title: colon organoids, MPXV clade IIa, no1

description:
TPM_for_GEO_upload_colon.txt
colon_west_Africa_1


title: G4 - Donor 3 confluency passage 2 + donor 2 day 2 proliferation

status: Public on Jun 06 2023

type: SRA

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

country: Netherlands

institute: MERLN Institute

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
The BCL files resulting from sequencing were transformed to FASTQ files with 10× Genomics Cell Ranger mkfastq following its mapping with Cell Ranger count. During sequencing, Read 1 was assigned 28 bp, and were used for identification of the Illumina library barcode, cell barcode and unique molecular identifier (UMI). R2 was used to map the human reference genome GRCh38. Filtering of empty barcodes was done in Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Corneal endothelium

growth_protocol: Human corneal endothelial cells were isolated and cultured as previously reported.5 Briefly, the stripped endothelium–Descemet’s layer was incubated with 2 mg/ml collagenase A (Roche) solution in human endothelial serum free media (SFM) (Thermo Fisher Scientific) for 2–5 h at 37°C followed by a 5 min incubation in TrypLE express (Thermo Fisher Scientific) to generate small clumps of corneal endothelial cells. Cells from each cornea were seeded equally across 2 wells of a 24-well plate coated with fibronectin collagen (FNC) coating mix (Athena Enzyme Systems) in M5 stabilization media (human endothelial SFM (Thermo Fisher Scientific) supplemented with 5% fetal bovine serum (FBS), 100 U/mL penicillin–streptomycin, and 0.25 μg/mL amphotericin B) supplemented with 10 μM Y-27632 (STEMCELL Technologies). Subsequently, corneal endothelial cells were cultured in M4 proliferation medium (1:1 Ham’s F12 (Thermo Fisher Scientific) and M199 (Thermo Fisher Scientific) supplemented with 5% FBS, 20 μg/mL ascorbic acid (Sigma), 1 × ITS (Thermo Fisher Scientific), 10 ng/mL human recombinant bFGF (Sigma), and 10 μM Y-27632 (STEMCELL Technologies)); media was refreshed every other day. Upon reaching 90% confluency, after approximately 8–10 days of culture, cells were cultured in M5 stabilization media for 7 days. After this, corneal endothelial cells were treated with TripLE express and passaged into wells pre-coated with FNC-coating mix at a seeding density of 10,500 cells/cm2 in M5 stabilization medium. All cell culture was performed in incubators with humidified atmosphere of 37°C and 5% CO2.

extract_protocol: scRNAseq of primary cultured CECs wasperformedat Single Cell Discoveries (Utrecht, the Netherlands)followingstandard 10× Genomics 3’V3.1chemistry protocol.Cells were rehydrated and loaded on the 10× Chromium controller as follows. Approximately 10,000 cells were loaded per each sample. Sequencing libraries were prepared following a standard 10× Genomics protocol and sequenced with an Illumina NovaSeq 6000 platform; read length: 150 bp, paired-end.

tag: tissue

value: Corneal endothelium

tag: cell type

value: primary corneal endothelial cells

tag: genotype

value: Caucasian Female + Male

tag: treatment

value: primary culture


title: Bulk RNA-Seq, 8858.3, Ligand exposed, day 90-120_3

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

country: USA

institute: Emory University

description:
40 million PE reads
8858-3_feature_counts.txt

library_source: transcriptomic

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38)
We used FeatureCounts to assemble transcripts and generate raw count matrices. Following generation of raw count data, we used DESeq2 to normalize matrices and to determine differential gene expression statistics.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw expression values for each sample.

source_name: organoid

growth_protocol: Human cortical organoids: Following 3D formation, spheroids were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142  P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, organoids were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, organoids were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, organoids were fed every 3 days with neural media only.

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen).
RNA libraries for RNA-seq were prepared using the NEB Next Ultra II kit using poly-A selection following manufacturer's protocols.

treatment_protocol:
Additon of ligands TGFB2, NLGN1, TSLP, DKK1, and BMP4
Purified human fetal tissue: Purified cells were spun and plated on poly-D-lysine-coated plastic coverslips in a Neurobasal/DMEM-based serum-free medium. We replaced the media every other day for 12 days with or without ligand addition.

value: organoid

tag: cell line

value: Ligand cocktail-exposed


title: colon organoids, MPXV clade IIa, no2

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description:
TPM_for_GEO_upload_colon.txt
colon_west_Africa_2

data_processing:
Sequencing was performed on an Illumina NextSeq500 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.17 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: iPS cell-derived colon organoids

growth_protocol: Normal human epidermal keratinocytes   NHEK-Ad (Normal Human Epidermal Kerationocytoes-Adult, Cat# 00192627, Lonza) were cultured with KGM-Gold Keratinocyte Growth Medium BulletKit (Cat# 00192060, Lonza). NHEK-Ad were seeded on 24-well cell culture plates (2.0×104 cells/2 cm2) and cultured for 7 days.    Human iPS cell-derived colon organoids   The iPS cell line, 1383D6, was maintained on 0.5 μg/cm2 recombinant human laminin 511 E8 fragments (iMatrix-511, Cat# 892 012, Nippi) with StemFit AK02N medium (Cat# RCAK02N, Ajinomoto) containing 10 μM Y-27632 (Cat# 034-24024FUJIFILM Wako Pure Chemical). To passage the cells, iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After the centrifugation, the cells were seeded on Matrigel® Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. To perform definitive endoderm differentiation, human iPS cells were treated with 100 ng/mL Activin A (Cat# 338-AC-01M, R&D Systems) and 10 μM Y-27632 in RPMI1640 medium (Cat# R8758-500, Sigma-Aldrich) supplemented with 1×B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), 1×GlutaMAX (Cat# 35050-079, Thermo Fisher Scientific), and 1×Penicillin-Streptomycin for 3 days. To perform hindgut differentiation, the cells were treated with 200 ng/uL FGF2 (Cat# 160-0010-3, Katayama Chemical Industries) in RPMI1640 medium supplemented with 1×B-27 Supplement Minus Vitamin A, 1×GlutaMAX, and 1×Penicillin-Streptomycin for 4 days. To generate colon organoids, the cells were dissociated and embedded in Matrigel Growth Factor Reduced Basement Membrane to generate organoids. To perform colonic differentiation, the cells were treated with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 0.5 μM A-83-01 (Cat# 035-24113, FUJIFILM Wako Pure Chemical), 50 ng/mL Noggin (Cat# 120-10C, PeproTech), 30 ng/uL Forskolin (Cat# 063-02193, FUJIFILM Wako Pure Chemical), and 50 ng/ml EGF (Cat# AF-100-15, PeproTech) in advanced DMEM/F12 supplemented with 1×N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), 1×B-27 Supplement Minus Vitamin A, 1×GlutaMAX, 0.05% bovine serum albumin, and 1×penicillin-streptomycin for 13 days. To perform the infection experiments, the colon organoids were recovered from Matrigel, and the suspension of colon organoids (small free-floating clumps) was seeded onto Matrigel-coated 24-well cell culture plates (1.0×105 cells/2 cm2) and cultured for 3 days.

extract_protocol:
Total RNA was isolated from infected keratinocytes and colon organoids using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Human iPS cell-derived colon organoids or keratinocytes were infected with MPXV (0.05 multiplicity of infection (MOI)) and cultured for 72 h. Three MPXV strains (clade I/Zr-599, clade IIa/Liberia, clade IIb/MPXV-2022) were used in this experiment.

value: iPS cell-derived colon organoids

value: colon organoids

value: wild type

value: MPXV clade IIa infected

tag: time

value: 3 dpi


title: colon organoids, mock, no3

description:
TPM_for_GEO_upload_colon.txt
colon_mock_3

value: mock


title: Bulk RNA-Seq, 8858.3, Ligand exposed, day 90-120_2


title: Bulk RNA-Seq, 8858.3, Ligand exposed, day 90-120_1


title: Cerebellum H5/H5 Sample 1

city: Bar Harbor

first: George

middle: C

last: Murray

state: ME

address: 600 Main St.

department: Research

institute: The Jackson Laboratory

data_processing:
nf-core RNASeq pipline v3.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Quality was assessed using FASTQC
Trimmed sequence reads were mapped to GRCm38/mm10 using Star
Read count extraction and normalization were performed using RSEM
Assembly: GRCm38 - mm10
Supplementary files format and content: tab-delimited text files include RSEM expected counts, TPM, and FPKM values for each Sample

organism: Mus musculus

source_name: cerebellum

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in MR1 buffer (Macherey-Nagel) using a gentleMACS dissociator (Miltenyi Biotec Inc). RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.
Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5.

