal files


title: RNA-seq 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep1
RNA-seq sample ZSWIM3_pft-a_editing_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR9

description: Library name: MLLr9_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR8

description: Library name: MLLr8_R


title: NBSD_PCGF1_G1_Ig

description:
Library name: NBSD_PCGF1_G1_Ig
CUT&RUN control IgG

data_processing:
Quality control tests for unmapped sequenced were performed using FASTQC software and aligned to the human GRCh38/hg38 genome with bowtie2 (v2.5.3) aligner. PCR duplicates were removed with Picard. Mapped reads were normalized to reads per kilobase per million (RPKM) and tracks for RPKM were created using bamCoverage tool as part of DeepTools (v3.5.3). Peak calling was performed against the input control using MACS2 (v2.2.9) software and the significance cut-offf of FDR ≤0.01.  Quantification of ChIP-seq signal under the curve (AUC) for peak regions was calculated by converting BigWig to bedGraph files using the UCSC utility bigWigToBedGraph (v3.7.7) . These files were then intersected with merged peak regions using bedtools v2.27.1, producing files that included overlapping signal segments for each peak. The intersected files were loaded into python as data frames, and each entry’s contribution to the AUC was calculated by multiplying the length of peak (i.e., end - start) with its associated signal intensity value. These values were then aggregated across all intervals corresponding to the same peak, resulting in peak-wise AUC.  MACS2-detected peaks for which log2(AUC+1) was ≤ 12, irrespective of the sample conditions, or overlapping with the ENCODE black-listed regions for hg38 were filtered. Peaks were annotated with the nearest hg38 gene using the annotatePeak function in ChIPseeker (v1.42.1) in R with promoters identified as within 3kb of the transcription start site. Log2 fold-change in AUC between conditions were determined Motif analysis was performed using HOMER (v5.1) platform with a P value cut-off of ≤0.01 and ChIP-seq binding peaks were visualized using Integrative Genomic Viewer (IGV) v2.9.0.
Heatmaps for global PCGF1, RING1B, and H2AK119Ub ChIP-seq tracks were created using computeMatrix and plotHeatmap tools available in deepTools. For consensus analysis in Figure 5G, rows were rank ordered according to highest to lowest changes in gene transcription with PCGF1 knockout RNA-sequencing in NB-SD. Metaplots on RPKM normalized enrichment were created using plotProfile in deepTools.
Assembly: Hg38
Supplementary files format and content: RPKM normalized bigwig signal files
Library strategy: CUT&Run


title: Arthrocelia, CellFree, 3

description: Library name: Arthrocelia_CellFree_3


title: NBSD_Chr2_Input

description:
Library name: NBSD_Chr2_Input
ChIP-seq input

value: Control


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR7

description: Library name: MLLr7_R


title: Arthrocelia, CellFree, 2

description: Library name: Arthrocelia_CellFree_2


title: RNA-seq 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep2
RNA-seq sample ZSWIM3_dmso_editing_rep2

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)


title: RNA-seq 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep1
RNA-seq sample ZSWIM3_dmso_editing_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR6

description: Library name: MLLr6_R


title: NBSD_Chr2_Ig

description:
Library name: NBSD_Chr2_Ig
CUT&RUN control IgG


title: NBSD_PCGF1_G1_H2AK119Ub

description:
Library name: NBSD_PCGF1_G1_H2AK119Ub
ChIP-seq for H2AK119Ub


title: Arthroconidia, CellFree, 2

description: Library name: Arthroconidia_CellFree_2


title: Mycelia, CellFree, 1

description: Library name: Mycelia_CellFree_1


title: RNA-seq 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep3
RNA-seq sample TYR_pft-a_editing_rep3


title: NBSD_Chr2_H2AK119Ub

description:
Library name: NBSD_Chr2_H2AK119Ub
ChIP-seq for H2AK119Ub


title: Arthrocelia, CellFree, 1

description: Library name: Arthrocelia_CellFree_1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR3

description: Library name: MLLr3_R


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR5

description: Library name: MLLr5_R


title: RNA-seq 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep3
RNA-seq sample ZSWIM3_dmso_editing_rep3


title: RNA-seq 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep2
RNA-seq sample TYR_pft-a_editing_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR2

description: Library name: MLLr2_R


title: RNA-seq 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep1
RNA-seq sample TYR_pft-a_editing_rep1


title: NBSD_PCGF1_G1_RING1B

description:
Library name: NBSD_PCGF1_G1_RING1B
CUT&RUN for RING1B


title: Arthroconidia, CellFree, 1

description: Library name: Arthroconidia_CellFree_1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR4

description: Library name: MLLr4_R


title: Spherule, 2

description: Library name: Spherule_2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, MR1

description: Library name: MLLr1_R


title: Spherule, 1

description: Library name: Spherule_1


title: NBSD_Chr2_RING1B

description:
Library name: NBSD_Chr2_RING1B
CUT&RUN for RING1B


title: NBSD_PCGF1_G1_PCGF1

description:
Library name: NBSD_PCGF1_G1_PCGF1
CUT&RUN for PCGF1


title: RNA-seq 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep3
RNA-seq sample TYR_dmso_editing_rep3


title: Mycelia, 3

description: Library name: Mycelia_3


title: RNA-seq 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep2
RNA-seq sample EMX1_pft-a_editing_rep2


title: NGP_XL177A_Input

description:
Library name: NGP_XL177A_Input
Input sample

source_name: NGP

value: NGP

value: 1 µM XL177A


title: RNA-seq 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep2
RNA-seq sample TYR_dmso_editing_rep2


title: NBSD_Chr2_PCGF1

description:
Library name: NBSD_Chr2_PCGF1
CUT&RUN for PCGF1


title: NGP_Vehicle_Input

description:
Library name: NGP_Vehicle_Input
Input sample

value: Vehicle


title: Acute Myeloid Leukemia Patient Blood Sample, PS_754422

description: Library name: AML1_R

value: Peripheral Blood


title: Arthrocelia, 2

description: Library name: Arthrocelia_2


title: RNA-seq 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep3
RNA-seq sample EMX1_pft-a_editing_rep3


title: Acute Myeloid Leukemia Patient Blood Sample, PS_743835

description: Library name: AML4_R


title: Arthrocelia, 3

description: Library name: Arthrocelia_3


title: Mycelia, 1

description: Library name: Mycelia_1


title: RNA-seq 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep1
RNA-seq sample TYR_dmso_editing_rep1


title: Acute Myeloid Leukemia Patient Blood Sample, PS_88351

description: Library name: AML2_R