title: 274_87_D-snRNA

description:
Library name: 274_87_Dc
10X 3prime v3.1


title: NC-3

status: Public on Apr 17 2025

type: SRA

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

library_source: transcriptomic

data_processing:
FASTX-toolkit (version 0.0.14) to obtain high-quality reads. the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by HISAT2 allowing one  mismatch.
FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: BHT101 cells

growth_protocol: The BHT101 cell line was purchased from Pricella (CL-0617, Pricella, Wuhan, China), validated by STR profiling, and tested negative for mycoplasma. The BHT101 cells were cultured in DMEM high sugar basic culture medium (PM150210, Pricella, Wuhan, China) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion).  The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using NanoPhotometer N50（IMPLEN）. The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads (N401, Vazyme, Nanjing, China). The purified RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional RNA-seq library preparation by VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina （NR605）. Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Adaptor (N323). After purification of ligation product and size fractioning to 300-500bps, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: Plasmid transfection of BHT101 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. The transfected cells were then harvested after 48h for RT-qPCR and following analysis.

tag: cell line

value: BHT101 cells

tag: treatment

value: BHT102 cell (control plasmid)


title: Blastema_14dpa_rep3

type: RNA

city: Bar Harbor

first: Prayag

last: Murawala

state: ME

address: 159 Old Bar Harbor Rd, Bar Harbor, ME 04609

country: USA

institute: MDI Biological Laboratory

description: Gene expression of Cherry+-sorted-CT cells 14 day post-amputation

hyb_protocol: Custom-designed 400K Agilent arrays (Name:Am400k_v2, Design ID: 084163, Design Format: 2x 400 K, Control Grid: IS-420288-2-v2_400kBY2_gx_eqc_20100210) were probed with 3.75 ug of cRNA per array according to the Agilent protocol.

scan_protocol: Scan was performed using the AgilentG3_GX_1Color Raw scan protocol

data_processing: Microarray data were imported and processed using limma v3.58.1 in R applying backgroud correction using the normexp method, quantile between array normalization, filtering out control and low-expressed probes, as well as probes assigned to multiple genes. Gene set over-representation analysis per cluster was performed with clusterprofile v4.10.01 and GO.db v3.18.0.

organism: Ambystoma mexicanum

source_name: Blastema 14dpa replicate 3

label_protocol: A custom Agilent 400K microarray (Agilent Technologies) was designed using the axolotl transcriptome assembly release 25 (https://www.axolotl-omics.org/assemblies, version Am_2.2). Three sense probes and one antisense probe were designed for each annotated transcript with known strandedness. For transcripts with unknown strandedness, which includes non-coding, partial, or novel sequences lacking homology to known proteins, three sense, and three antisense probes were generated, utilizing RNA-seq strandedness data to guide orientation. Additionally, 20,839 probes from a previously established EST and cDNA-based microarray (Knapp et al. 2013) were incorporated to ensure backward compatibility. Overall, the microarray used in this project comprises a total of 415,996 probes. Cy3-labeled cRNA probes were generated from 45 ng of purified total RNA using Agilent Low Input Quick Amp Gene Expression Labeling Kit (Agilent, 5190-2307).

growth_protocol: Axolotls were raised up to 9-cm long (from nouse to tail), and  were individually housed in 20% Holtfreter’s solution all the time.

extract_protocol: Tissue from the intact lower arm or from the blastema at different stages of regeneration (1, 3, 5, 7, 10, and 14 dpa), including tissue 2 mm behind the amputation plane, was collected and washed in 0.8x PBS buffer. Blastemas from 4-6 axolotls from the same clutch were pooled to collect a sufficient numbers of cells. Three biological replicates represent independently collected and processed samples from three separate animal batches.  Tissue was transferred into 1 ml of dissociation solution containing 0.35/ml of Liberase TM (Roche, 05401119001) and 100 U/ml of DNase1 (Roche, 04716728001) in 0.8x PBS. Tissue was dissected into small pieces using forceps and then rocked or pipetted for approximately 30 minutes at RT. The cell suspension was cooled on ice and filtered through a 70-µm filter before FACS-sorting. Cherry+ cells were sorted directly into the lysis buffer RLT (Qiagen, 79216). Total RNA from 150,000 to 250,000 cells per sample was purified using RNeasy mini kit (Qiagen, 74104) according to the manufacturer’s protocol.

treatment_protocol: Axolotls were anesthetized using 0.03% benzocaine (Sigma-Aldrich, E1501) diluted in 20% Holtfreter’s solution. Once the axolotls no longer responded to mechanical stimuli, they were transferred to a surgical plate under a stereoscope (Carl Zeiss Microscopy, Stemi DV4). The right forelimb was then amputated at the mid-zeugopod level, and any protruding bone was carefully trimmed using scissors to facilitate skin retraction and wound healing. Subsequently, axolotls were immediately transferred to fresh 20% Holtfreter’s solution to aid their recovery.

tag: gender

value: Unknown

tag: tissue

value: FACS-sorted Cherry+ cells

tag: developmental stage

value: 9-cm long axolotl

tag: strain


title: 274_62_D-snRNA

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

description:
Library name: 274_62_Db
10X 3prime v3.1

library_source: transcriptomic single cell

data_processing:
fastq files were generated from basecalls using CellRanger’s mkfastq implementation
snRNAseq fastqs were trimmed for read2 contaminants with cutadapt
trimmed reads were mapped with the STARsolo implementation of STAR (version: ) to GRCh38 with gencode reference annotation release #
count data was cleaned and annotated in R using the Seurat package  (version: )
Assembly: GRCh38; GENCODE release 37
Supplementary files format and content: .rds files of R objects for the package Seurat (Seurat library version: ; SeuratObject library version: ). Each object includes the gene expression, cell metadata and graph layout coordinates for cells/nuclei described in the associated manuscript.

molecule: nuclear RNA

source_name: lung

extract_protocol:
Nuclei for snMultiOme and PCLS were extracted from frozen tissue using the 10X Genomics nuclei extraction kit, per the manufacturer’s instructions.
Library construction for 10X Genomics “3prime v3.1” assays and 10X Genomics “Multiome ATAC + Gene Expression” were each constructed with the manufacturer’s recommended protocol.

treatment_protocol: In vivo lung samples were inflated and frozen after collection. Ex vivo precision cut lung slice (PCLS) were exposed for 5 days to either PBS or a fibrotic cocktail of TGF-b, PDGFa/b,TNFa and LPA

value: lung

tag: cell type

value: nuclei

tag: condition

value: control

tag: subject

tag: sample


title: CUT&RUN_REP2

city: Brisbane

first: Lachlan

middle: Ian

last: Harris

state: QLD

address: 300 Herston Road

department: Cancer Research Program

country: Australia

institute: QIMR Berghofer MRI

description:
Library name: CUT_RUN_REP2
PE100

library_source: genomic

data_processing:
scRNA-seq: CellRanger Count (Ver. 7.0.1) CUT&RUN The nf-core/cutandrun pipeline was used (v3.2). The uniquely mapped reads were aligned to the mm10 reference genome using Bowtie2. Peak calling was performed using SEACR with 0.01 seacr_peak_threshold. The BigWig file was visualized using the Integrative Genomics Viewer (IGV).
Assembly: scRNA-seq: refdata-gex-mm10-2020-A or Mycn data was mapped to a custom version of this genome, which had the Mycn gene deleted and replaced with two new contigs, corresponding to exon1 of the Mycn gene (Mycnex1) and exon 2/3 (Mycnex3). The gene encoding eGFP was also added to the custom genome. The genome was made with the cellRanger mkref command. CUT&RUN: mm10.
Supplementary files format and content: scRNA-seq: output from CellRanger Count (Ver. 7.0.1). CUT&RUN: bigWig files.
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: Brain

extract_protocol:
scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions (10x Genomics Chemistry, Single Cell version 3.0.1).  CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000  cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C  for 10 min. DNA was then purified using a DNA cleanup kit.
scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100.

value: Brain

value: Adult hippocampuse derived neural stem cell culture

value: adult hippocampal neural stem cells

tag: genotype

value: wildtype

value: no treatment


title: Blastema_10dpa_rep3

description: Gene expression of Cherry+-sorted-CT cells 10 day post-amputation

source_name: Blastema 10dpa replicate 3


title: NC-2

value: BHT101 cell (control plasmid)


title: 274_45_D-snRNA

description:
Library name: 274_45_Db
10X 3prime v3.1


title: Input ChIP-seq in iGMPs Replicate 2

city: Riverside

first: Reuben

last: Franklin

state: CA

address: 3401 Watkins Drive

institute: University of California, Riverside

description: Library name: ChIP_INPUT_NT_0H_Rep2

data_processing:
Paired-end (PE) fastqs for H3K27ac were processed with the ENCODE Uniform Processing Pipeline (Hitz et al. 2023) to produce quality control data, read alignments, and signal tracks. Read inputs included two reps each for target files and inputs. For this pipeline, reads were mapped to mm10 (mm10 no alt analysis set ENCODE) (bowtie2, v2.2.9), duplicates, and read mapping to multiple locations were removed. The pipeline produced base-pair resolution signal over background fold-change signal files for pooled reps with MACS2.
Assembly: mm10
Supplementary files format and content: H3K27ac signal fold-enrichment over input, pooled replicates. Bigwig format.

source_name: Blood

growth_protocol: Immortalized granulocyte-macrophage progenitor-like cells (iGMPs) with a GFP reporter at the Lyz2 locus and the ER-HOXA9 transgene (herein iGMPs or HOXA9-iGMPs) were cultured in RPMI-1640 supplemented with 10% FBS, 100U mL-1 penicillin, 100 µg mL−1 streptomycin, 2mM L-alanyl-L-glutamine dipeptide and stem cell factor (SCF). Depending on the batch, media was made with 1-2% SCF-conditioned media from SCF-secreting Chinese hamster ovary cells (a gift from David Sykes). Concentrations for each batch were determined with functional testing, exploiting the strict SCF-dependence of iGMPs. β-Estradiol (E2) was added to a final concentration of 150 ng/mL for normal culture.