value: cerebellum

tag: Sex

value: F

tag: age (wk)


title: Cerebellum DBA/1J Sample 3

value: M

value: DBA-WT


title: G2 - Donor 3 confluency passage 0 + donor 2 day 5 proliferation

description: 10x genomics


title: colon organoids, mock, no2

description:
TPM_for_GEO_upload_colon.txt
colon_mock_2


title: Cerebellum DBA/1J Sample 2


title: colon organoids, mock, no1

description:
TPM_for_GEO_upload_colon.txt
colon_mock_1


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_14

value: BMP4 Exposed


title: G1 - Donor 3 day 5 proliferation + donor 2 confluency passage 0

description: 10x genomics

value: Corneal endothelium


title: Donor8857-D10_TBX21andEOMESedited

city: St Louis

first: Todd

middle: A

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Paired-end reads were trimmed for adaptors and low-quality reads were removed using Cutadapt (v3.2). Trimmed reads were aligned to the human genome assembly hg38 using Bowtie2 (v2.4.1). Samtools (v1.3.1) was used to filter reads by alignment score and remove mitochondrial reads and PCR duplicates were removed using Picard (v2.25.0).
Peaks calling was performed using Genrich (v0.6) ATAC-seq mode (-j -d 100).
Assembly: GRCh38
Supplementary files format and content: narrowpeak files output from Genrich

molecule: genomic DNA

source_name: peripheral blood mononuclear cells

extract_protocol:
Donor peripheral blood NK cells were isolated from a LRS chamber and CRISPR-edited by electroporation with Cas9 mRNA and gRNA targeting EOMES and TBX21. Control NK cells were electroporated without gRNA. CRISPR-edited cells were either maintained in vitro in 1ng/mL IL-15. On Day 7 and Day 10 post CRISPR electroporation, NK cells were harvested from tissue culture plate for library preparation
Nuclei and libraries were prepared for ATAC sequencing following established protocol as reported in https://www.nature.com/articles/nmeth.2688. Nuclei were isolated and Illumina Tagment DNA TDE1 Enzyme and Buffer Kit was used to perform the tranposition reaction. PCR Amplification was performmed using the NEB kit with Illumina indexing primers. A qPCR reaction on the side was performed to identify the approciate number of PCR amplication cycles to perform so that amplification is stopped prior to saturation

value: natural killer cells


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_15


title: G3 - Donor 3 confluency passage 1 + donor 1 day 2 proliferation

description: 10x genomics

value: primary corneal endothelial cells

value: Caucasian Female + Male


title: Cerebellum DBA/1J Sample 1


title: Donor8857-D10_Control


title: colon organoids, MPXV clade I, no1

description:
TPM_for_GEO_upload_colon.txt
colon_Congo_1

value: MPXV clade I infected


title: Hippocampus H5/H5 Sample 2

source_name: hippocampus

value: hippocampus


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_12

value: organoid

value: DKK1 Exposed


title: Cerebellum H5/H5 Sample 2


title: Hippocampus H5/H5 Sample 3


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_13


title: Hippocampus DBA/1J Sample 3


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_11


title: Donor3688-D10_TBX21andEOMESedited


title: Donor8857-D7_Control


title: Donor3688-D10_Control


title: Hippocampus DBA/1J Sample 2


title: Hippocampus H5/H5 Sample 1


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_10


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_8

value: TSLP Exposed


title: Donor3688-D7_TBX21andEOMESedited


title: BCC_Normal_7

city: San Francisco

first: Vikas

last: Daggubati

state: CA

department: Radiation Oncology

institute: University of California, San Francisco

data_processing:
100 base pair single-ended sequencing on Illumina HiSeq 4000, basecalling with
Quality control performed by FASTQC
Reads were trimmed using Trimmomatic, removing leading and trailing bases with quality scores below 28, as well as any base that did not have an average quality score of 28 within a sliding window of 4 bases. Any read shorter than 75 bases was removed
Reads were mapped to GRCm38 or GRCh38 (depending on human or mouse origin) using HISAT2 default paramters
Differential analysis was performed using DESeq2 with "apeglm" parameters with a FDR of 0.05
Assembly: GRCm38, GRCh38
Supplementary files format and content: csv or xlsx files containing fold-change for identified genes, p-values, and FDR values

source_name: Skin

extract_protocol:
Qiagen Rneasy Mini Extraction
Illumina TruSeq stranded mRNA kit

value: Skin

value: mixture

value: wildtype

value: normal


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_9


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_7


title: Cortex H5/H5 Sample 3

source_name: cortex

value: cortex

value: F


title: Hippocampus DBA/1J Sample 1

value: DBA-WT


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day90-120_6

value: NLGN1 Exposed


title: Donor8857-D7_TBX21andEOMESedited


title: Donor168582_in vivo TRAC edited NK cells

description: 5'v2 10x Genomics scRNA-seq

data_processing:
Fastq files were aligned to human  genome (GRCh38) using 10x Genomics CellRanger 6.0.0 with default settings and for CITE-seq samples, feature barcoding reference file for hashtagging alignment and counts.
The filtered_feature_bc_matrix was used as input into Seurat for processing.
Assembly: GRCh38
Supplementary files format and content: matrix, features, and barcodes files consist of the 3 file types as output into the filtered_feature_bc_matrix from CellRanger and used as input into Seurat.

molecule: polyA RNA

extract_protocol:
Donor peripheral blood NK cells were isolated from a LRS chamber and CRISPR-edited by electroporation with Cas9 mRNA and gRNA targeting indicated gene. The next day. CRISPR-edited cells were either maintained in vitro in 1ng/mL IL-15 or injected into NSG mice supported with rhIL-15. One week later, live human NK cells were flow sorted and prepared for 10X Genomics library prep.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-18 cycles before being cleaned up using SPRIselect beads.The supernatant was then collected for the Cell Surface Protein Library. Samples were then run on a Bioanalyzer to determine the cDNA concentration for the GEX library preparation. GEX (Gene Expression) libraries were prepared as recommended by the 10x Genomics with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. Hashtag oligo libraries were prepared with TotalSeq™ anti-human Hashtag reagent from Biolegend according to manufacturer protocol. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 5’ Library and Gel Bead Kit. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the IlluminaNovaSeq6000instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x8x151 sequencing recipe according to manufacturer protocol.


title: Cortex H5/H5 Sample 2

value: M


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day90-120_5


title: Cortex DBA/1J Sample 3


title: Cortex H5/H5 Sample 1


title: Donor168582_in vitro TRAC edited NK cells

description: 5'v2 10x Genomics scRNA-seq

value: natural killer cells


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_2

value: TGFB2 Exposed


title: Donor214_in vivo TBET+EOMES edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day90-120_4


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_3


title: Cortex DBA/1J Sample 1


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 90-120_1


title: Brain H5/H5 Sample 3

source_name: brain hemisection

value: brain hemisection


title: Donor168582_in vitro TBET+EOMES edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Brain H5/H5 Sample 2


title: Bulk RNA-Seq, 8858.3, Control, day 61-91_3

value: Control


title: Donor3688-D7_Control


title: Donor214_in vitro TRAC edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Bulk RNA-Seq, 8858.3, Control, day 61-91_2


title: Donor214_in vivo TRAC edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Brain H5/H5 Sample 1


title: Donor168582_in vivo TBET+EOMES edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Donor3128_in vivo TBET+EOMES edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Donor3128_in vivo TRAC edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Brain DBA/1J Sample 2


title: Bulk RNA-Seq, 8858.3, Control, day 61-91_1


title: Donor3128_in vitro TBET+EOMES edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Bulk RNA-Seq, 8858.3, Ligand exposed, day 61-91_3

value: Ligand cocktail-exposed


title: Bulk RNA-Seq, 8858.3, Ligand exposed, day 61-91_2

value: organoid


title: Donor3128_in vitro TRAC edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Cortex DBA/1J Sample 2


title: Brain H4/H4 Sample 4


title: Donor3227_in vitro TRAC, TBET, EOMES, and TBET+EOMES edited NK cells

description: 5'v2 10x Genomics CITE-seq (cell hashtagging)


title: Donor214_in vitro TBET+EOMES edited NK cells

description: 5'v2 10x Genomics scRNA-seq


title: Brain DBA/1J Sample 1


title: L265P_dox_3

city: Ostrava

first: Matous

last: Hrdinka

address: Syllabova 19

country: Czech Republic

institute: University of Ostrava

data_processing:
Adapter trimming using TrimGalore v0.6.6; parameters: --illumina -q 20, --clip_R2 3
rRNA filtering with SortMeRNA v4.2.0;
Quantification of transcripts using Salmon v1.4.0; parameters: --gcBias, --reduceGCMemory, --seqBias, -l A, --validateMappings, --writeUnmappedNames
Differential expression analysis using DESeq2 v1.30.0
Assembly: GRCh38
Supplementary files format and content: *_salmon_quant.sf files; quantification file from salmon. This is a plain text, tab-separated file with single header line. Each file represents transcript quantification record of corresponding sample describing name, length, effective length of transcripts, salmon’s estimate of relative abudnace of transcripts in TPM and number of reads mapping to each transcript.
Supplementary files format and content: norm_counts_all.csv is a plain text comma separated file containing deseq2 normalized counts for all samples

