title: WT_2

city: Kiel

first: Konrad

last: Aden

address: Rosalind-Franklin-Straße 12

institute: Institute of Clinical Molecular Biology, CAU

description: Library name: H23225.L1_S9_L001

data_processing:
Raw reads were trimmed for adapter sequences and low-quality bases using Cutadapt.
Cleaned reads were aligned to the mouse reference genome (GRCm38) using TopHat2
Gene-level counts were calculated using HTSeq. Differential gene expression and principal component analysis (PCA) were performed using the DESeq2 package.
Venn diagrams were generated using the VennDiagram R package.
Gene Ontology enrichment analysis was performed using InnateDB. TFBSTools was used to analyze transcription factor binding site enrichment.
Assembly: GRCm38
Supplementary files format and content: CSV file with Ensembl gene IDs and sample-wise read counts generated using HTSeq.

source_name: Small intestine

growth_protocol: Organoid growth in intesticult medium

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
Total RNA was extracted and used for library preparation using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: no treatment

value: Small intestine

value: intestinal stem cell-derived organoid


title: WT_1

status: Public on Jun 17 2025

type: SRA

country: Germany

description: Library name: H23226.L1_S10_L001

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: WT_4

description: Library name: H23223.L1_S7_L001


title: WT_3

description: Library name: H23224.L1_S8_L001


title: RNaseH2bATG16L1_DKO_4

description: Library name: H23227.L1_S11_L001


title: ATG16L1_KO_3

description: Library name: H23232.L1_S16_L002


title: RNaseH2bATG16L1_DKO_3

description: Library name: H23228.L1_S12_L001


title: RNaseH2bATG16L1_DKO_2

description: Library name: H23229.L1_S13_L002


title: ATG16L1_KO_2

description: Library name: H23233.L1_S17_L002


title: ATG16L1_KO_1

description: Library name: H23234.L1_S18_L002


title: RNaseH2bKO_2

description: Library name: H23235.L1_S19_L002


title: ATG16L1_KO_4

description: Library name: H23231.L1_S15_L002


title: RNaseH2bKO_1

description: Library name: H23236.L1_S20_L002


title: flu infection smaller repeat reporter guide RNA #3

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

country: USA

institute: University of California, San Diego

description:
Library name: Sample 15
RNA reporter econding guide RNA

library_source: other

data_processing:
Data were processed with a custom pipeline described in the associated manuscript.
Assembly: Gecko V2
Supplementary files format and content: Individual counts of guide sequences and associated gene targets
Library strategy: CRISPR Screen

molecule: other

organism: Homo sapiens

growth_protocol: Samples were from infections of A549-Cas9 cells bearing a CRITR-seq library with a type III interferon reporter with guides cloned from the GECKO library. Cells were allowed to undergo editing or silencing for 10 days, after which they were infected by A/WSN/1933 bearing segment 8 from A/PR/8 with stop codons interrupting the NS1 reading frame at an MOI of 2 in influenza growth media. RNA and DNA harvested at 8 hours post infection. RNA more samples represent increased input of RNA, which we found to greatly improve the quality of the dataset. Silenced samples were processed for flu cap lengths using 5' RACE.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010), DNA by the Monarch spin gDNA extraction kit (NEB #T3010).
Custom amplicon sequencing

treatment_protocol: Infection at MOI 2 by A/WSN/1933 with segment 8 from A/PR/8 bearing stop codons in the NS1 reading frame for 8 hours.

tag: cell line

tag: treatment

value: CRITR-Seq with infection by flu lacking NS1


title: RNaseH2bATG16L1_DKO_1

description: Library name: H23230.L1_S14_L002


title: flu infection smaller repeat reporter guide RNA #2

description:
Library name: Sample 14
RNA reporter econding guide RNA


title: flu infection smaller repeat reporter guide RNA #1

description:
Library name: Sample 13
RNA reporter econding guide RNA


title: 20057-0011

type: RNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing: Raw data (.CEL files) were processed using the RMA (Robust Multi-array Average) normalization method implemented in the `oligo` package in R (version 4.0.3). Background correction and probe summarization were performed as described in the Affymetrix Clariom D Human array documentation. ProbeIDs were matched to Gene Symbols using the R package clariomdhumantranscriptcluster.db.

label: biotin

source_name: Ewing Sarcoma cell line

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol.

growth_protocol: All cell lines were cultured in RPMI 1640 with stable glutamine (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich) at 37°C in a fully humidified 5% CO2 atmosphere. Cell lines were routinely tested for Mycoplasma contamination using a custom nested PCR protocol.

extract_protocol: For RNA extraction, the NucleoSpin RNA kit from Macherey-Nagel (Duren, Germany) was used following the manufacturer’s protocol.

treatment_protocol: 96h Dox or no Dox

tag: shRNA

value: EIF4EBP1-targeting specific shRNA

tag: clone

value: UTR

value: Minus Dox

tag: duration of treatment


title: flu infection smaller repeat genomic guide DNA #2

description:
Library name: Sample 11
DNA encoding guide RNA


title: flu infection smaller repeat genomic guide DNA #1

description:
Library name: Sample 10
DNA encoding guide RNA


title: flu infection smaller repeat genomic guide DNA #3

description:
Library name: Sample 12
DNA encoding guide RNA


title: 20057-0005

value: SK-N-MC


title: Tension_Bio3_Region3

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

description:
Library name: Tension_Bio3_Region3
Column name in LCMSpTrTW_count.txt is Tension_Bio3_L3

data_processing: As the libraries from 3 replicates of 3 regions were pooled for sequencing with their specific sample indexes, demultiplexing was initially performed to extract the sample index and UMI sequences from the R2 reads. Only reads with a sample index that exactly mached one of the predefined sample index sets were retained. The sample index and UMI sequences were subsequently labeled in their corresponding R1 reads using the "extract" function from UMI-tools. The labeled R1 reads were then split into separate files according to their sample indexes. Subsequently, the R1 reads were trimmed to remove any 3’ poly-A sequence and reads shorter than 25 base pairs were discarded. The trimmed R1 reads were aligned to the P. trichocarpa reference genome using the STAR. The resulting BAM files were then processed using featureCounts to annotate reads with their corresponding gene IDs as gene tags. Based on UMI sequences and mapping locations, the annotated BAM files were then processed with UMI-tools functions, including “group”, “dedup”, and “count”, to accurately quantify each gene's transcript abundance by removing redundant reads generated during PCR amplification.    Assembly: Populus trichocarpa (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002775.5/)  Supplementary files format and content: LCMSpTrNW_count.txt contains UMI counts for normal samples, and LCMSpTrTW_count.txt contains those for tension samples. Each column corresponds to one sample.

molecule: polyA RNA

organism: Populus trichocarpa

source_name: SDX

growth_protocol: Five to twelve-month-old P. trichocarpa trees were propagated from branch cutting. Trees were grown in a glasshouse or a walk-in growth chamber (16/8 h light/dark cycle, 24–26°C) at National Taiwan University (Taipei, Taiwan). Stem samples were collected from below the 8th internode.

extract_protocol:
The debarked stem segments of normal and tension wood were frozen with liquid nitrogen and stored at -80℃. The segments were mounted vertically onto cryostat chucks with Tissue-Tek O.C.T. Compound (Sakura Finetek) and sectioned into 16-μm slices using a cryostat (Leica, CM1900) at −20℃. The sectioned samples were placed on PET membranes of metal-frame slides and dehydrated by 99.5% ethanol. Laser capture microdissection (LCM) technology was applied to collect normal or tension xylem samples at different differentiation stages on debarked stem cross-sections. Five regions were cut by laser capture microdissection (Leica, LMD7000), and Region 1, 2 and 3 were collected (Figures 5A and 5B). The width of each region was set to three times the average width of 10 consecutive libriform fibers. Approximately 1,600,000 μm2 of each region of samples were collected and pooled as one biological replicate. Three biological replicates were collected for normal and tension xylem. After laser dissection, the collected regions of samples fell into 500-μL tube caps containing 50 μL of RLT buffer (QIAGEN) with 1% beta-mercaptoethanol (Sigma-Aldrich), which was then frozen with liquid nitrogen within 30 min and stored at -80℃. Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) following the manufacturer instructions.
The sequencing library was constructed using QIAseq® UPX 3' Transcriptome Kit (QIAGEN) according to manufacturer's guidelines.

treatment_protocol: The stems of P. trichocarpa trees were bent from vertical position to a 90° angle relative to a horizontal line and maintained for the required duration of the experiments. The bending point was fixed at a height of 115 cm (Figure. S2). The stem segments were collected from the bending point for 16 cm above and 16 cm below both. Trees treated with 21-day bending were used for spatial transcriptomic analyses.

value: SDX

value: wild type


title: Tension_Bio3_Region1

description:
Library name: Tension_Bio3_Region1
Column name in LCMSpTrTW_count.txt is Tension_Bio3_L1


title: 20057-0003

value: CDS


title: 20057-0010

value: control shRNA

value: control

value: Plus Dox


title: 20057-0014


title: 20057-0007


title: 20057-0002


title: 19059-0038


title: 20057-0004


title: Tension_Bio3_Region2

description:
Library name: Tension_Bio3_Region2
Column name in LCMSpTrTW_count.txt is Tension_Bio3_L2


title: 20057-0009


title: 20057-0006


title: Tension_Bio2_Region3

description:
Library name: Tension_Bio2_Region3
Column name in LCMSpTrTW_count.txt is Tension_Bio2_L3


title: 20057-0012


title: 19059-0018


title: flu infection reporter guide more RNA #2

description:
Library name: Sample 8
RNA reporter econding guide RNA


title: 20057-0001


title: 20057-0013


title: Tension_Bio1_Region3

description:
Library name: Tension_Bio1_Region3
Column name in LCMSpTrTW_count.txt is Tension_Bio1_L3


title: 20057-0008


title: Tension_Bio2_Region1

description:
Library name: Tension_Bio2_Region1
Column name in LCMSpTrTW_count.txt is Tension_Bio2_L1


title: Tension_Bio1_Region2

description:
Library name: Tension_Bio1_Region2
Column name in LCMSpTrTW_count.txt is Tension_Bio1_L2


title: Tension_Bio2_Region2

description:
Library name: Tension_Bio2_Region2
Column name in LCMSpTrTW_count.txt is Tension_Bio2_L2


title: flu infection reporter guide more RNA #1

description:
Library name: Sample 7
RNA reporter econding guide RNA


title: Tension_Bio1_Region1

description:
Library name: Tension_Bio1_Region1
Column name in LCMSpTrTW_count.txt is Tension_Bio1_L1


title: Normal_Bio3_Region2

description:
Library name: Normal_Bio3_Region2
Column name in LCMSpTrNW_count.txt is Normal_Bio3_L2


title: Normal_Bio2_Region2

description:
Library name: Normal_Bio2_Region2
Column name in LCMSpTrNW_count.txt is Normal_Bio2_L2


title: flu infection reporter guide more RNA #3

description:
Library name: Sample 9
RNA reporter econding guide RNA


title: Normal_Bio3_Region3

description:
Library name: Normal_Bio3_Region3
Column name in LCMSpTrNW_count.txt is Normal_Bio3_L3


title: Normal_Bio2_Region3

description:
Library name: Normal_Bio2_Region3
Column name in LCMSpTrNW_count.txt is Normal_Bio2_L3


title: Human CALB2-expressing neuron 8908_S5 transfected with CellREADR

city: Durham

first: Jeffrey

last: Russ

state: NC

address: 311 Research Drive

institute: Duke University

description: Library name: X8908_S5

data_processing:
Data were aligned to the human genome (GRCh38, annotations from ENSEMBL v106). Raw count matrices from aligned data were analyzed using the Allen Institute scrattch.hicat (version 1.0.0) package in R (2022.07.1 Build 554). Normalized counts were calculated as log2(counts-per-million reads per cell) for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: csv file that includes raw counts for each sample

molecule: nuclear RNA

source_name: Human cortex

extract_protocol:
Clean nucleus extraction was confirmed visually with both DIC and fluorescent images. Nuclei were stored at -80C in 10μL of lysis buffer with RNase inhibitor (40 U/µL) and then processed for sequencing in batches (5-12 nuclei/batch).
Nuclear RNA was processed into cDNA libraries using the SMART-Seq v4 Ultra Low Input kit (Takara) using 19 PCR cycles. Nuclei that yielded >200 pg/µL cDNA were sequenced. Borderline cDNA (concentrations just below 200 pg/µL, and fragment sizes >500 bp) were re-amplified with 3 rounds of PCR, rechecked for cDNA quality, and included in the sequencing set if reamplification increased cDNA concentration above threshold.