extract_protocol:
H3K27ac ChIP-seq was performed as previously described (Franklin et al. 2022). For each ChIP, 10 million iGMPs were fixed in culture media with 4% formaldehyde for 15 minutes at room temperature. After fixing, cells were washed with DPBS and the cell pellet was flash frozen in liquid nitrogen and stored at -80 °C. Nuclei were isolated by lysing cells with cell lysis buffer (20mM Tris-HCl pH 8.0, 85mM KCl, 0.5% NP40) for 10 minutes at 4 °C and spinning at 12,000 RPM for 4 min at 4 °C. Nuclei were then lysed for 10 min at 4 °C in nuclear lysis buffer (10mM Tris-HCl pH7.5, 1% NP40, 0.5% Na Deoxycholate, 0.1%SDS). Lysed nuclei were sonicated using a Branson 250 probe sonifier at 40% amplitude for 5 minutes in an ice bath to garner 50% of fragments below 1000 bp, and less than 10% under 200 bp. Chromatin was stored at -80 °C while confirming input fragment distribution by gel electrophoresis or TapeStation. Sheared chromatin was supplemented with 167 mM NaCl and 1.2mM EDTA for immunoprecipitation. Protein A or G beads (for rabbit or mouse antibodies, respectively; 10002D/10004D, ThermoFisher) pre-conjugated with 2 µg of antibody were added to the sheared chromatin for 2 hours at 4 °C for each target. The following antibodies were used: H3K27ac (ab4729, Abcam). Immunoprecipitations were washed sequentially two times each with low salt buffer (0.1% DOC, 0.1% SDS, 1% Triton X-100, 140 mM NaCl, 1 mM EDTA, 20 mM Tris-HCl pH 8.0), high salt buffer (0.1% DOC, 0.1%SDS, 1% Triton X-100, 500 mM NaCl, 1 mM EDTA, 20 mM Tris-HCl pH 8.0), LiCl buffer (0.25 M LiCl, 1% NP40, 1% Na Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0) and then eluted in elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS). Immunoprecipitations were reverse crosslinked overnight at 65 °C after adding 7.25x reverse crosslinking buffer (250 mM Tris-HCl pH 6.5, 1.25 M NaCl, 62.5 mM EDTA, 5 mg/ml Proteinase K [EO0491, ThermoFisher], 62.5 ug/ml RNase A [EN0531, ThermoFisher]). Input samples were reverse crosslinked by diluting sheared chromatin 1:5 with water and adding 7.25x reverse crosslinking buffer overnight at 65 °C. Reverse-crosslinked DNA was isolated with 1.8x AMPure XP (A63880, Beckman Coulter) beads and used for library preparation.
NEB Ultra II DNA Library Prep and Index Kits (E7645, E6440) were used according to the manufacturer's protocol with modifications. Briefly, up to 10 ng DNA was used for end preparation and adapter ligation without size selection. NEB indexes were added with 2-step PCR using an optimized number of cycles (10-15) and reduced extension times (15 s). Fragment distribution of prepared libraries were confirmed by Bioanalyzer to contain over 90% fragments in the 200-600 bp range and then submitted to Illumina NovaSeq 6000 paired-end sequencing at the University of California, Irvine Genomics Research and Technology Hub.

value: Blood

value: granulocyte-macrophage progenitor

value: Untreated

tag: batch

tag: antibody


title: NC-1

value: BHT101 cells


title: 249_42_D-snRNA

description:
Library name: 249_42_D
10X 3prime v3.1


title: CUT&RUN_REP1

description:
Library name: CUT_RUN_REP1
PE100


title: Blastema_10dpa_rep2

source_name: Blastema 10dpa replicate 2


title: Human ETMR tumor, C19MC amplified, 8

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

description: 10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex

data_processing:
NovaSeq 6000 binary base call (bcl) files were demultiplexed into individual library fastq files using the mkfastq program from the Cellranger v7.1.0  Suite (10X Genomics). Feature-barcode matrices were obtained for each sample by aligning the raw fastq files to the GRCh38 reference genome using the cellranger multi pipeline (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files containing barcodes and features (genes) and matrix files containing count data.

molecule: polyA RNA

source_name: Brain tumor, FFPE sample

extract_protocol:
Sample preparation for deparafinization and isolation of cells from FFPE tissue sections following 10x Genomics for Fixed RNA seq - protocol CGO000632_RevB, using gentleMACS Octo dissociator with heaters (Miltenyi, Cat n. 140-004-386.06).
Protocol for probe hybridization, GEM generation and barcoding, amplification and library construction as per 10x Genomics Fixed RNA seq protocol CG000527_RevE, for multiplexed library (16 rxns x 16 BC): 1Mio cells per sample taken for probe hibridization; strategy washing -> pooling for pool preparation; targeted 80.000 cells per library.
Chromium Fixed RNA Profiling for Multiplexed Samples

value: Brain tumor, FFPE sample

tag: age (months)


title: Blastema_5dpa_rep2

description: Gene expression of Cherry+-sorted-CT cells 5 day post-amputation

source_name: Blastema 5dpa replicate 2

value: Unknown


title: Calu-3, d16i3a-infected, 24 hpi, Repeat 4

city: Hong Kong

first: Chon Phin

last: Ong

address: L3-53, Laboratory Block, 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Mutant 2

data_processing:
PE100
Sequencing reads filtering, genome mapping to homo sapiens GCF_000001405.38_GRCh38.p12
Gene expression calculation, differentially expressed gene detection
Hierarchical clustering analysis of DEG, Gene ontology analysis of DEG
Pathway analysis of DEG, alternative splicing detection and gene fusion detection
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: Files contain all raw counts detected for each sample

growth_protocol: Calu-3 lung adenocarcinoma cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine seurm (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Rneasy Mini kit (Qiagen).
General library: short-insert 160-180bp library, mostly according to BGI's protocol

treatment_protocol: Viral infection with MOI of 5 for 24 hours

value: Lung adenocarcinoma

value: WT

value: Infection with MOI of 5


title: 249_13_D-snRNA

description:
Library name: 249_13_D
10X 3prime v3.1

value: lung

value: nuclei


title: Human ETMR tumor, C19MC amplified, 7


title: Calu-3, d16i3a-infected, 24 hpi, Repeat 3

description: Mutant 2


title: T-cells, patient10, day28

city: Duarte

first: chintan

last: parekh

state: California

address: 1500 east duarte

department: Pediatrics

institute: Children's Hospital Los Angeles

description: Library name: Sample 33

data_processing:
Trimmomatic settings to remove adapter reads included LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 (Trichommatic v0.36).
Reads were aligned to the GRCh38 reference genome (STAR v2.5.2b).
Subread v1.5.2 was used to calculate gene counts. Settings for calculating gene counts via the Subread packager included -largestOverlap -t exon -g gene_id -s 0–p.
Assembly: GRCh38
Supplementary files format and content: .csv file of unnormalized  gene counts

growth_protocol: Peripheral blood mononuclear cells were thawed, blocked with intravenous immunoglobulin, and then stained with an anti-CD3 flow cytometry antibody to enable sorting of T-cells.

extract_protocol:
RNA was extracted from sorted CD3+ T-cells with a PicoPure RNA Isolation Kit (Thermo Fisher Scientific). 1-10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using SMART-Seq mRNA-Seq (Takara).

value: CD3+ T-cells

value: Day 28


title: 249_117_D-snRNA

description:
Library name: 249_117_D
10X 3prime v3.1

value: control


title: Human ETMR tumor, C19MC amplified, 6


title: Calu-3, d16i3a-infected, 24 hpi, Repeat 2

description: Mutant 2


title: T-cells, patient10, day14

description: Library name: Sample 32

value: Day 14


title: Blastema_14dpa_rep2

source_name: Blastema 14dpa replicate 2

value: FACS-sorted Cherry+ cells

value: 9-cm long axolotl


title: 248_95_D-snRNA

description:
Library name: 248_95_D
10X 3prime v3.1


title: Calu-3, d16i3a-infected, 24 hpi, Repeat 1

description: Mutant 2


title: Blastema_7dpa_rep2

description: Gene expression of Cherry+-sorted-CT cells 7 day post-amputation

source_name: Blastema 7dpa replicate 2


title: Human ETMR tumor, C19MC amplified, 4


title: T-cells, patient10, day0

description: Library name: Sample 31

value: Blood

value: Day 0


title: Blastema_1dpa_rep1

description: Gene expression of Cherry+-sorted-CT cells 1 day post-amputation

source_name: Blastema 1dpa replicate 1


title: Calu-3, d16-infected, 24 hpi, Repeat 4

description: Mutant 1


title: 248_111_D-snRNA

description:
Library name: 248_111_D
10X 3prime v3.1


title: T-cells, patient1, day28

description: Library name: Sample 30


title: Blastema_3dpa_rep3

description: Gene expression of Cherry+-sorted-CT cells 3 day post-amputation

source_name: Blastema 3dpa replicate 3


title: Calu-3, d16-infected, 24 hpi, Repeat 3

description: Mutant 1


title: T-cells, patient1, day14

description: Library name: Sample 29


title: Blastema_5dpa_rep3

source_name: Blastema 5dpa replicate 3


title: Blastema_3dpa_rep2

source_name: Blastema 3dpa replicate 2


title: Blastema_5dpa_rep1

source_name: Blastema 5dpa replicate 1


title: 222_68_D-snRNA

description:
Library name: 222_68_D
10X 3prime v3.1


title: Blastema_1dpa_rep3

source_name: Blastema 1dpa replicate 3


title: Human ETMR tumor, Dicer mutation, 1


title: Blastema_10dpa_rep1

source_name: Blastema 10dpa replicate 1


title: T-cells, patient1, day0

description: Library name: Sample 28


title: Human ETMR tumor, C19MC amplified, 3


title: Blastema_3dpa_rep1

source_name: Blastema 3dpa replicate 1


title: 248_70_D-snRNA

description:
Library name: 248_70_D
10X 3prime v3.1

source_name: lung


title: Human ETMR tumor, C19MC amplified, 5


title: Calu-3, d16-infected, 24 hpi, Repeat 2

description: Mutant 1


title: Calu-3, d16-infected, 24 hpi, Repeat 1

description: Mutant 1


title: T-cells, patient2, day28

description: Library name: Sample 27


title: Human ETMR tumor, C19MC amplified, 2


title: Blastema_1dpa_rep2

source_name: Blastema 1dpa replicate 2


title: Calu-3, WT-infected, 24 hpi, Repeat 4

description: Control


title: Human ETMR tumor, C19MC amplified, 1


title: 222_32_D-snRNA

description:
Library name: 222_32_Dc
10X 3prime v3.1


title: 222_66_D-snRNA

description:
Library name: 222_66_D
10X 3prime v3.1


title: Blastema_0dpa_rep2

description: Gene expression of Cherry+-sorted-CT cells from uninjured forelimbs upper arms

source_name: Blastema 0dpa replicate 2


title: 221_70_D-snRNA

description:
Library name: 221_70_Db
10X 3prime v3.1


title: Blastema_0dpa_rep3

source_name: Blastema 0dpa replicate 3


title: Calu-3, WT-infected, 24 hpi, Repeat 2

description: Control


title: T-cells, patient2, day0

description: Library name: Sample 25

source_name: Blood


title: FA-1

city: Tai’an

first: Fangjun

last: Ding

address: 249 Chuangye Road, High-tech Zone, Feicheng City, Shandong Province

institute: Shandong Agricultural University Fertilizer Science & Technology Co., Ltd

data_processing:
FPKM(Fragment Per Kilobase of transcript, per Million mapped reads)
Assembly: Homo_sapiens.GRCh38_release95.genome.fa
Supplementary files format and content: EXCELfile includes raw counts and FPKM for each Sample

extract_protocol:
Trizol method
After the samples were qualified, the library was constructed. The main process was as follows: (1) Eukaryotic mRNA was enriched by magnetic beads with Oligo (dT); (2) The Fragmentation Buffer was added to randomly interrupt the mRNA. (3) The first cDNA strand and the second strand were synthesized and purified from the mRNA. (4) The purified double-stranded cDNA was end repaired, A-tailed, ligated with sequencing adaptor, and then sequenced with AMPure XP beads Segment size selection; (5) cDNA library was obtained by PCR enrichment.

