title: MCF7 MPRA replicate 1

city: seattle

first: Samantha

last: Koplik

email: skoplik@uw.edu, kopliksam@gmail.com

state: Washington

address: 185 Stevens Way

department: Electrical and Computer Engineering

institute: University of Washington

description:
Library name: MCF7_R1
MPRA library RNA-Seq, replicate 1

data_processing:
DNA-seq reads were used to extract 20-nt barcodes from R2, anchored by a required 20-bp forward shared region (allowing up to 5 mismatches). Barcodes were clustered with starcode (distance = 1), and consensus barcode+insert sequences supported by ≥5 reads were assembled into a FASTA reference for STAR indexing. Reference FASTA entries were assembled from each unique 20-nt barcode cluster. For each barcode cluster and library member combination, the reference sequence consisted of the last 25 nt of Citrine exon 1, SMN2 intron 6, the variable exon and intronic flanks, SMN2 intron 7, Citrine exon 2, and the 20-nt barcode. The matched barcode+insert references were used to build STAR genome indexes for RNA-seq mapping.
RNA-seq reads were split based on barcode and mapped to the barcode+insert reference FASTA using STAR. Unique molecular identifiers (UMIs) were collapsed to remove PCR duplicates, and reads were remapped with STAR after collapsing. Splice isoform abundance was quantified by counting junction-spanning reads, from which percent spliced-in (PSI) values were calculated. PSI values were clipped to be [0.01, 0.99] and then logit-transformed to obtain logit(PSI), and ΔPSI and Δlogit(PSI) were computed relative to the corresponding wild-type reference sequence.
Assembly: Synthetic plasmid backbone reference sequence (Citrine exon 1 – SMN2 intron 6 – variable intron flank-exon-intron flank – SMN2 intron 7 – Citrine exon 2). Human genome build hg38 was used only for annotation of exons and their variants
Supplementary files format and content: Processed PSI values are provided in tab-delimited text/CSV format. Each row corresponds to a variant with columns for reference ID (1-indexed), event_id, gene_exon, gene_name, cell line, replicate, and computed values including inclusion reads, exclusion reads, PSI, clipped PSI (0.01–0.99), logit(PSI), ΔPSI, and Δlogit(PSI).

growth_protocol: Cells were cultured under standard conditions. HEK293, HeLa, K562, MCF7, and HMC3 cells were seeded at 200,000 cells/mL in 10 cm plates in appropriate growth medium supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted from cells 36–48 h after transfection using the Monarch RNA cleanup kit (NEB). Poly(A)+ mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). mRNA was reverse transcribed with SuperScript IV Reverse Transcriptase (Thermo Fisher) to generate cDNA using a primer downstream of the barcode region.
cDNA was amplified with KAPA HiFi HotStart ReadyMix using primers flanking the Citrine exon 1 splice junction and barcode region, which included offset sequences to increase base diversity. Following amplification, Illumina P5/P7 adapters were added via qPCR to selectively enrich for adapter-containing fragments and prevent over-amplification. Libraries were size-selected to retain fragments ≥100 nt, quantified with Qubit and qPCR, pooled with PhiX, and sequenced on an Illumina NextSeq 500 using 300-cycle kits and custom primers.

treatment_protocol: Cells were transfected with 15 µg of the plasmid MPRA library using Lipofectamine 3000 (Thermo Fisher). Cells were harvested 36–48 h post-transfection.

value: Breast adenocarcinoma

value: Exon Skipping MPRA


title: HEK293T_Acyclovir_250uM_Rep1

status: Public on Sep 08 2025

type: SRA

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

country: USA

institute: Weill Cornell Medicine

description:
Library name: HEK293T_Acyclovir_250uM_Rep1
Total RNA with rRNA depletion

library_source: transcriptomic

data_processing:
Raw FASTQ files were processed using nf-core/rnasplice (v1.0.4), a standardized and reproducible Nextflow-based pipeline (v24.10.0). Reads were aligned to the GRCh38 human genome reference, and all pipeline parameters—including trimming, alignment, quantification, and splicing analysis—were retained at their default settings.
For alternative splicing analysis, rMATS results from nf-core/rnasplice were used to compare branaplam-treated samples to branaplam controls and acyclovir-treated samples to acyclovir controls. Splicing events were quantified from rMATS output files reporting inclusion junction counts (IJC) and skipping junction counts (SJC) for each event. Events were retained if either condition had all replicates with IJC and SJC counts ≥ 10, ensuring robust splicing metric estimation. Significant alternative splicing events were defined as those with FDR < 0.05 and |ΔPSI| > 0.1. Individual splicing patterns were visualized using ggSashimi by merging triplicates and displaying mean coverage based on STAR-aligned BAM files and genomic coordinates extracted from the rMATS results.
For differential gene expression analysis, raw read count data were obtained from featureCounts output files generated by nf-core/splice. Raw counts were processed to retain only Ensembl gene identifiers. Counts for each gene were aggregated across samples and merged into a single count matrix for analysis with DESeq2. Genes with low expression (row sum ≤10) were removed prior to analysis. Differentially expressed genes were defined as those with an adjusted p-value < 0.05 and |log2 fold change| > 1.
All software versions, parameters, and computational workflows are fully documented in the nf-core/rnasplice pipeline. Complete DGE and rMATS datasets for branaplam- and acyclovir-treated samples are provided as additional files.
Assembly: GRCH38
Supplementary files format and content: "RNA-seq_DGE_raw_reads_count.xlsx"-RNAseq raw reads for all samples; raw reads count for each sample is in its subsheet, "RNA-seq_rMATS_acyclovir_250uM_vs_DMSO_250uM.xlsx"-rMATS output; each splicing type is in its subsheet, "RNA-seq_rMATS_acyclovir_500uM_vs_DMOS_500uM.xlsx"-rMATS output; each splicing type is in its subsheet, "RNA-seq_rMATS_branaplam_100nM_vs_DMSO_100nM.xlsx"-rMATS output; each splicing type is in its subsheet.

molecule: total RNA

organism: Homo sapiens

growth_protocol: HEK293T cells (ATCC CRL-3216) were maintained at 37 °C in a humidified 5 % CO₂ incubator in Dulbecco’s Modified Eagle Medium (DMEM, Thermo 11995065) supplemented with 10 % heat-inactivated fetal bovine serum, 100 U mL⁻¹ penicillin, and 100 µg mL⁻¹ streptomycin. Cells were sub-cultured at 70–80 % confluence by trypsinisation, counted with a TC20™ Automated Cell Counter, and seeded into 10 cm dishes at 2 × 10⁶ cells dish⁻¹ 24 h before drug treatment.

extract_protocol:
Total RNA was isolated with TRIzol LS (Invitrogen 10296010) according to the manufacturer’s instructions. RNA pellets were resuspended in RNase-free H₂O, treated with 1 U DNase I (NEB M0303) 10 min at 37 °C, and purified with the RNA Clean & Concentrator-25 kit (Zymo R1018). RNA integrity (RIN > 9) was verified on an Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Preparation Kit (with rRNA depletion) at the Weill Cornell Medicine Genomics Resources Core Facility. Sequencing was performed on an Illumina NovaSeq X Plus platform, generating ≥70million 150 bp paired-end reads per sample. The 500 µM acyclovir group generated ≥ 32 million 150 bp paired-end reads per sample.

treatment_protocol: Six conditions in biological triplicate: (1) 250uM DMSO (vehicle for 250uM acyclovir), (2) 100nM DMSO (vehicle for 100nM branaplam), (3) acyclovir 250 uM, (4) branaplam 100 nM, (5) 500uM DMSO, (6) acyclovir 500 uM. Drugs or vehicle were added directly to culture medium; cells were incubated 72 h before harvest.

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: genotype

value: WT

tag: treatment

value: Acyclovir 250uM for 3 days


title: HMC3 MPRA replicate 2

description:
Library name: HMC3_R2
MPRA library RNA-Seq, replicate 2

molecule: polyA RNA

value: Human microglia


title: K562 MPRA replicate 1

description:
Library name: K562_R1
MPRA library RNA-Seq, replicate 1

value: Chronic myelogenous leukemia


title: HEK293T_DMSO_250uM_Rep3

description:
Library name: HEK293T_DMSO_250uM_Rep3
Total RNA with rRNA depletion

value: DMSO 250uM for 3 days


title: K562 MPRA replicate 2

description:
Library name: K562_R2
MPRA library RNA-Seq, replicate 2


city: Cambridge

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

country: United Kingdom

institute: University of Cambridge

description: Library name: ChIPseq_SetD_antiH3K4me3_StPRDM9g4_line2

library_source: genomic

data_processing:
Bowtie2 (version 2.5.0) was used to map the PE150 bp read data in fastq format to the TAIR10 genome (--no-unal), and were converted to bam format using Samtools (version 1.10). Reads were de-duplicated using the samtools fixmate and markdup commands. Tracks were generated in DeepTools (version 3.5.1) using bamCoverage (--normalizeUsing RPGC, --effectiveGenomeSize 135000000 --binSize 10) with multicopy regions blacklisted (--blackListFileName) using the regions identified in (Klasfeld et al., 2022). For analysis of reads mapping to the centromere, a modified version of the previously described pipeline (Wlodzimierz et al., 2023) was used. Briefly, PE150 bp read data in fastq format were mapped to the Col-CEN genome (Naish et al., 2021) using Bowtie2 (version 2.2.5) with (--very-sensitive -k 200 --no-unal --no-discordant) and were filtered for primary alignments using samtools view (-F 256 -q 5) prior to deduplication and track generation, as above. Peaks were called using MACS2 (version 2.2.9.1) with default parameters. For the Quantseq, only read (*1.fq.gz) from PE150 bp data was used for downstream analysis. Reads were trimmed using cutadapt (version 1.18) and were mapped to the genome using STAR (version 2.7.10b) to the TAIR10 genome (--quantMode GeneCounts --alignIntronMax 10000 --outSAMmultNmax 20).
Assembly: TAIR10 for everything except for analysis relating to Figure 3, for which the Col-CEN assembly was used.
Supplementary files format and content: BigWig trackes were generated in DeepTools (version 3.5.1) using bamCoverage (--normalizeUsing RPGC, --effectiveGenomeSize 135000000 --binSize 10) with multicopy regions blacklisted (--blackListFileName) using the regions identified in (Klasfeld et al., 2022). For the QuantSeq genecount data, in accordance with the manufacturer’s (Lexogen) instructions, only read (*1.fq.gz) from PE150 bp data was used for downstream analysis. Briefly, reads were trimmed using cutadapt (version 1.18) and were mapped to the genome using STAR (version 2.7.10b) to the TAIR10 genome (--quantMode GeneCounts --alignIntronMax 10000 --outSAMmultNmax 20).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under 16h light: 8h dark condition on soil or plates.

extract_protocol:
All the material for ChIP used in this paper were from pooled 10-12 day old seedlings grown on Murashinge and Skoog agar plates (1/2X MS, 1.5% agar, pH5.7). 2-4g of seedling tissue was used for each sample. Samples were ground in liquid nitrogen and crosslinked for 10 or 12 minutes at room temperature in Nuclei Isolation buffer (50mM Hepes pH8, 1M sucrose, 5mM KCl, 5mM MgCl2, 0.6% triton X-100, 0.4 mM PMSF, 5 mM benzamidine hydrochloride, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)) containing 1% formaldehyde. The crosslinking reactions were stopped with 125 mM glycine by incubation at room temperature for 10 minutes. Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol (Villar and Kohler, 2018)). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with antibody. 7 µl of anti-HA (3F10, Merck) and 5 µl of anti-H3K4me3 (ab8580, abcam) were added to up to 2 ml of sheared chromatin per sample for pulldown. . 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers, for 5 minutes each at 4°C (buffer compositions are described in the published protocol (Villar and Kohler, 2018)) and eluted twice with 250 µl of elution buffer (1% SDS and 0.1 M NaHCO3) in a thermomixer at 65°C and 1000 rpm, 20 minutes for each elution. Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C. For the RNA-seq, plant material was extracted using the Direct-zol RNA miniprep kit (Zymo R2052) according to manufacturers instructions, including the in column DNase I treatment.
ChIP-seq libraries were generated using NuGen Ovation Ultra Low System V2 kits according to manufacturer’s instructions. Quantseq libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) according to manufacturer’s instructions.