value: Human cortex

value: Slice culture

value: Neuron


title: Human CALB2-expressing neuron 8908_S6 transfected with CellREADR

description: Library name: X8908_S6


title: Human CALB2-expressing neuron 8908_S9 transfected with CellREADR

description: Library name: X8908_S9


title: Normal_Bio1_Region3

description:
Library name: Normal_Bio1_Region3
Column name in LCMSpTrNW_count.txt is Normal_Bio1_L3


title: Human CALB2-expressing neuron 8908_S2 transfected with CellREADR

description: Library name: X8908_S2


title: Normal_Bio1_Region2

description:
Library name: Normal_Bio1_Region2
Column name in LCMSpTrNW_count.txt is Normal_Bio1_L2


title: Human CALB2-expressing neuron 8908_S11 transfected with CellREADR

description: Library name: X8908_S11


title: Normal_Bio3_Region1

description:
Library name: Normal_Bio3_Region1
Column name in LCMSpTrNW_count.txt is Normal_Bio3_L1


title: 19059-0037


title: ATAC day 3 late CHIR

city: Tucson

first: Bao

last: Thai

state: AZ

address: 1656 E Mabel St

institute: University of Arizona

description:
Library name: CHIRmulti5 ATAC
ATAC output from Cell Ranger ARC

library_source: genomic single cell

data_processing:
Cell Ranger ARC  was used to align reads and generate feature-barcode matrices.
ATAC-seq reads were aligned to the hg38 reference genome using Cell Ranger ARC.
Gene Expression reads were aligned to the hg38 transcriptome using Cell Ranger ARC.
Peaks were called using Cell Ranger ARC’s internal pipeline.
Fragment and gene count matrices were generated per cell using default Cell Ranger ARC settings.
Assembly: hg38 (GRCh38)
Supplementary files format and content: atac_fragments.tsv.gz: ATAC-seq fragment coordinates with cell barcodes.
Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered gene-barcode matrix from integrated RNA + ATAC profiling.

molecule: genomic DNA

source_name: hPSC

growth_protocol: Cells were cultured under standard pluripotent stem cell conditions in mTeSR1 medium on Matrigel-coated plates.

extract_protocol:
Nuclei were extracted using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression protocol
Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following the manufacturer’s protocol

treatment_protocol: Cells were treated with CHIR99021 for WNT pathway activation at the indicated timepoints.

value: hPSC

value: embryonic stem cell


title: Human CALB2-expressing neuron 8727_G transfected with CellREADR

description: Library name: X8727_G


title: 19059-0017


title: ATAC day 3 early CHIR

description:
Library name: CHIRmulti4 ATAC
ATAC output from Cell Ranger ARC


title: ATAC day 1.5 early CHIR

description:
Library name: CHIRmulti2 ATAC
ATAC output from Cell Ranger ARC


title: ATAC day 1.5 late CHIR

description:
Library name: CHIRmulti3 ATAC
ATAC output from Cell Ranger ARC


title: Human CALB2-expressing neuron 8554_M transfected with CellREADR

description: Library name: X8554.M


title: ATAC day 0

description:
Library name: CHIRmulti1 ATAC
ATAC output from Cell Ranger ARC


title: Human CALB2-expressing neuron 8554_P transfected with CellREADR

description: Library name: X8554.P


title: GEX day 3 late CHIR

description:
Library name: CHIRmulti5 GEX
GEX output from Cell Ranger ARC

library_source: transcriptomic single cell


title: Normal_Bio2_Region1

description:
Library name: Normal_Bio2_Region1
Column name in LCMSpTrNW_count.txt is Normal_Bio2_L1


title: GEX day 1.5 late CHIR

description:
Library name: CHIRmulti3 GEX
GEX output from Cell Ranger ARC


title: GEX day 3 early CHIR

description:
Library name: CHIRmulti4 GEX
GEX output from Cell Ranger ARC


title: Human CALB2-expressing neuron 8554_H transfected with CellREADR

description: Library name: X8554_H


title: Human CALB2-expressing neuron 8554_G transfected with CellREADR

description: Library name: X8554_G


title: PCD1-ST

city: Saint Louis

first: Khai

last: Nguyen

state: MO

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,

department: Pathology & Immunology

institute: Washington University in St. Louis

description: 10X Visium spatial transcriptomics of perianal fistula biopsies from FFPE block

data_processing:
Raw sequencing data was processed using CellRanger (scRNA-seq) or SpaceRanger (Spatial Transcriptomics) by the Washington University Genome Technology Access Center.
Assembly: hg38
Supplementary files format and content: tar  file containing CellRanger/SpaceRanger output
Library strategy: Spatial Transcriptomics

molecule: cytoplasmic RNA

source_name: Perianal Fistula

extract_protocol:
10X Chromium 5' (scRNA); 10X Visium (ST)
scRNA-seq/Spatial Transcriptomics

value: Perianal Fistula

tag: disease state

value: PCD


title: PCD9-scRNA

description: scRNA-seq of perianal fistula tract biopsy

data_processing:
Raw sequencing data was processed using CellRanger (scRNA-seq) or SpaceRanger (Spatial Transcriptomics) by the Washington University Genome Technology Access Center.
Assembly: hg38
Supplementary files format and content: tar  file containing CellRanger/SpaceRanger output


title: IPF3-ST

value: IPF


title: GEX day 1.5 early CHIR

description:
Library name: CHIRmulti2 GEX
GEX output from Cell Ranger ARC


title: IPF2-ST


title: PCD3-ST


title: Human CALB2-expressing neuron 8554_F transfected with CellREADR

description: Library name: X8554_F


title: GEX day 0

description:
Library name: CHIRmulti1 GEX
GEX output from Cell Ranger ARC


title: Normal_Bio1_Region1

description:
Library name: Normal_Bio1_Region1
Column name in LCMSpTrNW_count.txt is Normal_Bio1_L1


title: Human CALB2-expressing neuron 8908_S10 transfected with CellREADR

description: Library name: X8908_S10


title: PCD8-scRNA


title: Human CALB2-expressing neuron 8554_I transfected with CellREADR

description: Library name: X8554_I


title: Human CALB2-expressing neuron 8554_E transfected with CellREADR

description: Library name: X8554_E


title: PCD7-scRNA


title: PCD5-scRNA


title: Human CALB2-expressing neuron 8554_B transfected with CellREADR

description: Library name: X8554_B


title: PCD6-scRNA


title: PCD2-ST


title: PCD4-scRNA


title: Human CALB2-expressing neuron 8498_S9 transfected with CellREADR

description: Library name: X8498_S9


title: Human CALB2-expressing neuron 8498_S8 transfected with CellREADR

description: Library name: X8498_S8


title: IPF7-scRNA


title: PCD1-scRNA


title: IPF5-scRNA


title: PCD3-scRNA


title: IPF6-scRNA


title: IPF1-ST


title: PCD2-scRNA


title: Human CALB2-expressing neuron 8498_S11 transfected with CellREADR

description: Library name: X8498_S11


title: Human CALB2-expressing neuron  8498_S7 transfected with CellREADR

description: Library name: X8498_S7


title: Human CALB2-expressing neuron 8498_S10 transfected with CellREADR

description: Library name: X8498_S10


title: Human CALB2-expressing neuron 8498_S3 transfected with CellREADR

description: Library name: X8498_S3


title: IPF1-scRNA


title: ubp1MO St32 exp2

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

institute: University Freiburg Medical Center

description: Library name: Sample 23

data_processing:
Reads were aligned to the Xenopus laevis 9.2 genome using RNA STAR 2.7.11a (on usegalaxy.eu)
Duplicate reads were removed using RmDup 2.0.1 (on usegalaxy.eu)
Gene expression was measured using featureCounts 2.0.6 (on usegalaxy.eu)
Differential gene expression was calculated using DESeq2 2.11.40.8 (on usegalaxy.eu)
Assembly: XenLae9.2
Supplementary files format and content: Expression count tables from featureCounts as tabular files
Supplementary files format and content: Differential expression tables from DESeq2 as tabular files (with gene names)

organism: Xenopus laevis

source_name: epidermis, animal cap explant, st32

growth_protocol: Animal caps were excised in 1X MBS at stage 9 and transferred to 0.5X MBS until collection at stage 10

extract_protocol:
Standard TRIZOL extraction of total RNA.
500-1000 ng total RNA per sample was used, poly-A selection, TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation for mRNA-seq, unstranded, paired-end 150bp

treatment_protocol: Embryos were either uninjected or injected bilaterally at stage 2 with 1.5 pmol Foxi1 MO, or 3 pmol Ubp1 MO, or 1 pmol Dmrt2 MO in the animal pole

value: epidermis, animal cap explant, st32

value: wt

value: 3pmol Ubp1 MO

tag: batch


title: ubp1MO St32 exp3

description: Library name: Sample 24


title: ubp1MO St32 exp1

description: Library name: Sample 22


title: IPF4-scRNA


title: Human CALB2-expressing neuron 8554_D transfected with CellREADR

description: Library name: X8554_D


title: dmrt2MO St32 exp1

description: Library name: Sample 19

value: 1pmol Dmrt2 MO


title: dmrt2MO St32 exp2

description: Library name: Sample 20


title: dmrt2MO St32 exp3

description: Library name: Sample 21


title: foxi1MO St32 exp2

description: Library name: Sample 17

value: 1.5pmol Foxi1 MO


title: Human rheumatoid arthritis knee cartilage

city: Guangzhou

first: Xiaobin

state: Guangdong

address: 107 Yanjiang West Road, Yuexiu District, Guangzhou City, Guangdong Province

department: Department of Joint Surgury

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Library name: RA_Cartilage
10x Genomics

data_processing:
Umi tools were used for single-cell transcriptome analysis to identify the cell barcode whitelist, extract the cell barcode UMIs, and calculate the cell expression counts based on the filtered clean FASTQ data.
Assembly: Human
Supplementary files format and content: Matrix files and Seurat files

source_name: knee cartilage

extract_protocol:
Human fresh RA synovium tissues were dissected in 2 mm pieces and then digested in collagenase Ⅰ solution (2 mg/mL, Gibco; +10% FBS, Gibco; +1% penicillin-streptomycin, Gibco) for 2 h in 37℃, after which solution was filtered by 70 nm cell strainer (BIOFIL) and centrifuged at 1000 rpm for 5 minutes to obtain cells and made into single cell suspensions. Human fresh RA Meniscal and cartilage tissues were dissected in 2 mm pieces and then digested in collagenase P solution (2 mg/mL for meniscus and 0.25 mg/mL for cartilage, Roche; +10% FBS, Gibco; +1% penicillin-streptomycin, Gibco) for 6–8 h in 37℃ for cell suspensions.
Suspension cells were captured with 10x Genomics based on the NovaSeq platform. Fastp was applied with a default parameter for filtering the adaptor sequence and removing low-quality reads.

value: knee cartilage


title: Human rheumatoid arthritis knee meniscus

description:
Library name: RA_Meniscus
10x Genomics

source_name: knee meniscus

value: knee meniscus


title: max2, Root, Zaxinone, 6 hours, rep 4

city: Thuwal

first: Juan Camilo

last: Moreno Beltran

address: King Abdullah University of Science and Technology

country: Saudi Arabia

institute: KAUST

description:
MAX2_Z4_1
max2_Z_vs_max2_M.xls

data_processing:
Fastp was used to process Raw data of FASTQ format at first (Cock et al., 2010). This step removes adapter reads, poly-N sequences, and reads with low quality from the raw data.
In Parallel, Q20, Q30, and GC content of cleaned data were calculated. Final cleaned reads were used in all downstream analysis.
All cleaned Paired-end reads were mapped against reference genomes obtained from NCBI, UCSC, and Ensembl genomes and gene model annotations, using HISAT2 software.
HISAT2 enables fast and very accurate alignment of sequencing reads by using a large set of small GFM indexes that collectively cover the whole genome in combination with multiple alignment strategies.
The assembly was done using Stringtie to assemble transcript isoforms for each bam file generated from the mapping step. Gffcompare is able to compare Stringtie assemblies to the reference annotation files and assists in identifying new genes from declared ones.
Assembly: NCBI, UCSC, and Ensembl
Supplementary files format and content: gene id, Tair ATG identifier, normalized data, Log2Fold change, p-value, p-adjust, gene description, read counts and FPKM values for col0_Z_vs_col0_M, d14_Z_vs_d14_M, kai2_Z_vs_kai2_M, max2_Z_vs_max2_M