value: Ovarian cancer

value: treated with 100-ug/ml FA for 48 h


title: FA-3


title: FA-2


title: T-cells, patient3, day28

description: Library name: Sample 24


title: 221_45_D-snRNA

description:
Library name: 221_45_Db
10X 3prime v3.1


title: Calu-3, WT-infected, 24 hpi, Repeat 3

description: Control


title: 221_35_D-snRNA

description:
Library name: 221_35_Db
10X 3prime v3.1


title: T-cells, patient3, day14

description: Library name: Sample 23


title: Blastema_0dpa_rep1

source_name: Blastema 0dpa replicate 1


title: T-cells, patient2, day14

description: Library name: Sample 26


title: control-3


title: 145_94_D-snRNA

description:
Library name: 145_94_D
10X 3prime v3.1


title: T-cells, patient3, day0

description: Library name: Sample 22


title: 145_22_D-snRNA

description:
Library name: 145_22_D
10X 3prime v3.1


title: control-2


title: siTEAD4 2

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: kidney

growth_protocol: 786-O cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: 786-O cells were transfected with Control or siTEAD4.

value: kidney

value: Renal clear cell carcinoma


title: control-1


title: Calu-3, WT-infected, 24 hpi, Repeat 1

description: Control

value: Lung adenocarcinoma


title: 145_21_D-snRNA

description:
Library name: 145_21_Db
10X 3prime v3.1


title: siTEAD4 3


title: siTEAD4 1


title: dTAG-SPT5-HCT116, muALL_NVP2, Rep2_Inde5

city: NYC

first: Rui

last: Sun

state: New York

address: 1425 Madison

institute: Icahn school of medicine at Mount Sinai

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). PCR duplicates were removed using Picard Tools (version 3.1.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals

growth_protocol: dTAG-SPT5 HCT116 cells were cultured in McCoy’s 5A medium (Corning) supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) and 1× Penicillin-Streptomycin (Corning) at 37°C and 5% CO2.

extract_protocol:
About 20 million HCT116 cells grown on the 150 mm dish were cross-linked with 1% formaldehyde for 10 min at room temperature. Cross-linking was quenched with 125 mM glycine for 5 min. Cells were collected with a cell lifter (Costar) in 2 ml ChIP nuclei fractionation buffer [50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% Glycerol, 1% NP-40, 0.25% Triton X-100] with proteinase and phosphatase inhibitors and incubated on ice for 10 min. Cell nuclei were collected by centrifugation at 4 °C at 600 × g for 10 min and washed with wash buffer [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0)]. The pellets were lysed in 1.8 mL RIPA buffer with proteinase and phosphatase inhibitors and sheared by sonication in a Bioruptor (Diagenode) at high power, for 2× 20 min with cycles of 30 s ON and 30 s OFF. Lysates were clarified by centrifugation at 16,000 × g for 10 min at 4 °C. 600 μL pre-cleared lysates were incubated with 4 μg antibodies overnight at 4 °C with end-to-end rotation. 22 μL Protein G magnetic beads (New England Biolabs) were added to the tube on the second day and the samples were incubated for another 4 hours at 4 °C with end-to-end rotation. The beads were washed with RIPA buffer three times, IP wash buffer [100 mM Tris-HCl (pH 8.0), 500 mM lithium chloride, 1% NP-40, 1% sodium deoxycholate] three times and TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0)] twice. Reversal of cross-linking was done by incubating beads in the elution buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 1% SDS, 200mM NaCl, 0.8 U Proteinase K] at 55 °C with heated lid for 16 h. On the third day, 1 μg of RNase A was added and the samples were incubated at 37 °C for 30 min. DNA was purified by using DNA Cleanup Kit (5 μg) (New England Biolabs).
The purified DNA was used for qPCR and library preparation. Spike-In DNA (S. cerevisiae) (Cell Signaling Technology) were added to each sample and DNA libraries were prepared with NEBnext Ultra II DNA library kit (New England Biolabs).

treatment_protocol: 125 nM dTAGv-1 for 4 hours; 250 nM NVP2 for 1 hour in specified experiments

value: Human colon cancer cell line

tag: genetic modification

tag: chip antibody

value: Bethyl Laboratories;Cat. # A304-405A

value: dTAGv-1; NVP2


title: Control 3

value: Control


title: T-cells, patient8, day14

description: Library name: Sample 20

value: CD3+ T-cells


title: T-cells, patient8, day0

description: Library name: Sample 19


title: dTAG-SPT5-HCT116, muALL_NVP2, Rep1_Inde5


title: T-cells, patient6, day28

description: Library name: Sample 18

value: Day 28


title: Sample_14

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: 10X Genomics

data_processing:
A GENCODE v30 GTF file was modified to create a “pre-mRNA” GTF file so that pre-mRNAs would be included as counts in the subsequent analysis.
CellRanger-3.0.2 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq (https://support.illumina.com/) to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files.
The FASTQ files were then aligned to the human reference genome GRCh38 with RNAseq aligner STAR.
The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell.
The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Assembly: Genome_build: Human Gencode (GRCh38.p13.genome.fa)
Supplementary files format and content: Barcodes.tsv as input for single nuclei object
Supplementary files format and content: Matrix.mtx as input for single nuclei object
Supplementary files format and content: Features.tsv as input for single nuclei object

source_name: postmortem doroslateral prefrontal cortex

extract_protocol:
Nuclei were isolated from tissue based on a modified version of Luciano Martelotto’s Customer-Developed Protocol provided on the 10XGenomics website.
Libraries were prepared using the 10X Genomics 3’ Single Cell Gene Expression protocol. Paired-end sequencing of the libraries was conducted using a NovaSeq 6000 with an S2 chip (100 cycles).
Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, 4 rxns PN-120267, Chromium™ Single Cell A Chip Kit, 16 rxns PN-1000009, Chromium™ i7 Multiplex Kit, 96 rxns PN-120262.

treatment_protocol: AUD and control donors were selected to be as close as possible in terms of age, sex, post-mortem interval (PMI), pH of tissue, and cause of death

tag: disease status

tag: Sex

value: Male


title: Control 2

tag: cell line

tag: treatment


title: T-cells, patient6, day14

description: Library name: Sample 17

tag: tissue

value: Day 14


title: Sample_03

description: 10X Genomics

value: postmortem doroslateral prefrontal cortex

value: AUD


title: T-cells, patient8, day28

description: Library name: Sample 21

value: Blood


title: Control 1


title: dTAG-SPT5-HCT116, muALL_5, Rep2

description:
DRB2-CR-muALL-5-Rep2
DRB2-CR-muALL-5.scaled.bigwig
DRB2-CR-muALL-5.wave.bed

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals or Flag-SPT5 occupancy signals as indicated
Supplementary files format and content: bed files include RNAPII wave tracks
Library strategy: CUT&RUN

extract_protocol:
About 2 million freshly prepared cell nuclei were used for one CUT&RUN experiment. The procedures were described in the manual of CUT&RUN kit (Epicypher). For DRB RNAPII CUT&RUN, dTAG-SPT5 cells grown on 100 mm dish were first treated with 125 nM dTAGv-1 for 4 hours, then followed by adding 100 μM DRB (5,6-dichloro-1-β-D-ribofuranosyl-1H-benzimidazole) for another 3 hours. DRB were washed out and cells were incubated in the fresh medium with 125 nM dTAGv-1 at 37 °C for the indicated time course. Cells were collected in the medium containing 1 µg/ml of actinomycin D on ice. Cell nuclei were extracted and proceeded with procedures above.
Spike-In DNA (E.coli) (Epicypher) were added to each sample and DNA libraries were prepared with NEBnext Ultra II DNA library kit (New England Biolabs).

treatment_protocol: 125 nM dTAGv-1 for 4 hours; 100 uM DRB for 3 hour in specified experiments

tag: cut&run antibody

value: Santa Cruz Biotechnology; Cat. # sc-55492


title: dTAG-SPT5-HCT116, muALL_5, Rep1

description:
DRB2-CR-muALL-5-Rep1
DRB2-CR-muALL-5.scaled.bigwig
DRB2-CR-muALL-5.wave.bed


title: T-cells, patient6, day0

description: Library name: Sample 16

value: Day 0


title: dTAG-SPT5-HCT116, muALL_3, Rep2

description:
DRB2-CR-muALL-3-Rep2
DRB2-CR-muALL-3.scaled.bigwig
DRB2-CR-muALL-3.wave.bed


title: Sample_13

description: 10X Genomics


title: T-cells, patient4, day14

description: Library name: Sample 14


title: Pxyl, PrgA, t=5h, rep 2

city: Amsterdam

first: Mariah

last: Kes

address: De Boelelaan 1108

department: A-LIFE

country: Netherlands

institute: Vrije Universiteit Amsterdam

description:
Library name: X-PrgA-2
Normalized_counts_X-EV_X-PrgA.tabular

data_processing:
The data was processed using the online platform Galaxy (usegalaxy.org).
Read quality was assessed with FastQC, read trimming was performed with Trimmomatic.
The reads were aligned to a reference file containing the B. subtilis 168 genome complemented with the genes that are present on the expression plasmids (annotated BSU44441-BSU44452) using Bowtie2.
Gene feature counts were obtained using featureCounts and differential gene expression analysis was performed for each expression condition compared to its respective non-expressing condition with DESeq2.
Assembly: GCF_000009045.1
Supplementary files format and content: tabular file; each file containing 1 column with BSU numbers, 4 columns with normalized counts of 4 samples (DEseq2 output), 1 column with locus name and 1 column with locus description.

organism: Bacillus subtilis

growth_protocol: Cells were grown in LB with 50 µg/mL kanamycin at 37 °C while shaking. Samples for RNA-sequencing were taken at the start of the stationary growth phase (t = 5 h).

extract_protocol:
P/C/I extraction of RNA.
RNA-seq libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's protocol.

treatment_protocol: For cells harboring the inducible expression construct, inducion of Pxyl occurred at the end of the logarithmic growth phase (t = 3 h).