tag: tissue

value: seedling

tag: chip antibody

value: anti-H3K4me3 (ab8580, abcam)

tag: ecotype


description: Library name: ChIPseq_SetD_antiH3K4me3_StPRDM9g4_line1


title: HMC3 MPRA replicate 1

description:
Library name: HMC3_R1
MPRA library RNA-Seq, replicate 1


title: HeLa MPRA replicate 2

description:
Library name: HeLa_R2
MPRA library RNA-Seq, replicate 2

source_name: HeLa

value: HeLa

value: Cervical carcinoma


title: HEK293T_DMSO_250uM_Rep2

description:
Library name: HEK293T_DMSO_250uM_Rep2
Total RNA with rRNA depletion


title: ChIPseq_SetD_antiH3K4me3_rdr6_rep2

description: Library name: ChIPseq_SetD_antiH3K4me3_rdr6_rep2


title: HeLa MPRA replicate 1

description:
Library name: HeLa_R1
MPRA library RNA-Seq, replicate 1


title: HEK293T_DMSO_250uM_Rep1

description:
Library name: HEK293T_DMSO_250uM_Rep1
Total RNA with rRNA depletion


title: HEK293 MPRA replicate 1

description:
Library name: HEK293_R1
MPRA library RNA-Seq, replicate 1

value: Human embryonic kidney


title: ChIPseq_SetD_antiH3K4me3_rdr6_rep1

description: Library name: ChIPseq_SetD_antiH3K4me3_rdr6_rep1


title: HEK293 MPRA replicate 2

description:
Library name: HEK293_R2
MPRA library RNA-Seq, replicate 2


description: Library name: ChIPseq_SetC_antiHA_StSDG2gLRCEN3_withST_rep2

value: anti-HA (3F10, Merck)


title: ChIPseq_SetD_antiHA_rdr6_rep2

description: Library name: ChIPseq_SetD_antiHA_rdr6_rep2


title: shYTHDF2-IP-2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig normalized signal

source_name: Skin

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

tag: technology

tag: condition

value: YTHDF2 knockdown


title: MCF7 MPRA replicate 2

description:
Library name: MCF7_R2
MPRA library RNA-Seq, replicate 2


title: HTO Library for CEL230327LH

city: Portland

first: Laura

middle: M

last: Heiser

state: OR

address: 2730 S Moody Ave

department: Biomedical Engineering

institute: Oregon Health and Science University

description:
Library name: Sample 2
HTO

library_source: other

data_processing:
BCL files were converted to fastq using the bamtofastq tool (Illumina). Reads were aligned to GRCh38-2020-A and counted using CellRangre (v6.0.2, 10X Genomics) to produce bam file and count matrices.
The R package deMULTIplex was used to demultiplex the HTO and assign sample to each cell.
Assembly: GRCh38-2020-A
Supplementary files format and content: Filtered feature, barcode, and matrix output from Cellranger 6.0.2 (CEL230327LH_filtered_feature_barcodes.tsv.gz, CEL230327LH_filtered_feature_features.tsv.gz, CEL230327LH_filtered_feature_matrix.mtx.gz)
Supplementary files format and content: Hashtag oligonucleotide barcode and sample information (CEL230327LH_adt_features.csv.gz)
Library strategy: CITE-seq

molecule: protein

source_name: Mammary

growth_protocol: Cells were grown in medium consistingof DMEM/F12, 5% horse serum, 100 ng/mL cholera toxin, .5 ug/mL hydrocortisone, 10 ug/mL insulin, and 1% Pen/Strep.

extract_protocol:
Culture medium was removed, and cells were rinsed twice with PBS. Cells were then incubated in 0.05% trypsin-EDTA for about 5 minutes until they detached from the plate surface. After detachment, cells were gently triturated and the enzyme was neutralized using PBS containing 10% FBS. Cells were collected by centrifugation at 300 x g for 5 minutes and resuspended in PBS.
All samples were multiplexed and underwent hashtag oligo staining according to the vendor’s recommendations (TotalSeq-A, BioLegend). The library was prepared using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10X Genomics) to capture both gene expression and antibody-derived features.

treatment_protocol: Cells were plated 24 hours prior to treatment in growth media lacking EGF and insulin. After 24 hours the cells were treated with 10ng/mL OSM, 10 ng/mL EGF, or 20 ng/mL IFNG + 10 ng/mL EGF

value: Mammary

value: Epithelial

value: mixed sample

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0255 (shSCR_EGF), TotalSeq-A0256 (shSCR_IFNG), TotalSeq-A0257 (shSCR_OSM), TotalSeq-A0258 (shHIF1A_EGF), TotalSeq-A0259 (shHIF1A_IFNG), TotalSeq-A0260 (shHIF1A_OSM),


title: MCF10A (shSCR and shHIF1A), HTO multiplexed treated with ligand, gene expression

description:
Library name: Sample 1
10X Genomics

library_source: transcriptomic single cell

data_processing:
BCL files were converted to fastq using the bamtofastq tool (Illumina). Reads were aligned to GRCh38-2020-A and counted using CellRangre (v6.0.2, 10X Genomics) to produce bam file and count matrices.
The R package deMULTIplex was used to demultiplex the HTO and assign sample to each cell.
Assembly: GRCh38-2020-A
Supplementary files format and content: Filtered feature, barcode, and matrix output from Cellranger 6.0.2 (CEL230327LH_filtered_feature_barcodes.tsv.gz, CEL230327LH_filtered_feature_features.tsv.gz, CEL230327LH_filtered_feature_matrix.mtx.gz)
Supplementary files format and content: Hashtag oligonucleotide barcode and sample information (CEL230327LH_adt_features.csv.gz)

value: mRNA


description: Library name: ChIPseq_SetC_antiHA_StSDG2gLRCEN3_withST_rep1


title: shYTHDF2-IP-1


title: HEK293T_Acyclovir_250uM_Rep2

description:
Library name: HEK293T_Acyclovir_250uM_Rep2
Total RNA with rRNA depletion

value: human embryonic kidney cells

value: WT

value: Acyclovir 250uM for 3 days


title: Dam-HP1a in Ago2WT brain_rep2

city: Moscow

first: Yuri

last: Shevelyov

address: Kurchatov sq., 2

country: Russia

institute: National Research Centre “Kurchatov Institute”

description: Library name: E2C_DamHP1_rep2

data_processing:
DamID-seq reads were trimmed from Illumina adapters using trim_galore version 0.6.10.
For genome mapping, bowtie2 version 2.5.4 was used with standard settings, bam files then were filtered from unmapped reads (flag -F 4) and sorted with samtools version 1.9.
For genome profile generation, bamCoverage from deeptools version 3.5.4 was used with the settings "--binSize 50 --normalizeUsing CPM -of bigwig --effectiveGenomeSize 120000000" for multimappers or "--binSize 50 --minMappingQuality 40 --normalizeUsing CPM -of bigwig --effectiveGenomeSize 120000000" for unique mappers
All the subsequent data analysis is shown in the GitHub repository, associated with the article, including transposable element mapping
Assembly: dm3
Supplementary files format and content: processed data files are bigwig dm3 genome profiles with either all mapped reads including multimappers or only uniquely mapped reads
Library strategy: DamID-Seq

organism: Drosophila melanogaster

source_name: central brain

growth_protocol: Flies were grown according to standard protocols at room temperature

extract_protocol:
The central brain was extracted in two replicates from approximately one hundred third instar male larvae of the corresponding genotypes. Several micrograms of genomic DNA were isolated from the larval brain. After that, PCR amplification of methylated GATC-GATC fragments of the genome was carried out according to (Vogel et al. 2007). PCR-amplified methylated fragments were digested with DpnII to remove adaptors and were purified using PCR purification kit (Qiagen). After that, libraries from the samples containing ~0.5 µg DNA were prepared for next generation sequencing on Illumina.
Libraries were constructed according to standard protocol for sequencing on Illumina.

value: central brain

tag: developmental stage

value: late L3 instar male larvae


title: Dam-only in Ago2WT brain_rep1

description: Library name: E2C_Dam_rep1

value: Dam4-HT-intein@L127C/+; Ago2WT/Ago2WT


title: Dam-only in Ago2WT brain_rep2

description: Library name: E2C_Dam_rep2


title: shNC-IP-1 (YTHDF2 control)

value: Control


title: shYTHDF2-input-2

value: RNA-Seq


description: Library name: ChIPseq_SetC_antiHA_StSDG2gLRCEN3_noST_rep1

value: seedling


title: shYTHDF2-input-1


title: shNC-input-2 (YTHDF2 control)


title: Dam-only in Ago2mut brain_rep2

description: Library name: E2AGOM_Dam_rep2

value: Dam4-HT-intein@L127C/+; Ago2414/Ago2454


title: ChIPseq_SetC_antiHA_Col0_rep2

description: Library name: ChIPseq_SetC_antiHA_Col0_rep2

value: anti-HA (3F10, Merck)


title: Dam-only in Ago2mut brain_rep1

description: Library name: E2AGOM_Dam_rep1


title: shNC-input-1 (YTHDF2 control)


title: Simmental-Like fibroblast - Immortalized, Rep 2

city: Jerusalem

first: Shaun

last: Regenbaum

address: The Hebrew University of Jerusalem Edmond J. Safra Campus - Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
nf-core/rnaseq
Assembly: UMD3.1
Supplementary files format and content: raw counts

organism: Bos taurus

source_name: Immortalized line of Simmental-Like fibroblasts (biological rep 2)

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) according to manufacturer's directives.
Library construction was conducted using NEB Next® UltraTM5II RNA Library Kit (NEB) and NEXTSeq 75SR Kit6 (Illumina)


title: ChIPseq_SetC_antiHA_Col0_rep1

description: Library name: ChIPseq_SetC_antiHA_Col0_rep1


title: Simmental-Like fibroblast - Immortalized, Rep 3

source_name: Immortalized line of Simmental-Like fibroblasts (biological rep 3)


title: Dam-HP1a in Ago2mut brain_rep2

description: Library name: E2AGOM_DamHP1_rep2


title: Simmental-Like fibroblast - Immortalized, Rep 1

source_name: Immortalized line of Simmental-Like fibroblasts (biological rep 1)


title: Simmental-Like fibroblast - Senescent, Rep 2

source_name: Senescent stage Simmental-Like fibroblasts (biological rep 2)


title: shNC-IP-2 (YTHDF2 control)


title: Dam-HP1a in Ago2mut brain_rep1

description: Library name: E2AGOM_DamHP1_rep1


description: Library name: ChIPseq_SetC_antiH3K4me3_StSDG2gLRCEN3_withST_rep1

value: anti-H3K4me3 (ab8580, abcam)


description: Library name: ChIPseq_SetC_antiHA_StSDG2gLRCEN3_noST_rep2


title: Simmental-Like fibroblast - Senescent, Rep 3

source_name: Senescent stage Simmental-Like fibroblasts (biological rep 3)


title: Simmental-Like fibroblast - Primary, Rep 3

source_name: Primary culture of Simmental-Like fibroblasts (biological rep 3)


title: Dam-only in brain upon Lam-KD in neurons_rep2

description: Library name: E1LKD_Dam_rep2


title: Simmental-Like fibroblast - Primary, Rep 1

source_name: Primary culture of Simmental-Like fibroblasts (biological rep 1)


description: Library name: ChIPseq_SetC_antiH3K4me3_StSDG2gLRCEN3_noST_rep2


title: Simmental-Like fibroblast - Senescent, Rep 1

source_name: Senescent stage Simmental-Like fibroblasts (biological rep 1)


title: Dam-only in brain upon Lam-KD in neurons_rep1

description: Library name: E1LKD_Dam_rep1


title: Simmental-Like fibroblast - Primary, Rep 2

source_name: Primary culture of Simmental-Like fibroblasts (biological rep 2)


title: Dam-HP1a in Ago2WT brain_rep1

description: Library name: E2C_DamHP1_rep1


description: Library name: ChIPseq_SetC_antiH3K4me3_StSDG2gLRCEN3_noST_rep1


title: Holstein-Like  fibroblast - Immortalized, Rep 2

source_name: Immortalized line of Holstein-Like fibroblasts (biological rep 2)


title: Dam-HP1a in brain upon Lam-KD in neurons_rep2

description: Library name: E1LKD_DamHP1_rep2


title: ChIPseq_SetC_antiH3K4me3_Col0_rep2

description: Library name: ChIPseq_SetC_antiH3K4me3_Col0_rep2


title: Dam-HP1a in brain upon Lam-KD in neurons_rep1

description: Library name: E1LKD_DamHP1_rep1


title: Holstein-Like  fibroblast - Senescent, Rep 2

source_name: Senescent stage Holstein-Like fibroblasts (biological rep 2)