source_name: Blood

extract_protocol:
RNeasy Mini Kit (Qiagen, cat. n. 74106)
Poly-A selection

value: Blood

value: B cell lymphoma

value: Tet-On Inducible system for MyD88 L265P

value: Doxycycline Hyclate

tag: concentration

value: 250 ng/mL


title: Brain H4/H4 Sample 3


title: Donor89528_in vitro TRAC, TBET, EOMES, and TBET+EOMES edited NK cells


title: Brain H4/H4 Sample 2


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_13

value: BMP4 Exposed


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_14


title: Brain H4/H4 Sample 1


title: L265P_dox_2


title: Brain DBA/1J Sample 3


title: Brain H3/H3 Sample 4


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_12

value: DKK1 Exposed


title: Brain H3/H3 Sample 3

value: F


title: Bulk RNA-Seq, 8858.3, Ligand exposed, day 61-91_1


title: L265P_untreated_3


title: L265P_untreated_2


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_10


title: Brain H2/H2 Sample 4


title: L265P_untreated_1


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_9

value: TSLP Exposed


title: Brain H3/H3 Sample 1


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_8


title: L265P_dox_1


title: Brain H3/H3 Sample 2


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_15


title: Brain H2/H2 Sample 3


title: wt_dox_2

value: Tet-On Inducible system for MyD88 wt


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_6

value: NLGN1 Exposed


title: Brain H2/H2 Sample 2


title: wt_dox_1


title: wt_untreated_3


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_4


title: wt_untreated_2


title: Brain H1/H1 Sample 3

value: M


title: Brain H2/H2 Sample 1


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_5


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_3

value: TGFB2 Exposed


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_11


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_7


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_2


title: wt_dox_3


title: N2

city: Changchun

first: Song

last: He

address: No.1977 Xinzhu Road, Lvyuan District, Changchun City, Jilin Province

country: China

institute: Jilin University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9).
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: not provided
Supplementary files format and content: genes_fpkm_expression.xlsx: Excel file includes counts and FPKM values.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit. High-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: human malignant melanoma cell

value: WT


title: N3


title: Brain C57BL/6J Sample 3

value: brain hemisection


title: wt_untreated_1


title: Bulk RNA-Seq, 1363.1, Individual Control, day 90-120_4

description:
40 million PE reads
1363-1_Individual_Ligands_feature_counts.txt

value: organoid

value: Control


title: Bulk RNA-Seq, 8858.3, Individual Ligand exposed, day 61-91_1


title: LIDAR titrations, total, 500ng

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: counts.genes.titrations.txt

data_processing:
For LIDAR, LIDAR3 and NEB samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
Samples with UMI (LIDAR, LIDAR-3): UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed)
Reads were mapped sequentially with STAR v2.7.10a to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2 ver2.5.0, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP ver 2019-02-26 with SNP database provided, then to a custom GRCm39 genome with all of the sequences above masked and provided as extra scaffolds, using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

source_name: cells

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

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

value: cells

value: ESC serum

tag: input amount_(ng)


title: H3

value: HOPX overexpression


title: LIDAR titrations, total, 100ng

description: counts.genes.titrations.txt


title: ADNP sgRNA S3

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

data_processing:
Samples were sequenced using an Illumina Novaseq6000 running a single-read 50bp protocol
Sequence data were trimmed to remove adaptors and sequences with a quality score below 30 using Trim Galore (v0.50, Babraham Bioinformatics)
sequences were aligned to the mouse genome (GRCm38) using STAR (v2.6.0a, Spliced Transcripts Alignment to a Reference, Alexander Dobin)
differential expression calculated using DEseq2 (v1.18.1)
Supplementary files format and content: GRCm38
Supplementary files format and content: DEseq2 output file

source_name: Spleen

growth_protocol: Naïve CD4+ T cells were isolated from Rosa26Cas9EGFP x Il13tdTom mice and cultured on anti-CD3 coated plates (2B Scientific, 145-2C11, 5 mg ml-1, 37oC, 1 h), supplemented with anti-CD28 (2B Scientific, 37.51, 2 mg ml-1) and IL-2 (10 ng ml-1) for 24 hr.

extract_protocol:
Cells were flow sorted into PBS 50% FCS and RNA was extracted using RNeasy Plus micro kit (Qiagen). After assessment using a Bioanalyser (Agilent), RNA was processed for RNA-sequencing using an Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220,
and bar-coded using Ovation Ultralow Library Systems (Nugen)

treatment_protocol: Cells were collected and mixed with retroviruses and spinoculated on retronectin-coated plates (Takara, 4 mg cm-2, non-TC-treated plate) at 37oC for 1 h. Cells were incubated further for 3 h at 37oC before transfer to fresh TC-treated plates until day 6. Fresh media containing 10 ng ml-1 IL-2 was supplemented at day 3. On day 6, cells were transferred to anti-CD3 coated plates and cultured in the presence of anti-CD28 (2 mg ml-1), IL-2 (10 ng ml-1), IL-4 (10 ng ml-1) and anti-IFNg neutralising antibody (2B Scientific, 1 mg ml-1). After 3 days of differentiation, GFP+ BFP+ cells were sorted into IL13Tom+ and IL13Tom- populations.

value: Spleen

value: Primary cells

value: Primary mouse TH2 cells

value: wt

value: ADNP sgRNA


title: N1


title: H2


title: H1


title: Bulk RNA-Seq, 1363.1, Individual Control, day 90-120_3


title: LIDAR titrations, total, 10ng

description: counts.genes.titrations.txt


title: ADNP sgRNA S2


title: G3

value: GADD45B overexpression


title: Bulk RNA-Seq, 1363.1, Individual Control, day 90-120_1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_10

value: BMP4 Exposed


title: pA, total, NPC, b3

description: counts.genes.txt

value: NPC


title: Brain H1/H1 Sample 2

value: F


title: ADNP sgRNA S1


title: Brain C57BL/6J Sample 1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_9


title: LIDAR titrations, total, 1ng

description: counts.genes.titrations.txt


title: pA, total, NPC, b2

description: counts.genes.txt


title: NT sgRNA S3

value: NT sgRNA


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_8

value: DKK1 Exposed


title: NT sgRNA S2


title: G2

value: human malignant melanoma cell


title: NT sgRNA S1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_7

value: organoid


title: TLE1_KO_Pred_24hr_Rep3

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Reads were mapped to the human genome using bowtie2
Differential enrichment analysis was performed using DESeq2
Assembly: hg19
Supplementary files format and content: text file of raw counts for each replicate

source_name: CRISPR/Cas9 edited Nalm6 (ALL cell line)

growth_protocol: Nalm6 and TLE1 KO cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
RNA was extracted from cell lines using the Rneasy Mini Kit (Cat #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nalm6 cells were treated with prednisolone at a concentration of 5uM for 24 hours. TLE1 KO cells were treated with CHIR-99021 at a concentration of 0.5uM for 24 hours.

value: ALL

tag: treatement

value: PRED (5uM, 24hrs)

tag: replicate


title: TLE1_KO_Pred_24hr_Rep2


title: Th2, ATAC, ADNP-flox S1

data_processing:
Pooled libraries were sequenced using an Illumina NovaSeq6000 running a single-read 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Assembly: GRCm38
Supplementary files format and content: bed file and macs2 output

source_name: Cd4Cre Adnpflox

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
Nuclei were immediately used in the transposase reaction (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease- free water) for 30 min at 37 °C, followed by sample purification (Qiagen MinElute kit). Then, we amplified library fragments using Kappa HiFi HotStart Ready mix and 1.25 M of custom Nextera PCR primers. Libraries were purified using dual (0.5x-0.7x) SPRI Ampure XP beads (Beckman Coulter), pooled and were subjected to high-throughput sequencing

value: Cd4Cre Adnpflox


title: pA, total, NPC, b1

description: counts.genes.txt

value: cells


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_6

value: TSLP Exposed


title: pA, total, mES, serum-free, b2

description: counts.genes.txt

value: ESC, serum-free


title: Th2, ATAC, ADNP-flox S2


title: pA, total, mES, serum-free, b3

description: counts.genes.txt


title: NEB, <50nt, NPC, b3

description:
counts.genes.txt
counts.biotypes.txt


title: pA, total, mES, serum-free, b1

description: counts.genes.txt


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_5


title: TLE1_KO_Ctrl_Rep3


title: TLE1_KO_Pred_24hr_Rep1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_3

value: NLGN1 Exposed


title: Th2, ATAC, cont S1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_4


title: Th2, ATAC, cont S2


title: TLE1_KO_Ctrl_Rep2


title: G1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_2

value: TGFB2 Exposed


title: NEB, <50nt, NPC, b2

description:
counts.genes.txt
counts.biotypes.txt


title: TLE1_KO_Ctrl_Rep1


title: Nalm6_CHIR_24hr_Rep3

source_name: Nalm6 (ALL cell line)