value: BSB1, trp+, aprE, nprE & spoIIE knockout

value: 1% xylose at t = 3 h

tag: time

value: t = 5 h


title: dTAG-SPT5-HCT116, muALL_3, Rep1

description:
DRB2-CR-muALL-3-Rep1
DRB2-CR-muALL-3.scaled.bigwig
DRB2-CR-muALL-3.wave.bed

tag: cell type


title: Pxyl, PrgA, t=5h, rep 1

description:
Library name: X-PrgA-1
Normalized_counts_X-EV_X-PrgA.tabular


title: Sample_58

description: 10X Genomics


title: Sample_06

description: 10X Genomics


title: dTAG-SPT5-HCT116, muALL_1, Rep2

description:
DRB2-CR-muALL-1-Rep2
DRB2-CR-muALL-1.scaled.bigwig
DRB2-CR-muALL-1.wave.bed


title: Pxyl, GFPnb, t=5h, rep 1

description:
Library name: X-GFPnb-1
Normalized_counts_X-EV_X-GFPnb.tabular


title: Sample_10

description: 10X Genomics


title: dTAG-SPT5-HCT116, muALL_0, Rep1


title: Pxyl, GFPnb, t=5h, rep 2

description:
Library name: X-GFPnb-2
Normalized_counts_X-EV_X-GFPnb.tabular


title: Sample_12

description: 10X Genomics


title: dTAG-SPT5-HCT116, muALL_1 Rep1

description:
DRB2-CR-muALL-1-Rep1
DRB2-CR-muALL-1.scaled.bigwig
DRB2-CR-muALL-1.wave.bed


title: Sample_16

description: 10X Genomics


title: T-cells, patient4, day28

description: Library name: Sample 15


title: Pxyl, XynA, t=5h, rep 2

description:
Library name: X-XynA-2
Normalized_counts_X-EV_X-XynA.tabular


title: Sample_02

description: 10X Genomics


title: Pxyl, XynA, t=5h, rep 1

description:
Library name: X-XynA-1
Normalized_counts_X-EV_X-XynA.tabular


title: T-cells, patient7, day14

description: Library name: Sample 11


title: T-cells, patient4, day0

description: Library name: Sample 13


title: dTAG-SPT5-HCT116, muALL, TT, Rep2

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). PCR duplicates were removed using Picard Tools (version 3.1.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Reads mapped introns were counted through HTseq (version 2.0.5).
BedGraph files were generated through the genomecov function in bedtools (version 2.30). Reads were normalized and scaled based on the sizeFactors used in DEseq2. BedGraph files were converted into bigwig files for later analysis. The bigwig files of replicates were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts on introns
Supplementary files format and content: bigwig files include stranded nascent RNA signals

extract_protocol:
Total RNA was extracted from cells with Trizol (Thermo Fisher Scientific). Drosophila RNA from 4sU labeled S2 cells were added to samples (1:50) for spike-in.
RNA samples were fragmented by adding 1 M NaOH (0.2 M final concentration) and incubating on ice for 20 min. Reaction was stopped by adding 1 M Tris buffer (pH 6.8) (0.5 M final concentration). RNA samples were biotinylated with MTSEA biotin-XX (Biotium) and incubated in the dark for 30 min at room temperature. RNA was purified with RNA clean-up kit (500 μg) (New England Biolabs). Biotinylated RNA was enriched with hydrophilic streptavidin magnetic beads (New England Biolabs). Ribosome RNA (rRNA) was removed with NEB rRNA removal module (New England Biolabs). Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: 125 nM dTAGv-1 for 4 hours, cells were pulsed labeled with 0.5 mM 4sU (Sigma-Aldrich) for 15 mins at 37 °C


title: Sample_22

description: 10X Genomics


title: T-cells, patient7, day0

description: Library name: Sample 10


title: Pxyl, EV, t=5h, rep 2

description:
Library name: X-EV-2
Normalized_counts_X-EV_X-XynA.tabular
Normalized_counts_X-EV_X-PrgA.tabular
Normalized_counts_X-EV_X-GFPnb.tabular


title: dTAG-SPT5-HCT116, muALL, TT, Rep1


title: Sample_19

description: 10X Genomics


title: T-cells, patient7, day28

description: Library name: Sample 12


title: T-cells, patient11, day28

description: Library name: Sample 9


title: Pxyl, EV, t=5h, rep 1

description:
Library name: X-EV-1
Normalized_counts_X-EV_X-XynA.tabular
Normalized_counts_X-EV_X-PrgA.tabular
Normalized_counts_X-EV_X-GFPnb.tabular


title: dTAG-SPT5-HCT116, muR1R2, TT, Rep3


title: Sample_18

description: 10X Genomics


title: T-cells, patient11, day14

description: Library name: Sample 8


title: dTAG-SPT5-HCT116, muR1R2, TT, Rep2


title: PamyQ, GFPnb, t=5h, rep 2

description:
Library name: C-GFPnb-2
Normalized_counts_C-EV_C-GFPnb.tabular


title: Sample_17

description: 10X Genomics


title: T-cells, patient5, day28

description: Library name: Sample 6


title: T-cells, patient11, day0

description: Library name: Sample 7


title: PamyQ, GFPnb, t=5h, rep 1

description:
Library name: C-GFPnb-1
Normalized_counts_C-EV_C-GFPnb.tabular


title: Sample_11

description: 10X Genomics

value: Female


title: dTAG-SPT5-HCT116, muR2, TT, Rep3

value: Human colon cancer cell line


title: Sample_09

description: 10X Genomics


title: T-cells, patient5, day0

description: Library name: Sample 4


title: PamyQ, PrgA, t=5h, rep 1

description:
Library name: C-PrgA-1
Normalized_counts_C-EV_C-PrgA.tabular


title: T-cells, patient5, day14

description: Library name: Sample 5


title: Sample_23

description: 10X Genomics


title: PamyQ, XynA, t=5h, rep 2

description:
Library name: C-XynA-2
Normalized_counts_C-EV_C-XynA.tabular


title: dTAG-SPT5-HCT116, muR2, TT, Rep2


title: dTAG-SPT5-HCT116, muR2, TT, Rep1


title: T-cells, patient9, day28

description: Library name: Sample 3


title: PamyQ, XynA, t=5h, rep 1

description:
Library name: C-XynA-1
Normalized_counts_C-EV_C-XynA.tabular


title: Sample_21

description: 10X Genomics


title: PamyQ, EV, t=5h, rep 2

description:
Library name: C-EV-2
Normalized_counts_C-EV_C-XynA.tabular
Normalized_counts_C-EV_C-PrgA.tabular
Normalized_counts_C-EV_C-GFPnb.tabular


title: Sample_05

description: 10X Genomics


title: PamyQ, PrgA, t=5h, rep 2

description:
Library name: C-PrgA-2
Normalized_counts_C-EV_C-PrgA.tabular


title: Sample_20

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1R2, TT, Rep1


title: dTAG-SPT5-HCT116, muR1, TT, Rep1


title: T-cells, patient9, day14

description: Library name: Sample 2


title: PamyQ, EV, t=5h, rep 1

description:
Library name: C-EV-1
Normalized_counts_C-EV_C-XynA.tabular
Normalized_counts_C-EV_C-PrgA.tabular
Normalized_counts_C-EV_C-GFPnb.tabular


title: dTAG-SPT5-HCT116, muR1, TT, Rep2


title: Sample_15

description: 10X Genomics


title: PNOC005-33_D56, bulkRNA

city: San Francisco

first: Aaron

last: Diaz

institute: UCSF

description: Library name: PNOC005-33_D56_bulkRNA

data_processing:
Quality control of bulk and RNA exome sequencing data was performed using FASTQC (v0.11.0). Adapter sequences (Illumina TruSeq: AGATCGGAAGAGC) and polyA/G tails were trimmed using fastp (v0.23.4). Reads with Phred scores <20 or lengths <16 bp were excluded. Processed reads were aligned to either the human (GRCh38) or mouse (mm10) reference genome using STAR (v2.7.10b) with two-pass mode, based on sample origin. Gene-level counts were generated using featureCounts (v2.0.1).
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separated files include raw counts

source_name: PBMC

extract_protocol:
Peripheral whole blood samples were collected in EDTA tubes and either processed directly or used for PBMC isolation via density gradient centrifugation with Ficoll-Paque. Total RNA was extracted from whole blood or PBMCs using a silica column-based method, including on-column DNase treatment to remove residual genomic DNA. All samples were processed promptly to preserve RNA integrity and ensure suitability for downstream library construction.
Approximately 100 ng of total RNA was used for library preparation following the 3′ Tag-Seq protocol. Polyadenylated transcripts were captured using anchored oligo(dT) primers during reverse transcription, incorporating unique molecular identifiers (UMIs) and sample-specific barcodes. Second-strand synthesis and PCR amplification were performed to generate sequencing-ready libraries with Illumina adapters. Libraries were sequenced on an Illumina NextSeq using single-end reads, following the standard 3′ Tag-Seq workflow.

value: PBMC

value: Medulloblastoma

value: MV-NIS


title: dTAG-SPT5-HCT116, WT, TT, Rep3


title: Input ChIP-seq in iGMPs Replicate 1

description: Library name: ChIP_INPUT_NT_0H_Rep1

value: granulocyte-macrophage progenitor

value: Untreated


title: T-cells, patient9, day0

description: Library name: Sample 1

value: CD3+ T-cells


title: PNOC005-33_D28, bulkRNA

description: Library name: PNOC005-33_D28_bulkRNA


title: H3K27ac ChIP-seq in iGMPs Replicate 2

description: Library name: ChIP_H3K27ac_NT_0H_Rep2


title: PNOC005-31_D56, bulkRNA

description: Library name: PNOC005-31_D56_bulkRNA


title: H3K27ac ChIP-seq in iGMPs Replicate 1

description: Library name: ChIP_H3K27ac_NT_0H_Rep1


title: dTAG-SPT5-HCT116, WT, TT, Rep1


title: dTAG-SPT5-HCT116, muALL, RNA, Rep2

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1).
Reads mapped to exons were counted through HTseq (version 2.0.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts on exons

extract_protocol:
Total RNA was extracted from cells with Trizol (Thermo Fisher Scientific). Drosophila RNA from S2 cells were added to samples (1:50) for spike-in.
NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) was used to select mRNA. RNA-seq library was prepared with xGen™ RNA Library Preparation Kit (IDT).