description: Library name: ChIPseq_SetC_antiH3K4me3_StSDG2gLRCEN3_withST_rep2


title: Holstein-Like  fibroblast - Senescent, Rep 1

source_name: Senescent stage Holstein-Like fibroblasts (biological rep 1)


title: Dam-only in control for Lam-KD brain_rep2

description: Library name: E1C_Dam_rep2


title: Holstein-Like  fibroblast - Primary, Rep 3

source_name: Primary culture of Holstein-Like fibroblasts (biological rep 3)


description: Library name: ChIPseq_SetB_antiHA_StSDG2g4_lineCB12_rep2

source_name: seedling


title: Dam-only in control for Lam-KD brain_rep1

description: Library name: E1C_Dam_rep1


title: Holstein-Like  fibroblast - Primary, Rep 2

source_name: Primary culture of Holstein-Like fibroblasts (biological rep 2)


title: Holstein-Like  fibroblast - Primary, Rep 1

source_name: Primary culture of Holstein-Like fibroblasts (biological rep 1)


description: Library name: ChIPseq_SetB_antiHA_StSDG2g4_lineCB10_rep2


title: Thymic iNKT cells, Prkd2/3-deficient, bulkTCR-seq

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: Prkd2/3-deficient, bulkTCR-seq
Takara

data_processing:
Sequencing was performed on MiSeq platform in a 301+301-base paired-end mode.
Illumina RTA 1.18.54 software was used for base calling.
Generated reads were processed with MiXCR v3.0.11 using commands (align, assemble, assembleContigs, exportClones) and deafult MiXCR v3.0.11 VDJ reference.
Assembly: Deafult MiXCR v3.0.11 VDJ reference
Supplementary files format and content: fullVDJ.tsv: output file of mixcr exportClones command with option (-nFeature VDJRegion --preset full) including nucleotide sequence of VDJRegion
Library strategy: TCR-Seq

organism: Mus musculus

source_name: Thymus

extract_protocol:
Thymocytes were resuspended in 2%FBS/RPMI1640 medium and stained with anti-mouse TCRb-FITC and alpha-Galactosylceramide (a-GalCer)-loaded mouse CD1d tetramer-APC and anti-APC microbeads. Thymic iNKT cells were enriched by MACS magnetic separator (Miltenyi). Thereafter cells were passed through 0.45 um mesh, stained with propium iodide (PI) and purified for TCRβ+CD1d tetramer+PI- cells by a cell sorter (SH800S, Sony). Purified thymic iNKT cells were washed with PBS (-), suspended in QIAzol Lysis Reagent (QIAGEN) for RNA purification and applied to bulk TCR-seq analysis using SMARTer mouse TCR a/b profiling kit (Takara).
Library construction was conducted using SMARTer mouse TCR a/b profiling kit (Takara) following the manufacturer’s instructions. In brief, after reverse transcription of RNA obtained from 1~10 x10⁴ thymic iNKT cells, cDNA was amplified by 21 cycles for PCR1 and 24 cycles for PCR2, and amplified libraries were purified using magnetic beads for sequencing.

value: Thymus

value: iNKT cells

value: Prkd2/3 deficient


title: Holstein-Like  fibroblast - Immortalized, Rep 3

source_name: Immortalized line of Holstein-Like fibroblasts (biological rep 3)


description: Library name: ChIPseq_SetB_antiHA_StSDG2g4_lineCB12_rep1


title: Dam-HP1a in control for Lam-KD brain_rep2

description: Library name: E1C_DamHP1_rep2

source_name: central brain


title: Dam-HP1a in control for Lam-KD brain_rep1

description: Library name: E1C_DamHP1_rep1


title: endothelial cells untreated - rep 2

city: Brescia

first: Martina

last: Tambassi

state: Italy

address: Via Bianchi, 9

department: Risk Analysis and Genomic Epidemiology Unit

country: Italy

institute: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, VAT IT00284840170

description: Library name: Ec-C-060624

data_processing:
The bioinformatic analysis was performed using the Galaxy platform (Galaxy Community). Specifically, reads were checked for quality by using FastQC software, version 0.12.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then trimmed with Trimmomatic software, version 0.39 (Bolger et al., 2014). STAR aligner version 2.7.11a (Dobin et al., 2013) was used to map the trimmed reads to the reference genome of Canis lupus familiaris CanFam3.1. Determination of adjusted P-values for differential gene expression comparisons was done using DESeq2 (Love at al., 2014).
Assembly: GCA_000002285.2
Supplementary files format and content: tab-delimited text file includes row counts for each sample

organism: Canis lupus familiaris

source_name: aorta

growth_protocol: CnAOEC and culture medium were purchased from Cell Applications, Inc (San Diego, CA, USA. n. Cn304-05). Cells were maintained in an incubator at 37°C and 5% CO2 and were always handled under a hood to maintain sterility. Medium (Canine Endothelial Cell Basal Medium n. Cn210-485 + Canine Endothelial Cell Growth Supplement n. Cn211-GS) was supplemented with penicillin/streptomycin (Corning, 100X solution, n. 30-002-CI), amphotericin B (Corning, n. 30-003-CF, starting concentration 250 µg/ml diluted 100-fold for use) and 10% FBS (fetal bovine serum) (Gibco, n. A5256701).

extract_protocol:
RNA extraction was performed using the NucleoSpin RNA II kit following manufacturer’s instructions (Macherey-Nagel, No. 740955.50). An additional DNA digestion step with rDNase in solution was performed in order to further reduce DNA contamination, followed by RNA precipitation with sodium acetate and ethanol.
The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, San Diego, California, USA) was used to prepare transcriptomic libraries using 10 ng of RNA input. Libraries were quantified using Quantus dsDNA kit (Promega, Madison, Wisconsin) and their average fragment length was assessed using Agilent High Sensitivity D1000 kit on the Agilent TapeStation system (Agilent Technologies, Inc, Waldbronn, Germany).

treatment_protocol: Cells were seeded in 24-well plates and treated with polystyrene nanoplastics with a diameter of 100 nm (Sigma-Aldrich 43302-5ML-F) 25 µg/mL.

value: aorta

value: CnAOEC

value: endothelial cells

value: control


title: Thymic iNKT cells, WT, bulkTCR-seq

description:
Library name: WT, bulkTCR-seq
Takara

value: Wild type


title: endothelial cells treated with nanoplastics - rep 3

description: Library name: Ec-25-030724

value: nanoplastics


description: Library name: ChIPseq_SetB_antiHA_StSDG2g4_lineCB10_rep1


title: C2C12 myoblasts, Hnrnpl shRNA knockdown condition, n=2

city: Minneapolis

first: Peter

middle: B

last: Kang

state: MN

address: 2101 6th Street SE

department: Neurology

institute: University of Minnesota

description: Library name: Hnrnpl-knockdown-RNA2

data_processing:
RNAseq data was basecalled using Guppy v.6.0.1, and bases called were counted with NanoPlot v1.32.1
Basecalled data was mapped to the mouse genome (GRCm39) using splice-aware Minimap2 v.2.17, and the number of bases and reads mapped were counted with SAMtools stats v.1.9
Gene transcript numbers were counted using HTSeq v.0.9.1.
Assembly: GRCm39
Supplementary files format and content: ens_count files (tab-deliminated text file) produced by HTSeq of the raw counts

growth_protocol: C2C12 myoblast cultures were established and maintained in growth medium containing DMEM (Corning) +10% fetal bovine serum (FBS) (GenClone) + 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was extracted from two biological replicates each of scrambled and Hnrnpl shRNA-treated C2C12 myoblasts using the PureLink RNA Mini Kit (Invitrogen). RNA concentration and purity was verified using a NanodropOne Spectrophotometer (Thermofisher Scientific), and RNA integrity was determined using a 2100 Bioanalyzer (Agilent).
1ug of total RNA was used for nanopore direct RNA sequencing (SQK-RNA002) on R9.4.1 flow cells using a GridION sequencer (Oxford Nanopore Technologies).

treatment_protocol: C2C12 myoblasts were transfected with either a cocktail of three different shRNAs targeting mouse-Hnrnpl or scrambled shRNA control (catalog number MSH092806-CU6, GeneCopoeia) using Lipofectamine 3000 (Invitrogen). The 3 shRNAs target the following sequences on mouse Hnrnpl – NM_177301.5: Hnrnpl (1) – ATTGACGGAGTAGTGGAAGCT; Hnrnpl (2) – CTACTCCATAACCACGGATGT; Hnrnpl (3) – ATGGTCTATGGCTTGGATCAA. The plasmids containing the shRNA sequences also expressed an eGFP reporter. Clones expressing the eGFP reporter were isolated and stable cells were selected using puromycin 3µg/mL (Sigma – P8833). eGFP expression was detected using Leica DM IL LED microscope (Leica). The eGFP-positive clones were expanded, the knockdown efficiency was evaluated with qPCR, and the cells were used for further experimentation. Replicates for each experiment were obtained from different passages of the same selected stable cell line.

value: myoblast

value: WT

value: Hnrnpl shRNA

tag: batch


title: Holstein-Like  fibroblast - Senescent, Rep 3

source_name: Senescent stage Holstein-Like fibroblasts (biological rep 3)


title: endothelial cells untreated - rep 3

description: Library name: Ec-C-030724


title: endothelial cells untreated - rep 1

description: Library name: Ec-C-050624


title: ChIPseq_SetB_antiHA_rdr6_rep2

description: Library name: ChIPseq_SetB_antiHA_rdr6_rep2


title: ChIPseq_SetC_antiH3K4me3_Col0_rep1

description: Library name: ChIPseq_SetC_antiH3K4me3_Col0_rep1


title: endothelial cells treated with nanoplastics - rep 1

description: Library name: Ec-25-050624


title: Holstein-Like  fibroblast - Immortalized, Rep 1

source_name: Immortalized line of Holstein-Like fibroblasts (biological rep 1)


title: C2C12 myoblasts, Hnrnpl shRNA knockdown condition, n=1

description: Library name: Hnrnpl-knockdown-RNA1


title: endothelial cells treated with nanoplastics - rep 2

description: Library name: Ec-25-060624


title: ChIPseq_SetB_antiHA_rdr6_rep1

description: Library name: ChIPseq_SetB_antiHA_rdr6_rep1


title: C2C12 myoblasts, scrambled shRNA control, n=2

description: Library name: Hnrnpl-scrambled-RNA2

value: scrambled shRNA


title: Outer hair cells, P0, WT, ATAC-Seq, rep2

first: Jaime

last: Garcia-Anoveros

address: 303 E Chicago Ave, Ward 10-070, Chicago, IL 60657

department: Anesthesiology

description:
Library name: P0_OHC2_ATAC
OHC2

data_processing:
Adaptor sequences were trimmed from reads using Trimmomatic
Trimmed reads were aligned to the GRCm39/mm39 mouse genome using Bowtie2
ATAC-seq peaks were identified for each cell type using Genrich
Tag directories were generated using HOMER's makeTagDirectory module
BigWig files were generated using HOMER's makeMultiWigHub.pl module
ATAC-seq peaks for both cell types were combined into a single file using BedTools
Number of reads under each peak was quantified using HOMER's annotatePeaks.pl without normalization
Assembly: mm39
Supplementary files format and content: tab-delimited file with raw counts under each peak for each sample
Supplementary files format and content: BigWig file for each sample, NarrowPeak file for each cell type

source_name: Organ of Corti

extract_protocol:
Atoh1-GFP positive inner hair cells (IHCs) and Atoh1-GFP; Insm1-GFP-Cre and R26-TdTomato positive sensory outer hair cells (OHCs) were FACS-sorted from P0 cochleae into 500 uL 1x PBS with 2% FBS.
Cells were centrifuged at 700g for 20 min at 4°C. The supernatant was removed and cells were lysed in 20 uL lysis buffer (10mM Tris HCl, 5mM MgCl2, 10% DMF, 0.2% NP-40) at 4°C. 30 uL reaction buffer (10mM Tris-HCl pH 8, 5 mM MgCl2, 10% DMF, 3000 u Tn5 transposase from Segil lab) was added, and sample was incubated at 37°C for 30 min. Fragments were purified using the MinElute Reaction Cleanup Kit (Qiagen), and DNA fragments were eluted into 23 uL elution buffer from kit. A 5-cycle PCR was peformed using a mix with 20 uL DNA fragments solution, 2.5 ul primer 1 (25 uM), 2.5 uL primer 2 with barcode (25 uM), 0.3ul SYBR Green and 25 uL 2x NEB Next High-Fidelity PCR Master MIix to give a final volume of 50 uL, using an intial elongation step of 3 min at 72°C followed by 5 cycles of 98°C for 10s, 63°C for 30s and 72°C for 1 min, and a final elongation step at 72°C for 3 min. 5 ul of each sample was taken and run in a QuantStudi 7 Flex Real-Time PCR System (Applied Biosystems) with an intitial denaturaiton at 98°C for 1 min, followed by 40 cycles at 98°C for 10s, 63°C for 30s and 72°C for 1 min.  The number of cycles to reach 1/4 saturation point was determined for each sample, and the remaining 45 uL of the sample was run with an initial denaturation temperature at 98°C for 1 min, followed by the required number of cycles to reach 1/4 saturation point at 98°C for 10s, 63°C for 30s and 72°C for 1 min. 45 uL AMPure XP Reagent (Beckman Coulter) was added then added to PCR products following the reaction. Tubes were placed on a magnetic beads separation rack, and the supernatant was discarded. Beads were washed twice using 200 uL 80% ethanol, and DNA was eluted from the beads using 22 uL nuclease-free water. Samples were sent to the NUSeq core facility at Northwestern University for size selection for fragments between 200bp and 1kb, and sequencing using the Illumina NextSeq 500 sequencer. Samples were sequenced using 37bp paired-end reads to a depth of about 50 million reads.