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Arabidopsis thaliana col-0, d14, kai2 and max2 seeds were germinated in boxes with water for 7 days. Then, water was replaced for Hoagland solution (+Pi) for seven days. Then seedlings were transferrred to black 50 mL falcon tubes and transferred to a growth chamber with 16 h light/8 h dark and 180 µmol m-1 s-1 illumination at 21C day/18C night for three weeks.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Plus Kit (Zymo Research according to the manufacturer’s instructions).  A total of 2ug were used for libraries preparation.
RNA sequencing was performed by Novogene (Novogene Co., Ltd., Beijing, China). A total of 2000 ng total RNA was used to extract messenger RNA, using poly-T oligo-attached magnetic beads. Random hexamer primers were used to synthesize the first strand of cDNA from the fragmented RNA. The second strand was synthesized using either dUTP or dTTP, depending on whether the library was directional or non-directional. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was quantified using Qubit and real-time PCR and detected size distribution using a bioanalyzer device. Libraries were pooled and sequenced using Illumina sequencing and paired-end reads were generated.

treatment_protocol: Arabidopsis col-0, d14, kai2 and max2 plants were treated with zaxinone (20 μM; dissolved in 1% acetone) and Mock (acetone 1%) by adding zaxinone or mock into the hydroponic media. Root samples were harvested after 6 hours of treatment.

value: root

tag: harvest time_point

value: after 6 hours of treatment

tag: age

value: 5 weeks old

value: zaxinone


title: IPF8-scRNA


title: max2, Root, Zaxinone, 6 hours, rep 3

description:
MAX2_Z3_1
max2_Z_vs_max2_M.xls


title: HHL5 cells transfected with Flag-DDX49 following OA/PA treatment for 24 hours, replicate 3, RIP-seq

city: Shanghai

first: Jin

last: Hou

address: 800 Xiangyin Road

institute: Second Military Medical University

description:
Library name: O3
OAPA3

data_processing:
Basecalls performed using CASAVA version 1.4
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts and normalized counts for every sample

source_name: liver

extract_protocol:
The cells were cross-linked using ultraviolet light and harvested. RIP was performed using the Magna RIP® RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to the manufacturer’s instruction. Cell lysates were subjected to RIP by the indicated antibodies. The co-immunoprecipitated RNAs were isolated by TRIzol for sequencing.
RIP-seq was performed by Biotechnology Corporation (Shanghai, China)

value: liver

value: HHL5 cell line

value: embryonic liver cells

value: WT


title: ctrl. St32 exp3

description: Library name: Sample 15

value: Uninjected


title: HHL5 cells transfected with Flag-DDX49 following OA/PA treatment for 24 hours, replicate 2, RIP-seq

description:
Library name: O2
OAPA2


title: HHL5 cells transfected with Flag-DDX49 following OA/PA treatment for 24 hours, replicate 1, RIP-seq

description:
Library name: O1
OAPA1


title: foxi1MO St32 exp1

description: Library name: Sample 16


title: max2, Root, Zaxinone, 6 hours, rep 1

description:
MAX2_Z1_1
max2_Z_vs_max2_M.xls


title: max2, Root, Zaxinone, 6 hours, rep 2

description:
MAX2_Z2_1
max2_Z_vs_max2_M.xls


title: max2, Root,Mock, 6 hours, rep 4

description:
MAX2_M4_1
max2_Z_vs_max2_M.xls

value: Mock (acetone)


title: ctrl. St32 exp2

description: Library name: Sample 14

value: epidermis, animal cap explant, st32


title: ctrl. St32 exp1

description: Library name: Sample 13

value: wt


title: VPSP-ASD-BA9

city: Los Angeles

first: Nasser

last: Elhajjaoui

address: 695 Charles E Young Dr S

department: Human Genetics

institute: University of California, Los Angeles

description: Library name: Sample 49

library_source: genomic

data_processing:
We aligned the snmCT-seq data to the GENCODE v40 reference (GRCh38.p13 genome and genic annotation files), building upon the settings described extensively in the flagship manuscript for snmCT-seq1. Core changes are the implementation of paired-end alignment and quantification methods, increasing mapping rate and coverage and ensuring that read 1 and read 2 features are not quantified twice when insert size is low. Additionally, we add read deduplication to the RNA reads. Detailed descriptions are available on the pipeline git repository (github.com/chooliu/snmCTseq_Pipeline, release v1.1.0) and summarized below.
We used cell barcodes specific to each reaction well (of 384-well plate) to demultiplex sequence reads into individual nuclei with custom scripts, then trimmed Phred score base calls, Illumina adapter sequences and components specific to snmCT-seq library (the well-barcode, adaptase tail) using fastp2 v0.23.2 (-f 17 -t 10 -F 15 -T 10 -l 30 --cut_right -q 20 -u 50 -y -Y 15 -x --adapter_fasta).
Methylome reads for each nuclei are then mapped using Bismark3 v0.24.0 in a two-stage process in order to increase mapping efficiency for PBAT-based reactions and other single-cell methylome preparations4: (i) first, reads are mapped in paired-end mode, then (ii) reads unable to map in stage i and singleton reads are mapped in single-end mode. We define singletons as reads without its pair passing trimming quality control. The --maxins 2000 and --pbat (for paired-end and read 1) flags are used, with default settings otherwise. PCR and sequencer optical duplicates (pixel distance 2500) are then removed using Picard MarkDuplicates5. Reads with mapping score ≤ 10 were excluded (samtools view -h -q 10; samtools6 v1.16.1). A core innovation of the snmCT-seq bench workflow is its simultaneous profiling of RNA and DNA in one reaction well without requiring their physical separation; instead, we perform in silico separation of fully methylated RNA libraries introduced by methylated dNTPs (resulting in full methylation, including at CpH- contexts) from the low mCH/CH levels present in libraries originating from genomic DNA. Using the “XM:Z” alignment flag, we then therefore classified the Bismark alignments containing at least three CpH-context cytosines and mCH/CH ≤ 0.50 as DNA reads. Finally, the final resultant DNA reads were used to infer cytosine-level methylation states: for each cytosine c, we tabulated the number of alignments suggesting that the cytosine is methylated (mc; C>T bisulfite conversion) versus unmethylated (uc; no conversion) using allcools7 v1.0.8 (“.allc” file, github.com/lhqing/ALLCools).
In parallel, RNA-originating reads were mapped with STAR8 v2.7.10a, also using the two-stage (paired-end, followed by single-end) mapping procedure for RNA quantification. Non-default mapping settings included --alignEndsType EndToEnd --sjdbOverhang 149 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 as established previously. Alignments that were duplicates identified by Picard or had mapping score ≤ 10 were excluded. To retain RNA reads, each alignment with at least three CpH- context cytosines and mCH/CH ≥0.90 based on the “MD:Z” flag were retained. Finally, RNA counts of each gene were then quantified using featureCounts9.
We re-validated the performance of the in silico separation of RNA and DNA in this paired-end workflow by using three datasets generated with the related, DNA methylation-only array10 (snmC-seq2). Using existing data of this DNA-only assay profiling similar nuclei (BA10 cortex from 25 year old male; Sequence Read Archive SRR6911760, SRR6911772, SRR6911776), we again found high in silico discrimination between RNA and DNA based on alignment mCH/CH. When the RNA pipeline (STAR 🡪 mCH/CH filtering) was applied to these DNA-only reads, the majority (98.9%) of these bisulfite-converted DNA-only reads failed to align to the genome, and only 0.09% of reads were ultimately incorrectly classified as RNA reads and 0.0089% were quantified as transcript counts using featureCounts. With the DNA pipeline (Bismark 🡪 mCH/CH filtering), 0.075% of reads were incorrectly classified as RNA reads and discarded.
Assembly: hg38
Supplementary files format and content: tab delimited text files of methylcytosine calls (CGN)
Supplementary files format and content: tab delimited text files of methylcytosine calls (CAN)
Supplementary files format and content: tab delimited pseudo-bulk count matrix of genes (row names) by cell-type (column names)

source_name: brodmann area 9

extract_protocol:
Nuclei were isolated from postmortem human cortical tissue (Brodmann area 9) stored at −80°C. Tissue was pulverized in liquid nitrogen using a pre-chilled mortar and pestle, and resuspended in NIBT buffer (250 mM sucrose, 10 mM Tris-Cl pH 8.0, 25 mM KCl, 5 mM MgCl₂, 0.1% Triton X-100, 1 mM DTT, protease inhibitors, and RNase inhibitors). Lysates were homogenized in a Dounce homogenizer (40 strokes loose and tight pestles), mixed with 20% iodixanol, and overlaid on a 25% iodixanol cushion. Nuclei were pelleted by centrifugation at 10,000×g at 4°C for 20 minutes. Nuclei were resuspended in DPBS supplemented with RNase inhibitors, stained with Hoechst 33342 (2 μM), blocked with 5 mg/mL BSA, and labeled with anti-NeuN AlexaFluor-488 antibody (clone A60, MilliporeSigma MAB377XMI). Nuclei were sorted into 384-well plates containing reverse transcription reagents and stored on ice until library preparation.
Single-nucleus libraries were prepared using the snmCT-seq and snm3C-seq3 protocols (PMID: 35419551, protocols.io [https://www.protocols.io/view/snmcat-v2-x54v9jby1g3e/v2] and [https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1]). Reverse transcription included Superscript II RT, 5mM DTT, 0.1% Triton X-100, dNTPs, a biotinylated oligo-dT primer (dT30VN_4_5bio), random primer (N6_2), and template-switching oligo (TSO_4_5bio), with RNase inhibitors. Following RT, cDNA was amplified with KAPA2G polymerase for 14–16 cycles depending on neuronal identity. Unincorporated oligos were digested using uracil DNA glycosylase. Bisulfite conversion was performed with Zymo EZ DNA Methylation-Direct kit reagents, followed by multiple rounds of clean-up with M-Binding and M-Wash Buffers. Libraries were prepared using random priming, exonuclease digestion, SPRI bead clean-up, Adaptase-mediated end repair and ligation, and final indexing with KAPA HiFi HotStart ReadyMix and custom indexing primers. Libraries were purified and quantified using the Qubit dsDNA BR Assay Kit. Sequencing was performed using the Illumina NovaSeq 6000 with S4 flowcells in 100 bp paired-end mode.