treatment_protocol: 500 nM dTAGv-1 for 24 hours,


title: PNOC005-31_D28, bulkRNA

description: Library name: PNOC005-31_D28_bulkRNA


title: Sample_04

description: 10X Genomics


title: dTAG-SPT5-HCT116, muALL, RNA, Rep1


title: PNOC005-33_D07, bulkRNA

description: Library name: PNOC005-33_D07_bulkRNA


title: PNOC005-31_D07, bulkRNA

description: Library name: PNOC005-31_D07_bulkRNA


title: Sample_01

description: 10X Genomics

value: Male


title: dTAG-SPT5-HCT116, muR1R2, RNA, Rep2


title: Sample_38

description: 10X Genomics

value: postmortem doroslateral prefrontal cortex


title: dTAG-SPT5-HCT116, muR1R2, RNA, Rep1


title: PNOC005-31_D00, bulkRNA

description: Library name: PNOC005-31_D00_bulkRNA

value: Pre-MV-NIS


title: Sample_37

description: 10X Genomics

value: AUD


title: Lung, untreated, rep4

city: Columbia

first: Ti

last: Lu

state: MO

address: 1201 Rollins St, 311 Bond Life Science Center

institute: University of Missouri-Columbi

description: Library name: C_Naive_4

data_processing:
Raw sequencing data were processed using the bcl-convert pipeline to generate FASTQ files
Sequences were aligned to the mm10 genome to generate gene expression counts according to the default settings of Space Ranger
Gene expression levels of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: aligned_fiducials.JPG: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.JPG: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in JSON format
Supplementary files format and content: tissue_hires_image.PNG: high resolution tissue image
Supplementary files format and content: tissue_lowres_image.PNG: low resolution tissue image
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and coordinates of corresponding spots
Library strategy: Spatial Transcriptomics

source_name: Lung

growth_protocol: S. flexneri 2a 2457T challenge strains were grown on tryptic soy agar containing 0.025% Congo red at 37°C, subcultured in tryptic soy broth to an A600 of 1.0, and diluted to 1 x 10⁶ CFU in 30 µl PBS for intranasal (IN) challenge. Mice were monitored for two weeks, with euthanasia criteria including >25% weight loss or blood glucose ≤100 mg/dL. Remaining mice were euthanized on Day 14 post-infection

extract_protocol:
Sample preparation for mouse lung for spatial transcriptomics To prepare for tissue collection, isopentane was chilled in a metal beaker placed on dry ice to ensure rapid tissue freezing. Lung samples were collected from both naïve and vaccinated mice (n=4 per group) based on a published protocol (20). Mice were sacrificed, and a laparotomy was performed to expose the thoracic cavity.  Lungs were perfused via a tracheal needle with an Optimal Cutting Temperature (OCT)/PBS solution (1:1) (20). After inflation, extracted lungs were rinsed in OCT, coated with room-temperature OCT in a pre-cooled cryomold, and placed in chilled isopentane until OCT solidified and turned white (20). Samples were stored at -80°C for subsequent cryo-sectioning and analysis. Tissue sectioning, staining and imaging Tissue samples were cut using a Leica CM3050 S cryostat (Leica Biosystems, Deer Park, IL), and 10 µm thick sections were placed on capture areas of Visium spatial gene expression slides v1 (10X Genomics, Pleasanton, CA), as described previously  (21). Slides were fixed in pre-chilled methanol (-20°C) for 30 minutes and stained with Mayer’s hematoxylin for 7 minutes. Sections were washed in nuclease-free water, incubated in bluing buffer (Dako) for 2 minutes, counterstained with eosin for 1 minute, briefly rinsed, and dried on a slide warmer at 37°C for 5 minutes. Images of individual capture areas with stained sections were acquired using a Zeiss Axiovert 200M motorized microscope (Carl Zeiss Microscopy, White Plains, NY) with a 5x Plan Apochromat objective and a Leica DFC290 camera. Image tiles were stitched using Metamorph software (Molecular Devices, LLC, San Jose, CA). The pixel size of the final composite images was 1.275 µm. Permeabilization, reverse transcription, second strand synthesis, and cDNA PCR amplification. The optimal enzymatic permeabilization time for the tissue type was pre-determined using the 10X Genomics Tissue Optimization kit, as described previously (21).  The stained and imaged slides were incubated in the permeabilization enzyme solution for 8 min at 37˚C.  Following the permeabilization wash step, the reverse transcription master mixture was added and incubated for 45 min at 53˚C.  After degradation of the mRNA with KOH, the second strand synthesis was carried out for 15 minutes at 65˚C by adding a second strand mixture containing the second strand enzyme and primer. The second strand cDNA was released by denaturation of the double-stranded cDNA with KOH, neutralized with 1 M Tris-HCl and transferred from the slide section to an 8-tube strip.  After determinating the optimal PCR cycle number by KAPA SYBR FAST qPCR Master Kit, the cDNA was amplified for 15 cycles using the PCR cycling conditions provided in the 10X Genomics Visium Spatial Gene Expression protocol. The cDNA was purified using 0.6X AxyPrep Mag magnetic beads. The quality and concentration were confirmed by the Fragment Analyzer (Agilent) using the High Sensitivity NGS kit.
The cDNA library for the Illumina platform was prepared by following the 10X Genomics spatial gene expression library construction protocol, as described previously (21).  Briefly, the double-stranded cDNA was fragmented, the end was repaired, and an A-tail was added in a single step.  The A-tailed fragments were size selected using double-sided AxyPrep Mag magnetic beads with a bead-to-reaction solution ratio of 0.6X for the first step and 0.8X for the second step. The adaptor was ligated and purified with 0.8X AxyPrep Mag magnetic beads. The final Illumina libraries were amplified by PCR, which added the sample dual indexes.  The PCR amplified libraries were purified and size selected using double-sided AxyPrep Mag magnetic beads with a bead-to-reaction solution ratio of 0.6X for the first step and 0.8X for the second step. The individual library was analyzed by Fragment Analyzer (Agilent) to determine the quality and average fragment size and quantified using the Qubit (Invitrogen) DNA assay.  The libraries were pooled in equal molar ratios with a total concentration of 5 nM and sequenced on the Illumina Novaseq 6000.

treatment_protocol: Mouse experiments were approved by the Office of Animal Research (OAR) and the institutional IACUC at the University of Missouri (Protocol: 38241). Six-to-eight-week-old female C57BL/6 mice (Charles River Laboratories, Wilmington, MA) were used in this study. For intranasal administration, 30 µL of either PBS, pH 7.4 (placebo) or 10 µg L-DBF/ME was prepared. Mice were anesthetized using isoflurane and vaccine formulations administered intranasally (IN) as previously described (4, 9). Vaccinations were conducted on Days 0 and 14 (prime and boost, respectively), with groups of 22 mice divided as follows: 10 for survival, 4 for pre-challenge immune assessment, 4 for post-challenge immune assessment, and 4 for spatial transcriptomic sample collection (Figure 1A). Notably, the survival curve, antibody titers, cytokine analysis, and spatial transcriptomics were all conducted within a single animal study.

value: Lung

value: Naïve


title: Lung, vaccinated, rep4

description: Library name: D_Vaccine_4

value: Vaccinated


title: Lung, vaccinated, rep3

description: Library name: D_Vaccine_1


title: Lung, untreated, rep3

description: Library name: C_Naive_2


title: dTAG-SPT5-HCT116, muR2, RNA, Rep2


title: Sample_36

description: 10X Genomics


title: PNOC005-29_D28, bulkRNA

description: Library name: PNOC005-29_D28_bulkRNA


title: Lung, vaccinated, rep2

description: Library name: B_Vaccine_3


title: dTAG-SPT5-HCT116, WT, TT, Rep2


title: dTAG-SPT5-HCT116, muR2, RNA, Rep1


title: Sample_08

description: 10X Genomics


title: PNOC005-29_D07, bulkRNA

description: Library name: PNOC005-29_D07_bulkRNA


title: Sample_32

description: 10X Genomics


title: PNOC005-29_D00, bulkRNA

description: Library name: PNOC005-29_D00_bulkRNA


title: Sample_31

description: 10X Genomics


title: dTAG-SPT5-HCT116, WT, RNA, Rep2


title: Sample_07

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1, RNA, Rep1


title: PNOC005-28_D28, bulkRNA

description: Library name: PNOC005-28_D28_bulkRNA


title: Sample_29

description: 10X Genomics


title: PNOC005-28_D56, bulkRNA

description: Library name: PNOC005-28_D56_bulkRNA


title: Lung, vaccinated, rep1

description: Library name: B_Vaccine_2


title: Lung, untreated, rep1

description: Library name: A_Naive_1


title: Lung, untreated, rep2

description: Library name: A_Naive_3


title: dTAG-SPT5-HCT116, WT, RNA, Rep1


title: IgG CUT&Tag in iGMPs Replicate 2

description: Library name: CnT_IgG_NT_0H_Rep2

data_processing:
Paired-end (PE) fastqs were processed with the ENCODE Uniform Processing Pipeline (Hitz et al. 2023) to produce quality control data, read alignments, and signal tracks. Read inputs included fastq files for two reps and IgG control reads. For this pipeline, reads were mapped to mm10 (mm10 no alt analysis set ENCODE) (bowtie2, v2.2.9), duplicates were removed, and multimapping and discordant reads were excluded. The pipeline produces base-pair-resolution fold-enrichment (signal over IgG) signal files using MACS2.
Assembly: mm10
Supplementary files format and content: signal tracks of fold-enrichment over IgG in bigwig format.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag for H3K27me3 in iGMPs was performed as previously described, using EpiCypher’s CUTANA CUT&Tag Kit (14-1102; Kaya-Okur et al. 2019). Briefly, 200,00 cells were incubated in Nuclei Extraction Buffer (21-1021, 1x protease inhibitor, 0.5 mM spermidine) for 10 min on ice. Nuclei were spun and resuspended in Nuclei Extraction Buffer and then bound to concavalin A beads (21-1401, EpiCypher) and incubated for 10 min at room temperature. After binding, supernatant was removed, and nuclei were resuspended in Antibody Buffer with primary antibody and then incubated overnight at 4 °C. The following antibodies were used: H3K27me3 (1:50, 13-0055, EpiCypher) and IgG (1:50, 13-0042, EpiCypher). After primary antibody incubation, nuclei were washed (Wash Buffer 1) and then incubated with 1:100 Anti-Rabbit Secondary Antibody (13-0047) for 30 min at room temperature. Nuclei were then washed twice with Wash Buffer 1 and resuspended in Wash Buffer 2 for incubation with 1:20 pAG-Tn5 (15-1017) for 1 h at room temperature. Nuclei were then washed twice with Wash Buffer 2 and resuspended in Tagmentation Buffer (Wash Buffer 2, 10 mM MgCl2) and tagmented for 1 h at 37 °C. Nuclei were then washed with Pre-Wash Buffer and then SDS Release Buffer was added to each sample and incubated for 1 h at 58 °C. Reactions were quenched with SDS Quench Buffer.
Samples were indexed with i5 and i7 Primers performing PCR according to manafacturer's recommendations and DNA was purified with SPRIselect beads (21-1405). Indexed samples were sequenced PE150 on a NovaSeq X Plus at the University of California, Irvine Genomics Research and Technology Hub.