value: Organ of Corti

value: Outer hair cell


title: Outer hair cells, P0, WT, ATAC-Seq, rep1

description:
Library name: P0_OHC1_ATAC
OHC1


title: C2C12 myoblasts, scrambled shRNA control, n=1

description: Library name: Hnrnpl-scrambled-RNA1


title: Coptotermes gestroi_3_Worker Head_Pre-Molting

city: College Station

first: Kyung

middle: Seok

last: Kim

state: TX

address: 2556 F&B ROAD

department: Dept of Entomology

institute: Texas A&M University

description:
Library name: Cg_3_WH_PreM
Column name in raw_counts_All_Samples.txt: Cg_3_WH_PreM

data_processing:
To obtain clean reads, reads mapped to rRNAs were removed, low-quality reads (those with greater than 20% of the base quality scores lower than 10), and reads with unknown bases (N bases > 5%) were filtered. The remaining clean reads were mapped to a C. formosanus reference genome (GCA_013340265.1_CopFor1.0_NCBI_20221021) using Bowtie2 (Langmead B, Salzberg SL, 2012 https://doi.org/10.1038/nmeth.1923), and then gene expression level was calculated with RSEM (Li and Dewey, 2011, DOI:10.1186/1471-2105-12-323).
Finally, differentially expressed genes (DEGs) for pairwise expression comparison were identified using Deseq2
Assembly: The remaining clean reads were mapped to a C. formosanus reference genome (GCA_013340265.1_CopFor1.0_NCBI_20221021) using Bowtie2
Supplementary files format and content: csv files include raw counts and length for each sample

organism: Coptotermes gestroi

source_name: Head

extract_protocol:
Total RNA was extracted using the Trizol method and silica membrane-based columns to capture RNA.
RNA-seq library was prepared using the Hieff NGS™ Ultima Dual-mode mRNA Library Prep Kit (Catalogue #: 12309ES96, Yeasen Biotechnology, Shanghai, China) ) according to the manufacturer’s protocols.

value: Head


title: Inner hair cells, P0, WT, ATAC-Seq, rep2

description:
Library name: P0_IHC2_ATAC
IHC2

value: Inner hair cell


title: Coptotermes gestroi_3_Worker Head_Post-Molting

description:
Library name: Cg_3_WH_PoM
Column name in raw_counts_All_Samples.txt: Cg_3_WH_PoM


title: Inner hair cells, P0, WT, ATAC-Seq, rep1

description:
Library name: P0_IHC1_ATAC
IHC1


title: Coptotermes formosanus_3_Worker Head_Pre-Molting

description:
Library name: Cf_3_WH_PreM
Column name in raw_counts_All_Samples.txt: Cf_3_WH_PreM

organism: Coptotermes formosanus


title: Coptotermes gestroi_3_Worker Head_Inter-Molting

description:
Library name: Cg_3_WH_IM
Column name in raw_counts_All_Samples.txt: Cg_3_WH_IM


title: Coptotermes formosanus_3_Worker Head_Post-Molting

description:
Library name: Cf_3_WH_PoM
Column name in raw_counts_All_Samples.txt: Cf_3_WH_PoM


title: Total thymocytes (Input)

first: Eri

last: Ishikawa

address: 3-1 Yamadaoka

institute: Osaka University

description:
Library name: Thy_Input
Analysis by Active Motif

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500 and bcl2fastq2 (v2.20)) were mapped to the genome using the BWA algorithm (v0.7.12, “bwa aln/samse” with default settings). Alignment information for each read was stored in the BAM format using Samtools (v0.1.19). Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were removed.
Since the 5´-ends of the aligned reads (tags) represent the end of ChIP/IP-fragments, the tags were extended in silico (using Active Motif software) at their 3´-ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. This information (“signal map”; histogram of fragment densities) was stored in a bigWig file (wigToBigWig, v4).
The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals were defined by the chromosome number and a start and end coordinate. Peaks were called using MACS 2.1.0. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks. Peak filtering was performed by removing false ChIP-seq peaks as defined within the ENCODE blacklist.
Spike-in adjusted normalization was performed. The number of test tags were adjusted by a factor that would result in the same number of spike-in Drosophila tags for each sample.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Thymocytes from iNKT-iPS cell-derived mice were resuspended in 2%FBS/RPMI1640 medium and stained with alpha-Galactosylceramide (a-GalCer)-loaded mouse CD1d tetramer-APC and anti-APC microbeads. Thymic iNKT cells were purified by MACS magnetic separator (Miltenyi). Total thymocytes from wild-type mice and purified thymic iNKT cells were washed with PBS and cell pellets were snap-frozen in liquid nitrogen. Frozen cells were sent to Active Motif for further analysis. Active Motif fixed cells and chromatin was extracted and applied to sonication after quenching.
Active Motif performed ChIP reactions, library generation and barcoding for next-generation sequencing and data analysis. Spike-in of Drosophila chromatin was performed before ChIP for normalization. 30 ug of chromatin and 30 ul of anti-Ikaros antibody (Cell Signaling Technology, #14859) were used for the ChIP reaction and the reaction was validated by qPCR. Library generation, library quality check and barcoding were performed and next-generation sequencing was done using Illumina NextSeq 500. As an input, equal amounts of unprecipitated genomic DNA from each sample were used to generate a next-generation sequencing libraries, and sequenced in parallel with the ChIP-seq samples.

value: Thymus

value: Thymocytes


title: Thymic iNKT cells, Ilaros (ChIP)

description:
Library name: NKT_Ikaros, ChIP
Analysis by Active Motif

value: Thymic iNKT cells

value: iNKT-iPS cell-derived mice

value: Ikaros  (Cell Signaling Technology, #14859)


title: Coptotermes gestroi_3_Worker Body_Post-Molting

description:
Library name: Cg_3_WB_PoM
Column name in raw_counts_All_Samples.txt: Cg_3_WB_PoM

source_name: thorax and abdomen with gut removed

value: thorax and abdomen with gut removed


title: Thymic iNKT cells (Input)

description:
Library name: NKT_Input
Analysis by Active Motif


title: Coptotermes gestroi_2_Worker Head_Pre-Molting

description:
Library name: Cg_2_WH_PreM
Column name in raw_counts_All_Samples.txt: Cg_2_WH_PreM


title: Coptotermes gestroi_3_Worker Body_Pre-Molting

description:
Library name: Cg_3_WB_PreM
Column name in raw_counts_All_Samples.txt: Cg_3_WB_PreM


title: Total thymocytes, Ilaros (ChIP)

description:
Library name: Thy_Ikaros, ChIP
Analysis by Active Motif


title: Coptotermes formosanus_3_Worker Body_Pre-Molting

description:
Library name: Cf_3_WB_PreM
Column name in raw_counts_All_Samples.txt: Cf_3_WB_PreM


title: Coptotermes formosanus_3_Worker Head_Inter-Molting

description:
Library name: Cf_3_WH_IM
Column name in raw_counts_All_Samples.txt: Cf_3_WH_IM


title: Znhit2_MUT_s9

city: Amherst

first: Jesse

last: Mager

state: Massachusetts

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

data_processing:
Raw reads were trimmed for sequence quality and to remove adapters or primers using trimmomatic (v0.39), and the quality was evaluated by fastqc (v0.11.9). Trimmed reads were aligned to the mouse genome assembly GRCm39 using STAR (v2.7.6a). Single embryo genotypes were confirmed by viewing read alignment to genes/exons targeted for knockout on IGV (v2.16.2).
Differential gene expression analysis was performed in R (v4.2.1) using DESeq2 (v1.36.0). Adjusted p-values were calculated by DEseq2 using the Benjamini-Hochberg method.
Assembly: Mus Musculus(GRCm39)
Supplementary files format and content: RPKM_summary.xlsx contains normalized read counts. DEGs_summary.xlsx contains differential gene expression results between MUT embryos compared to WT or HET embryos.

source_name: Single embryo

growth_protocol: For OG samples, Blastocysts were harvested at E3.5 and cultured individually in iBiTreat dishes with DMEM containing 10% fetal bovine serum. Embryos were kept in culture for 72 hrs at 37°C and 5% CO2  atmosphere in a humidified incubator.

extract_protocol:
RNA was extracted from E3.5, E6.5, or OG embryos individually using the Zymo kit as previously described. Total RNA was analyzed using the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico assay. RNaseq libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina following manufacturer instructions. The quantity of library was assayed using the Qubit DNA HS assay, and quality was analyzed on Bioanalyzer.
Libraries were sequenced on Illumina NextSeq 500 platform using NextSeq 500/550 Mid Output v2.5 kit (150 cycles) with 76 bp paired-end sequencing chemistry. RNAseq library preparation and Illumina Next-Generation Sequencing was performed at Genomics Resource Laboratory (RRID:SCR_017907), Institute for Applied Life Sciences, University of Massachusetts Amherst, MA.

tag: time

value: Single embryo


title: Znhit2_HET_s6


title: Coptotermes formosanus_2_Worker Head_Pre-Molting

description:
Library name: Cf_2_WH_PreM
Column name in raw_counts_All_Samples.txt: Cf_2_WH_PreM


title: Coptotermes gestroi_2_Worker Head_Post-Molting

description:
Library name: Cg_2_WH_PoM
Column name in raw_counts_All_Samples.txt: Cg_2_WH_PoM


title: Znhit2_MUT_s8


title: Il27ra knockout, scRNA-seq

city: Milwaukee

first: Yi-Guang

last: Chen

state: WI

address: 9200 W. Wisconsin Ave.