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 90-120_1


title: Bulk RNA-Seq, 1363.1, Individual Control, day 61-91_2

value: Control


title: Th2, anti-INP cont S2

data_processing:
Pooled libraries were sequenced using anIllumina NovaSeq6000
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Assembly: GRCm38
Supplementary files format and content: macs2 output files with peak calling data

extract_protocol:
Chromatin extracts from in vitro expanded Th2 cells (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)

tag: chip antibody

value: Input


title: Th2, anti-INP cont S1


title: NEB, <50nt, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum


title: NEB, <50nt, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: Nalm6_CHIR_24hr_Rep1


title: Bulk RNA-Seq, 1363.1, Individual Control, day 61-91_1


title: Nalm6_Ctrl_Rep3


title: NEB, <50nt, NPC, b1

description:
counts.genes.txt
counts.biotypes.txt

value: NPC


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_9

value: BMP4 Exposed


title: NEB, <50nt, mES_serum-free, b1

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum-free


title: Nalm6_CHIR_24hr_Rep2


title: NEB, <50nt, mES_serum, b1

description:
counts.genes.txt
counts.biotypes.txt


title: Th2, anti-HP1g, ADNP-flox S1


title: Nalm6_Ctrl_Rep2


title: Th2, anti-INP, ADNP-flox S2


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_8

value: DKK1 Exposed


title: Th2, anti-HP1g cont S2


title: Th2, anti-HP1g, ADNP-flox S2


title: NEB, <200nt, NPC, b3

description:
counts.genes.txt
counts.biotypes.txt


title: NEB, <200nt, NPC, b2

description:
counts.genes.txt
counts.biotypes.txt


title: Th2, anti-INP, ADNP-flox S1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_7


title: Nalm6_Ctrl_Rep1


title: Th2, anti-HP1g cont S1


title: Nalm6_IgG_Epicypher_Control

data_processing:
Sequencing data was processed with the publicly available nf-core/cutandrun pipeline (version 2.0).
The following customized parameters were used: genome: hg19; normalisation_mode: Spikein; peakcaller: macs2; run_narrow_peak: true.
NarrowPeaks with a p-value threshold of 0.05 were used to construct reproducible and consensus peak sets.
Reproducible peaks were defined as genomic intervals present in all three replicates within each experimental condition.
Assembly: hg19
Supplementary files format and content: narrowPeak files for each experimental sample
Library strategy: Cut&Run

growth_protocol: Nalm6 cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
Briefly, Nalm6 cells were processed using the CUTANA ChIC/CUT&RUN Kit (Version 3, Cat# 14-1048) exactly according to manufacturer's instructions
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with prednisolone at a concentration of 5uM (Nalm6 cells) or vehicle control for 24 hours

tag: antibody

value: IgG Epicypher (Rabbit pAb #13-0042K)


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_10

value: organoid


title: Th2, anti-H3K27ac, ADNP-flox S2


title: NEB, <200nt, mES_serum-free, b3

description:
counts.genes.txt
counts.biotypes.txt


title: Th2, anti-H3K27ac, ADNP-flox S1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_5


title: LEF1_Nalm6_Pred_24hr_Rep2

value: ALL

value: LEF1 Rabbit mAb (Cell Signaling #2230)


title: Th2, anti-H3K27ac cont S2


title: LEF1_Nalm6_Pred_24hr_Rep1

value: PRED (5uM, 24hrs)


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_4


title: NEB, <200nt, mES_serum-free, b2

description:
counts.genes.txt
counts.biotypes.txt

value: cells


title: NEB, <200nt, mES_serum-free, b1

description:
counts.genes.txt
counts.biotypes.txt


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_3


title: LEF1_Nalm6_Ctrl_Rep3


title: Th2, anti-H3K27ac cont S1


title: Th2, anti-BRG1, ADNP-flox S2

value: Cd4Cre Adnpflox


title: NEB, <200nt, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: LEF1_Nalm6_Ctrl_Rep2


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_1


title: NEB, <200nt, NPC, b1

description:
counts.genes.txt
counts.biotypes.txt


title: NEB, <200nt, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_2


title: LEF1_Nalm6_Ctrl_Rep1


title: Bulk RNA-Seq, 1363.1, Individual Ligand exposed, day 61-91_6

value: TSLP Exposed


title: NEB, <200nt, mES_serum, b1

description:
counts.genes.txt
counts.biotypes.txt


title: Th2, anti-BRG1, ADNP-flox S1


title: LEF1_Nalm6_Pred_24hr_Rep3


title: Th2, anti-BRG1 cont S2


title: SH-SY5Y-3 (short-read)

first: Yi

last: Xing

state: PA

address: 9054 Colket Translational Research Bldg. 3501 Civic Center Blvd.

department: Executive Director, Department of Biomedical and Health Informatics

institute: The Children’s Hospital of Philadelphia

data_processing:
Basecalling was performed in fast mode with Guppy (version 4.0.15) for all Nanopore sequencing data in this study (https://community.nanoporetech.com/downloads). Basecalling of direct RNA and cDNA libraries were done using config files rna_r9.4.1_70bps_fast.cfg and dna_r9.4.1_450bps_fast.cfg respectively.
Reads were then mapped to either the SIRVome or hg19 reference genome using minimap2 (v2.17) with parameters “-a -x splice -ub -k 14 -w 4 --secondary=no” and either SIRV transcript annotations or GENCODE v34 annotations (https://www.gencodegenes.org/human/release_34lift37.html).
Alignment files (SAM format) were next processed by ESPRESSO (https://github.com/Xinglab/espresso) using default settings and either SIRV transcript annotations or GENCODE v34 annotations. Reads that either map to the mitochondrial genome or contain large continuous insertions (≥20 nt) in the raw alignment were filtered out by ESPRESSO.
Assembly: hg19, SIRVome
Supplementary files format and content: .esp files are tab-delimited matrices generated by ESPRESSO that contain read count estimates for all identified isoforms (rows) across all samples (columns); .gtf files generated by ESPRESSO are in GTF format and provide genomic coordinates for all identified transcript isoforms and their corresponding exons
Paired-end Illumina sequencing data with 150-bp read length for SH-SY5Y cells were generated from libraries prepared following the TruSeq Stranded mRNA protocol (Illumina, Cat. #20020595)
Reads from the 3 samples were pooled and aligned to the GRCh37/hg19 reference genome using STAR on two-pass mode with default settings and transcript annotations from GENCODE v34.
Exon skipping events were detected and quantified from short-read alignment files using rMATS (v4.1.1) with default settings.
Assembly: hg19
Supplementary files format and content: SH-SY5Y_SE.MATS.JC.txt is a tab-delimited file that contains coordinates and junction read counts associated with all identified exon skipping events

growth_protocol:
SH-SY5Y human neuroblastoma cells (ATCC, #CRL-2266) were cultured in DMEM/F-12 (Gibco, #11330032) supplemented with 10% fetal bovine serum (FBS, Corning, #45000-734) and 100 U/ml penicillin-streptomycin (Gibco, #15140122). SH-SY5Y cells were maintained at 37°C in a humidified chamber with 5% CO2. The SH-SY5Y cell line was authenticated by short tandem repeat analysis and verified to be mycoplasma-free.
See above

extract_protocol:
Total RNA of  SH-SY5Y cell line was extracted using TRIzol reagent (Invitrogen, #15596018).
A 1 μg aliquot of total RNA extracted from SH-SY5Y cells, together with 25 pg of SIRV-set4 RNA, was used to prepare short-read sequencing libraries by following the TruSeq Stranded mRNA protocol (Illumina, Cat. #20020595).
See above
See above

tag: lineage

value: human neuroblastoma

tag: nanopore library type

value: TruSeq Stranded mRNA protocol


title: Th2, anti-BRG1 cont S1


title: SH-SY5Y-2 (short-read)


title: Bulk RNA-Seq, 1363.1, Ligand exposed, day 90-120_1

description:
40 million PE reads
1363-1_Ligand_Cocktail_feature_counts.txt

value: Ligand cocktail-exposed


title: Th2, anti-CHD4, ADNP-flox S2


title: NEB, total, sperm, b1

description:
counts.genes.txt
counts.biotypes.txt

source_name: mouse sperm

value: mouse sperm

value: sperm

value: below detection


title: SH-SY5Y-1 (short-read)


title: NEB, total, NPC, b3

description:
counts.genes.txt
counts.biotypes.txt

value: NPC


title: Th2, anti-CHD4, ADNP-flox S1


title: Bulk RNA-Seq, 1363.1, Ligand exposed, day 90-120_3


title: Bulk RNA-Seq, 1363.1, Control, day 90-120_4

value: Control


title: Th2, anti-CHD4 cont S2


title: Bulk RNA-Seq, 1363.1, Control, day 90-120_3


title: NEB, total, NPC, b2

description:
counts.genes.txt
counts.biotypes.txt


title: NEB, total, NPC, b1

description:
counts.genes.txt
counts.biotypes.txt


title: HEK293T cells, HA-nsp13 2, 24 h

city: Wuhan

first: Aixin

last: Li

state: Hubei Province

address: No.299, Bayi Road, Wuchang District, Wuhan City, Hubei Province

department: School of Basic Medical Sciences

institute: Wuhan University

data_processing:
RNA reads were aligned to the human genome (UCSC hg38) using Bowtie 1.1.2.
Differential gene expression was performed with EdgeR (Empirical analysis of digital gene expression data in R) version 3.08