value: Blood

value: IgG


title: PNOC005-28_D07, bulkRNA

description: Library name: PNOC005-28_D07_bulkRNA


title: dTAG-SPT5-HCT116, IgG

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals or Flag-SPT5 occupancy signals as indicated
Supplementary files format and content: bed files include RNAPII wave tracks

value: Epicypher; Cat. # 14-1048

value: Mock


title: Sample_52

description: 10X Genomics

value: Control


title: Sample_50

description: 10X Genomics


title: IgG CUT&Tag in iGMPs Replicate 1

description: Library name: CnT_IgG_NT_0H_Rep1


title: H3K27me3 CUT&Tag in iGMPs Replicate 2

description: Library name: CnT_H3K27me3_NT_0H_Rep2


title: Sample_55

description: 10X Genomics


title: Sample_26

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1_Flag, Rep2

value: Human colon cancer cell line

value: Cell Signaling Technology; Cat. # 14793


title: PNOC005-27_D56, bulkRNA

description: Library name: PNOC005-27_D56_bulkRNA

value: PBMC

value: Medulloblastoma

value: MV-NIS


title: dTAG-SPT5-HCT116, muR1_Flag, Rep1


title: H3K27me3 CUT&Tag in iGMPs Replicate 1

description: Library name: CnT_H3K27me3_NT_0H_Rep1

value: granulocyte-macrophage progenitor

value: Untreated


title: Sample_72

description: 10X Genomics

value: postmortem doroslateral prefrontal cortex

value: Male


title: PNOC005-27_D28, bulkRNA

description: Library name: PNOC005-27_D28_bulkRNA


title: IgG CUT&RUN in iGMPs Replicate 2

description: Library name: CnR_IgG_NT_0H_Rep2

data_processing:
Paired-end (PE) fastqs were processed with the ENCODE Uniform Processing Pipeline (Hitz et al. 2023) to produce quality control data, read alignments, and signal tracks. Read inputs included fastq files for two reps of each target reads, and IgG control reads. For this pipeline, reads were mapped to mm10 (mm10 no alt analysis set ENCODE) (bowtie2, v2.2.9), duplicates were removed, and multimapping and discordant reads were excluded. The pipeline produces base-pair-resolution fold-enrichment (signal over IgG) signal files using MACS2.
Assembly: mm10
Supplementary files format and content: signal tracks of fold-enrichment over IgG in bigwig format.
Library strategy: CUT&Run

extract_protocol:
H3K4me1 and H3K9me3 CUT&RUN was performed as previously described in uninduced iGMPs using the CUTANA ChIC/CUT&RUN Kit (14-1048, EpiCypher; Franklin et al. 2022; Skene et al. 2018). Briefly, 1 million cells were collected for each sample. Cells were washed twice (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, protease inhibitor) and bound to concavalin A beads (21-1401, EpiCypher), and incubated overnight at 4 °C with 1:100 or 1:50 (IgG) dilution of primary antibody (Wash Buffer, 0.01% digitonin, 2 mM EDTA). The following antibodies were used: H3K4me1 (ab8895, Abcam), H3K9me3 (ab8898, Abcam), and IgG (13-0042, EpiCypher). Cells were then washed twice with wash buffer. pAG-MNase (15–1116, EpiCypher) was then used at 1:20 dilution for each 50 μL CUT&RUN reaction and incubated for 10 min at room temperature. Cells were then washed twice with wash buffer and 2 mM CaCl2 was added for 2 hours at 4 °C. Stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 50 µg/mL glycogen) was added at 1.5x dilution, with 0.5 ng E. coli spik-in DNA per reaction, and incubated for 10 min at 37 °C. DNA was purified with CUTANA DNA purification kit (14-0050, EpiCypher).
NEB Ultra II DNA Library Prep and Index Kits (E7645, E6440) were used according to the manufacturer's protocol with modifications. Briefly, up to 10 ng DNA was used for end preparation and adapter ligation without size selection. NEB indexes were added with 2-step PCR using an optimized number of cycles (12-14) and short extension times (10 s). Fragment distribution of prepared libraries were confirmed by Bioanalyzer to contain nucleosomal and sub-nucleosomal enrichment and then submitted to Illumina Novaseq 6000 PE100 sequencing at the University of California Irvine Genomics Research and Technology Hub.

value: IgG Epicypher 13-0042


title: Sample_30

description: 10X Genomics

value: AUD


title: IgG CUT&RUN in iGMPs Replicate 1

description: Library name: CnR_IgG_NT_0H_Rep1


title: Sample_25

description: 10X Genomics


title: PNOC005-27_D00, bulkRNA

description: Library name: PNOC005-27_D00_bulkRNA

value: Pre-MV-NIS


title: dTAG-SPT5-HCT116, muL_Flag, Rep2


title: dTAG-SPT5-HCT116, muL_Flag, Rep1


title: H3K9me3 CUT&RUN in iGMPs Replicate 2

description: Library name: CnR_H3K9me3_NT_0H_Rep2

value: Blood

value: H3K9me3 Abcam ab8898


title: PNOC005-27_D07, bulkRNA

description: Library name: PNOC005-27_D07_bulkRNA


title: H3K9me3 CUT&RUN in iGMPs Replicate 1

description: Library name: CnR_H3K9me3_NT_0H_Rep1


title: PNOC005-26_D28, bulkRNA

description: Library name: PNOC005-26_D28_bulkRNA


title: dTAG-SPT5-HCT116, muR1, RNA, Rep2


title: Sample_70

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR2_8, Rep2_inde1

value: Santa Cruz Biotechnology; Cat. # sc-55492


title: dTAG-SPT5-HCT116, WT_Flag, Rep2


title: dTAG-SPT5-HCT116, WT_Flag, Rep1


title: PNOC005-17_D28, bulkRNA

description: Library name: PNOC005-17_D28_bulkRNA

source_name: Whole blood

value: Whole blood


title: PNOC005-17_D14, bulkRNA

description: Library name: PNOC005-17_D14_bulkRNA


title: H3K4me1 CUT&RUN in iGMPs Replicate 2

description: Library name: CnR_H3K4me1_NT_0H_Rep2

value: H3K4me1 Abcam ab8895


title: PNOC005-28_D00, bulkRNA

description: Library name: PNOC005-28_D00_bulkRNA


title: H3K4me1 CUT&RUN in iGMPs Replicate 1

description: Library name: CnR_H3K4me1_NT_0H_Rep1


title: dTAG-SPT5-HCT116, muR2_8, Rep1_inde1

value: Human colon cancer cell line


title: Sample_49

description: 10X Genomics

value: Control


title: PNOC005-26_D07, bulkRNA

description: Library name: PNOC005-26_D07_bulkRNA

value: PBMC


title: Sample_68

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR2_0, Rep1_inde1


title: Sample_24

description: 10X Genomics


title: FACS sorted CD45+ single cell 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 2

city: St. Louis

first: Julie

last: Choi

address: 4370 Duncan Avenue

department: Genetics

institute: Washington University in St. Louis

description:
Library name: Nmnat2 V98M/R232Q Single CD45+ Cell Sciatic 2
10X Genomics
TH_WT_2-3mo_sc_CD45+_sciatic_processed.rds

data_processing:
The reads were aligned to mouse genome version GRCm38/mm10 using CellRanger 8.0.1-7.1.0 from 10X Genomics which includes intronic reads in alignment by default. For nuclei, CellBender was used for ambient RNA removal (v0.3.0), followed by QC filtering to remove nuclei with numbers of genes outside the threshold (nFeatures <500 and >7500) and high mitochondrial percentage (>1%). Doublets were removed using Scrublet (v0.2.3). For single cell, the low-quality cells were removed from down-stream analysis by filtering for number of genes over the threshold (nFeatures <500 and >7500) and high mitochondrial percentage (>10%). The single cell and single nuclei libraries were normalized by SCTransform (v2) and integrated using Harmony in Seurat (v5.1.0) in R (v2023.03.0). The CD45+ libraries were normalized using SCTransform (v2) and integrated using the IntegrateData function in Seurat (v5.1.0) in R (v2023.03.0). The dimensions were reduced using principal component analysis (PCA) and visualized using UMAP. Standard Seurat pipeline was applied throughout the analysis process.
Assembly: Mouse mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: RDS file of integrated single cell and single nucleus from WT and Nmnat2 V98M/R232Q
Supplementary files format and content: RDS file of integrated single cell immune subclusters and CD45+ FACS cells from WT and Nmnat2 V98M/R232Q

source_name: Sciatic nerve

extract_protocol:
Single Cells For single cell RNA-sequencing, sciatic nerves from 2 mice were pooled. Mice were euthanized and perfused with ice cold PBS. Nerves were collected and immediately kept on ice in DMEM with 1% FBS, RNase-In RNase inhibitor (Promega N2518), and SUPERase-In RNase Inhibitor (Invitrogen AM2696) at 1:1000 ratio. The nerves were mechanically dissociated with shears and incubated in DMEM with 1% FBS containing collagenase II (4 mg/mL; Worthington Biochemical LS004176) and Dispase II (2 mg/mL; Sigma-Aldrich D4693-1G) at 37˚C for 30 minutes with gentle shaking. The samples were pipetted up and down at 15 minutes. The cells were filtered through pre-wet 70-µm cell strainers and washed twice with buffer containing DMEM, 1% FBS, RNase-In, and SUPERase-In. Myelin was removed using Myelin Removal Beads II (Miltenyi Biotec 130-096-731) and LS columns (Miltenyi Biotec 130-042-401) per manufacturer’s manuals (Miltenyi Biotec IM0001691). Additional debris and dead cells from the single cell suspensions were excluded by immediate FACS using propidium iodide (PI). Cells were collected into PBS with 10% FBS prior to library preparation.  Single Nuclei For single nucleus RNA-sequencing, sciatic nerves from 2 mice were pooled. Mice were euthanized and perfused with ice cold PBS. The nerves were collected and immediately fresh frozen in dry ice. The nerves were mechanically dissociated with shears in cold lysis buffer containing 10mM Tris buffer, 5mM CaCl2, 3mM Mg(Ac)2, 0.05% CHAPS, 320mM sucrose, 1mM DTT, 5X EDTA-free protease inhibitor (Millipore Sigma 11873580001), RNase-In RNase inhibitor (Promega N2518), and SUPERase-In RNase Inhibitor (Invitrogen AM2696) at 1:1000 ratio in nuclease-free water. The samples were transferred into a glass Dounce homogenizer on ice and mechanically dounced with 10 loose strokes and 20 tight strokes. The samples were filtered through a pre-wet 40-µm cell strainer (Fisher Scientific MT4040) and washed twice with cold wash buffer containing PBS, 0.1% BSA, RNase-In, and SUPERase-In. After removing the supernatant, the nuclear pellet was washed with 3mL of cold wash buffer. The samples were further purified using Anti-Nucleus MicroBeads (Miltenyi Biotec 130-132-997) per manufacturer’s manuals.  CD45+ Single Cells For CD45+ scRNA-seq, sciatic nerves from 5-9 mice were pooled per genotype for one replicate. The samples were processed using the same procedure described above until the myelin removal step. After myelin removal, cells were incubated in CD45+ antibody (Invitrogen MCD4528; 1:250) for 20 minutes and FAC sorted using highly modified Beckman Coulter MoFlo at the Siteman Flow Cytometry core at Siteman Cancer Center. Additional debris and dead cells from the single cell suspensions were excluded during FAC sorting using propidium iodide (PI) as well. Cells were collected into PBS with 10% FBS prior to library preparation.
Single Cells (All and CD45+) The purified single cells were used to prepare scRNA-seq libraries following the 10X Genomics manufacturer’s manuals at the Genome Technology Access Center (GTAC) @ McDonnell Genome Institute (MGI) using 10X Genomics v3.1 chemistry.  Single Nuclei The purified single nuclei were used to prepare scRNA-seq libraries following the 10X Genomics manufacturer’s manuals at the Genome Technology Access Center (GTAC) @ McDonnell Genome Institute (MGI) using 10x Genomics GEM-X v3.4 chemistry.  All libraries were sequenced using Illumina NovaSeq 6000/X accordingly to the manufacturer’s manuals at the GTAC @ MGI at Washington University in St. Louis.