department: Pediatrics

institute: Medical College of Wisconsin

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islets

extract_protocol:
Pancreata from mixed bone marrow chimera mice were inflated using a 30-gauge needle by injecting 3-5 mL of HBSS containing 0.5 U/mL collagenase P solution and 10 μg/mL DNase into the bile duct. The inflated pancreas was digested at 37°C for 15 min. Digested pancreata were washed three times with 10 mL of HBSS containing 2% FBS. Each individual pancreas was then suspended in 5 mL complete RPMI 1640.  Islets were visualized under a dissecting microscope and hand-picked.  Pelleted islets were suspended in 200 μL of enzyme free cell dissociation buffer.  Cells were then washed with 500 μL of HBSS, resuspended in RPMI 1640. Islet cells were stained with antibodies for CD45.1, CD45.2, CD11c, and CD19, and sorted into CD45.1 and CD45.2 T cells on a FACSAria III (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: pancreatic islets

value: T cells

tag: age

value: 9-12 weeks post transfer

tag: strain

tag: Sex

value: female


title: wildtype, scRNA-seq

description:
Library name: Sample 1
10x Genomics


title: Znhit2_HET_s4


title: Coptotermes gestroi_2_Worker Head_Inter-Molting

description:
Library name: Cg_2_WH_IM
Column name in raw_counts_All_Samples.txt: Cg_2_WH_IM


title: Coptotermes formosanus_3_Worker Body_Post-Molting

description:
Library name: Cf_3_WB_PoM
Column name in raw_counts_All_Samples.txt: Cf_3_WB_PoM


title: Znhit2_WT_s3


title: Znhit2_WT_s2


title: Coptotermes formosanus_2_Worker Head_Post-Molting

description:
Library name: Cf_2_WH_PoM
Column name in raw_counts_All_Samples.txt: Cf_2_WH_PoM


title: Coptotermes gestroi_2_Worker Body_Pre-Molting

description:
Library name: Cg_2_WB_PreM
Column name in raw_counts_All_Samples.txt: Cg_2_WB_PreM


title: Znhit2_WT_s1


title: Coptotermes formosanus_2_Worker Head_Inter-Molting

description:
Library name: Cf_2_WH_IM
Column name in raw_counts_All_Samples.txt: Cf_2_WH_IM


title: Znhit1_MUT_s9

value: Znhit1 MUT


title: Coptotermes gestroi_2_Worker Body_Post-Molting

description:
Library name: Cg_2_WB_PoM
Column name in raw_counts_All_Samples.txt: Cg_2_WB_PoM


title: Znhit1_MUT_s7


title: Coptotermes formosanus_2_Worker Body_Pre-Molting

description:
Library name: Cf_2_WB_PreM
Column name in raw_counts_All_Samples.txt: Cf_2_WB_PreM


title: Znhit1_HET_s6

value: Znhit1 HET


title: Coptotermes gestroi_2_Worker Body_Inter-Molting

description:
Library name: Cg_2_WB_IM
Column name in raw_counts_All_Samples.txt: Cg_2_WB_IM


title: Coptotermes formosanus_2_Worker Body_Post-Molting

description:
Library name: Cf_2_WB_PoM
Column name in raw_counts_All_Samples.txt: Cf_2_WB_PoM


title: Znhit2_HET_s5


title: Znhit1_WT_s3

value: Znhit1 WT


title: Znhit1_WT_s1


title: Coptotermes gestroi_1_Worker Head_Pre-Molting

description:
Library name: Cg_1_WH_PreM
Column name in raw_counts_All_Samples.txt: Cg_1_WH_PreM


title: Znhit1_WT_s2


title: Coptotermes formosanus_2_Worker Body_Inter-Molting

description:
Library name: Cf_2_WB_IM
Column name in raw_counts_All_Samples.txt: Cf_2_WB_IM


title: Coptotermes gestroi_1_Worker Head_Post-Molting

description:
Library name: Cg_1_WH_PoM
Column name in raw_counts_All_Samples.txt: Cg_1_WH_PoM


title: CTinput_9.5dpcPI_mb_RING1Blot2

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

data_processing:
The fastq files were trimmed and QC-ed by Trim Galore (version 0.6.7).
Trimmed sequences were mapped and counted on mm10 genome.
BAM files were converted into bigWig files by in-house software.
Assembly: mm10
Supplementary files format and content: plain text

source_name: midbrain

growth_protocol: Standard ES/EB medium.

extract_protocol:
Qiagen Rneasy Mini Kit
NEBNext poly(A) mRNA magnetic isolation module

value: midbrain

value: embryo


title: Coptotermes formosanus_1_Worker Head_Pre-Molting

description:
Library name: Cf_1_WH_PreM
Column name in raw_counts_All_Samples.txt: Cf_1_WH_PreM

value: Head


title: CTinput_9.0dpc_mb_RING1Blot2


title: Coptotermes gestroi_1_Worker Body_Post-Molting

description:
Library name: Cg_1_WB_PoM
Column name in raw_counts_All_Samples.txt: Cg_1_WB_PoM


title: CT_9.5dpc_mb_RING1Blot1


title: Coptotermes gestroi_1_Worker Head_Inter-Molting

description:
Library name: Cg_1_WH_IM
Column name in raw_counts_All_Samples.txt: Cg_1_WH_IM


title: Coptotermes formosanus_1_Worker Head_Post-Molting

description:
Library name: Cf_1_WH_PoM
Column name in raw_counts_All_Samples.txt: Cf_1_WH_PoM


title: CTinput_9.0dpc_mb_RING1Blot1


title: Coptotermes formosanus_1_Worker Head_Inter-Molting

description:
Library name: Cf_1_WH_IM
Column name in raw_counts_All_Samples.txt: Cf_1_WH_IM


title: CT_9.5dpcPI_mb_RING1Blot2


title: mus_Hif1a5_S19

city: Schlieren

first: Christian

last: Grimm

state: Zürich

address: Wagistrasse 14

department: Department of Ophthalmology

country: Switzerland

institute: Universität Zürich

description:
Library name: mus_Hif1a5_S19
rawcounts_mus.csv

data_processing:
Rsubread (v2.18.0) for alignment of reads with gencode M36 basic annotation gtf file in paired-end mode.
Gene-level quantification was performed with featureCounts() (Rsubread), using antisense strand-specific mode and the same GTF annotation.
Assembly: GRCm39
Supplementary files format and content: csv, raw counts as output from Rsubread's featurecount over a gene body.

source_name: retina

extract_protocol:
Retinas were isolated through a slit in the cornea and snap-frozen in liquid nitrogen. RNA from retinas or cells was isolated using an RNA isolation kit (Nucleo Spin RNA, Macherey-Nagel GmbH & Co.KG, Düren, Germany) according to the manufacturer’s instructions.
mRNA from 661W cells and murine retina was prepared using Illumina Stranded mRNA Prep to generate antisense paired-end reads and according to Illumina protocols.

value: retina


title: CT_9.5dpcPI_mb_RING1Blot1


title: CTinput_9.5dpc_mb_RING1Blot2


title: Coptotermes formosanus_1_Worker Body_Pre-Molting

description:
Library name: Cf_1_WB_PreM
Column name in raw_counts_All_Samples.txt: Cf_1_WB_PreM


title: mus_Hif1a4_S28

description:
Library name: mus_Hif1a4_S28
rawcounts_mus.csv


title: CTinput_9.5dpc_mb_RING1Blot1


title: Coptotermes formosanus_1_Worker Body_Post-Molting

description:
Library name: Cf_1_WB_PoM
Column name in raw_counts_All_Samples.txt: Cf_1_WB_PoM


title: CT_9.0dpc_mb_RING1Blot2


title: mus_Hif1a3_S18

description:
Library name: mus_Hif1a3_S18
rawcounts_mus.csv


title: CT_9.0dpc_mb_RING1Blot1


title: Hybrid G_3_Worker Head_Pre-Molting

description:
Library name: HyG_3_WH_PreM
Column name in raw_counts_All_Samples.txt: HyG_3_WH_PreM

organism: Coptotermes formosanus x Coptotermes gestroi


title: mus_Hif1a2_S20

description:
Library name: mus_Hif1a2_S20
rawcounts_mus.csv


title: CT_Skp1aKO_mb_RING1Blot1


title: CT_Skp1aKO_mb_RING1Blot2


title: CT_Pcgf1cont_mb_RING1Blot1


title: CT_Pcgf1contPI_mb_RING1Blot2


title: Hybrid G_3_Worker Head_Inter-Molting

description:
Library name: HyG_3_WH_IM
Column name in raw_counts_All_Samples.txt: HyG_3_WH_IM


title: CT_9.5dpc_mb_RING1Blot2


title: CTinput_9.5dpcPI_mb_RING1Blot1


title: mus_Hif1a1_S25

description:
Library name: mus_Hif1a1_S25
rawcounts_mus.csv


title: CT_Pcgf1contPI_mb_RING1Blot1


title: mus_EGFP5_S15

description:
Library name: mus_EGFP5_S15
rawcounts_mus.csv


title: Hybrid G_3_Worker Body_Pre-Molting

description:
Library name: HyG_3_WB_PreM
Column name in raw_counts_All_Samples.txt: HyG_3_WB_PreM


title: CT_Pcgf1cont_mb_RING1Blot2


title: CTinput_Skp1acont_mb_RING1Blot2


title: mus_EGFP4_S29

description:
Library name: mus_EGFP4_S29
rawcounts_mus.csv


title: Hybrid G_3_Worker Body_Post-Molting

description:
Library name: HyG_3_WB_PoM
Column name in raw_counts_All_Samples.txt: HyG_3_WB_PoM


title: CTinput_Skp1acontPI_mb_RING1Blot2


title: mus_EGFP3_S17

description:
Library name: mus_EGFP3_S17
rawcounts_mus.csv


title: CTinput_Skp1acont_mb_RING1Blot1


title: CTinput_Skp1acontPI_mb_RING1Blot1


title: Hybrid G_3_Worker Body_Inter-Molting

description:
Library name: HyG_3_WB_IM
Column name in raw_counts_All_Samples.txt: HyG_3_WB_IM


title: CTinput_Skp1aPcgf1dKO_mb_RING1Blot2


title: mus_EGFP2_S27

description:
Library name: mus_EGFP2_S27
rawcounts_mus.csv


title: Hybrid G_2_Worker Head_Pre-Molting

description:
Library name: HyG_2_WH_PreM
Column name in raw_counts_All_Samples.txt: HyG_2_WH_PreM


title: Hybrid G_3_Worker Head_Post-Molting

description:
Library name: HyG_3_WH_PoM
Column name in raw_counts_All_Samples.txt: HyG_3_WH_PoM


title: mus_EGFP1_S22

description:
Library name: mus_EGFP1_S22
rawcounts_mus.csv


title: Hybrid G_2_Worker Head_Post-Molting

description:
Library name: HyG_2_WH_PoM
Column name in raw_counts_All_Samples.txt: HyG_2_WH_PoM


title: CTinput_Skp1aPcgf1dKO_mb_RING1Blot1


title: LPS3

city: Shanghai

first: Yijie

last: Gao

address: 150 Jimo Road, Pudong New Area

department: Department of Obstetrics

country: China

institute: Tongji University Dongfang Hospital

description: Library name: PTB-3

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 25M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Cervical tissues

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Cervical tissues

value: Sprague-Dawley

value: WT

value: LPS


title: CTinput_Skp1aPcgf1cont_mb_RING1Blot2


title: 661W_Hif1a4_S23

description:
Library name: 661W_Hif1a4_S23
rawcounts_661W.csv

tag: cell line


title: Hybrid G_2_Worker Head_Inter-Molting

description:
Library name: HyG_2_WH_IM
Column name in raw_counts_All_Samples.txt: HyG_2_WH_IM


title: LPS1

description: Library name: PTB-1


title: 661W_Hif1a3_S30

description:
Library name: 661W_Hif1a3_S30
rawcounts_661W.csv


title: CTinput_Skp1aPcgf1cont_mb_RING1Blot1


title: PBS4

description: Library name: NC-4

value: PBS


title: 661W_Hif1a2_S26

description:
Library name: 661W_Hif1a2_S26
rawcounts_661W.csv


title: Hybrid G_2_Worker Body_Pre-Molting

description:
Library name: HyG_2_WB_PreM
Column name in raw_counts_All_Samples.txt: HyG_2_WB_PreM

value: thorax and abdomen with gut removed


title: CTinput_Skp1aPcgf1contPI_mb_RING1Blot2


title: PBS3

description: Library name: NC-3


title: CTinput_Skp1aPcgf1contPI_mb_RING1Blot1


title: Hybrid G_2_Worker Body_Post-Molting

description:
Library name: HyG_2_WB_PoM
Column name in raw_counts_All_Samples.txt: HyG_2_WB_PoM


title: Hybrid G_2_Worker Body_Inter-Molting

description:
Library name: HyG_2_WB_IM
Column name in raw_counts_All_Samples.txt: HyG_2_WB_IM


title: PBS2

description: Library name: NC-2


title: 661W_EGFP4_S24

description:
Library name: 661W_EGFP4_S24
rawcounts_661W.csv


title: LPS4

description: Library name: PTB-5


title: PBS1

description: Library name: NC-1


title: Hybrid G_1_Worker Head_Pre-Molting

description:
Library name: HyG_1_WH_PreM
Column name in raw_counts_All_Samples.txt: HyG_1_WH_PreM


title: CT_Pcgf1KO_mb_RING1Blot2


title: 661W_EGFP3_S21

description:
Library name: 661W_EGFP3_S21
rawcounts_661W.csv


title: CTinput_Skp1aKO_mb_RING1Blot2


title: LPS2

description: Library name: PTB-2


title: Hybrid G_1_Worker Head_Post-Molting

description:
Library name: HyG_1_WH_PoM
Column name in raw_counts_All_Samples.txt: HyG_1_WH_PoM