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin sulfate, and cultured at 37℃ with 5% CO2.

extract_protocol:
Total cellular RNA was extracted by the RNApure Tissue & Cell Kit (Cowin Biotech, China).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: HEK293T cells were co-transfected with pEF1α-Luc and pHA-nsp13 or empty vector for 24 h.

value: HEK293T cells

value: Overexpression nsp13

tag: treatment time


title: NEB, total, mES_serum-free, b3

description:
counts.genes.txt
counts.biotypes.txt

tag: tissue

value: ESC serum-free


title: Th2, anti-CHD4 cont S1

tag: cell type


title: NEB, total, sperm, b3

description:
counts.genes.txt
counts.biotypes.txt


title: Bulk RNA-Seq, 1363.1, Control, day 90-120_2

value: organoid


title: Bulk RNA-Seq, 1363.1, Control, day 90-120_1


title: HEK293T cells, HA-nsp13 1, 24 h


title: HEK293T cells, Vector 3, 24 h

value: Overexpression Vector


title: Bulk RNA-Seq, 1363.1, Ligand exposed, day 90-120_2


title: Bulk RNA-Seq, 1363.1, Ligand exposed, day 61-91_3


title: NEB, total, mES_serum-free, b2

description:
counts.genes.txt
counts.biotypes.txt


title: Th2, anti-CTCF, ADNP-flox S1

tag: genotype

value: CTCF


title: HEK293T cells, Vector 2, 24 h

tag: treatment


title: NEB, total, mES_serum-free, b1

description:
counts.genes.txt
counts.biotypes.txt

value: cells

tag: cell line


title: Th2, anti-CTCF cont S2


title: Bulk RNA-Seq, 1363.1, Ligand exposed, day 61-91_2


title: HEK293T cells, HA-nsp13 3, 24 h


title: HEK293T cells, Vector 1, 24 h


title: NEB, total, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum


title: Bulk RNA-Seq, 1363.1, Ligand exposed, day 61-91_1


title: Th2, anti-CTCF cont S1


title: Brain C57BL/6J Sample 2

value: brain hemisection

value: F


title: Bulk RNA-Seq, 1363.1, Individual Control, day 90-120_2


title: KO-1-3

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
10X Genomics CellRanger v3.0.2
Seurat v4
Genome_build: GRCh38.p12, Gencode v28
Supplementary_files_format_and_content: raw counts matrix for filtered cells/nuclei in H5AD format

source_name: induced pluripotent stem cells, wild type WTC-11 line from Gladstone Institute

growth_protocol: Cerebral organoid protocol from Stemcell Technologies and Lancaster et al., 2013

extract_protocol:
nuclei extraction method following Habib et al., 2017 and Ayhan et al., 2021
Chromium Single Cell 3’ v3
10X Chromium single-nuclei

value: CRISPR gene edited, isogenic to the wild type samples


title: Th2, anti-CTCF, ADNP-flox S2

value: Cd4Cre Adnpflox


title: Brain H1/H1 Sample 1


title: Bulk RNA-Seq, 1363.1, Control, day 61-91_3

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38)
We used FeatureCounts to assemble transcripts and generate raw count matrices. Following generation of raw count data, we used DESeq2 to normalize matrices and to determine differential gene expression statistics.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw expression values for each sample.

source_name: organoid

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen).
RNA libraries for RNA-seq were prepared using the NEB Next Ultra II kit using poly-A selection following manufacturer's protocols.


title: KO-1-2


title: Th2, anti-JUNB cont S2

value: JUNB


title: Th2, anti-JUNB, ADNP-flox S1


title: KO-1-1


title: Bulk RNA-Seq, 1363.1, Control, day 61-91_2


title: ovary_R_TP2G_rep6

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

institute: University of East Anglia

description: NER0008751_obj1_exp1_ovary_all_expressed_genes.csv

data_processing:
Sequencing reads were pseudoaligned to the Bombus terrestris transcriptome using Kallisto v0.46.1 with parameter --rf-stranded
Estimated transcript counts were summarised per gene in R v4.0.1 using the tximport package v1.16.1 with parameter type="kallisto"
Differential expression analysis was conducted in R v4.0.1 using the DESeq2 package v1.28.1, with technical replicates (sequencing the same library on different lanes of the sequencing machine) collapsed using the collapseReplicates() function.
Genome_build: Bombus_terrestris.Bter_1.0.cdna.all.fa
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in brain
CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body (Represents the 22 samples used for the final analysis, as 2 samples did not meet our threshold for the number of reads pseudoaligned to the Bombus terrestris transcriptome with Kallisto. The 2 excluded samples had large numbers of bee virus reads present.)
CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary

organism: Bombus terrestris

source_name: ovary

growth_protocol: Bumble bee colonies were maintained under standard conditions. See the publication for further details.

extract_protocol:
Bumble bee queens were flash-frozen in liquid nitrogen and stored at -80oC. Queens were then defrosted and the brain, fat body and ovaries were dissected out, flash-frozen in liquid nitrogen, and stored at -80oC. Each sample (one tissue from a single queen) was then ground in liquid nitrogen using a micropestle with the resulting powder resuspended in Tri-reagent (Sigma-Aldrich, UK). RNA was extracted using the Direct-zolTM RNA extraction kit (Zymo Research, USA) according to the manufacturer's protocol. An additional DNase treatment was performed using TurboTM DNA-free kit (Thermo Fisher Scientific, UK), according to the manufacturer's protocol.
Illumina TruSeq stranded mRNA-seq libraries constructed by Edinburgh Genomics (Edinburgh, UK)

treatment_protocol: Egg removal (R) treatment (to increase the costs of reproduction) and an egg removal and replacement (C) treatment (to control for the effects of disturbance caused by egg removal).

value: ovary

value: removal (R), eggs removed

tag: time point

value: time point 2 (TP2G), after 60% of the members of the cohort had died

tag: biological replicate


title: NEB, total, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: Bulk RNA-Seq, 1363.1, Control, day 61-91_1

value: Control


title: LIDAR3, <50nt, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt


title: LIDAR3, <50nt, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: LIDAR, <50nt, NPC, b3

description:
counts.genes.txt
counts.biotypes.txt

value: NPC


title: NEB, total, mES_serum, b1

description:
counts.genes.txt
counts.biotypes.txt


title: Th2, anti-JUNB cont S1


title: ovary_R_TP2G_rep5


title: Bulk RNA-Seq, 1363.1, Control, day 61-91_4


title: Th2, anti-JUNB, ADNP-flox S2


title: Th2, anti-BATF, ADNP-flox S2

value: BATF


title: 36 hpf Zebrafish trunk region Bulk_CUT&TAG (Igg)

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

description: Zebrafish.36 hpf.Bulk_cuttag

data_processing:
For scRNA-seq  and scATAC-seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters, using the GRCz11 reference genome.
For STRT-seq, raw reads were first de-multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells, then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously, UMI sequences in reads 2 were integrated into reads 1. The template switching oligo (TSO) sequence, polyA sequence and the low-quality reads (N > 10%) in reads 1 were subsequently removed by Python scripts and Trimmomatic (version 0.36). Next, the clean reads were aligned to the zebrafish genome (GRCz11 from Ensembl) using HISAT2 (version 2.1.0) with known gene annotation. Only protein-coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded.
For cut&tag, reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. After merging replicates, MACS2 was used for the peak calling.
Assembly: GRCz11
Library strategy: Cut&Tag

organism: Danio rerio

source_name: Zebrafish trunk region

extract_protocol:
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, 40,000 mCherry+ GFP- cells, 40,000 mCherry+ GFP+ cells and 30,000 mCherry- GFP+ cells were sorted from Tg (kdrl:mCherry/runx1:enGFP) at 36 hpf. For STRT-seq in zebrafish, single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells were sorted from the trunk region of Tg (spi2: Gal4;UAS:GFP/ kdrl:mCherry) at 36 hpf. For scRNA-seq of spi2 morphants at 36 hpf in zebrafish, ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) were sorted. For bulk CUT&TAG in zebrafish, fli1a-flag-spi2-EGFP+ cells were sorted from the trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, we loaded ~20,000 cells for further 10x Genomics-based scRNA-seq and ~90,000 cells for further 10x Genomics-based scATAC-seq. For scRNA-seq, libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For ATAC-seq, nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit, and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired-end reads. For 10x Genomics-based scRNA-seq in mice, libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For STRT-seq in zebrafish, the end-repair and dA-tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. After the adaptor ligation step, the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For bulk CUT&TAG, libraries were prepared according to Hyperactive In-Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired-end reads.

value: Zebrafish trunk region 36hpf

tag: cells

value: fli1a-flag-spi2-EGFP+ cells sorted from the trunk region of Tg (fli1a-flag-spi2-GFP) embryos

tag: Stage

value: 36 hours post fertilization


title: Th2, anti-BATF, ADNP-flox S1


title: ovary_R_TP2G_rep4


title: LIDAR, <50nt, NPC, b2

description:
counts.genes.txt
counts.biotypes.txt

tag: input amount_(ng)


title: 36 hpf Zebrafish trunk region Bulk_CUT&TAG (flag)

description: Zebrafish.36 hpf.Bulk_cuttag


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

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum-free


title: Th2, anti-BATF cont S2


title: ovary_R_TP2G_rep2


title: ovary_R_TP2G_rep3


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

description:
counts.genes.txt
counts.biotypes.txt

value: cells


title: Th2, anti-BATF cont S1


title: LIDAR, <50nt, mES_serum-free, b1

description:
counts.genes.txt
counts.biotypes.txt


title: DP2_36hpf

data_processing:
For scRNA-seq  and scATAC-seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters, using the GRCz11 reference genome.
For STRT-seq, raw reads were first de-multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells, then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously, UMI sequences in reads 2 were integrated into reads 1. The template switching oligo (TSO) sequence, polyA sequence and the low-quality reads (N > 10%) in reads 1 were subsequently removed by Python scripts and Trimmomatic (version 0.36). Next, the clean reads were aligned to the zebrafish genome (GRCz11 from Ensembl) using HISAT2 (version 2.1.0) with known gene annotation. Only protein-coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded.
For cut&tag, reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. After merging replicates, MACS2 was used for the peak calling.
Assembly: GRCz11
Library strategy: STRT-seq

value: single spi2:Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2:Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells


title: Th2, anti-GATA3, ADNP-flox S2


title: DP1_36hpf


title: ovary_R_TP2G_rep1


title: LIDAR, <50nt, NPC, b1

description:
counts.genes.txt
counts.biotypes.txt


title: 36 hpf Zebrafish VDA scATAC_seq

data_processing:
For scRNA-seq and scATAC-seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters, using the GRCz11 reference genome.
For STRT-seq, raw reads were first de-multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells, then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously, UMI sequences in reads 2 were integrated into reads 1. The template switching oligo (TSO) sequence, polyA sequence and the low-quality reads (N > 10%) in reads 1 were subsequently removed by Python scripts and Trimmomatic (version 0.36). Next, the clean reads were aligned to the zebrafish genome (GRCz11 from Ensembl) using HISAT2 (version 2.1.0) with known gene annotation. Only protein-coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded.
For cut&tag, reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. After merging replicates, MACS2 was used for the peak calling.
Genome_build: mm10  GRCz11

source_name: Zebrafish VDA

extract_protocol:
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, 40,000 mCherry+ GFP- cells, 40,000 mCherry+ GFP+ cells and 30,000 mCherry- GFP+ cells were sorted from Tg (kdrl:mCherry/runx1:enGFP) at 36 hpf. For STRT-seq in zebrafish, single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells were sorted from the trunk region of Tg (spi2: Gal4;UAS:GFP/ kdrl:mCherry) at 36 hpf. For scRNA-seq of spi2 morphants at 36 hpf in zebrafish, ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) were sorted. For bulk CUT&TAG in zebrafish, fli1a-flag-spi2-EGFP+ cells were sorted from the trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, we loaded ~20,000 cells for further 10x Genomics-based scRNA-seq and ~90,000 cells for further 10x Genomics-based scATAC-seq. For scRNA-seq, libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For ATAC-seq, nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit, and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired-end reads. For 10x Genomics-based scRNA-seq in mice, libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For STRT-seq in zebrafish, the end-repair and dA-tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. After the adaptor ligation step, the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For bulk cell RNA-seq, libraries were prepared according to STRT-seq method and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired-end reads.

value: Zebrafish VDA 36hpf

value: VDA-derived kdrl+runx1-, kdrl+runx1+, and kdrl-runx1+ cells


title: Th2, anti-GATA3, ADNP-flox S1


title: ovary_C_TP2G_rep6

value: control (C), eggs removed and replaced


title: LIDAR, <50nt, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum


title: ovary_C_TP2G_rep5


title: Th2, anti-GATA3 cont S2


title: LIDAR, <50nt, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: 4h_nZVI (3d)

city: Liberec

first: Alena

last: Sevcu

state: Liberec

address: Bendlova 1409/7

department: Applied Biology

institute: Technical University of Liberec

description:
development stage: cell culture on mid-log phase
T4nZVI3_L4

data_processing:
Approximately five million 2 × 79-bp paired end reads were generated respectively from each library by the means of Illumina sequencing on a NextSeq 500/550 High Output v2 platform. The Illumina TruSeq adapter sequences (34 nucleotides) were then clipped by Illumina bcl2fastq2 Conversion Software v2.19.1 using standard parameters.
The FASTQ files were first trimmed (minimum quality 3, minimum read length to be kept 36 bp) using the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014). The processed sequence reads were then mapped to R. subcapitata ATCC 22662 reference genome (GenBank Accession number: BDRX01000001.1) (Suzuki et al., 2018) using HISAT2 (Kim et al., 2019). SAMtools (Danecek et al., 2021) was then applied to access the transcripts level in order to get quantitative assignments and to generate the BAM files.
After that, BAM files were selected for the determination of read counts and identification of differentially expressed genes (DEGs). To define the transcripts abundance, read counts for each BAM file were determined by bedtools v2.27.1 and its option multicov (Quinlan and Hall, 2010). The established read count table was then imported into idep 1.0 (Ge et al., 2018). Then, the gene expression level in counts per million (CPMs) were calculated and visualized in box and PCA plot. To identify DEGs, the BAM files were loaded and processed in R using Rsamtools package (Morgan et al., 2022).
Prior than that, gene models were imported and queried using GenomicFeatures (Lawrence et al., 2013) package and followed by using GenomicAlignments (Lawrence et al., 2013) package to create the Summarized Experiment object that contains the fragment counts for each gene and sample.
Differential gene expression for each condition was illustrated using relative log expression function of the DESEQ2 (Love et al., 2014) package and statistical analysis was through the function p.adjust in R. Venn diagrams were plotted by VennDiagram (Chen and Boutros, 2011) package. Genes showing log2(fold change) ≥ 1.5 and ≤ −1.5, and adjusted p-value less than 0.05 were considered to be significantly expressed. Furthermore, a log2(fold change) ≥ 1.5 and ≤ −1.8 cutoff was applied only to the sample T1nZVI (nZVI exposure at 1 h) versus T1neg (control at 1 h), due to high number of DEGs. Clustering and visualization of the dissimilarity matrix was achieved using ClustVis – a web tool for visualizing clustering of multivariate data (http://biit.cs.ut.ee/clustvis/) (Metsalu and Vilo, 2015) and pheatmap packages. The heatmap function was applied with default setting (Manhattan distance and average linkage were used). Principal component analysis was performed based on PCAtools package. Following the differential gene expression analysis, functional annotation and genes classification into metabolic pathway subtypes were grouped using the KEGG database (https://www.kegg.jp/kegg/) (Kanehisa and Goto, 2000) and JGI Algal Genome Portal PhycoCosm (https://phycocosm.jgi.doe.gov) (Grigoriev et al., 2021; Nordberg et al., 2014). Annotation improvement was further performed using alpha version of protein sequence observation service (PSOS) (https://psos-staging.computational.bio/) and UniProtKB database (https://www.uniprot.org/) (Bateman et al., 2022). The differentially expressed genes were then co-analyzed using protein-protein interaction (PPI) software to analyze for possible gene interactions and was performed using STRING online database version 11.5 (https://string-db.org/) (Szklarczyk et al., 2021) with k-means clustering and interaction score of (medium confidence > 0.4) as the cut off criterion. For every p-value presented in PPI analysis, the false discovery rate (FDR) was controlled using the Benjamini–Hochberg method (Benjamini and Hochberg, 1995). Construction and visualization of PPI network was performed using Cytoscape software version 3.9.1 (Shannon et al., 2003) with Cytoscape stringApp 2.0 installed in the software (Doncheva et al., 2022).
Assembly: R. subcapitata ATCC 22662 genome (GenBank Accession number: BDRX01000001.1)
Supplementary files format and content: 50 genes with the highest variance across samples (rlog transformed counts).csv Format: csv Content: rlog transformed counts of 50 highly expressed genes
Supplementary files format and content: converted_counts_data.csv Format: csv Content: counts per million of all treatment conditions
Supplementary files format and content: T1Fe versus T1neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 1-Fe treatment versus Time 1 neg. control)
Supplementary files format and content: T1nZVI versus T1Fe DESEQ.csv Format: csv Differential gene expression for each condition (Time 1- nZVI treatment versus Time 1-Fe treatment)
Supplementary files format and content: T1nZVI versusT1neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 1- nZVI treatment versus Time 1-neg. control)
Supplementary files format and content: T4 versus T1 DESEQ.csv Format: csv Differential gene expression for each condition (Time 4 versus Time 1)
Supplementary files format and content: T4Fe versus T4neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 4-Fe treatment versus Time 4-neg. control)
Supplementary files format and content: T4nZVI versus T4Fe DESEQ.csv Format: csv Differential gene expression for each condition (Time 4-nZVI treatment versus Time 4-Fe treatment )
Supplementary files format and content: T4nZVI versus T4neg DESEQ.csv Format: csv Differential gene expression for each condition (Time 4- nZVI treatment versus Time 4- neg. control)

organism: Raphidocelis subcapitata

source_name: R. subcapitata exposed to 100 mg/L nZVI (4 h)

growth_protocol: Raphidocelis subcapitata ATCC 22662 (formerly known as Pseudokirchneriella subcapitata) was obtained from the Culture Collection of Autotrophic Organisms (CCALA, Czech Republic) and maintained in Bold’s Basal Medium (BBM) at 24°C.