value: brodmann area 9

tag: donor

value: VPSP

tag: donor alt

tag: Sex

value: male

tag: genome build

tag: diagnosis

value: ASD

tag: age category

value: Mid

tag: age detailed

tag: brainbank

value: ABN

tag: pmi

tag: rin


title: ubp1MO St20 exp2

description: Library name: Sample 11

source_name: epidermis, animal cap explant, st20

tag: tissue

value: epidermis, animal cap explant, st20

tag: genotype

tag: treatment

value: 3pmol Ubp1 MO


title: ubp1MO St20 exp3

description: Library name: Sample 12


title: max2, Root,Mock, 6 hours, rep 1

description:
MAX2_M1_1
max2_Z_vs_max2_M.xls

value: root

value: after 6 hours of treatment

value: 5 weeks old


title: PZ65-CTL-BA9

description: Library name: Sample 48

value: CTL


title: PH2A-CTL-BA9

description: Library name: Sample 47


title: max2, Root,Mock, 6 hours, rep 2

description:
MAX2_M2_1
max2_Z_vs_max2_M.xls


title: Human rheumatoid arthritis knee synovium

description:
Library name: RA_Synovium
10x Genomics

source_name: knee synovium

value: knee synovium


title: foxi1MO St32 exp3

description: Library name: Sample 18

value: 1.5pmol Foxi1 MO


title: ubp1MO St20 exp1

description: Library name: Sample 10


title: PA3P-ASD-BA9

description: Library name: Sample 46


title: NEPX-ASD-BA9

description: Library name: Sample 45

value: NEPX

value: Young


title: kai2, Root, Zaxinone, 6 hours, rep 4

description:
KAI2_Z4_1
kai2_Z_vs_kai2_M.xls

value: zaxinone


title: KMC3-ASD-BA9

description: Library name: Sample 44

value: brodmann area 9

value: Old


title: dmrt2MO St20 exp3

description: Library name: Sample 9

value: wt

value: 1pmol Dmrt2 MO


title: kai2, Root, Zaxinone, 6 hours, rep 3

description:
KAI2_Z3_1
kai2_Z_vs_kai2_M.xls


title: dmrt2MO St20 exp2

description: Library name: Sample 8


title: kai2, Root, Zaxinone, 6 hours, rep 2

description:
KAI2_Z2_1
kai2_Z_vs_kai2_M.xls


title: Hct002-CTL-BA9

description: Library name: Sample 43

value: male

value: UM-BTB

tag: ancestry

value: White


title: max2, Root,Mock, 6 hours, rep 3

description:
MAX2_M3_1
max2_Z_vs_max2_M.xls

value: Mock (acetone)


title: HQ4T-CTL-BA9

description: Library name: Sample 42

value: Mid

value: ABN


title: kai2, Root,Mock, 6 hours, rep 4

description:
KAI2_M4_1
kai2_Z_vs_kai2_M.xls

value: root

value: after 6 hours of treatment

value: 5 weeks old


title: kai2, Root, Zaxinone, 6 hours, rep 1

description:
KAI2_Z1_1
kai2_Z_vs_kai2_M.xls


title: foxi1MO St20 exp3

description: Library name: Sample 6

value: epidermis, animal cap explant, st20

value: 1.5pmol Foxi1 MO

tag: batch


title: G7YU-CTL-BA9

description: Library name: Sample 41

value: CTL


title: foxi1MO St20 exp2

description: Library name: Sample 5


title: FXMW-ASD-BA9

description: Library name: Sample 40

value: FXMW

value: FXMN

value: ASD


title: EUFW-CTL-BA9

description: Library name: Sample 39

value: brodmann area 9

value: EUFW


title: kai2, Root,Mock, 6 hours, rep 2

description:
KAI2_M2_1
kai2_Z_vs_kai2_M.xls

tag: harvest time_point


title: dmrt2MO St20 exp1

description: Library name: Sample 7

value: wt

value: 1pmol Dmrt2 MO


title: ctrl. St20 exp3

description: Library name: Sample 3

value: Uninjected


title: kai2, Root,Mock, 6 hours, rep 1

description:
KAI2_M1_1
kai2_Z_vs_kai2_M.xls

tag: age

value: Mock (acetone)


title: ctrl. St20 exp2

description: Library name: Sample 2


title: d14, Root, Zaxinone, 6 hours, rep 4

description:
D14_Z4_1
d14_Z_vs_d14_M.xls

value: zaxinone


title: kai2, Root,Mock, 6 hours, rep 3

description:
KAI2_M3_1
kai2_Z_vs_kai2_M.xls


title: E4FN-CTL-BA9

description: Library name: Sample 38

tag: donor

value: male

value: Mid

value: ABN


title: foxi1MO St20 exp1

description: Library name: Sample 4


title: CQ56-CTL-BA9

description: Library name: Sample 37

tag: donor alt


title: ctrl. St20 exp1

description: Library name: Sample 1


title: iPSC-CM_IndC_VEH_24h_H3K27ac_CT

city: Galveston

first: Michelle

middle: C.

last: Ward

email: miward@UTMB.edu, ermatthe@UTMB.edu

state: TX

address: 301 University Blvd., MRB 7.150

department: Biochemistry and Molecular Biology

institute: UTMB-Galveston

description: Library name: IndC_VEH_24h_CT

data_processing:
Raw sequencing reads were assessed for quality using FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and visualized with MultiQC (Ewels, 2016 Bioinformatics). Cutadapt (version 4.0, Martin,M 2011 EMBnet.journal) was run in PE legacy mode to remove any adapter sequences present and FastQC was performed again
Paired-end sequencing reads were aligned to hg38 using bowtie2 with the settings –local–very-sensitive -loca l–no-mixed –no-discordant –phred33 -I 10 -X 700 -fr (Langmead and Salzberg, 2012).
Reads were filtered using samtools (Daneck, 2021 GigaScience) to remove reads mapping to more than one genome location. Picard Tools (https://broadinstitute. github.io/picard/) was used  to remove duplicate reads.
Peaks were called on each file using MACS2 callpeak -f BAMPE -g hs –keep-dup all (Zhange et al. 2008, Genome Biology).
A master peak set was created with BEDtools (Quinlan 2010 Bioinformatics) by first concatenating, then merging all .narrowPeak files together as one large peak file. The BEDtools multiinter function was called to generate intersections of all .narrowPeak files with the merged large peak file.  A set of high confidence intersections was created by filtering out intersections found in > 5 .narrowPeak files. Next, BEDtools intersect was used between the merged peaks set and the filtered intersections files using -wa -u flags to create a final set of high confidence peaks (n = 20,137). Subread featureCounts (Liao, 2014 Bioinformatics) was used to collect counts across each .bam file using the high confidence peak set as features.
Assembly: hg38
Supplementary files format and content: Matthews_H3K27ac_counts.txt
Library strategy: CUT&Tag

growth_protocol: Human iPSC-dervied cardiomyocytes were maintained in Cardiomyocyte Maintenance Media (500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (MT35015CV, Corning), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL Penicillin/Streptomycin) on Matrigel-coated dishes at 37°C, 5% CO2 and atmospheric O2.

extract_protocol:
Samples were fast-thawed and centrifuged at 4 °C for four min at 1000 x g. The supernatant was poured off and the cell pellet retained. The pellets were resuspended and washed twice in 1 mL of Wash Buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Protease inhibitor cocktail; Roche 11873580001). Nuclei were extracted by incubating cells for 10 min on ice in 200 µL/sample of cold Nuclei Extraction buffer (NE buffer: 20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 1x Protease Inhibitor cocktail). Following incubation, nuclei were centrifuged at 4 °C for four min at 1300 x g and drained by inverting onto a paper towel. The cells were resuspended in PBS and fixed with 0.1% formaldehyde solution for two min at room temperature, with the termination of cross-linking by adding 2.5 M glycine to twice the molar concentration of formaldehyde. After fixation, the nuclei were centrifuged at 4 °C for four min at 1300 x g, and the liquid was poured off through inversion over a paper towel. The pellet was resuspended in 1.5 mL of Wash Buffer. Concanavalin A coated magnetic beads (Bangs Laboratories Inc, BP531; Lot 16963) were prepared as previously described (Skene, Elife, 2017) and 10 µL of activated beads were added to each sample and incubated for 15 min at room temperature on an end-over-end rotator. Beads with sample were collected via magnet and unbound supernatant was discarded. The sample was resuspended in 50 µL of ice-cold Antibody Buffer (Wash Buffer with 2 mM EDTA and 0.1% BSA) with appropriate antibody dilution (H3K27ac, Active Motif, 39034; Lots 31521015, manufacturer recommendation of 1:50). Samples were incubated at 4 °C overnight on a tilt table. After incubation, the primary antibody was removed by magnetic pelleting to clear the supernatant and discarding the non-bound supernatant. Each pellet was resuspended in 100 µL of secondary antibody, Guinea Pig anti-Rabbit IgG (Heavy & Light Chain) Preabsorbed Antibodies (Antibodies-Online ABIN101961; Lot NE-200-032309), diluted 1:100 in Wash Buffer. The samples were incubated for one hr at room temperature on a tilt table. The secondary antibody was removed using a magnet stand to clear the supernatant. The bound samples were washed twice with 1 mL of Wash Buffer for five min each wash. After washing, 50 µL of a solution of pAG-Tn5 (CUTANA™ pAG-Tn5, Epicypher 15-1017; Lot 23243004-C1) diluted 1:20 in 300 Buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor cocktail) was added to each sample and samples were incubated on a tilt table for one hr at room temperature. Samples were collected using a magnet stand and washed twice with 1 mL of 300 Buffer. Next, samples were resuspended in 300 µL Tagmentation Buffer (10 mM MgCl2 in 300 Buffer) and incubated in a water bath at 37 °C for one hr. To stop tagmentation, 10 µL of 0.5 M EDTA, 3 µL of 10% SDS, and 2.5 µL of 20 mg/mL Proteinase K were added to each 300 µL of sample, vortexed and incubated in a water bath at 55 °C for one hr. DNA was extracted using PCI-Chloroform separation, extracting the aqueous layer, placing it in a new tube, discarding the rest. The samples were chilled on ice and centrifuged at 4 °C for 10 min at 16,000 x g. The liquid was decanted, and pellets were resuspended with 100% ethanol, followed by centrifugation at 4 °C for one min at 16,000 x g. Supernatant was decanted, and pellets were allowed to air dry before dissolving in 30 µL TE buffer (1 mM Tris-HCl pH 8, 0.1 mM EDTA).
To amplify and index libraries, 21 µL of DNA was combined with 2 µL of a 10 µM uniquely barcoded i5 and 2 µL of a uniquely barcoded i7 primer (Buenrostro, Nature, 2015), using a different barcode combination for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a thermocycler with a heated lid using the following cycling conditions: 72 °C for five min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 10 s; final extension at 72 °C for one min and hold at 8 °C. Post-PCR clean-up was performed by adding 1.3× volume of AMpureXP beads (Beckman Counter), and libraries were incubated with beads for 10 min at room temperature, washed twice gently in 80% ethanol, and eluted in 25 µL 10 mM Tris pH 8.0. Libraries additionally underwent a double-sided clean-up to eliminate the large and small fragments, using AMpureXP beads at a 0.55 x and then 1.8 x ratio, respectively.

treatment_protocol: 400,000 iPSC-CMs were plated in 12-well plates. On Days 27-29, iPSC-CMs were treated with 0.5 µM DNR, DOX, EPI, MTX, TRZ, or vehicle in fresh cardiomyocyte maintenance media. iPSC-CMs  were collected 3- and 24-hours post-treatment,  by washing twice with ice-cold PBS and manually scraping into seperate tubes with cold PBS on ice.  Samples pelleted through centrifugation at 500 x g for 10 min.  Supernatant was removed and cells were resuspended in 50 uL of cryo-media (50% FBS, 40% cardiomyocyte maintenance media, 10% DMSO) ). Cells were then placed into a CoolCell (Corning, 432000 )at -80 ˚C for 24 hours, before removing vials on ice and storing at  -80˚C until processing.