title: 661W_EGFP2_S31

description:
Library name: 661W_EGFP2_S31
rawcounts_661W.csv


title: Hybrid G_1_Worker Head_Inter-Molting

description:
Library name: HyG_1_WH_IM
Column name in raw_counts_All_Samples.txt: HyG_1_WH_IM


title: CRISPRoff_NTC_Donor2

city: San Francisco

first: Laine

last: Goudy

state: CA

address: 400 Parnassus Ave

institute: University of California, San Francisco

description:
Library name: 33b_Neg_D2
normalized_counts_Co013.csv

data_processing:
RNA-seq sequencing data was aligned and counts were generated using the RNAseq pipeline of nf-core (v 3.18)69.  Raw sequencing reads were quantified using Salmon and summarized to gene-level counts using tximport. Differential gene expression analysis was conducted using the limma-voom framework, with donor variation included as a covariate in the statistical model. Gene expression was normalized using the trimmed mean of M-values (TMM) method, and low-expressed genes were filtered prior to analysis. Differentially expressed genes were identified by comparing treated samples to non-targeting controls (NTC), with significance criteria set at adjusted p-value < 0.05 (Empirical-Bayes moderated statistics with Benjamini–Hochberg correction) and absolute log2 fold change > 1. Results were visualized using volcano plots displaying log2 fold change versus -log10(adj. P-value), with genes colored based on significance thresholds or target gene.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each file

source_name: primary

growth_protocol: Human peripheral blood Leukopaks enriched for peripheral blood mononuclear cells (PBMCs) from deidentified healthy donors were purchased from STEMCELL Technologies (#200-0092). CD3+ T cells were isolated using the EasySep Human T cell isolation kit (#100-069) per manufacturer-provided instructions. After isolation, T cells were seeded at 1×106 cells ml–1 and activated with anti-CD3/CD28 Dynabeads (Life Technologies, #40203D). T cells were maintained in culture at 1×106 cells ml–1 density throughout and cultured in complete X-VIVO-15 (cX-VIVO), consisting of X-VIVO 15 (Lonza Bioscience, Visp, Switzerland #04-418Q) supplemented with 5% FCS (R&D systems, lot M19187), 5 ng μl–1 IL-7, and 5 ng μl–1 IL-15, unless otherwise indicated. CD4+CD25low Tconv were isolated from washed PBMCs using the EasySep Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, catalog no. 18063) according to manufacturer’s protocol. Tconv were activated using Immunocult CD2/CD3/CD28 T Cell Activation reagent (STEMCELL Technologies #10990) at 12.5 μl ml–1. Tconv were maintained in culture in cX-VIVO supplemented with 300 IU ml-1 of IL2 and passaged every 2-3 days.

extract_protocol:
Human primary T cells were harvested 27 days post-electroporation (CD55, CD81) or 7 days post-electroporation (FAS, PTPN2, RC3H1, SUV39H1, MED12). 1×106 cells were harvested per condition, and RNA was isolated using a Quick-RNA MicroPrep Kit (Zymo #R1050). Isolated RNA was treated with TURBO DNase (Invitrogen #AM2239) and concentrated using RNA Clean and Concentrate Kit (Zymo #NC0622892).
Library preparation was carried out using 96 prep QuantSeq FWD V2 with UDI Set A1 kit and UMI Module (Lexogen #191.96). Final libraries were assessed using a 4200 TapeStation (Agilent), quantified using Qubit ds HS Assay Kit (Invitrogen), and sequenced as single-end 50 base pair reads on a HiSeq 4000 (Illumina) or NextSeq 500 (Illumina)

treatment_protocol: For experiments using Cas9, CRISPRi, or CRISPRoff mRNA, fresh CD3+ T cells were activated with a 1:1 bead-to-cell ratio with anti-CD3/CD28 Dynabeads (Life Technologies, #40203D). in the presence of 5 ng μl–1 IL-7 and 5 ng μl–1 IL-15 at 1×106 cells ml–1. After two days of stimulation, T cells were magnetically de-beaded, washed with PBS, and resuspended in TheraPEAK P3 buffer with supplement (Lonza #G4LP3-126000) at 0.75×106 cells in 20 μl. Cas9, CRISPRi and CRISPRoff mRNA were added to 20 μl cells at an equimolar ratio (1 μg, 1.07 μg, or 1.6 μg, respectively) with 2 μg chemically modified sgRNA (Synthego), and cells were electroporated on a Lonza 4D Nucleofector using pulse code DS137. Immediately after electroporation, 80μl pre-warmed cX-VIVO was added to each electroporation well, and cells were incubated for 30 min in a CO2 incubator at 37°C followed by distribution of each electroporation reaction into three wells of a 96-well round-bottom plate. Each well was brought to 200 μl with cX-VIVO. Cells were maintained and expanded by addition of cX-VIVO every 2 or 3 days and re-stimulated with ImmunoCult Human CD2/CD3/CD28 T Cell Activation reagent (STEMCELL Technologies #10990) every 9–10 days at 6.25 μl ml–1.

value: primary

tag: cell type

value: Bulk T cells

value: CRISPRoff

value: Day 28


title: CRISPRoff_NTC_Donor1

description:
Library name: 33b_Neg_D1
normalized_counts_Co013.csv

tag: genotype


title: CTinput_Skp1aKO_mb_RING1Blot1


title: 661W_EGFP1_S16

description:
Library name: 661W_EGFP1_S16
rawcounts_661W.csv


title: CTinput_Pcgf1cont_mb_RING1Blot2


title: CRISPRoff_CD81_Donor2

description:
Library name: 81_33b_D2
normalized_counts_Co013.csv

tag: treatment


title: Hybrid G_1_Worker Body_Pre-Molting

description:
Library name: HyG_1_WB_PreM
Column name in raw_counts_All_Samples.txt: HyG_1_WB_PreM

tag: tissue


title: 661W_Hif1a1_S32

description:
Library name: 661W_Hif1a1_S32
rawcounts_661W.csv


title: RNA_Skp1a_fl_fl_ESClot2

data_processing:
The fastq files were trimmed and QC-ed by Trim Galore (version 0.6.7).
Trimmed sequences were mapped and counted on GRCm38 cDNA library.
Assembly: mm10
Supplementary files format and content: plain text

source_name: embryoid body

value: embryoid body


title: heart tissue, IR_24h_3

first: Xiaokai

last: Zhang

state: Please Select

address: 180 Fenglin Road

institute: Zhongshan hosipital

description:
Library name: IR_24h_3
G15

data_processing:
fastp software was used to process raw reads in fastq format. clean reads were obtained after low-quality reads were removed for subsequent data analysis.
Clean reads were compared with mm39 reference genome using HISAT2 software, and gene expression volume (FPKM) was calculated. The reads of each gene were obtained by HTSeq-count.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: heart tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit(Ambion) followingthe manufacturer's protocol. 4 μg of total RNA was used to construct sequencing libraries.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number(RIN)≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (llumina, San Diego, CA, USA) according to the manufacturer's instructions. Then these libraries were sequenced on the llumina sequencing platform.

value: heart tissue


title: heart tissue, IR_24h_2

description:
Library name: IR_24h_2
G14


title: Hybrid G_1_Worker Body_Post-Molting

description:
Library name: HyG_1_WB_PoM
Column name in raw_counts_All_Samples.txt: HyG_1_WB_PoM


title: Hybrid G_1_Worker Body_Inter-Molting

description:
Library name: HyG_1_WB_IM
Column name in raw_counts_All_Samples.txt: HyG_1_WB_IM


title: CRISPRoff_CD81_Donor1

description:
Library name: 81_33b_D1
normalized_counts_Co013.csv


title: RNA_Skp1a_fl_fl_EBd2lot12


title: RNA_Skp1a_fl_fl_ESClot1


title: heart tissue, IR_24h_1

description:
Library name: IR_24h_1
G13


title: CRISPRoff_CD55_Donor1

description:
Library name: 55_33b_D1
normalized_counts_Co013.csv


title: CRISPRoff_CD55_Donor2

description:
Library name: 55_33b_D2
normalized_counts_Co013.csv


title: Hybrid F_3_Worker Head_Post-Molting

description:
Library name: HyF_3_WH_PoM
Column name in raw_counts_All_Samples.txt: HyF_3_WH_PoM


title: Hybrid F_3_Worker Head_Pre-Molting

description:
Library name: HyF_3_WH_PreM
Column name in raw_counts_All_Samples.txt: HyF_3_WH_PreM


title: RNA_Skp1a_fl_fl_EBd2lot1


title: heart tissue, IR_6h_3

description:
Library name: IR_6h_3
G12


title: Outer hair cells, P0, WT, rep6

description: Library name: P0_OHC6_RNA

data_processing:
Adaptor sequences were trimmed from reads using Trimmomatic
Trimmed sequences were mapped to GRCm39/mm39 mouse genome using STAR
Read counts were geneated using HTSeq with the intersection_nonempty mode
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each gene for each sample

extract_protocol:
Atoh1-GFP positive inner hair cells (IHCs) and Atoh1-GFP; Insm1-GFP-Cre and R26-TdTomato positive sensory outer hair cells (OHCs) were FACS-sorted from P0 cochleae into 350μL RNA lysis buffer (Qiagen), and RNA was extracted using RNeasy Micro Kit (Qiagen).
Libraries were synthesized by the Beijing Genomics Insititute (BGI) at their facility and the Children's Hospital of Philiadelphia. Genomic DNA was first removed using DNAse I, and ribosomal RNA (rRNA) was removed using RiboZero (Epicentre).The mRNA was fragmented into short fragments of about 200bp. First strand cDNA synthesis was done using random hexamers and the NuGEN Ovation RNA-Amplification System V2. Buffer, dNTPs, RNase H, and DNA polymerase I were added to synthesize the second strand. Double-stranded cDNA was purified with magnetic beads, end reparation and 3′-end single nucleotide A (adenine) addition were performed, and sequencing adaptors were ligated to the fragments, which were enriched by PCR amplification. Libraries were qualified and quantified with an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR. Libraries were sequenced using the Illumina HiSeq4000 sequencer using 100bp pair-end reads, to a depth of about 100 million reads per sample.

value: Organ of Corti

value: Outer hair cell


title: Hybrid F_3_Worker Head_Inter-Molting

description:
Library name: HyF_3_WH_IM
Column name in raw_counts_All_Samples.txt: HyF_3_WH_IM


title: heart tissue, IR_6h_2

description:
Library name: IR_6h_2
G11


title: Outer hair cells, P0, WT, rep5

description: Library name: P0_OHC5_RNA


title: heart tissue, IR_6h_1

description:
Library name: IR_6h_1
G10


title: RNA_Skp1a_KO_ESClot1

source_name: embryonic stem cell

value: embryonic stem cell


title: Hybrid F_3_Worker Body_Pre-Molting

description:
Library name: HyF_3_WB_PreM
Column name in raw_counts_All_Samples.txt: HyF_3_WB_PreM


title: Outer hair cells, P0, WT, rep4

description: Library name: P0_OHC4_RNA


title: heart tissue, IR_1h_3

description:
Library name: IR_1h_3
G9


title: RNA_Skp1a_KO_EBd2lot2


title: Hybrid F_3_Worker Body_Post-Molting

description:
Library name: HyF_3_WB_PoM
Column name in raw_counts_All_Samples.txt: HyF_3_WB_PoM


title: heart tissue, IR_1h_2

description:
Library name: IR_1h_2
G8


title: RNA_Skp1a_KO_EBd2lot1


title: Hybrid F_3_Worker Body_Inter-Molting

description:
Library name: HyF_3_WB_IM
Column name in raw_counts_All_Samples.txt: HyF_3_WB_IM


title: Hybrid F_2_Worker Head_Pre-Molting

description:
Library name: HyF_2_WH_PreM
Column name in raw_counts_All_Samples.txt: HyF_2_WH_PreM

value: Head


title: heart tissue, IR_1h_1

description:
Library name: IR_1h_1
G7


title: Outer hair cells, P0, WT, rep2

description: Library name: P0_OHC2_RNA


title: RNA_wt9.5dpcPI_mblot1

source_name: embryo

value: embryo


title: Hybrid F_2_Worker Head_Post-Molting

description:
Library name: HyF_2_WH_PoM
Column name in raw_counts_All_Samples.txt: HyF_2_WH_PoM