extract_protocol:
RNA isolation of microalgae R. subcapitata involved two major steps: the cell lysis and then the RNA extraction procedure. RNA was harvested from three biological replicates after 1 and 4 h from R. subcapitata exposed with nZVI and nFe3O4 respectively. Cell pellets were obtained through centrifugation at 10,000 × g, 4°C for 2 min, followed by overnight cell lyophilization and phenol-chloroform extraction method adapted from a previous work (Yeap et al., 2021). The integrity and concentration of the RNA extracts were determined with an Agilent 2100 Bioanalyzer system (Agilent Technologies, Germany) and Nanodrop (Thermo Scientific, USA) was for RNA concentration quantification. All electropherogram of ribosomal RNA peaks were computed and analyzed by 2100 Expert software (Agilent Technologies, Germany).
To prepare for whole transcriptome sequencing of the directional RNA-seq library, up to 1 µg of total RNA (RIN > 6) was used with a TruSeq® stranded mRNA Library Prep kit (Illumina Inc., USA) after capturing poly-adenylated transcripts and mRNA fragmentation. The resulting cDNA libraries were pooled and sequenced in paired-end mode (2 × 79 bp) on an Illumina NextSeq 500/550 High Output v2 platform.

treatment_protocol: For NPs experiments, R. subcapitata was cultivated in Sueoka’s high salt medium (HSM) (Sueoka, 1960), with gentle mixture of 1% CO2 and air bubbling supply under a 130 µmol photons·m−2·s−1 of constant white light illumination at room temperature (24°C). The algae in mid-log exponential phase were harvested after 48 h at an initial cell density of 1.575 × 107 cells/mL for R. subcapitata, and then added to a flask containing NPs. R. subcapitata was exposed to two different forms of activated iron NPs (100 mg/L of nZVI and nFe3O4 respectively), while NP-free condition was served as a control. Three replicates for each condition were conducted in 550 mL of HSM, starting with 45 mL of pre-grown algal culture. 15 mL of the culture was sampled every 24 h before NPs exposure (up to 48 h) and after the start of NPs exposure at 0, 1, 4 h and thereafter every 24 h up to 120 h. Cultures (35 mL) were sampled after NPs exposure at 1 and 4 h for RNA extraction. All the measurements were recorded in three technical replicates per biological sample for each time point and averaged prior to data analysis.

tag: strain

value: Strain ATCC 22662

value: biol rep 3

value: algae cell culture, time:4 h

value: R. subcapitata + nZVI


title: ovary_C_TP2G_rep4

value: ovary

value: time point 2 (TP2G), after 60% of the members of the cohort had died


title: Th2, anti-GATA3 cont S1


title: LIDAR, <50nt, mES_serum, b1

description:
counts.genes.txt
counts.biotypes.txt


title: SP_36hpf


title: 4h_nZVI (3c)

description:
development stage: cell culture on mid-log phase
T4nZVI3_L3

tag: replicate


title: Th2, anti-ADNP, ADNP-flox S2

value: Cd4Cre Adnpflox

tag: chip antibody

value: ADNP


title: ovary_C_TP2G_rep3


title: ovary_C_TP2G_rep2


title: Th2, anti-ADNP, ADNP-flox S1


title: 4h_nZVI (3a)

description:
development stage: cell culture on mid-log phase
T4nZVI3_L1


title: ovary_C_TP2G_rep1


title: 4h_nZVI (2d)

description:
development stage: cell culture on mid-log phase
T4nZVI2_L4

value: biol rep 2


title: Th2, anti-ADNP, cont S2


title: LIDAR3, <200nt, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: ovary_R_TP1G_rep6

value: removal (R), eggs removed

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: LIDAR, <200nt blocked, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: cells

value: below detection


title: Th2, anti-ADNP, cont S1


title: LIDAR, <200nt blocked, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: 4h_nZVI (2c)

description:
development stage: cell culture on mid-log phase
T4nZVI2_L3


title: ovary_R_TP1G_rep4


title: 4h_nZVI (2b)

description:
development stage: cell culture on mid-log phase
T4nZVI2_L2


title: 4h_nZVI (2a)

description:
development stage: cell culture on mid-log phase
T4nZVI2_L1


title: LIDAR, <200nt, NPC, b3

description:
counts.genes.txt
counts.biotypes.txt

value: NPC


title: ovary_R_TP1G_rep5


title: Ythdf2 cKO, r3, Cage #2

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) using HISAT (version 2.1.0).
Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package in R requiring at least 20 read counts in at least three samples with adjusted p-value < 0.05, and batch effect (mice cages) removed by introducing the batch in the design of the experiment as design = ~ batch + condition.
Assembly: mm10
Supplementary files format and content: text files include read counts for each Sample

source_name: B16F10 tumors

growth_protocol: 3×105 B16F10 tumor cells in 100 μL DPBS were injected subcutaneously into the flank

extract_protocol:
Tumors were harvested and minced into small pieces. Tumor tissue was submerged in RPMI with 10 U/mL DNase I (Thermo Fisher Scientific, EN0521) and 1 mg/ml collagenase IV (Gibco, 17104019) and digested at 37 °C for 1 hour. The suspension was filtered through a 70-mm cell strainer. Red blood cells were lysed with ACK Lysing Buffer (Gibco, A1049201) and resuspended in FACS buffer (DPBS with 2% FBS). Tumor-infiltrating lymphocytes were enriched by CD4 (TIL) Microbeads (Miltenyi Biotec, 130-116-475).  Enriched lymphocytes were stained DAPI, CD45, and CD4. Live CD45+CD4+GFP+ Treg cells were sorted at 4 °C into Trizol (Invitrogen). RNAs were isolated by chloroform and precipitated by isopropanol following the manufacturer’s protocol. Genomic DNA was removed by DNase I and purified by RNA Clean & Concentrator.
RNA libraries were constructed with the SMARTer Stranded Total RNA-Seq Kit v2 (Takara, 634412).

value: B16F10 tumors

value: CD45+ CD4+Foxp3-GFP+ Treg cells


title: Ythdf2 cKO, r2, Cage #2


title: 4h_nZVI (1d)

description:
development stage: cell culture on mid-log phase
T4nZVI1_L4

value: biol rep 1


title: LIDAR3, <200nt, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum


title: 4h_nZVI (3b)

description:
development stage: cell culture on mid-log phase
T4nZVI3_L2

value: Strain ATCC 22662

value: biol rep 3


title: LIDAR, <200nt, NPC, b2

description:
counts.genes.txt
counts.biotypes.txt


title: ovary_R_TP1G_rep2


title: ovary_R_TP1G_rep1


title: Ythdf2 cKO, r1, Cage #1


title: ovary_R_TP1G_rep3


title: 4h_nZVI (1b)

description:
development stage: cell culture on mid-log phase
T4nZVI1_L2

value: algae cell culture, time:4 h

value: R. subcapitata + nZVI


title: 4h_nZVI (1c)

description:
development stage: cell culture on mid-log phase
T4nZVI1_L3


title: WT Control, r2, Cage #1


title: ovary_C_TP1G_rep6

value: ovary

value: control (C), eggs removed and replaced


title: LIDAR, <200nt, mES_serum-free, b2

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum-free


title: LIDAR, <200nt, mES_serum-free, b1

description:
counts.genes.txt
counts.biotypes.txt


title: WT Control, r1, Cage #1


title: 4h_nFe3O4 (3d)

description:
development stage: cell culture on mid-log phase
T4Fe3_L4

source_name: R. subcapitata exposed to 100 mg/L nFe3O4 (4 h)

value: R. subcapitata + nFe3O4


title: ovary_C_TP1G_rep4


title: 4h_nZVI (1a)

description:
development stage: cell culture on mid-log phase
T4nZVI1_L1


title: 9p21+/- -Y-primary BM stromal cells-1 [CITE-seq, HTO]

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

library_source: other

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and read counting performed using HT-seq to make count tables
Assembly: mm10
Supplementary files format and content: txt. Formatted counts table

molecule: protein

source_name: bone marrow and bone (10-month-old mouse)

growth_protocol: For bulk RNA-seq: To prepare BM-MSCs, femur and tibia were dissected from mice that were euthanized with CO2. Each cleaned bone was transferred into a single PCR tube with a whole at the bottom which was punched by an 18G needle. The combined PCR tube was inserted into a 1.5 ml Eppendorf tube and centrifuged at 16,000 g for 20 seconds. The flushed BM cells were suspended and cultured in 20 ml low glucose DMEM medium supplemented with 10% fetal bovine serum (FBS), 1% MEM-NEAA and 1% penicillin/streptomycin at 37°C in a humidified atmosphere at 5% CO2. The medium was replenished every 2-3 days for a week. For CITE-seq, no growth cultre

extract_protocol:
For bulk RNA-seq, total RNA were extracted using TRIzol Plus purification kit (ThermoFisher), and cDNA libraries were prepared with TruSeq Stranded Total RNA with Ribo-Zero Globin.RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. For CITE-seq, Post staining and sorting, cells were run through the standard 10x Chromium (v3) protocol up until cDNA amplification, with the following modification: during cDNA PCR and 1 pmol of hashtagging oligonucleotide (HTO) additive primer were added to the cDNA amplification master mix. Post cDNA amplification, a 0.6X Solid Phase Reversible Immobilisation (SPRI) bead clean-up was performed to separate the cDNA fraction (on beads) from HTO fraction (in supernatant). The cDNA fraction was converted into a 3’ tag gene expression library according to the 10x Genomics Single Cell Genomics Protocol (v3). Supernatant from cleanup was kept for ADT and HTO preparation. To the supernatant, another 1.4X SPRI was added to bring the total SPRI concentration to 2X. After washing the beads in 80% ethanol and eluting in water, a second round of 2X SPRI cleanup was performed to remove any residual primer carryover from the cDNA PCR.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For osteigenic differetiation:  The attached cells were collected and seeded at a density of 10,000 cells per well in a 24-well plate and switched into osteogenic medium (low glucose DMEM supplemented with 10% FBS plus 100 ug/ml ascorbic acid, 10 mM β-glycerophosphate, 1% MEM-NEAA and 1% penicillin/streptomycin) after reaching 80% confluency.

value: BM lin-CD31-CD71- cells

tag: library type

value: HTO

tag: antibodies/tags

value: CD45/H-2; BM lin-CD31-CD71- cells; WT-Y- primary BM stromal cells-1 -- /2564WT


title: 9p21+/- -O-primary BM stromal cells-2 [CITE-seq, HTO]

source_name: bone marrow and bone (16-month-old mouse)

value: CD45/H-2; BM lin-CD31-CD71- cells; 9p21+/- -O-primary BM stromal cells-2 --/2588het_mutant


title: 4h_nFe3O4 (3c)

description:
development stage: cell culture on mid-log phase
T4Fe3_L3


title: ovary_C_TP1G_rep3

value: time point 1 (TP1G), after 10% of the members of the cohort had died


title: WT- O- primary BM stromal cells-2 [CITE-seq, HTO]

value: bone marrow and bone (16-month-old mouse)

value: WT

value: CD45/H-2; BM lin-CD31-CD71- cells; WT-Y- primary BM stromal cells-1 -- /8527WT


title: LIDAR, <200nt, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

data_processing:
For LIDAR, LIDAR3 and NEB samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
Samples with UMI (LIDAR, LIDAR-3): UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed)
Reads were mapped sequentially with STAR v2.7.10a to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2 ver2.5.0, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP ver 2019-02-26 with SNP database provided, then to a custom GRCm39 genome with all of the sequences above masked and provided as extra scaffolds, using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

source_name: cells

value: cells

value: ESC serum


title: LIDAR, <200nt, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: LIDAR, <200nt, NPC, b1

description:
counts.genes.txt
counts.biotypes.txt

value: NPC


title: LIDAR, <200nt, mES_serum, b1

description:
counts.genes.txt
counts.biotypes.txt


title: 4h_nFe3O4 (3a)

description:
development stage: cell culture on mid-log phase
T4Fe3_L1

value: Strain ATCC 22662

value: biol rep 3

value: algae cell culture, time:4 h


title: WT Control, r3, Cage #2

value: B16F10 tumors

value: CD45+ CD4+Foxp3-GFP+ Treg cells


title: LIDAR, <200nt, mES_serum-free, b3

description:
counts.genes.txt
counts.biotypes.txt

value: ESC serum-free


title: LIDAR3, total, sperm, b3

description:
counts.genes.txt
counts.biotypes.txt

value: mouse sperm

value: sperm


title: ovary_C_TP1G_rep1

value: ovary

value: control (C), eggs removed and replaced


title: 4h_nFe3O4 (2d)

description:
development stage: cell culture on mid-log phase
T4Fe2_L4

value: biol rep 2

value: R. subcapitata + nFe3O4


title: fatbody_R_TP2G_rep6

description: NER0008751_obj1_exp1_fatbody_all_expressed_genes.csv

source_name: fat body

value: fat body

value: removal (R), eggs removed

value: time point 2 (TP2G), after 60% of the members of the cohort had died


title: LIDAR3, total, sperm, b1

description:
counts.genes.txt
counts.biotypes.txt


title: 9p21+/- -Y-primary BM stromal cells-1 [CITE-seq, mRNA]

value: bone marrow and bone (10-month-old mouse)

value: BM lin-CD31-CD71- cells

value: mRNA


title: fatbody_R_TP2G_rep5


title: 4h_nFe3O4 (2b)

description:
development stage: cell culture on mid-log phase
T4Fe2_L2

value: Strain ATCC 22662


title: 4h_nFe3O4 (2a)

description:
development stage: cell culture on mid-log phase
T4Fe2_L1

value: algae cell culture, time:4 h


title: 4h_nFe3O4 (1d)

description:
development stage: cell culture on mid-log phase
T4Fe1_L4

value: biol rep 1


title: 4h_nFe3O4 (2c)

description:
development stage: cell culture on mid-log phase
T4Fe2_L3


title: LIDAR3, total, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: cells

value: ESC serum


title: WT-Y- primary BM stromal cells-1 [CITE-seq, mRNA]

value: WT


title: 4h_nFe3O4 (3b)

description:
development stage: cell culture on mid-log phase
T4Fe3_L2

value: biol rep 3


title: 9p21+/- BM-MSC-2s, Day 7 [1945M_7d_S31]

source_name: bone marrow

value: bone marrow

value: cultured mesenchymal stromal cells

value: osteogenic differentiation

tag: time

value: Day 7


title: WT- O- primary BM stromal cells-2 [CITE-seq, mRNA]

value: bone marrow and bone (16-month-old mouse)


title: LIDAR3, total, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: LIDAR, total blocked, sperm, b3

description:
counts.genes.txt
counts.biotypes.txt

value: mouse sperm

value: sperm

value: below detection


title: 4h_nFe3O4 (1c)

description:
development stage: cell culture on mid-log phase
T4Fe1_L3

value: R. subcapitata + nFe3O4


title: fatbody_R_TP2G_rep3

value: fat body

value: removal (R), eggs removed

value: time point 2 (TP2G), after 60% of the members of the cohort had died


title: LIDAR, total blocked, sperm, b1

description:
counts.genes.txt
counts.biotypes.txt


title: 9p21+/- -O-primary BM stromal cells-2 [CITE-seq, mRNA]

value: BM lin-CD31-CD71- cells

value: mRNA


title: 9p21+/- BM-MSCs-1, Day 7 [287M_7d_S29]


title: LIDAR, total blocked, mES_serum, b3

description:
counts.genes.txt
counts.biotypes.txt

value: cells

value: ESC serum


title: 4h_nFe3O4 (1b)

description:
development stage: cell culture on mid-log phase
T4Fe1_L2

value: Strain ATCC 22662

value: biol rep 1

value: algae cell culture, time:4 h


title: fatbody_R_TP2G_rep1


title: fatbody_C_TP2G_rep6

value: control (C), eggs removed and replaced


title: LIDAR, total blocked, mES_serum, b2

description:
counts.genes.txt
counts.biotypes.txt


title: fatbody_R_TP2G_rep4


title: 4h_nFe3O4 (1a)

description:
development stage: cell culture on mid-log phase
T4Fe1_L1


title: WT BM-MSCs-1, Day 7 [289WT_7d_S28]

value: bone marrow

value: cultured mesenchymal stromal cells

value: WT

value: osteogenic differentiation

value: Day 7


title: LIDAR, total, sperm, b3

description:
counts.genes.txt
counts.biotypes.txt

value: mouse sperm

value: sperm

value: below detection


title: fatbody_C_TP2G_rep5

value: fat body

value: time point 2 (TP2G), after 60% of the members of the cohort had died


title: fatbody_R_TP2G_rep2

value: removal (R), eggs removed


title: 4h_control (3d)

description:
development stage: cell culture on mid-log phase
T4neg3_L4

source_name: R. subcapitata-nanoparticle free (4 h)

value: biol rep 3

value: negative control:R. subcapitata


title: 4h_control (3c)

description:
development stage: cell culture on mid-log phase
T4neg3_L3

value: Strain ATCC 22662


title: fatbody_C_TP2G_rep4


title: fatbody_C_TP2G_rep2


title: fatbody_C_TP2G_rep3


title: WT BM-MSCs-2, Day 0 [1461WT_0d_S26]

value: Day 0

value: mRNA