tag: Sex

value: female

tag: cell line

tag: cell type

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM vehicle

tag: antibody


title: d14, Root, Zaxinone, 6 hours, rep 3

description:
D14_Z3_1
d14_Z_vs_d14_M.xls

value: root

value: after 6 hours of treatment

value: 5 weeks old


title: iPSC-CM_IndC_VEH_3h_H3K27ac_CT

description: Library name: IndC_VEH_3h_CT


title: 8XCF-ASD-BA9

description: Library name: Sample 35

tag: genome build

tag: diagnosis

value: ASD

tag: age category

tag: age detailed


title: d14, Root, Zaxinone, 6 hours, rep 2

description:
D14_Z2_1
d14_Z_vs_d14_M.xls

tag: tissue


title: d14, Root,Mock, 6 hours, rep 4

description:
D14_M4_1
d14_Z_vs_d14_M.xls

tag: genotype


title: d14, Root, Zaxinone, 6 hours, rep 1

description:
D14_Z1_1
d14_Z_vs_d14_M.xls

tag: treatment


title: 75QW-CTL-BA9

description: Library name: Sample 34

value: brodmann area 9

value: CTL

value: Old

tag: brainbank

tag: pmi

tag: rin


title: 6096-CTL-BA9

description: Library name: Sample 33

tag: age

value: UM-BTB

tag: ancestry

value: White


title: iPSC-CM_IndC_MTX_24h_H3K27ac_CT

description: Library name: IndC_MTX_24h_CT

value: 0.5 uM mitoxantrone

tag: batch


title: d14, Root,Mock, 6 hours, rep 2

description:
D14_M2_1
d14_Z_vs_d14_M.xls

tag: harvest time_point

value: Mock (acetone)


title: 9714-ASD-BA9

description: Library name: Sample 36

tag: donor

tag: donor alt

tag: Sex

value: male

value: Harvard-ATP


title: d14, Root,Mock, 6 hours, rep 3

description:
D14_M3_1
d14_Z_vs_d14_M.xls


title: 6041-ASD-BA9

description: Library name: Sample 32

tag: genome build

value: Mid


title: iPSC-CM_IndC_MTX_3h_H3K27ac_CT

description: Library name: IndC_MTX_3h_CT

value: female

tag: cell line

tag: cell type

tag: antibody


title: iPSC-CM_IndC_EPI_3h_H3K27ac_CT

description: Library name: IndC_EPI_3h_CT

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM epirubicin


title: 5978-ASD-BA9

description: Library name: Sample 31

tag: tissue

tag: diagnosis

tag: age category

value: Young

tag: age detailed


title: d14, Root,Mock, 6 hours, rep 1

description:
D14_M1_1
d14_Z_vs_d14_M.xls

value: root

value: after 6 hours of treatment

tag: genotype

tag: treatment


title: 5969-ASD-BA9

description: Library name: Sample 30

value: ASD

tag: age

tag: brainbank

tag: pmi

tag: rin


title: iPSC-CM_IndC_DOX_24h_H3K27ac_CT

description: Library name: IndC_DOX_24h_CT

value: 0.5 uM doxorubicin

tag: batch


title: Col-0, Root, Zaxinone, 6 hours, rep 4

description:
col0_Z4_1
col0_Z_vs_col0_M.xls

tag: harvest time_point

value: 5 weeks old

value: wild type

value: zaxinone


title: Col-0, Root, Zaxinone, 6 hours, rep 3

description:
col0_Z3_1
col0_Z_vs_col0_M.xls


title: 5895-CTL-BA9

description: Library name: Sample 28

value: brodmann area 9

tag: donor

tag: donor alt

tag: Sex

value: CTL

value: Old

value: UM-BTB

tag: ancestry

value: Black


title: iPSC-CM_IndC_DNR_24h_H3K27ac_CT

description: Library name: IndC_DNR_24h_CT

tag: cell line

tag: cell type

value: 0.5 uM daunorubicin

tag: antibody


title: Col-0, Root, Zaxinone, 6 hours, rep 2

description:
col0_Z2_1
col0_Z_vs_col0_M.xls

tag: tissue


title: 5842-ASD-BA9

description: Library name: Sample 27

value: male

tag: genome build

tag: diagnosis

tag: age category

value: Mid

tag: age detailed

value: White


title: iPSC-CM_IndC_DNR_3h_H3K27ac_CT

description: Library name: IndC_DNR_3h_CT

value: female

value: induced pluripotent stem cell-derived cardiomyocytes

tag: treatment


title: iPSC-CM_IndB_VEH_3h_H3K27ac_CT

description: Library name: IndB_VEH_3h_CT

value: 0.5 uM vehicle


title: iPSC-CM_IndB_MTX_24h_H3K27ac_CT

description: Library name: IndB_MTX_24h_CT

value: 0.5 uM mitoxantrone


title: Col-0, Root, Zaxinone, 6 hours, rep 1

description:
col0_Z1_1
col0_Z_vs_col0_M.xls

value: root

value: after 6 hours of treatment

tag: age

tag: genotype


title: iPSC-CM_IndB_VEH_24h_H3K27ac_CT

description: Library name: IndB_VEH_24h_CT

tag: batch


title: iPSC-CM_IndC_EPI_24h_H3K27ac_CT

description: Library name: IndC_EPI_24h_CT

value: 0.5 uM epirubicin


title: Col-0, Root,Mock, 6 hours, rep 4

description:
col0_M4_1
col0_Z_vs_col0_M.xls

tag: harvest time_point

value: 5 weeks old

value: wild type

value: Mock (acetone)


title: 5565-ASD-BA9

description: Library name: Sample 23

value: brodmann area 9

tag: donor

value: ASD

value: Young

tag: brainbank

tag: pmi

tag: rin


title: 5577-CTL-BA9

description: Library name: Sample 25

tag: donor alt

tag: Sex

value: CTL

value: UM-BTB

tag: ancestry


title: Col-0, Root,Mock, 6 hours, rep 3

description:
col0_M3_1
col0_Z_vs_col0_M.xls

tag: tissue


title: 5576-CTL-BA9

description: Library name: Sample 24

value: male

tag: genome build

value: Black


title: Col-0, Root,Mock, 6 hours, rep 1

description:
col0_M1_1
col0_Z_vs_col0_M.xls


title: Col-0, Root,Mock, 6 hours, rep 2

description:
col0_M2_1
col0_Z_vs_col0_M.xls


title: iPSC-CM_IndB_EPI_3h_H3K27ac_CT

description: Library name: IndB_EPI_3h_CT

value: female

tag: cell line

tag: cell type

tag: antibody


title: iPSC-CM_IndB_EPI_24h_H3K27ac_CT

description: Library name: IndB_EPI_24h_CT

value: induced pluripotent stem cell-derived cardiomyocytes

tag: treatment


title: 5558-CTL-BA9

description: Library name: Sample 22

tag: diagnosis

tag: age

tag: age category

tag: age detailed

value: White


title: iPSC-CM_IndB_DNR_24h_H3K27ac_CT

description: Library name: IndB_DNR_24h_CT

value: 0.5 uM daunorubicin

tag: batch


title: HSPCs_cocultured_with_Genetically_modified_Bone_Marrow_MSCs_2

city: Bagayam, Vellore

first: Srujan Kumar

last: Marepally

state: Tamil Nadu

address: Christian Medical College Campus,

country: India

institute: Centre for Stem Cell Research

description: Library name: HSPC_GM_BM_MSCs_2

data_processing:
The data processing steps for RNA-seq analysis, as depicted in the image, begin with sequencing, where raw sequence data (.fastq files) is generated. This is followed by pre-processing, which involves adapter trimming and quality filtration using adapter sequence files (.fa files). Next, contamination removal is performed using Bowtie2 to align and filter out contaminant sequences, such as rRNA, tRNA, and mitochondrial DNA, utilizing contamination files (.fa files). The cleaned reads are then aligned to the reference genome using STAR or HISAT2, with reference genome files (.fa files) and gene annotation files (.gtf files). Read counts and gene expression levels are quantified using HTSeq or featureCounts, relying on gene annotation files (.gtf files). Count normalization is performed using DESeq2 based on the geometric mean/size factor, producing normalized read counts. Differential expression analysis is then conducted using DESeq2, leading to gene ontology and pathway analysis through tools such as clusterProfiler or RDAVIDWeb Service. The final results can be used for Overrepresentation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA).
Assembly: GRCh38
Supplementary files format and content: raw count, normalised count and FPKM for each samples

source_name: Hematopoietic Stem and Progenitor Cells

extract_protocol:
Total RNA was isolated using the Qiagen RNA isolation kit and quantified with the Qubit RNA HS Assay. RNA purity was evaluated using the QIAxpert system, and RNA integrity was assessed on the Agilent TapeStation with RNA HS ScreenTapes (Cat# 5067-5579)
Library preparation for total RNA sequencing (RNA-seq) was performed according to the NEB Ultra II Directional RNA-Seq Library Prep Kit protocol. The libraries were quantified using the Qubit High Sensitivity Assay (Invitrogen, Cat# Q32852).

value: Hematopoietic Stem and Progenitor Cells


title: 5917-CTL-BA9

description: Library name: Sample 29

tag: donor

value: Old

tag: brainbank


title: 5408-CTL-BA9

description: Library name: Sample 21

tag: pmi

tag: rin


title: HSPCs_cocultured_with_Genetically_modified_Bone_Marrow_MSCs_1

description: Library name: HSPC_GM_BM_MSCs_1


title: iPSC-CM_IndB_DNR_3h_H3K27ac_CT

description: Library name: IndB_DNR_3h_CT

tag: Sex


title: 5360-CTL-BA9

description: Library name: Sample 19

tag: donor alt

tag: ancestry


title: 5308-ASD-BA9

description: Library name: Sample 18

tag: tissue

tag: genome build


title: iPSC-CM_IndA_VEH_3h_H3K27ac_CT

description: Library name: IndA_VEH_3h_CT

tag: cell line

tag: cell type

value: 0.5 uM vehicle


title: HSPCs_Standard_Condition_1

description: Library name: HSPC_SC_1

tag: treatment


title: 5841-ASD-BA9

description: Library name: Sample 26

tag: diagnosis


title: iPSC-CM_IndA_VEH_24h_H3K27ac_CT

description: Library name: IndA_VEH_24h_CT

tag: antibody


title: HSPCs_Standard_Condition_2

description: Library name: HSPC_SC_2


title: iPSC-CM_IndA_MTX_24h_H3K27ac_CT

description: Library name: IndA_MTX_24h_CT

value: 0.5 uM mitoxantrone


title: iPSC-CM_IndB_DOX_3h_H3K27ac_CT

description: Library name: IndB_DOX_3h_CT

value: 0.5 uM doxorubicin


title: Genetically_modified_Bone_Marrow_MSCs_2

description: Library name: GM_BM_MSCs_2

source_name: Mesenchymal Stromal Cells

value: Mesenchymal Stromal Cells

tag: genotype


title: 5242-CTL-BA9

description: Library name: Sample 15

value: brodmann area 9

tag: age

tag: age category

tag: age detailed


title: Wild_type_Bone_Marrow_MSCs_2

description: Library name: Wild_type_BM_MSCs_2


title: 5302-ASD-BA9

description: Library name: Sample 17

tag: donor

value: ASD

tag: brainbank


title: 5294-ASD-BA9

description: Library name: Sample 16

value: Mid

tag: pmi

tag: rin


title: Genetically_modified_Bone_Marrow_MSCs_1

description: Library name: GM_BM_MSCs_1


title: iPSC-CM_IndA_DOX_24h_H3K27ac_CT

description: Library name: IndA_DOX_24h_CT

tag: Sex

tag: batch


title: Wild_type_Bone_Marrow_MSCs_1

description: Library name: Wild_type_BM_MSCs_1


title: 4670-CTL-BA9

description: Library name: Sample 12

tag: tissue

tag: donor alt

value: CTL

value: Young

tag: ancestry


title: iPSC-CM_IndA_DNR_24h_H3K27ac_CT

description: Library name: IndA_DNR_24h_CT

tag: cell line

tag: cell type


title: 5144-ASD-BA9

description: Library name: Sample 14

value: male

tag: genome build

tag: diagnosis

value: UM-BTB


title: 5403-ASD-BA9

description: Library name: Sample 20


title: 5115-ASD-BA9

description: Library name: Sample 13


title: iPSC-CM_IndA_DOX_3h_H3K27ac_CT

description: Library name: IndA_DOX_3h_CT

value: female

tag: treatment

tag: antibody


title: iPSC-CM_IndA_DNR_3h_H3K27ac_CT

description: Library name: IndA_DNR_3h_CT

value: induced pluripotent stem cell-derived cardiomyocytes


title: 4337-CTL-BA9

description: Library name: Sample 11

tag: age

tag: age category

value: Black


title: YZ1 MUT#2 NPC, POU3F2 pull-down, replicate 1

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: CB183

data_processing:
FastQC was performed to assess read quality and reads were aligned to the hg38 genome index using bowtie2. Alignments were filtered with samtools to remove unmapped reads, reads with duplicate mapping and reads > 300 bp. Peaks were calls with MACS2 and compared to the corresponding input sample, and differential peaks between wildtype and mutant samples were scored using DiffBind. Peaks were annotated and screened for enrichment of known motifs using HOMER.
Assembly: Human hg38
Supplementary files format and content: Bedgraph file of treatment pileup (POU3F2 pull-down)
Supplementary files format and content: Bedgraph file of control lambda (input)
Supplementary files format and content: NarrowPeak file of MACS2-defined peaks
Library strategy: CUT&Run

growth_protocol: In brief, iPSCs were grown in StemFlex media until confluent. Cells were dissociated with collagenase IV and transferred to non-adherent 6-well plates. For the following six days (D2-D7), cells were maintained as embryoid bodies in suspension and fed once every two days with DMEM-F12/N2/B27-RA media containing dual-SMAD inhibitors, 100 nM LDN193189 (Stemgent, #04-0074) and 10 uM SB431542 (STEMCELL Technologies, #72234). On D7, embryonic bodies were resuspended in dual-SMAD inhibition media with the addition of 1 ug/mL laminin (Life Technologies, #23017-015) and transferred to poly-ornithine (Sigma, #P3655-50mg) / laminin (POL) coated 6-well plates. For the following seven days (D8-D14), cells were washed and fed once every two days with dual-SMAD inhibition media with the addition of laminin. On D14, neural rosettes were selected with STEMdiffTM neural rosette selection reagent (STEMCELL Technologies, #05832), which allows for the isolation of NPC-dominant neural rosettes while leaving behind non-NPC cell types that may arise during embryoid body formation (i.e., fibroblasts). Rosettes were resuspended in NPC media (DMEM-F12/N2/B27-RA with the addition of 1 ug/mL laminin and 20 ng/mL FGF2 (Peprotech, #100-18B)) and transferred to POL-coated 6-well plates. For the following seven days (D15-D21), cells were washed and fed once every two days with NPC media. After D21, NPCs were expanded on growth-factor reduced (GFR) Matrigel (Corning, #354230) at high density and fed with NPC media every two days for up to 3 passages.

extract_protocol:
NPCs were cultured and dissociated with 1:1 accutase:PBS (Invitrogen, #A1110501). CUT&RUN of POU3F2 in NPC samples was performed according to manufacturer instructions from Cell Signaling Technologies with minor modifications (Cell Signaling Technologies, #86652). Briefly, cells were collected (100k cells/reaction) and washed in buffer containing protease inhibitor cocktail and spermidine. Cells were bound to Concanavalin A Beads and incubated with primary antibody overnight at 4C at a 1:50 dilution (POU3F2: Cell Signaling Technologies, #12137S; H3K4me3: Cell Signaling Technologies, #9751). Input samples were prepared via treatment with proteinase K and RNase A, and chromatin was fragmented by sonication in a Bioruptor Plus (15 cycles of 30 seconds on/30 seconds off, high intensity setting). Input lysates were clarified and stored at -20C until library preparation. For the CUT&RUN samples, cells were permeabilized with digitonin and pAG-MNase enzyme was bound and activated by treatment with calcium chloride. DNA fragments were released from the cell and isolated via centrifugation. Input and CUT&RUN samples were purified using spin columns and assessed for concentration of DNA with a Qubit dsDNA high sensitivity assay (ThermoFisher, #Q33230).
Library preparation was performed per manufacturer instructions (Cell Signaling Technologies, #56795) and sent for paired end (2x75bp) sequencing (Harvard Biopolymers Facility).

value: NPC

tag: genotype

value: MUT


title: YZ1 MUT#2 NPC, POU3F2 pull-down, replicate 2

description: Library name: CB184


title: YZ1 WT NPC, POU3F2 pull-down, replicate 2

description: Library name: CB182

value: WT


title: 3HUF-ASD-BA9

description: Library name: Sample 8

tag: donor

tag: age detailed

tag: brainbank

value: ABN


title: 4334-ASD-BA9

description: Library name: Sample 10

tag: Sex

tag: pmi

tag: rin


title: iPSC-CM_IndA_MTX_3h_H3K27ac_CT

description: Library name: IndA_MTX_3h_CT

value: 0.5 uM mitoxantrone

tag: batch


title: YZ1 WT NPC, POU3F2 pull-down, replicate 1

description: Library name: CB181


title: 35BV-ASD-BA9

description: Library name: Sample 7

tag: tissue

tag: donor alt

value: Old


title: YZ1 MUT#2 NPC, input, replicate 2

description: Library name: CB172

tag: cell line

tag: cell type

value: input


title: KO Male Th2 3

city: Sydney

first: Kylie

last: James

state: NSW

address: 384 Victoria Street, Darlinghurst

department: Translational Genomics

country: Australia

institute: Garvan Institute of Medical Research

description:
sample 31
4598STDY10004945

data_processing:
The raw sequencing reads were aligned to the mouse genome version Ensembl GRCh38.91 with STAR 2.5.3a
Assembly: GRCm38.91
Supplementary files format and content: txt file includes the raw gene counts for each sample

source_name: Spleen

extract_protocol:
RNA was extracted from purified cell populations using QIAzol and miRNeasy RNA extraction kits (QIAGEN) according to manufacturer’s instructions. RNA yield was quantified and checked for quality using a Nanodrop spectrophotometer before quality control and further quantification using an Agilent bioanalyser prior to RNAseq.
Pooled cDNA libraries were sequenced on one lane of an Illumina Novaseq 6000 S4 flow-cell at 100PE

treatment_protocol: The spleens and lymph nodes of WT or Malat1-/- mice were extracted, then passed through a 70 um filter. Resulting cell pellets were then treated with 3ml ACK lysis buffer. Naïve CD4+ T cells were then purified via MACS column isolation (Naive CD4+ T Cell Isolation Kit, mouse, catalogue number 130-104-453) normally resulting in purity of >90%. For Th2 polarisation, purified naïve CD4+ T cells (typically 500,000 cells per well) were typically stimulated with 10 μg/ml plate-bound anti-CD3ε (clone 145-2C11) and 2 μg/ml soluble anti-CD28 (37.51) in RPMI 1640 in flat-bottom 96-well plates in the presence of 30 ng/ml mouse rIL-4 and 5 μg/ml anti–IFN-γ (XMG1.2). Anti-CD3/anti-CD28–dependent activation (4 days) was followed by rest in 10 U/ml human recombinant IL2 for 2 days.

value: Spleen

value: CD4+ T

value: Malat1 KO


title: 3152-CTL-BA9

description: Library name: Sample 6

value: brodmann area 9

tag: genome build

tag: diagnosis

value: CTL

value: Mid

tag: ancestry


title: YZ1 MUT#2 NPC, input, replicate 1

description: Library name: CB171

tag: antibody


title: KO Male Th2 2

description:
sample 30
4598STDY10004944

value: male

tag: treatment


title: KO Male Th2 1

description:
sample 29
4598STDY10004943

tag: genotype


title: 2NA6-ASD-BA9

description: Library name: Sample 5

tag: donor

value: ASD

tag: age

tag: age category

value: Young


title: 2GGP-CTL-BA9

description: Library name: Sample 4

tag: Sex

tag: age detailed

tag: brainbank


title: YZ1 WT NPC, input, replicate 2

description: Library name: CB170


title: YZ1 WT NPC, input, replicate 1

description: Library name: CB169


title: 285A-ASD-BA9

description: Library name: Sample 3

tag: pmi

tag: rin


title: 13161-ASD-BA9

description: Library name: Sample 2

tag: tissue

tag: donor alt

value: UM-BTB

value: Black


title: Multiplexed: YZ1 WT and BR33 MUT#2 NPCs

description: Library name: CB20

data_processing:
Reads were demultiplexed, processed with CellRanger, and imported into Seurat. Cells were filtered to remove cells with >10% mitochondrial reads and cells with <200 or >6000 features detected. Harmony was performed to regress the effect of sex (BR33 = male, YZ1 = female) on NPC clustering. Clusters were defined using UMAP dimensional reduction and annotated with expression of cell-fate markers. Single-cell data from POU3F2WT and POU3F2MUT NPCs were integrated with (1) single-nucleus RNA-seq data from iPSC-derived brain cell types and (2) single-cell RNA-seq data from Eze and Bhaduri, et al. 2021 comprising the fetal brain at Carnegie Stage 14 (CS14). For iPSC-derived brain cell types, Harmony was performed the regress the effect of sex and batch. For the CS14 fetal brain data, all brain regions were utilized. Data was imported into Seurat and cells were filtered to remove cells with >10% mitochondrial reads and cells with <200 or >6000 features detected. Harmony was performed the regress the effect of origin (i.e., ‘brain’ vs. ‘NPC’) and UMAP dimensional reduction was used to visualize integration and assign clusters.
Assembly: Human hg38
Supplementary files format and content: Tab-separated barcode, feature, and matrix files
Supplementary files format and content: Comma-separated table of barcode assignments
Supplementary files format and content: RDS file of NPC data integrated with CS14 human fetal brain (Eze and Bhaduri, et al. 2021)
Supplementary files format and content: RDS file of NPC data integrated with iPSC-derived brain cell types

source_name: pooled BR33 and YZ1

extract_protocol:
NPCs were grown to confluency and dissociated with 1:1 accutase:PBS (Invitrogen, #A1110501). Cells were filtered for debris and non-dissociated aggregates using 30 um filters (Sysmex, #04-0042326). Cells were encapsulated into lipid droplets using a 10X Chromium Controller (NeuroTechnology Studio, BWH).
Synthesis of cDNA was performed, followed by library preparation and sequencing (Harvard Biopolymers Facility).

tag: cell line

value: pooled BR33 and YZ1

tag: cell type

value: NPC

value: pooled WT and MUT

value: pooled male and female


title: WT Male Th2 4

description:
sample 28
4598STDY10004942

value: WT


title: 4332-CTL-BA9

description: Library name: Sample 9

tag: genome build

tag: diagnosis


title: WT Male Th2 2

description:
sample 26
4598STDY10004940


title: WT Male Th2 3

description:
sample 27
4598STDY10004941


title: Multiplexed: BR33 WT and YZ1 MUT#2 NPCs

description: Library name: CB19


title: 00493-ASD-BA9

description: Library name: Sample 1

value: Harvard-ATP


title: WT Male Th2 1

description:
sample 25
4598STDY10004939

value: Spleen


title: KO Male Th2 4

description:
sample 32
4598STDY10004946

value: CD4+ T


title: YZ1 MUT#2 NPC, replicate 2

description: Library name: AH53

data_processing:
Fastq files were assessed for quality using fastqc. Reads were pseudo-aligned using Kallisto and imported into Sleuth for differential expression analysis. Counts were normalized, filtered for low abundance transcripts, and batch effects were regressed using ComBat in the sva package. Principal component analysis (PCA) was performed on the batch-corrected, log-transformed expression matrix using the R function prcomp. Differential expression was assessed using the Sleuth package in R. Pathway enrichment was calculated (queried against the Reactome pathway database) using the R package clusterProfiler and enrichment dot-plots were created using the R package enrichplot. Heatmaps were produced for using the R package pheatmap with color palettes from the R package Seurat.
Assembly: Human hg38
Supplementary files format and content: Comma-separated expression matrix (normalized TPM, batch-corrected for line ID in ComBat)
Supplementary files format and content: Comma-separated expression matrix (normalized TPM)

extract_protocol:
RNA was harvested using the PureLink RNA Mini Kit (ThermoFisher, #12183018A). Quality and integrity of RNA extractions was assessed using a Tapestation RNA Screen Tape (Agilent Technologies, #5067-5576).
Samples were sent to Genewiz (Azenta) for library preparation and sequencing.

value: MUT

value: female


title: KO Female Th2 4

description:
sample 24
4598STDY10004938

value: Malat1 KO


title: YZ1 MUT#2 NPC, replicate 1

description: Library name: AH52


title: KO Female Th2 3

description:
sample 23
4598STDY10004937


title: 90

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

country: Belgium

institute: Universite libre de Bruxelles

description: Library name: DLRMS00109

data_processing:
The RiboMethSeq was conducted exactly as described in Marchand et al. 201635 for data in Extended Data Fig. 1g. Analysis: Adapter sequences were trimmed from raw reads using Trimmomatic v0.39 with the following parameters: LEADING:30, TRAILING:30, SLIDINGWINDOW:4:15, AVGQUAL:30, and MINLEN:17. Quality control of the raw and trimmed reads was assessed using FastQC (v0.11.9). Alignment to the reference rRNA sequence was done by Bowtie2 (v2.3.5.1), with default parameters. Sorting, indexing and extraction of mapped reads was done using Samtools (v1.15.1), with option -F 4 to exclude the unmapped reads. Subsequent analysis was conducted using R: the quantification of ribosomal RNA (rRNA) 2′-O-Me residues was performed using the RNAmodR.RiboMethSeq package (v1.18.0), the final processed data were exported using the writexl (v1.5.0) package, display output were generated with the Prism software (v10.3.0).
Assembly: The rRNA reference sequence used are 18S: NR_003286.4; 5.8S: NR_003285.2; and 28S: NR_003287.4
Supplementary files format and content: The processed data are in the MethScores_ExtendedF1G.xlsx file that includes MethScores for every sample

extract_protocol:
Total RNA was harvested in 200 μL 1X Buffer RLT (QIAGEN, 79216) and isolated using the QIAGEN RNeasy Mini Kit (74104), followed by 1 hr of DNase treatment using TURBO DNase (ThermoFisher, AM2238). DNase-digested RNA was then further purified with the Zymo RNA Clean and Concentrator-25 kit (R1017).
RNA was hydrolyzed in bicarbonate buffer and the reaction was stopped by ethanol precipitation. The resulting fragments were then end-repaired and converted into an Illumina library using the NEB Next Small RNA Library Prepkit (Bioke, E7300S), according to the manufacturer’s protocol.


title: 60

description: Library name: DLRMS00108


title: Control

description: Library name: DLRMS00105


title: YZ1 MUT#1 NPC, replicate 1

description: Library name: AH49


title: KO Female Th2 2

description:
sample 22
4598STDY10004936


title: YZ1 WT NPC, replicate 2

description: Library name: AH47


title: RTA-408 (100mg/kg) biol rep 2

city: Hangzhou

first: Meidan

last: Ying

address: No.866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: Zhejiang University

description: Library name: SAMPLE 9

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Tumor

growth_protocol: SK-N-BE(2) cells were transduced with shCtrl or shKLHL37 (#1 and #2) lentivirus. On the 2nd day of lentivirus infection, SK-N-BE(2) cells were injected into the underarm of female nude mice SK-N-DZ cells  were injected into the underarm of female nude mice

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq® RNA sample preparation kit (Illumina, USA) following TruSeq® RNA sample preparation guide.

treatment_protocol: The mice beared SK-N-DZ cells were treated daily for two weeks either with a solvent (CMC-Na suspension) or with RTA-408 administered intragastrically

value: Tumor

value: SK-N-DZ

value: Neuroblastoma

tag: batch


title: KO Female Th2 1

description:
sample 21
4598STDY10004935

tag: treatment


title: WT Female Th2 4

description:
sample 20
4598STDY10004934

tag: genotype


title: RTA-408 (50mg/kg) biol rep 2

description: Library name: SAMPLE 7


title: YZ1 WT NPC, replicate 1

description: Library name: AH46


title: RTA-408 (50mg/kg) biol rep 1

description: Library name: SAMPLE 6


title: RTA-408 (100mg/kg) biol rep 1

description: Library name: SAMPLE 8


title: WT Female Th2 3

description:
sample 19
4598STDY10004933


title: BR33 MUT#1 NPC, replicate 2

description: Library name: AH41

value: male


title: BR33 MUT#2 NPC, replicate 1

description: Library name: AH43


title: Con biol rep 2

description: Library name: SAMPLE 5

value: Solvent


title: BR33 WT NPC, replicate 2

description: Library name: AH38


title: BR33 MUT#1 NPC, replicate 1

description: Library name: AH40


title: YZ1 MUT#1 NPC, replicate 2

description: Library name: AH50


title: KO Male Naïve 4

description:
sample 16
4598STDY10004930

value: Naïve


title: shKLHL37 #2

description: Library name: SAMPLE 3

value: shKLHL37  #2


title: WT Female Th2 1

description:
sample 17
4598STDY10004931


title: KO Male Naïve 3

description:
sample 15
4598STDY10004929


title: Con biol rep 1

description: Library name: SAMPLE 4


title: BR33 WT NPC, replicate 1

description: Library name: AH37

value: NPC


title: BR33 MUT#2 NPC, replicate 2

description: Library name: AH44


title: KO Male Naïve 1

description:
sample 13
4598STDY10004927


title: shCtrl

description: Library name: SAMPLE 1

value: shCtrl


title: iPSC-CM IndD_VEH_24hr_ATAC

description: Library name: IndD_VEH_24hr_ATAC

data_processing:
Reads were assessed for quality using the MultiQC package (Ewels et al. 2016) in Linux.
Cutadapt (Martin,M et al. 2011 was run in PE legacy mode to remove any adapter sequences present.
Paired-end reads were aligned to hg38 using Bowtie2 (Langmead and Salzberg, 2012) with the settings -D 20 -R 3 -N 1 -L 20 .
Reads were filtered using samtools (Daneck,  2021 GigaScience) to remove reads mapping to mitochondria and reads mapping to more than one genome location.
Picard Tools (https://broadinstitute. github.io/picard/) was used to remove duplicate reads.
Peaks were called on each file using MACS2 callpeak -f BAMPE -g hs –keep-dup all (Zhange et al. 2008, Genome Biology).
A master peak set was created with BEDtools (Quinlan 2010 Bioinformatics) by first concatenating, then merging all .narrowPeak files together as one large peak file.  The BEDtools multiinter function was called to generate intersections of all .narrowPeak files with the master peak set .  A set of high-confidence intersections was created by filtering out intersections found in < 5 .narrowPeak files. Next, BEDtools intersect was used between the master peak set and the filtered intersections files using -wa -u flags.
We further filtered out annotated blacklist regions to create a master set of high-confidence open chromatin regions (n = 172,481).
Subread featureCounts (Liao, 2014 Bioinformatics) was used to collect counts across each .bam file using the high-confidence master open chromatin regions as features.
Assembly: hg38
Supplementary files format and content: ATAC-seq counts for all indiviudals and conditions based on high-confidence regions of open chromatin.

extract_protocol:
iPSC-CMs were washed twice with ice-cold PBS and manually scraped using cold PBS on ice.
[transposase protocol] iPSC-derived cardiomyocytes were processed using the Active Motif ATAC-Seq Kit (53150 ATAC-Seq Kit, Active Motif, Carlsbad, CA, USA) following the manufacturer’s directions. Briefly, approximately 100,000 scraped cells in PBS were pelleted by centrifugation at 500 g for 5 min. Cell pellets were resuspended in 100 μl cold ATAC Lysis Buffer. This solution was pelleted by centrifugation at 500 g for 5 min at 4 °C. Lysis buffer was removed and isolated nuclei were resuspended in 50 μl transposition mix. The tagmentation reaction was carried out at 37 °C for 30 min in a thermomixer set at 800 rpm. Transposed DNA was purified following the manufacturers recommendation and resuspended in 35 μl elution buffer, and stored at −20 °C.
Paired-end ATAC-seq library preparation was performed on four individuals, in time and treatment balanced batches, following the Active Motif ATAC-Seq kit manufacturer’s directions, and amplified for 14 cycles. Libraries were then purified and bioanalyzed to determine library quality. One sample was collected for each time, treatment, and individual for a total of twelve samples per individual. Libraries for each individual (n = 12) were quantified by qPCR before being pooled and run on an Illumnia Nextseq 2000, 50 bp PE reads in 4 treatment and time balanced batches.

treatment_protocol: 400,000 iPSC-CMs were plated in 12-well plates. On Days 27-29, iPSC-CMs were treated with 0.5 µM DNR, DOX, EPI, MTX, TRZ, or vehicle in fresh cardiomyocyte maintenance media. iPSC-CMs and cell culture media were collected 3- and 24-hours post-treatment, resulting in 48 samples from 4 individuals.

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM vehicle


title: BR33 SOX13 MUT#2 NPC, replicate 3

description: Library name: CB76

data_processing:
Fastq files were assessed for quality using fastqc. Reads were pseudo-aligned using Kallisto and imported into Sleuth for differential expression analysis. Counts were normalized, filtered for low abundance transcripts, and batch effects were regressed using ComBat in the sva package. Principal component analysis (PCA) was performed on the batch-corrected, log-transformed expression matrix using the R function prcomp. Differential expression was assessed using the Sleuth package in R. Pathway enrichment was calculated (queried against the Reactome pathway database) using the R package clusterProfiler and enrichment dot-plots were created using the R package enrichplot. Heatmaps were produced for using the R package pheatmap with color palettes from the R package Seurat.
Assembly: Human hg38
Supplementary files format and content: Comma-separated expression matrix (normalized TPM)


title: KO Male Naïve 2

description:
sample 14
4598STDY10004928


title: WT Female Th2 2

description:
sample 18
4598STDY10004932

value: WT


title: iPSC-CM IndD_TRZ_24hr_ATAC

description: Library name: IndD_TRZ_24hr_ATAC

value: 0.5 uM trastuzumab


title: WT Male Naïve 4

description:
sample 12
4598STDY10004926

value: Spleen

value: CD4+ T


title: BR33 SOX13 MUT#2 NPC, replicate 1

description: Library name: CB74

value: MUT


title: iPSC-CM IndD_MTX_24hr_ATAC

description: Library name: IndD_MTX_24hr_ATAC

value: female

value: 0.5 uM mitoxantrone


title: WT Male Naïve 3

description:
sample 11
4598STDY10004925


title: BR33 SOX13 MUT#1 NPC, replicate 3

description: Library name: CB73


title: iPSC-CM IndD_DOX_24hr_ATAC

description: Library name: IndD_DOX_24hr_ATAC

value: 0.5 uM doxorubicin


title: shKLHL37 #1

description: Library name: SAMPLE 2

value: Tumor

value: Neuroblastoma

value: shKLHL37  #1


title: WT Male Naïve 1

description:
sample 9
4598STDY10004923

value: male

value: Naïve


title: BR33 SOX13 MUT#1 NPC, replicate 2

description: Library name: CB72

value: NPC


title: KO Female Naïve 3

description:
sample 7
4598STDY10004921

value: Malat1 KO


title: iPSC-CM IndD_VEH_3hr_ATAC

description: Library name: IndD_VEH_3hr_ATAC

value: induced pluripotent stem cell-derived cardiomyocytes


title: BR33 SOX13 MUT#1 NPC, replicate 1

description: Library name: CB71


title: KO Female Naïve 2

description:
sample 6
4598STDY10004920


title: KO Female Naïve 4

description:
sample 8
4598STDY10004922


title: BR33 SOX13 WT NPC, replicate 3

description: Library name: CB70


title: iPSC-CM IndD_TRZ_3hr_ATAC

description: Library name: IndD_TRZ_3hr_ATAC


title: iPSC-CM IndD_DNR_24hr_ATAC

description: Library name: IndD_DNR_24hr_ATAC

value: 0.5 uM daunorubicin


title: BR33 SOX13 WT NPC, replicate 2

description: Library name: CB69

value: WT


title: KO Female Naïve 1

description:
sample 5
4598STDY10004919


title: BR08 NPCs

description: Library name: CB53

data_processing:
Fastq files were assessed for quality using fastqc. Reads were pseudo-aligned using Kallisto and imported into Sleuth for differential expression analysis. Counts were normalized, filtered for low abundance transcripts, and batch effects were regressed using ComBat in the sva package. Principal component analysis (PCA) was performed on the batch-corrected, log-transformed expression matrix using the R function prcomp. Differential expression was assessed using the Sleuth package in R. Pathway enrichment was calculated (queried against the Reactome pathway database) using the R package clusterProfiler and enrichment dot-plots were created using the R package enrichplot. Heatmaps were produced for using the R package pheatmap with color palettes from the R package Seurat.
Assembly: Human hg38
Supplementary files format and content: Comma-separated expression matrix (normalized TPM, genes with var = 0 removed)
Supplementary files format and content: Comma-separated expression matrix (normalized TPM)

value: non-cognitively impaired


title: iPSC-CM IndD_MTX_3hr_ATAC

description: Library name: IndD_MTX_3hr_ATAC


title: WT Female Naïve 4

description:
sample 4
4598STDY10004918

value: Spleen


title: iPSC-CM IndD_DOX_3hr_ATAC

description: Library name: IndD_DOX_3hr_ATAC


title: BR65 NPCs

description: Library name: CB52


title: BR33 SOX13 MUT#2 NPC, replicate 2

description: Library name: CB75


title: WT Female Naïve 3

description:
sample 3
4598STDY10004917

value: CD4+ T


title: WT Male Naïve 2

description:
sample 10
4598STDY10004924


title: WT Female Naïve 2

description:
sample 2
4598STDY10004916


title: iPSC-CM IndD_DNR_3hr_ATAC

description: Library name: IndD_DNR_3hr_ATAC


title: iPSC-CM IndD_EPI_24hr_ATAC

description: Library name: IndD_EPI_24hr_ATAC

value: 0.5 uM epirubicin


title: BR15 NPCs

description: Library name: CB51

value: female

value: Alzheimer's disease


title: iPSC-CM IndC_VEH_24hr_ATAC

description: Library name: IndC_VEH_24hr_ATAC

value: 0.5 uM vehicle


title: BR59 NPCs

description: Library name: CB50


title: WT Female Naïve 1

description:
sample 1
4598STDY10004915


title: iPSC-CM IndC_TRZ_24hr_ATAC

description: Library name: IndC_TRZ_24hr_ATAC

value: 0.5 uM trastuzumab


title: Myt1l striatum-wildtype 6

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage and the pups are weaned on P18~P28.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: strain

value: Striatum


title: BR68 NPCs

description: Library name: CB49


title: Myt1l striatum-wildtype 5

tag: age


title: iPSC-CM IndC_MTX_24hr_ATAC

description: Library name: IndC_MTX_24hr_ATAC

value: 0.5 uM mitoxantrone


title: BR46 NPCs

description: Library name: CB48


title: BR83 NPCs

description: Library name: CB47

value: male


title: iPSC-CM IndC_DOX_24hr_ATAC

description: Library name: IndC_DOX_24hr_ATAC

value: 0.5 uM doxorubicin


title: Myt1l striatum-wildtype 4


title: iPSC-CM IndD_EPI_3hr_ATAC

description: Library name: IndD_EPI_3hr_ATAC


title: iPSC-CM IndC_EPI_24hr_ATAC

description: Library name: IndC_EPI_24hr_ATAC


title: Myt1l striatum-wildtype 3


title: BR33 SOX13 WT NPC, replicate 1

description: Library name: CB68

value: NPC


title: BR69 NPCs

description: Library name: CB46


title: BR64 NPCs

description: Library name: CB45


title: iPSC-CM IndC_VEH_3hr_ATAC

description: Library name: IndC_VEH_3hr_ATAC


title: iPSC-CM IndC_DNR_24hr_ATAC

description: Library name: IndC_DNR_24hr_ATAC


title: Myt1l striatum-hetero 6


title: iPSC-CM IndC_MTX_3hr_ATAC

description: Library name: IndC_MTX_3hr_ATAC


title: BR50 NPCs

description: Library name: CB42


title: Myt1l striatum-wildtype 1


title: iPSC-CM IndC_DOX_3hr_ATAC

description: Library name: IndC_DOX_3hr_ATAC


title: iPSC-CM IndC_TRZ_3hr_ATAC

description: Library name: IndC_TRZ_3hr_ATAC


title: iPSC-CM IndC_EPI_3hr_ATAC

description: Library name: IndC_EPI_3hr_ATAC


title: BR54 NPCs

description: Library name: CB41


title: Myt1l striatum-hetero 3


title: BR48 NPCs

description: Library name: CB43


title: Myt1l striatum-wildtype 2


title: Myt1l striatum-hetero 4


title: Myt1l striatum-hetero 5


title: BR60 NPCs

description: Library name: CB40


title: Myt1l striatum-hetero 2


title: BR67 NPCs

description: Library name: CB39


title: iPSC-CM IndB_VEH_24hr_ATAC

description: Library name: IndB_VEH_24hr_ATAC


title: Myt1l striatum-hetero 1


title: BR63 NPCs

description: Library name: CB44


title: BR73 NPCs

description: Library name: CB38


title: iPSC-CM IndB_TRZ_24hr_ATAC

description: Library name: IndB_TRZ_24hr_ATAC


title: Myt1l hippocampus-wildtype 6

value: Hippocampus


title: Myt1l hippocampus-wildtype 5


title: BR62 NPCs

description: Library name: CB36


title: BR58 NPCs

description: Library name: CB35


title: Myt1l hippocampus-wildtype 4


title: iPSC-CM IndB_EPI_24hr_ATAC

description: Library name: IndB_EPI_24hr_ATAC

value: induced pluripotent stem cell-derived cardiomyocytes


title: iPSC-CM IndB_DOX_24hr_ATAC

description: Library name: IndB_DOX_24hr_ATAC


title: iPSC-CM IndB_DNR_24hr_ATAC

description: Library name: IndB_DNR_24hr_ATAC

value: 0.5 uM daunorubicin


title: BR14 NPCs

description: Library name: CB34


title: BR66 NPCs

description: Library name: CB32


title: BR40 NPCs

description: Library name: CB33


title: iPSC-CM IndC_DNR_3hr_ATAC

description: Library name: IndC_DNR_3hr_ATAC


title: Myt1l hippocampus-wildtype 3


title: Myt1l hippocampus-hetero 5


title: iPSC-CM IndB_TRZ_3hr_ATAC

description: Library name: IndB_TRZ_3hr_ATAC


title: iPSC-CM IndB_VEH_3hr_ATAC

description: Library name: IndB_VEH_3hr_ATAC


title: Myt1l hippocampus-wildtype 1


title: BR57 NPCs

description: Library name: CB30


title: Myt1l hippocampus-hetero 4


title: iPSC-CM IndB_EPI_3hr_ATAC

description: Library name: IndB_EPI_3hr_ATAC


title: Myt1l hippocampus-hetero 3


title: iPSC-CM IndB_DOX_3hr_ATAC

description: Library name: IndB_DOX_3hr_ATAC


title: Myt1l hippocampus-hetero 2


title: BR89 NPCs

description: Library name: CB37


title: BR11 NPCs

description: Library name: CB28


title: iPSC-CM IndB_MTX_24hr_ATAC

description: Library name: IndB_MTX_24hr_ATAC


title: iPSC-CM IndB_DNR_3hr_ATAC

description: Library name: IndB_DNR_3hr_ATAC


title: Myt1l hippocampus-hetero 1


title: Myt1l hippocampus-wildtype 2


title: Myt1l prefrontal cortex-wildtype 6

value: Prefrontal cortex


title: iPSC-CM IndA_VEH_24hr_ATAC

description: Library name: IndA_VEH_24hr_ATAC


title: BR37 NPCs

description: Library name: CB26

value: non-cognitively impaired


title: BR29 NPCs

description: Library name: CB27


title: iPSC-CM IndA_TRZ_24hr_ATAC

description: Library name: IndA_TRZ_24hr_ATAC


title: Myt1l prefrontal cortex-wildtype 5


title: Myt1l prefrontal cortex-wildtype 4


title: iPSC-CM IndA_MTX_24hr_ATAC

description: Library name: IndA_MTX_24hr_ATAC


title: iPSC-CM IndB_MTX_3hr_ATAC

description: Library name: IndB_MTX_3hr_ATAC


title: BR30 NPCs

description: Library name: CB24


title: BR41 NPCs

description: Library name: CB31


title: iPSC-CM IndA_EPI_24hr_ATAC

description: Library name: IndA_EPI_24hr_ATAC


title: BR36 NPCs

description: Library name: CB29


title: Myt1l prefrontal cortex-wildtype 2


title: BR04 NPCs

description: Library name: CB25


title: iPSC-CM IndA_DNR_24hr_ATAC

description: Library name: IndA_DNR_24hr_ATAC


title: BR33 NPCs

description: Library name: CB22


title: BR43 NPCs

description: Library name: CB23


title: Myt1l prefrontal cortex-wildtype 3


title: iPSC-CM IndA_VEH_3hr_ATAC

description: Library name: IndA_VEH_3hr_ATAC


title: BR21 NPCs

description: Library name: CB21


title: iPSC-CM IndA_TRZ_3hr_ATAC

description: Library name: IndA_TRZ_3hr_ATAC


title: BR24 MUT#2 NPC, Wnt3a-treated, replicate 3

description: Library name: CB121

data_processing:
Fastq files were assessed for quality using fastqc. Reads were pseudo-aligned using Kallisto and imported into Sleuth for differential expression analysis. Counts were normalized, filtered for low abundance transcripts, and batch effects were regressed using ComBat in the sva package. Principal component analysis (PCA) was performed on the batch-corrected, log-transformed expression matrix using the R function prcomp. Differential expression was assessed using the Sleuth package in R. Pathway enrichment was calculated (queried against the Reactome pathway database) using the R package clusterProfiler and enrichment dot-plots were created using the R package enrichplot. Heatmaps were produced for using the R package pheatmap with color palettes from the R package Seurat.
Assembly: Human hg38
Supplementary files format and content: Comma-separated expression matrix (normalized TPM, batch-corrected for line ID)
Supplementary files format and content: Comma-separated expression matrix (normalized TPM, batch-corrected for line ID and POU3F2 genotype)
Supplementary files format and content: Comma-separated expression matrix (normalized TPM)

treatment_protocol: Mouse fibroblasts that were untransfected (Control; ATCC, #CRL-2648) or stably transfected with a Wnt3a overexpression vector (Wnt3a; ATCC, #CRL-2647) were used to harvest control or Wnt3a conditioned media, respectively. Briefly, fibroblasts were maintained in DMEM (ATCC, #30-2002) containing 10% fetal bovine serum (ThermoFisher, #10131035). Media was harvested according to recommendations from ATCC. Control and Wnt3a media were filtered, aliquoted, and stored at -80C. For treatment, a full media change with either L or Wnt3a conditioned media was performed and the cells were incubated for 24 hours before harvesting.

value: MUT

value: Wnt3a conditioned media


title: iPSC-CM IndA_DOX_24hr_ATAC

description: Library name: IndA_DOX_24hr_ATAC


title: BR24 MUT#2 NPC, Wnt3a-treated, replicate 2

description: Library name: CB120


title: Myt1l prefrontal cortex-hetero 4


title: iPSC-CM IndA_MTX_3hr_ATAC

description: Library name: IndA_MTX_3hr_ATAC


title: Myt1l prefrontal cortex-hetero 3


title: iPSC-CM IndA_EPI_3hr_ATAC

description: Library name: IndA_EPI_3hr_ATAC

value: 0.5 uM epirubicin


title: iPSC-CM IndA_DOX_3hr_ATAC

description: Library name: IndA_DOX_3hr_ATAC

value: female


title: Myt1l prefrontal cortex-hetero 1


title: Myt1l prefrontal cortex-hetero 2


title: BR24 WT NPC, Wnt3a-treated, replicate 3

description: Library name: CB118

value: WT


title: BR24 WT NPC, Wnt3a-treated, replicate 2

description: Library name: CB117


title: Myt1l P56-wildtype 5

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

value: wild-type

value: whole brain


title: BR24 WT NPC, Wnt3a-treated, replicate 1

description: Library name: CB116


title: iPSC-CM_IndA_DNR_3hr_ATAC

description: Library name: IndA_DNR_3hr_ATAC


title: Molm-13, 100nm VTP, 2500nM PF-9363, 6hrs, rep 2

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Nextseq
Reads were aligned to human genome (hg38)
Adapters were trimmed from raw reads using Trim Galore v0.4.3.
Trimmed reads were aligned to the human genome (GRCh38.78) using HiSAT2 v2.2.1
Reads assigned to genes using htseq-count
Assembly: Hg38
Supplementary files format and content: counts matrix in tsv format
Supplementary files format and content: molm_counts_raw_upload.txt

growth_protocol: Molm-13 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 100 IU/ml Penicillin, 100 μg/ml streptomycin and 2 mM Glutamax, and

extract_protocol:
Qiagen RNAeasy Kit
Libraries were prepared using the QuantSeq 3’ mRNA-seq Library Prep kit (Lexogen)

treatment_protocol: Molm-13 cell were treated with either 2500nM PF-9363, 100nm VTP, 2500nM PF-9363 and 100nm VTP, or vehicle for 6 and 24 hours.

value: acute myeloid leukemia


title: Molm-13, 100nm VTP, 2500nM PF-9363, 6hrs, rep 3


title: Myt1l prefrontal cortex-hetero 5


title: Myt1l prefrontal cortex-wildtype 1


title: Myt1l P56-wildtype 4


title: Myt1l P56-wildtype 3


title: BR33 MUT#1 NPC, Wnt3a-treated, replicate 2

description: Library name: CB108