title: RNA_wt9.5dpcPI_mblot2


title: heart tissue, IR_0h_3

description:
Library name: IR_0h_3
G6


title: Inner hair cells, P0, WT, rep6

description: Library name: P0_IHC6_RNA

value: Inner hair cell


title: heart tissue, IR_0h_2

description:
Library name: IR_0h_2
G5


title: RNA_Skp1a_KO_ESClot12


title: RNA_wt9.0dpc_mblot1


title: heart tissue, IR_0h_1

description:
Library name: IR_0h_1
G4


title: Inner hair cells, P0, WT, rep5

description: Library name: P0_IHC5_RNA


title: Hybrid F_2_Worker Body_Pre-Molting

description:
Library name: HyF_2_WB_PreM
Column name in raw_counts_All_Samples.txt: HyF_2_WB_PreM


title: Inner hair cells, P0, WT, rep4

description: Library name: P0_IHC4_RNA


title: heart tissue, Sham3

description:
Library name: Sham3
G3

value: Sham


title: RNA_Skp1acont9.5dpc_mblot2


title: Hybrid F_2_Worker Body_Post-Molting

description:
Library name: HyF_2_WB_PoM
Column name in raw_counts_All_Samples.txt: HyF_2_WB_PoM


title: Inner hair cells, P0, WT, rep3

description: Library name: P0_IHC3_RNA

value: WT


title: heart tissue, Sham2

description:
Library name: Sham2
G2


title: Outer hair cells, P0, WT, rep3

description: Library name: P0_OHC3_RNA


title: Hybrid F_2_Worker Body_Inter-Molting

description:
Library name: HyF_2_WB_IM
Column name in raw_counts_All_Samples.txt: HyF_2_WB_IM


title: Hybrid F_1_Worker Head_Pre-Molting

description:
Library name: HyF_1_WH_PreM
Column name in raw_counts_All_Samples.txt: HyF_1_WH_PreM


title: RNA_Skp1acont9.5dpcPI_mblot2


title: Outer hair cells, P0, WT, rep1

description: Library name: P0_OHC1_RNA


title: heart tissue, Sham1

description:
Library name: Sham1
G1


title: Inner hair cells, P0, WT, rep1

description: Library name: P0_IHC1_RNA


title: NSC, ATAC, cKO, 3

city: Beijing

first: Ligong

address: Shuangqing Road No.30

institute: tsinghua university

description: Library name: Sample5

data_processing:
Clean fastq files were mapped to the GRCm38/mm10 using Bowtie2 with default parameters.
peaks were called using MACS2 (parameters:  -g mm --nomodel --shift -100 --extsize 200 -q 0.005)
Assembly: mm10
Supplementary files format and content: BIGWIG files containing dense and continuous genomic information

source_name: hippocampus

growth_protocol: NSCs were isolated from P0 WT and cKO mouse hippocampus, dissociated into single cells, and cultured as neurospheres in DMEM-F12 medium supplemented with B27, N2, EGF, and bFGF at 37°C in 5% CO2.

extract_protocol:
Nuclei isolated from 5×104 neural stem cells were used for ATAC-seq. Cells were harvested at 500 g 4°C for 5 min, and then cell pellets were re-suspended in 100 μL of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and then nuclei were centrifuged at 500 g 4°C for 15 min. The nuclei pellets were re-suspended in the transposition reaction mix containing Tn5 transposase (Vazyme Biotech, Nanjing, China).
The library was sequenced on an Illumina HiSeq X Ten sequencer.

value: hippocampus

value: neural stem cell

value: cKO


title: RNA_wt9.5dpc_mblot2


title: RNA_wt9.0dpc_mblot2


title: NSC, ATAC, cKO, 2

description: Library name: Sample4

value: primary


title: Hybrid F_2_Worker Head_Inter-Molting

description:
Library name: HyF_2_WH_IM
Column name in raw_counts_All_Samples.txt: HyF_2_WH_IM


title: Mouse sagittal brain, Control

city: Stanford

first: Arjun

last: Rajan

state: California

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

description:
Library name: E200028590
Fresh frozen

data_processing:
FASTQ corresponding to barcode indexes per sample along with the DNA nanoball (DNB) mask file were processed using the SAW v8.1.3 count pipeline
A reference file for GRCm39vM30 was assembled and reads were aligned using STAR. We used default parameters for SAW count pipeline which utilizes STAR and performs alignment, annotation, MID correction and deduplication, and binning.
The outputted gene expression file (GEF) contained the spatial gene expression matrix at different bin sizes.
Assembly: GRCm39vM30
Supplementary files format and content: h5ad (annotated h5 file with gene expresion by bin, at bin20 resolution)
Supplementary files format and content: gef (gene expression matrix with various bin sizes)
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
Animals were euthanized on day 6 (post-ICH / sham), and brain tissues were extracted and snap-frozen in isopentane prechilled in liquid nitrogen in Tissue-Tek OCT and transferred to a -80°C freezer for storage. Cryosections were cut sagittally at a thickness of 10 μm on a Leica CM1860 cryostat. Sections were matched to include equivalent regions of olfactory bulb, striatum, lateral and 4th ventricles, thalamus, midbrain, and cerebellum. Stereo-seq experiments followed STOmics stereo-seq chip-on-a-slide (1cm * 1cm) v1.3 kit.
Libraries were constructed and barcoded using STOmics barcode library preparation kit v1.0. We fragmented amplified 300ng cDNA with 10uL of KMB in a total reaction volume of 45 μL, and incubated in a thermocycler 95°C – 5 min, 40°C – 3 min. Reaction was stopped by adding 5 μL of KME, then incubated at 37C for 10min. Fragmented DNA was cleaned up using AMPure beads with a ratio of 1:0.8 beads following manufacturer’s protocol. DNA was eluted in 25 uL of 1X TE, and combined with 25 μL of a unique barcode mix, and 50 μL of 2X PCR master mix, and amplified using the following program: 95°C 5 min, 13 cycles of : 98°C – 20 sec, 58°C – 20 sec, 72°C – 30 sec, followed by 72°C   – 5 min. Final product was cleaned up using a double sided AMPure bead cleanup with a 1:0.55 bead ratio following manufacturer’s protocol. Libraries were eluted in 20uL of 1X TE. Prepared libraries were then sequenced using a DBSEQ-T7RS sequencer at the Stanford Genomics core, targeting 1.5 billion 75bp PE reads per sample.

value: brain

value: 3-4 month old


title: RNA_Skp1acont9.5dpcPI_mblot1


title: Hybrid F_1_Worker Head_Post-Molting

description:
Library name: HyF_1_WH_PoM
Column name in raw_counts_All_Samples.txt: HyF_1_WH_PoM


title: Hybrid F_1_Worker Body_Pre-Molting

description:
Library name: HyF_1_WB_PreM
Column name in raw_counts_All_Samples.txt: HyF_1_WB_PreM

value: thorax and abdomen with gut removed


title: RNA_Skp1acont9.5dpc_mblot1


title: Mouse sagittal brain, ICH + UCC

description:
Library name: E200028579
Fresh frozen

value: ICH + UCC


title: Hybrid F_1_Worker Body_Post-Molting

description:
Library name: HyF_1_WB_PoM
Column name in raw_counts_All_Samples.txt: HyF_1_WB_PoM


title: NSC, ATAC, WT, 1

description: Library name: Sample1


title: Hybrid F_1_Worker Body_Inter-Molting

description:
Library name: HyF_1_WB_IM
Column name in raw_counts_All_Samples.txt: HyF_1_WB_IM


title: NSC, ATAC, cKO, 1

description: Library name: Sample3


title: Inner hair cells, P0, WT, rep2

institute: Northwestern University

description: Library name: P0_IHC2_RNA


title: heart, ggti, rep2

status: Public on Sep 07 2025

first: Lek Wen

last: Tan

address: 450 Serra Mall,

data_processing:
ATAC-seq sequencing reads in FASTQ format were quality-controlled and trimmed with trim_galore in paired-end mode. The trimmed reads were aligned to the human genome (hg38) using Burrows-Wheeler Aligner v0.7.17 (BWA-MEM). Duplicate reads were subsequently removed with Picard MarkDuplicates. Peak-calling for each ATAC-seq replicate was performed using macs2 (v2.2.7.1) callpeaks with the options –nomodel –shift -37 –extsize 73 –SPMR. The quality of ATAC-seq peaks was assessed with the R package ATACseqQC. For ChIP-seq, peak-calling was performed using DFilter with the parameters: -ks=10 -bs=50 -lpval=6 -wig -nonzero -refine. The signal was converted into bigwig format, and visual inspection of the peak quality was performed using WashU Epigenome Browser.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: heart

extract_protocol:
For ATAC-seq samples, 50,000 iPSC-ECs treated with simvastatin or vehicle control were collected as previously reported.5 Transposition reaction was conducted using Nextera Tn5 Transposase. Transposed DNA was purified and amplified according to Buenrostro’s protocol.
Transposition reaction was conducted using Nextera Tn5 Transposase. Transposed DNA was purified and amplified according to Buenrostro’s protocol.

value: heart

value: GGTI


title: heart, ggti, rep1


title: NSC, ATAC, WT, 2

description: Library name: Sample2


title: RNA_Skp1aKO9.5dpc_mblot1


title: RNA_Skp1aKO9.5dpc_mblot2


title: heart, sim, rep1

value: Simvastatin


title: heart, sim, rep2


title: heart, dia, rep2

value: Diabetic


title: Mouse sagittal brain, Control + UCC

description:
Library name: E200028637
Fresh frozen

value: UCC


title: heart, control, rep2

value: Control


title: Hybrid F_1_Worker Head_Inter-Molting

description:
Library name: HyF_1_WH_IM
Column name in raw_counts_All_Samples.txt: HyF_1_WH_IM

value: Head


title: heart, control, rep1


title: control_a

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

data_processing:
Raw sequencing reads were mapped and counted against human reference genome (GRCh38) using 10X Genomics Cell Ranger 6.1.0. Multi-copy reads were discarded and only uniquely mapping reads were carried forward to unique molecular identifier (UMI) counting. The UMI count matrices were imported into the R package Seurat in the R statistical environment
Assembly: hg38
Supplementary files format and content: tsv:cells & barcodes, mtx: counts

source_name: blood

extract_protocol:
Cell concentrations were adjusted to 1000 cells/μl and cell suspensions were loaded onto a Chromium Next GEM Chip G (10X Genomics) for a target output of 10,000 cells per sample.Single-cell droplet capture was performed on the Chromium Controller (10X Genomics) by Children’s Medical Research Institute single cell sequencing centre
cDNA library preparation was performed in accordance with the Chromium Next GEM Single Cell 3’ v3.1 (dual index) protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood within 6 hours of sample collection using a Ficoll density medium (Cytiva) in SepMate tubes (Stemcell Technologies). PBMCs were cryopreserved in 10% dimethyl sulfoxide (Amrescro, WN182-10ML) in foetal bovine serum (FBS, Thermo Fisher Scientific) and stored in liquid nitrogen until analysis with 10X Genomics single cell RNA sequencing. PBMCs were thawed from liquid nitrogen, stained using DAPI, and sorted into a single cell suspension of live cells. A small aliquot was used to assess viability of the single cell suspensions using 0.4% Trypan Blue staining on a Countess II Automated Cell Counter (Invitrogen)

value: blood


title: pt_b_pre

value: PreIVIG


title: control_b


title: RNA_wt9.5dpc_mblot1

value: embryo


title: pt_a_pre


title: iEC, sim, 72h, rep2

data_processing:
ATAC-seq sequencing reads in FASTQ format were quality-controlled and trimmed with trim_galore in paired-end mode. The trimmed reads were aligned to the human genome (hg38) using Burrows-Wheeler Aligner v0.7.17 (BWA-MEM). Duplicate reads were subsequently removed with Picard MarkDuplicates. Peak-calling for each ATAC-seq replicate was performed using macs2 (v2.2.7.1) callpeaks with the options –nomodel –shift -37 –extsize 73 –SPMR. The quality of ATAC-seq peaks was assessed with the R package ATACseqQC. For ChIP-seq, peak-calling was performed using DFilter with the parameters: -ks=10 -bs=50 -lpval=6 -wig -nonzero -refine. The signal was converted into bigwig format, and visual inspection of the peak quality was performed using WashU Epigenome Browser.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: iPSC-derived Endothelial Cells