value: Sciatic nerve

tag: age

value: Nerve cells


title: PNOC005-17_D07, bulkRNA

description: Library name: PNOC005-17_D07_bulkRNA

value: Medulloblastoma

value: MV-NIS


title: FACS sorted CD45+ single cell 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 1

description:
Library name: Nmnat2 V98M/R232Q Single CD45+ Cell Sciatic 1
10X Genomics
TH_WT_2-3mo_sc_CD45+_sciatic_processed.rds


title: dTAG-SPT5-HCT116, muR1_8, Rep2_inde1


title: Sample_69

description: 10X Genomics

value: postmortem doroslateral prefrontal cortex


title: PNOC005-17_D01, bulkRNA

description: Library name: PNOC005-17_D01_bulkRNA


title: PNOC005-17_D00, bulkRNA

description: Library name: PNOC005-17_D00_bulkRNA


title: Single cell 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 1

description:
Library name: Nmnat2 V98M/R232Q Single Cell Sciatic 1
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: dTAG-SPT5-HCT116, muR1_8, Rep1_inde1


title: Sample_66

description: 10X Genomics

value: Female


title: Sample_65

description: 10X Genomics

value: Male


title: Sample_64

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1_0, Rep2_inde1


title: PNOC005-16_D28, bulkRNA

description: Library name: PNOC005-16_D28_bulkRNA


title: FACS sorted CD45+ single cell 2-3-month WT sciatic nerves rep 2

description:
Library name: WT Single CD45+ Cell Sciatic 2
10X Genomics
TH_WT_2-3mo_sc_CD45+_sciatic_processed.rds

value: WT


title: dTAG-SPT5-HCT116, WT_8, Rep2_inde1


title: Sample_67

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1_0, Rep1_inde1


title: PNOC005-16_D14, bulkRNA

description: Library name: PNOC005-16_D14_bulkRNA


title: Single cell 2-3-month WT sciatic nerves rep 2

description:
Library name: WT Single Cell Sciatic 2
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: PNOC005-16_D00, bulkRNA

description: Library name: PNOC005-16_D00_bulkRNA

value: Pre-MV-NIS


title: dTAG-SPT5-HCT116, WT_8, Rep1_inde1


title: PNOC005-15_D28, bulkRNA

description: Library name: PNOC005-15_D28_bulkRNA


title: dTAG-SPT5-HCT116, WT_0, Rep2_inde1


title: Single cell 2-3-month WT sciatic nerves rep 1

description:
Library name: WT Single Cell Sciatic 1
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: PNOC005-15_D14, bulkRNA

description: Library name: PNOC005-15_D14_bulkRNA


title: Sample_43

description: 10X Genomics

value: AUD


title: Sample_47

description: 10X Genomics


title: C57BL/6 male mice, PP-MP containing food, 71weeks, rep3

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

country: South Korea

institute: Chung-Ang

description: Library name: Sample6

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to GRCm39 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: GRCm39
Supplementary files format and content: txt file

source_name: liver

growth_protocol: C57BL/6 male mice were reared over a period of 71 weeks in a controlled environment, with temperatures consistently maintained between 18 to 22 degrees Celsius.

extract_protocol:
Total RNA was isolated from liver using Direct-Zol™ RNA microprep kit (Zymo research, CA, USA) according to the manufacturer’s protocol.
RNA Libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA magnetic Isolation Module and NEBNext Ultra II Derectional RNA Library Prep Kit for Illumina

treatment_protocol: Chow containing PS-MP

value: liver

value: Chow containing PP-MP


title: dTAG-SPT5-HCT116, WT_0, Rep1_inde1

value: Santa Cruz Biotechnology; Cat. # sc-55492


title: Single cell 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 2

description:
Library name: Nmnat2 V98M/R232Q Single Cell Sciatic 2
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: Sample_44

description: 10X Genomics


title: PNOC005-15_D00, bulkRNA

description: Library name: PNOC005-15_D00_bulkRNA

value: Whole blood


title: FACS sorted CD45+ single cell 2-3-month WT sciatic nerves rep 1

description:
Library name: WT Single CD45+ Cell Sciatic 1
10X Genomics
TH_WT_2-3mo_sc_CD45+_sciatic_processed.rds


title: C57BL/6 male mice, PP-MP containing food, 71weeks, rep2

description: Library name: Sample5


title: PNOC005-14_D28, bulkRNA

description: Library name: PNOC005-14_D28_bulkRNA


title: Sample_61

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1R2_5, Rep2

value: Human colon cancer cell line


title: Sample_73

description: 10X Genomics

value: Control


title: dTAG-SPT5-HCT116, muR1R2_5, Rep1


title: PNOC005-14_D14, bulkRNA

description: Library name: PNOC005-14_D14_bulkRNA


title: Sample_63

description: 10X Genomics


title: C57BL/6 male mice, PP-MP containing food, 71weeks, rep1

description: Library name: Sample4


title: Sample_59

description: 10X Genomics


title: C57BL/6 male mice, normal food, 71weeks, rep3.

description: Library name: Sample3

value: Normal Chow


title: C57BL/6 male mice, normal food, 71weeks, rep2.

description: Library name: Sample2


title: dTAG-SPT5-HCT116, muR1R2_3, Rep1


title: dTAG-SPT5-HCT116, muR1R2_1, Rep2


title: PNOC005-14_D01, bulkRNA

description: Library name: PNOC005-14_D01_bulkRNA


title: PNOC005-14_D04, bulkRNA

description: Library name: PNOC005-14_D04_bulkRNA


title: Sample_62

description: 10X Genomics


title: Sample_60

description: 10X Genomics


title: C57BL/6 male mice, normal food, 71weeks, rep1.

description: Library name: Sample1


title: dTAG-SPT5-HCT116, muR1R2_1 Rep1


title: iGMPs Rep2 RNA-seq

data_processing:
For bulk RNA-seq data analysis, we used STAR aligner (v2.7) 67, setting,  --outFilterMultimapNmax 20 --alignSJoverhangMin 8 –alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 1 Sequencing reads (PE fastq) were mapped to the mouse mm10 reference genome (Gencode M25 primary assembly).
Read counts for individual genes were quantified with subread featureCounts (-B -p --countReadPairs -s 2 -C -g gene_id), excluding multimapping reads and reads that map to overlapping features, using the Gencode M25 primary assembly annotation file.
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for all samples with gene IDs, gene symbols, and gene types.

growth_protocol: Immortalized granulocyte-macrophage progenitor-like cells with a GFP reporter at the Lyz2 locus and the ER-HOXA9 transgene (herein GMPs or HOXA9-iGMPs)32,33 were cultured in RPMI-1640 supplemented with 10% FBS, 100U mL-1 penicillin, 100 µg mL−1 streptomycin, 2mM L-alanyl-L-glutamine dipeptide and stem cell factor (SCF). Depending on the batch, media was made with 1-2% SCF-conditioned media from SCF-secreting Chinese hamster ovary cells (a gift from David Sykes). Concentrations for each batch were determined with functional testing, exploiting the strict SCF-dependence of iGMPs. β-Estradiol (E2) was added to a final concentration of 150 ng/mL for normal culture.

extract_protocol:
Cells were collected in TRIzol (ThermoFisher) at 10 million cells/mL TRIzol. RNA was extracted with the Direct-zol RNA miniprep plus kit (R2072, Zymo Research) by adding an equal volume of 100% ethanol to TRIzol collection. Mixture was then added to columns from the kit. Bound RNA was washed with Wash Buffer and incubated for 15 min on the column with DNase I. Bound RNA was then washed with Pre-wash Buffer and Wash Buffer. Columns were dried by centrifugation at >15,000 x g and RNA was eluted with 50 µL pure water. The quantity and purity of collected RNA was checked with a NanoDrop spectrophotometer. RNA quality was assessed using an Agilent 2100 Bioanalyzer or TapeStation to confirm RNA integrity (RIN) values were above 9.
RNA-seq libraries were prepared with the NEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep kit (E7405L, E7765S, NEB) using unique dual indices (E6440, NEB). 1 µg total RNA was input for each library. RNA was hybridized with rRNA probes by denaturation for 2 min at 95 °C and gradual temperature decrease (-0.1 °C/s) to 22 °C. RNase H digestion was then performed followed by DNase I digestion. rRNA and DNA depleted total RNA was purified and then fragmented and primed with random primers. Double-stranded cDNA was synthesized, purified, and ends were repaired and prepared with A-tailing. Adaptors were diluted according to RNA input quantity (1:5 for 1 µg total RNA input). cDNA and adapters were ligated followed by USER Enzyme digestion. The ligation mix was purified and eluted with 17 µL 0.1x TE. Purified ligations were then enriched with PCR using unique dual index primers and 7 amplification cycles. Amplified libraries were quantified with Qubit and analyzed with an Agilent 2100 Bioanalyzer or Agilent 4150 TapeStation. The molecular weights of library fragments within 200-700 bp and their percentages of total were calculated with Bioanalyzer or TapeStation results.

treatment_protocol: For LacO-shChaf1b expression (CAF-1 OFF condition), IPTG was added at a concentration of 500 µM to iGMPs cultured with E2. For neutrophil differentiation, HOXA9 was deactivated by rinsing cells with PBS twice to remove E2 and then cultured in the otherwise complete iGMP media lacking E2. For tetO-shSupt6 expression (SPT6 OFF condition), cells were treated with DOX at 1 µg/mL.

value: Blood

value: granulocyte-macrophage progenitor

value: Untreated


title: iGMPs Rep1 RNA-seq


title: PNOC005-14_D00, bulkRNA

description: Library name: PNOC005-14_D00_bulkRNA

value: Medulloblastoma


title: Sample_34

description: 10X Genomics

value: postmortem doroslateral prefrontal cortex


title: dTAG-SPT5-HCT116, muR1R2_0, Rep2


title: Sample_39

description: 10X Genomics

value: Female


title: PNOC005-12_D28, bulkRNA

description: Library name: PNOC005-12_D28_bulkRNA

value: MV-NIS


title: dTAG-SPT5-HCT116, muR1R2_0, Rep1


title: Neutrophils 48 h Rep2 RNA-seq

value: E2 withdrawal 48 h


title: PNOC005-12_D14, bulkRNA

description: Library name: PNOC005-12_D14_bulkRNA


title: PNOC005-14_D07, bulkRNA

description: Library name: PNOC005-14_D07_bulkRNA


title: Neutrophils 48 h Rep1 RNA-seq


title: dTAG-SPT5-HCT116, muR1_5, Rep2


title: Sample_42

description: 10X Genomics


title: CAF-1 OFF 48 h Rep2 RNA-seq

value: 500 uM IPTG 48 h


title: dTAG-SPT5-HCT116, muR1R2_3, Rep2


title: dTAG-SPT5-HCT116, muR1_5, Rep1


title: Sample_33

description: 10X Genomics

value: AUD

value: Male


title: Sample_28

description: 10X Genomics


title: CAF-1 OFF 48 h Rep1 RNA-seq


title: dTAG-SPT5-HCT116, muR1_3, Rep2


title: PNOC005-12_D07, bulkRNA

description: Library name: PNOC005-12_D07_bulkRNA


title: SPT6 OFF 48 h Rep2 RNA-seq

value: 1 ug/mL DOX 48 h


title: Sample_51

description: 10X Genomics


title: PNOC005-12_D01, bulkRNA

description: Library name: PNOC005-12_D01_bulkRNA


title: Sample_27

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1_3, Rep1

value: Santa Cruz Biotechnology; Cat. # sc-55492


title: dTAG-SPT5-HCT116, muR1_1, Rep2


title: SPT6 OFF 48 h Rep1 RNA-seq


title: PNOC005-09_D28, bulkRNA

description: Library name: PNOC005-09_D28_bulkRNA

value: Whole blood


title: Sample_46

description: 10X Genomics


title: dTAG-SPT5-HCT116, muR1_1 Rep1

value: Human colon cancer cell line


title: PNOC005-09_D14, bulkRNA

description: Library name: PNOC005-09_D14_bulkRNA


title: Sample_41

description: 10X Genomics


title: iGMPs Rep1 ATAC-seq

data_processing:
Reads were processed with the ENCODE Uniform processing pipeline71 to produce quality control data, read alignments, and signal tracks. For this pipeline, reads were trimmed with cutadapt and aligned against the mm10 reference genome (mm10 no alt analysis set ENCODE) using bowtie2 (v0.7.17) 72. The pipeline also filters out reads mapping to the mitochondrial genome or to multiple locations and duplicate reads. The pipeline then shifts reads to account for Tn5 insertions and calls peaks with the filtered, shifted reads using MACS2.
macs3 (v3.0.0a7) callpeak (--nomodel --shift -25 --extsize 50 -B --SPMR) was used to generate counts per million signal files with processed alignment file inputs.
Assembly: mm10
Supplementary files format and content: signal tracks of counts per million mapped reads for each library.

extract_protocol:
To generate ATAC-seq libraries, two clonal replicates for used for each condition. 100,000 cells were used with the Active Motif ATAC-seq kit (#53150). Briefly, collected cells were washed in PBS, and lysed in ATAC Lysis Buffer.
Nuclei were spun down and resuspended in the Tagmentation Master Mix containing assembled Tn5 transposomes. Transposase reactions were incubated at 37 °C for 30 min and then DNA from transposed nuclei was isolated and PCR-amplified using barcoded Nextera primers (Illumina). Library quality control and quantitation was carried out using high-sensitivity DNA Bioanalyzer or TapeStation and Qubit.


title: PNOC005-09_D00, bulkRNA

description: Library name: PNOC005-09_D00_bulkRNA

value: Pre-MV-NIS


title: dTAG-SPT5-HCT116, muR1_0, Rep1


title: Neutrophils 48 h Rep2 ATAC-seq


title: PNOC005-12_D04, bulkRNA

description: Library name: PNOC005-12_D04_bulkRNA


title: dTAG-SPT5-HCT116, muR1_0, Rep2


title: Sample_71

description: 10X Genomics

value: Control


title: PNOC005-08_D28, bulkRNA

description: Library name: PNOC005-08_D28_bulkRNA


title: Sample_54

description: 10X Genomics


title: dTAG-SPT5-HCT116, WT_5, Rep1


title: PNOC005-12_D00, bulkRNA

description: Library name: PNOC005-12_D00_bulkRNA


title: Sample_53

description: 10X Genomics


title: CAF-1 OFF 48 h Rep2 ATAC-seq

value: Blood


title: PNOC005-08_D01, bulkRNA

description: Library name: PNOC005-08_D01_bulkRNA


title: Neutrophils 48 h Rep1 ATAC-seq

value: granulocyte-macrophage progenitor


title: PNOC005-08_D04, bulkRNA

description: Library name: PNOC005-08_D04_bulkRNA


title: dTAG-SPT5-HCT116, WT_3, Rep2


title: CAF-1 OFF 48 h Rep1 ATAC-seq


title: SPT6 OFF 48 h Rep2 ATAC-seq


title: iGMPs Rep2 ATAC-seq

value: Untreated


title: dTAG-SPT5-HCT116, WT_5, Rep2


title: dTAG-SPT5-HCT116, WT_3, Rep1


title: PNOC005-08_D00, bulkRNA

description: Library name: PNOC005-08_D00_bulkRNA

value: Medulloblastoma


title: Sample_56

description: 10X Genomics

value: postmortem doroslateral prefrontal cortex


title: Sample_45

description: 10X Genomics


title: SPT6 OFF 48 h Rep1 ATAC-seq


title: Sample_57

description: 10X Genomics


title: Sample_48

description: 10X Genomics

value: Female


title: PNOC005-13_D28, RNAexome

description: Library name: PNOC005-13_D28_RNAexome

value: MV-NIS


title: dTAG-SPT5-HCT116, WT_1, Rep2


title: iBAT, YBKO_3

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly differential expression.
Assembly: mouse reference genome(GRCm38/mm10)
Supplementary files format and content: Excel; fpkm of each gene

source_name: iBAT

extract_protocol:
Ythdc1flox/flox and Ythdc1-BKO mice were fed with normal chow for 8 weeks.Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

value: iBAT


title: dTAG-SPT5-HCT116, WT_1 Rep1


title: PNOC005-08_D14, bulkRNA

description: Library name: PNOC005-08_D14_bulkRNA


title: PNOC005-13_D14, RNAexome

description: Library name: PNOC005-13_D14_RNAexome


title: Sample_40

description: 10X Genomics


title: Sample_35

description: 10X Genomics


title: iBAT, YBKO_2


title: dTAG-SPT5-HCT116, WT_0, Rep2


title: iBAT, YBKO_1


title: PNOC005-06_D28, RNAexome

description: Library name: PNOC005-06_D28_RNAexome


title: Frame-shift Mutant clone2, replicate 2, day 70

city: NY

first: zhixiong

last: sun

state: NY

address: 3908 pardes building, NYSPI

department: Psychiatry

institute: Columbia University

data_processing:
Columbia University Genome center STRPOLYA 20m 2x100bp NOVASEQ
We used RTA (Illumina) for base calling and bcl2fastq (Illumina, version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to the reference human genome (UCSC/hg38) using STAR (version 2.5.4b)
Read counts and normalization of the read count data and analysis of DEGs was performed using DESeq2
Assembly: hg38

source_name: independent clone 2

growth_protocol: Forebrain organoids were maintained in medium supplemented with 10% fetal bovine serum (FBS),1% Matrigel and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using miRNeasy mini kit (Qiagen). Approximately 100 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared from ~400 ng of total RNA using the STRYPOLYA library prep kit (Illumina) and were sequenced at the Columbia Genome Center on a Novaseq 6000 instrument (Illumina) with 100bp paired-end reads.

treatment_protocol:
Forebrain organoids were transduced with the AAV-hSYN-GFP virus (Addgene, 105539-AAV1) at DIV55, to label neurons with GFP. Sorting of neurons labelled with GFP at DIV70 was conducted using a BD influx cell sorter in 1.5 ml tubes pre-coated with 10% FBS. Sorted neurons were then collected by centrifugation at 400g at 4°C for 10 min, followed by ice-cold PBS wash.
Total RNA was extracted from sorted GFP positive neurons at DIV70 using RNeasy Mini Kit (Qiagen). Quality of RNA samples was assessed using a Bioanalyzer (Agilent 2100 bioanalyzer) to ensure the RNA Integrity Number (RIN)>9.0 for all samples.

value: independent clone 2

value: Neurons

value: Frame-shift Mutant

value: Fluorescence-activatedcellsorting

value: Day 70


title: dTAG-SPT5-HCT116, WT_0, Rep1

value: Santa Cruz Biotechnology; Cat. # sc-55492


title: iBAT, FF_2


title: Frame-shift Mutant clone2, replicate 3, day 70


title: PNOC005-13_D00, RNAexome

description: Library name: PNOC005-13_D00_RNAexome

value: Whole blood


title: iBAT, FF_3


title: dTAG-SPT5-HCT116, muR1R2, Inde2

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). PCR duplicates were removed using Picard Tools (version 3.1.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals

value: Human colon cancer cell line

value: Bethyl Laboratories;Cat. # A304-405A


title: PNOC005-06_D07, RNAexome

description: Library name: PNOC005-06_D07_RNAexome


title: WT clone2, replicate 3, day 70

value: WT


title: dTAG-SPT5-HCT116, muR2, Inde2


title: iBAT, FF_1


title: Frame-shift Mutant clone2, replicate 1, day 70


title: dTAG-SPT5-HCT116, muR1, Inde2


title: dTAG-SPT5-HCT116, WT, Inde2


title: PNOC005-06_D01, RNAexome

description: Library name: PNOC005-06_D01_RNAexome


title: WT clone2, replicate 2, day 70


title: dTAG-SPT5-HCT116, muALL, Inde5


title: PNOC005-06_D00, RNAexome

description: Library name: PNOC005-06_D00_RNAexome

value: Pre-MV-NIS


title: C57BL/6 male mice, PB-MP containing food, 71weeks, rep2

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to GRCm39 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

treatment_protocol: Chow containing PB-MP

value: liver

tag: strain

value: male

value: Chow containing PB-MP


title: dTAG-SPT5-HCT116, muR1R2, Rep2_Inde4

value: dTAGv-1; NVP2


title: WT clone2, replicate 1, day 70


title: C57BL/6 male mice, PB-MP containing food, 71weeks, rep1


title: PNOC005-06_D14, RNAexome

description: Library name: PNOC005-06_D14_RNAexome

value: Medulloblastoma

value: MV-NIS


title: WT clone1, replicate 3, day 70

source_name: independent clone 1

value: independent clone 1


title: PNOC005-05_D28, RNAexome

description: Library name: PNOC005-05_D28_RNAexome


title: C57BL/6 male mice, normal food (control), 71weeks, rep3

value: Normal Chow


title: PNOC005-05_D14, RNAexome

description: Library name: PNOC005-05_D14_RNAexome


title: C57BL/6 male mice, normal food (control), 71weeks, rep2


title: WT clone1, replicate 2, day 70

value: Neurons


title: dTAG-SPT5-HCT116, muR1R2, Rep1_Inde4


title: dTAG-SPT5-HCT116, muR1R2, Inde4


title: WT clone1, replicate 1, day 70

value: Fluorescence-activatedcellsorting


title: PNOC005-06_D04, RNAexome

description: Library name: PNOC005-06_D04_RNAexome


title: C57BL/6 male mice, normal food (control), 71weeks, rep1


title: C57BL/6 male mice, PB-MP containing food, 71weeks, rep3


title: dTAG-SPT5-HCT116, WT, Inde4


title: BMMCs of M5 AML (relapse) from Patient 1 [AML03M5_RE]

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

data_processing:
The Cell Ranger software pipeline (version 2.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: primary isolated cells

growth_protocol: These samples were directly isolated from AML patients without cell culture.

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v2 Kits according to the manufacturer’s protocol.

treatment_protocol: All of dead cells were removed using dead cell removal kit (Miltenyi Biotec). Furthermore, all of patients at relapse and partial remission stages were already treated with HSCs transplantation.

value: primary isolated cells

value: human bone marrow cells

value: post HSCs transplantation