value: iPSC-derived Endothelial Cells

value: Simvastatin 72h


title: Mouse sagittal brain, ICH

description:
Library name: E200028568
Fresh frozen

value: ICH


title: iEC, sim, 24h, rep2

value: Simvastatin 24h


title: iEC, sim, 24h, rep1


title: iEC, sim,12h, rep1

value: Simvastatin 12h


title: iEC, sim, 12h, rep2


title: iEC, dia, rep2


title: iEC, control, rep1


title: iEC, control, rep2


title: platelet derived from healthy controls, rep2

first: Tingting

last: Liu

state: Shanghai

address: No. 197 Ruijin Second Road

institute: Shanghai Jiao Tong University

data_processing:
Raw data of platelets encoded in FASTQ-files were subjected to a standardized RNA-seq alignment pipeline, as described previously. Here, RNA-seq reads were subjected to 5’-end quality trimming and clipping of sequence adapters by Trimmomatic (version 0.22), mapped to the human reference genome Ensembl 91 version (ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/) using STAR (version 2.5.1b).
Read summarization of only reads spanning introns (intron-spanning reads) was performed with HTSeq (version 0.6.0), using union intersection of uniquely aligned reads, which was guided by the Ensembl gene annotation version 75. All subsequent statistical and analytical analyses were performed in R (version 3.3.0) and R-studio (version 0.99.902).
Diferential expression analysis of two conditions (APS group and healthy control group) was performed using the edgeR package(1.10.1). Corrected read counts were converted to counts-per-million, log2-transformed, and multiplied by the TMM-normalization factor calculated by the calcNormFactors-function of the R-package edgeR. RNAs with a p value corrected for multiple hypothesis testing (FDR) below 0.05 were considered as statistically significant.
Assembly: the human reference genome Ensembl 91 version (ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: platelet

growth_protocol: The platelets was isolated from peripheral blood of APS patients and healthy controls

extract_protocol:
Whole blood collected was subjected to platelet isolation within 12 hours after blood collection. Platelet pellets were isolated by two continuous steps of centrifugation, followed by resuspension in RNAlater (Thermo Scientific) and isolation of total RNA using RNAeasy Micro Kit (50) RNA (Ambion, Thermo Scientific, cat nr. AM1560). Platelet RNA quality was evaluated by Qubit2.0 Fluorometer and RNA 6000 Picochip (Bioanalyzer 2100, Agilent).
Platelet RNA isolation, frozen platelets were thawed on ice and total RNA was isolated using the RNeasy Micro Kit（50）RNA (Ambion, Thermo Scientific, cat nr. AM1560). Platelet RNA was eluated in 30 μL elution buffer. We evaluated the platelet RNA quality using the Qubit2.0 Fluorometer and RNA 6000 Picochip (Bioanalyzer 2100, Agilent), and included as a quality standard for subsequent experiments only platelet RNA samples with a RIN-value >7 and/or distinctive rRNA curves. A total amount of 3ug RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were geneated using NEBNext® UItra TM rna Library prep kit for Illumina® (NEB,USA) following manufacturer's redcommendation s and index codes were added to attribute suquences to each sample.

value: platelet

tag: gender

value: Female


title: platelet derived from healthy controls, rep3

treatment_protocol: The platelets was isolated from peripheral blood of APS patients and healthy controls

value: male


title: platelet derived from healthy controls, rep1


title: platelet derived from antiphospholipid syndrome (APS) patients, rep3


title: heart, dia, rep1

value: heart


title: platelet derived from antiphospholipid syndrome (APS) patients, rep2


title: Riboseq of mouse small intestine

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: WenYi west street

institute: Zhejiang University School of Medicine

description: No treatment

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using STAR.
Assembly: GRCm39
Supplementary files format and content: rpkm files containing rpkm for each transcripts,which are seperated by Tab.
Library strategy: Ribo-seq

source_name: small intestine

extract_protocol:
Freshly collected mouse tissues were washed twice with cold PBS and the excess liquid was carefully aspirated. Then, 500 μl of lysis buffer (containing 8 mM HEPES, pH 7.4, 80 mM KCl, 4 mM MgCl2, 2% Triton X-100, and 200 μg/ml cycloheximide) was added to the tissues, which were thoroughly lysed. The lysate was then transferred to RNase-free tubes and centrifuged at 12,000 rpm for 12 minutes at 4°C. The supernatant was collected and sent to Novogene (China) for RNA-seq library construction. Additionally, approximately 100 μl of the supernatant was treated with RNase I (Thermo Fisher Scientific) for 3 hours, followed by RNA extraction using TRIzol™ LS.
The extracted RNA was denatured at 65°C, 20 min and run on a 15% TBE-Urea gel. The band around 25-35 nt was excised and eluted overnight in RNA elution buffer (300 mM NaAc,1 mM EDTA) at 4°C. The RNA was precipitated with an equal volume of isopropanol. The RNA was treated by T4 Polynucleotide Kinase (NEB), and then polyadenylated using E. coli Poly(A) polymerase (NEB) for 37°C, 30min. The cDNA was generated using Template Switching RT Enzyme Mix from NEB (NEB) according to the manufacturer’s instructions. A portion of the resulting cDNA was amplified by PCR using Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific) with barcoded primers. The PCR products were run on a 8% TBE gel, and the band around 180 bp was excised and recovered using DNA PAGE Gel Extraction Kit ( Beyotime). The recovered DNA was sent to Novogene for sequencing.

value: small intestine

value: WT

value: 4 weeks old


title: tho2

city: Nan Jing

first: La

middle: yu

last: mei

state: Jiang Su

address: XuanWu

institute: Nanjing Agricultural University

description:
Library name: Sample 3
14-day-old seeding

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapped to TAIR10 whole genome using bowtie2 (v2.3.5).
Deduplicated reads by bismark (v0.22.1).
methylation extracting by bismark.
Assembly: TAIR10
Supplementary files format and content: Matrix table with wig file for every sample

source_name: seeding

growth_protocol: soil,16 hour light, 8 hour dark cycle

extract_protocol:
14-day-old seeding of tho2-8 ,Col-LUC and ros1-7 plants were grown in soil
DNA libraries were prepared for sequencing using standard Illumina protocols

value: seeding

value: Col-LUC

value: the whole plant


title: iEC, sim, 72h, rep1


title: Riboseq of mouse lung

description: No treatment

source_name: lung

value: lung


title: Riboseq of mouse heart

description: No treatment


title: Riboseq of mouse kidney

description: No treatment

source_name: kidney

value: kidney


title: tho2-8_rep2

description:
Library name: SAMPLES4
14-day-old seeding

data_processing:
Raw sequencing data was removed of 3' adapters by Cutadapt (v 1.18).
Sequences (18-26 nt in length) were mapped using Bowtie (v 1.2.2) to the TAIR10 assembly.
Counts were made with intersetBed, from bedtools suite (v 3.2.1).
TAIR10 assembly.
Assembly: TAIR10
Supplementary files format and content: Matrix table with wig file for every sample

extract_protocol:
Total RNA was isolated from 14-day-old seeding with Plant Total RNA Isolation Kit (Vazyme, China) according to the manufacturer's instructions.2 μg total RNAs
smallRNA sequencing library prepared by using Stranded smallRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the  standard Illumina protocols


title: Riboseq of mouse brain

description: No treatment

value: brain


title: Col-LUC_rep2

description:
Library name: SAMPLES2
14-day-old seeding


title: ros1-7

description:
Library name: Sample 2
14-day-old seeding


title: tho2-8_rep1

description:
Library name: SAMPLES3
14-day-old seeding


title: Riboseq of mouse colon

description: No treatment

source_name: colon

value: colon


title: RNAseq of raw264.7 with 24h LPS treatment, Rep1

description: with 24 LPS treatment

growth_protocol: Raw264.7 were grown in DMEM medium containing 10% FBS at 37°C with 5% CO₂.

extract_protocol:
Cells were washed twice with cold PBS. 500 μl lysis buffer (8 mM HEPES, pH 7.4, 80 mM KCl, 4 mM MgCl2, 2% Triton x-100, and 200 μg/ml cycloheximide) was then added, and the cells were quickly scraped and collected into RNase-free tubes. The sample were centrifuged at 12,000 rpm for 12 minutes at 4°C, and the supernatant was sent to Novogene (China) for RNA-seq library construction. Approximately 100 μl of supernatant were treated with RNase I (Thermo Fisher Scientific) for 3 hours, followed by RNA extraction using TRIzol™ LS.
The extracted RNA was denatured at 65°C, 20 min and run on a 15% TBE-Urea gel. The band around 25-35 nt was excised and eluted overnight in RNA elution buffer (300 mM NaAc,1 mM EDTA) at 4°C. The RNA was precipitated with an equal volume of isopropanol. The RNA was treated by T4 Polynucleotide Kinase (NEB), and then polyadenylated using E. coli Poly(A) polymerase (NEB) for 37°C, 30min. The cDNA was generated using Template Switching RT Enzyme Mix from NEB (NEB) according to the manufacturer’s instructions. A portion of the resulting cDNA was amplified by PCR using Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific) with barcoded primers. The PCR products were run on a 8% TBE gel, and the band around 180 bp was excised and recovered using DNA PAGE Gel Extraction Kit ( Beyotime). The recovered DNA was sent to Novogene for sequencing.

treatment_protocol: When the RAW264.7 cells reach about 60% confluence as fully adherent cells, they are treated with 1 μg/mL of LPS for 0, 6, 12, and 24 hours.

value: monocyte-macrophage

value: with 24 LPS treatment


title: Col-LUC_rep1

description:
Library name: SAMPLES1
14-day-old seeding


title: RNAseq of raw264.7 with 24h LPS treatment, Rep2

description: with 24 LPS treatment


title: tho2-8_rep2

data_processing:
Raw sequencing data was first filtered by Trimmomatic low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed clean
Reads mapped to the exon regions of each gene by Hisat2 (v 2.1.0) and counted by featureCounts (v 1.6.3).
Genes differentially expressed between groups were identified using the DESeq2 (v 1.24.0). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge.
Assembly: TAIR10
Supplementary files format and content: Matrix table with count file for every sample

extract_protocol:
Total RNA was isolated from 14-day-old seeding with Plant Total RNA Isolation Kit (Vazyme, China) according to the manufacturer's instructions.2 μg total RNAs
RNA sequencing library prepared by using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the  standard Illumina protocols


title: iEC, dia, rep1

value: iPSC-derived Endothelial Cells

value: Diabetic


title: tho2-8_rep1


title: RNAseq of raw264.7 with 6h LPS treatment, Rep1

description: with 6h LPS treatment

value: with 6h LPS treatment


title: RNAseq of raw264.7 with 12h LPS treatment, Rep2

description: with 12h LPS treatment

value: with 12h LPS treatment


title: RNAseq of raw264.7 with 12h LPS treatment, Rep1

description: with 12h LPS treatment


title: RNAseq of raw264.7 with 6h LPS treatment, Rep2

description: with 6h LPS treatment


title: C49

city: Norwich

first: Alice

last: Godden

state: Not applicable

address: School of Biological Sciences, University of East Anglia, Norwich Research Park

institute: University of East Anglia

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

data_processing:
Standard QIIME2 pipeline was applied: https://docs.qiime2.org/2022.2/tutorials/overview/
Demultiplex, cutadapt, denoise, feature table, taxonomic assignment, differential abundance
Assembly: SILVA release 132: silva_132_99_16S.fna  , from https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip
Supplementary files format and content: OTU_matrix_2023.csv - differential abundance data
Supplementary files format and content: taxonomy_2023.csv -- the taxa associated to the OUT in the OUT_matrix_2023.csv file
Library strategy: 16S Amplicons V3-V4

organism: Danio rerio

source_name: intestine

growth_protocol: standard zebrafish growth, supplemented with Gum Arabic food

extract_protocol:
genomic DNA was extracted from whole intestines of adult fish. This was done using a homogenizer and the FastDNA™ SPIN Kit for Soil kit from MP Biomedical.
IDT for Illumina-Nextera DNA Unique Dual Indexes

treatment_protocol: Organs were harvested from euthanized zebrafish and flash frozen in liquid nitrogen before storage at -80 C

value: intestine

tag: block

value: D

value: male

value: WT AB

value: 0% GA


title: RNAseq of raw264.7 without LPS treatment, Rep2

description: without LPS treatment

value: WT

value: without LPS treatment


title: GA28

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: B

value: female


title: GA57

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: Col-LUC

description:
Library name: Sample 1
14-day-old seeding

value: seeding

value: Col-LUC

value: the whole plant

value: wild type


title: T7

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: 6% GA


title: RNAseq of raw264.7 without LPS treatment, Rep1

description: without LPS treatment

value: monocyte-macrophage


title: platelet derived from antiphospholipid syndrome (APS) patients, rep1

value: platelet

value: Female


title: GA49

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine