title: ProE_Mettl3_KO_rep3

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description: Library name: RNAseq_ProE_Mettl3_KO_rep3

data_processing:
For RNA-seq data analysis, raw sequencing data were filtered by fastp (0.23.4), transcript-level expression were quantified using Kallisto (v0.48.0) with the mouse reference genome (mm10), and then merged to gene-level by R package tximport. Differential expression analysis was performed by DESeq2 (v2_1.44.0) for pairwise comparisons, with the cutoff of a fold change of ≥ 1.5, adjusted P of< 0.05, and ≥ 1 transcript per million (TPM) at least in one group. Principal component analysis (PCA) was done on log-transformed normalized counts in gene expression analysis. GO enrichment analyses were applied by Metascape. GO terms and pathways with a q-value of < 0.001 were considered significant.m6A-seq:raw sequencing data from all input and immunoprecipitated (IP) samples were processed by fastp, Kallisto and tximport to quantify the gene-level abundance. To evaluate the relative m6A level of each gene, fold-change between IP and input sample read counts was calculated by DESeq2, representing m6A enrichment level. High-confidence m6A-tagged genes were identified using the following criteria: TPM > 1 in input samples, log2(fold-change) for IP/input > 0 with adjusted p< 0.05.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: Bone marrow

extract_protocol: Mouse erythroid progenitor cells and proerythroblasts were sorted, collected, and washed twice with PBS, then amplified by the Smart-Seq2 method. An Oligo-dT primer was used in the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and a magbeads purification step to clean up the product.  Next, the cDNA was randomly fragmented by ultrasonic waves prior to Illumina library preparation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.For m6A-seq, m6A immunoprecipitation was performed according to the standard protocol. The cDNA was fragmented to ~300 bp using Tn5 transposase and processed using the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501). Final libraries were amplified with the Tn5 adaptor and 3' primer (AATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTAATACGACTCACTATA) and sequenced as 150-bp paired-end reads on an Illumina HiSeq X Ten platform.

value: Bone marrow

value: Erythroid cells


title: EA.hy926 cells, Mock, poly(I:C) 24 h_rep1

status: Public on Jun 09 2025

type: SRA

city: CHAPEL HILL

first: Yukako

last: Kayashima

state: NC

address: 710 BRINKHOUS-BULLITT BUILDING CB #7525

department: Pathology Lab Med

country: USA

institute: University of North Carolina at Chapel Hill

description:
Library name: Sample 10
10_24H_LF1_TAACTCGC-GAGCGGTT_S2_L001_R1_001.fastq.gz

library_source: transcriptomic

data_processing:
Raw 101 bp paired‐end reads were obtained from a NextSeq 200 run and demultiplexed (allowing one mismatch) with bclconvert v3.8.2-12. These reads were then aligned to the GRCh38 reference genome and Gencode v44 for annotation via STAR, producing sorted BAM files. StringTie was subsequently used to quantify gene and transcript expression, yielding TPM, FPKM, and raw count values. The prepDE.py script from StringTie was run to assemble gene- and transcript-level count matrices, which were then imported into R.
After performing filtering and normalization, the voom transformation was applied to the normalized counts, and linear models incorporating experimental groups and time points were fitted using limma. Empirical Bayes moderation was applied to these fitted models, and subgroup contrasts were analyzed using the DREAM method. Finally, preranked GSEA was conducted with fgsea to identify enriched pathways
Assembly: GRCh38 reference genome and Gencode v44 for annotation
Supplementary files format and content: Gene/Transcript count matrix: CSV files with one row per ENST|TranscriptID and columns of raw counts per sample.
Supplementary files format and content: Limma subgroup analysis files: tab-delimited text containing columns for gene ID (ENSG|GeneName), log2 fold change (logFC), average expression (AveExpr, log2 CPM), moderated t-statistic (t), raw p-value (P.Value), adjusted p-value (adj.P.Val), and B-statistic (B) for each condition–timepoint contrast. GSEA result files: tab-delimited text files listing pathway names, enrichment score (ES), normalized enrichment score (NES), nominal p-value (pval), FDR (padj), number of more extreme permutations (nMoreExtreme), gene set size (size), and comma-separated leading-edge gene IDs.

molecule: total RNA

organism: Homo sapiens

source_name: human umbilical vein

growth_protocol: EA.hy926 human umbilical vein endothelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin/100 μg/mL streptomycin in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNAeasy mini kit (Qiagen).
RNA libraries for RNAseq were prepared using KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer's protocol.

treatment_protocol: EA.hy926 cells were transfected with 10 nM siRNA. Forty-eight hours after the transfection, cells were stimulated with 1 μg/ml poly(I:C) and incubated for 24 h. Cells before (0 h) or after (24 h) the poly(I:C) stimulation were lysed for RNA extraction.

tag: tissue

value: human umbilical vein

tag: cell line

tag: cell type

value: vascular endothelial cells

tag: genotype

value: Mock transfection

tag: treatment

value: poly(I:C) 24 h


title: EA.hy926 cells, siELMO1, poly(I:C) 0 h_rep3

description:
Library name: Sample 9
9_0H_E3_TATGCGGT-TAGGTGCT_S18_L001_R1_001.fastq.gz

value: ELMO1 siRNA

value: poly(I:C) 0 h


title: ProE_Mettl3_KO_rep2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

country: China

description: Library name: RNAseq_ProE_Mettl3_KO_rep2

organism: Mus musculus


title: No_captured_Illumina_RNA-seq_control

city: Taipei

first: Hsueh-Ping

last: Chu

address: No. 1 Sec. 4 Roosevelt Road

department: Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

description:
No captured Illumina RNA-seq: control
TERRA-region_count_Illumina-datasets.txt

data_processing:
For Nanopore dataset, the raw fast5 files were processed using Guppy base caller (guppy_GPUv5.0.7) with default settings to convert them into fastq files. Outputs from this step were merged and compressed by 'cat' and 'gzip' commands. For Illumina datasets, fastq files are raw data, no base calling step
For Nanopore dataset, fastq files will automatically split into 'pass' (Q>7) and 'fail' (Q<7) groups during base calling, all reads passed quality filter were merged into a single fastq file. For Illumina datasets, adapter sequence and low-quality reads were removed by Trimgalore (v0.6.3) using default options.
Reads were mapped to the Homo sapiens T2T-CHM13 reference genome by different alignment tools. For Illumina datasets, alignment was performed using STAR (v2.7.9a) with default parameters. For Nanopore dataset, alignment was performed using minimap2 (v2.22) with options: -ax splice, -uf, -k14
SAM format files were converted to BAM, sorted and indexed by samtools (v1.9)
Bigwig files were generated by deepTools (v3.1.1) bamCoverage with parameters: --normalizeUsing RPKM
Compared bigwig files were generated by deepTools (v3.1.1) bamCompare with parameters: --scaleFactorsMethod None, --normalizeUsing RPKM, --operation log2
TERRA transcription regions were defined on chromosome ends of T2T-CHM13 genome and recorded as a BED format file.
Reads mapped to TERRA regions were extracted from BAM file using samtools v1.17 according to the defined TERRA transcription region bed file. (samtools view -b -h -M -L TERRA_region.bed TERRA-captured_RNA-seq.bam -o TERRA_selected.bam) The number of extracted reads of each group were quantified.
Assembly: T2T-CHM13
Supplementary files format and content: tab-delimited text files include raw read counts that was mapped to TERRA regions. (Illumina and Nanopore datasets)
Supplementary files format and content: bigwig or bw are read coverage files (Illumina dataset)
Supplementary files format and content: bam file is alignment result (Nanopore dataset)
Supplementary files format and content: bed file contains TERRA transcription regions defined on the T2T-CHM13 genome.

growth_protocol: U2OS cells were cultured using Gibco Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum, L-glutamine, and 1% penicillin/streptomycin in a 37℃, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from 1 x 10^7 cells using TRIzol™ Reagent (Invitrogen™, Cat:15596018) following the manufacturer's protocol.
For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010). The TERRA-captured RNA sample was divided into two equal halves for the reverse transcription reaction. Half of the TERRA-captured sample was reverse transcribed using 2 μM random hexamers (Thermo Fisher Scientific, 48190011), while the other half using 1 μM of telomeric C-rich primer. These two groups are referred to as the random and specific groups, respectively. The rest steps were performed as the protocol provided by manufactor. For Nanopore sequencing, TERRA-enriched sample was polyadenylated using E. coli Poly (A) polymerase (New England Biolabs, #M0276S) at a final concentration of 0.25 U/μl in 1X Poly(A) Polymerase Reaction Buffer with 1 mM dATP and 2 Unit/μl RNaseOUT, (Thermo Fisher Scientific, Cat: 10777019) at 37°C for 30 minutes. The reaction was terminated by adding 10 mM EDTA. The RNA sample was purified by AMPureXP RNA beads (Beckman Coulter, A66514) then subjected to Nanopore direct RNA sequencing protocol (Cat#SQK-RNA002).


title: EA.hy926 cells, siELMO1, poly(I:C) 0 h_rep2

description:
Library name: Sample 8
8_0H_E2_CTCATCAC-GGTGGCAC_S17_L001_R1_001.fastq.gz


title: MEF, 1 hour Thapsigargin, CLIP, replicate 2

city: Baton Rouge

first: Anastasios

middle: A.

last: Vourekas

state: LA

address: 202 life sciences building

institute: Louisiana State University

data_processing:
sequence reads were trimmed for adapter sequence/ low quality sequences using cutadapt version 4.1 with python 3.9.13 with the options -n 1 -e 0.15.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner version 2.7.0d and UCSC gene transfer format for annotations.
Read counts table extraction using CLIPSEQTOOLS with the option count_reads_on_genic_elements.
Normalization and other data processing for the count reads tables were performed using custom python scripts which can be found in the following GitHub page: https://github.com/Abdelmonsif/DDX3X.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing raw counts for each sample
Supplementary files format and content: Tab-delimited file containing TPM values for each sample

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts were maintained in DMEM supplemented with 10% defined FBS, 2mM L-glutamine, 100 units/mL  penicillin,   and 100 ug/mL streptomycin in humidified atmosphere with 5% CO2  at 37C.

extract_protocol:
CCells were grown to ~80% confluency and treated with control (DMSO) or Thapsigargin (400 nM) containing full medium to induce ER stress. The cells where then collected by trypsinization and kept in ice-cold HBSS during UV crosslinking (254 nm, 3x400 mJ/cm2). For the IP step our own custom rabbit polyclonal DDX3X antibody was used. The rest of the CLIP-Seq procedure was performed as previously described (Vourekas and Mourelatos, 2014).
RNA  libraries  for RNA-seq were prepared using Illumina Stranded mRNAs prep Ligation Reference Guide, Document # 1000000124518 V03 protocol without changes.

treatment_protocol: ER stress was induced  by treating cells with 400 nM Thapsigargin for 1 hour for MEFs

value: MEF

value: Mouse embryonic fibroblast

value: Wt

value: Thapsigargin


title: TERRA_captured_Illumina_RNA-seq_specific

description:
TERRA captured Illumina RNA-seq: specific group.
TERRA-region_count_Illumina-datasets.txt


title: EA.hy926 cells, siELMO1, poly(I:C) 24 h_rep2

description:
Library name: Sample 17
17_24H_E2_ACCGTCCT-GTCCGACC_S9_L001_R1_001.fastq.gz


title: ProE_Mettl3_KO_rep1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_ProE_Mettl3_KO_rep1


title: EA.hy926 cells, siNT, poly(I:C) 24 h_rep3

description:
Library name: Sample 15
15_24H_C3_GTTATATA-GTAGTGAT_S7_L001_R1_001.fastq.gz

value: non-targeting siRNA


title: ProE_Control_rep3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_ProE_Control_rep3


title: EA.hy926 cells, siNT, poly(I:C) 0 h_rep3

description:
Library name: Sample 6
6_0H_C3_TGCATTGC-GTCCTGTT_S15_L001_R1_001.fastq.gz


title: Adipose, replicate 1, snRNA-seq

city: Shenzhen

first: juan

middle: li

last: chen

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Sus scrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa domesticus

source_name: Adipose tissue

extract_protocol: One male and one female Meishan pig, aged 180 days , were obtained from a commercial pig farming company. Each tissue was minced into 5-10 pieces weighing approximately 50-100 mg each on ice with sterilized scissors, which were then snap-frozen in liquid nitrogen and stored at -80℃ until nuclear extraction was performed.Briefly, the tissue samples were homogenized using the Dounce homogenizer with 25 strokes of the loose pestle A and then 25 strokes of the tight pestle B in 1 ml of ice-cold homogenization buffer. After this, the mixture was filtered through a 40-μm cell strainer into a 1.5-ml tube. To collect dissociated single nuclei, the sample was centrifuged at 500g for 5 min at 4℃, and the supernatant was discarded. After centrifugation, the nucleus pellet was resuspended using the desired amount of 1× PBS/0.5% BSA with RNase inhibitor, filtered through a 40-μm cell strainer, and counted. A final concentration of 1,000 nuclei per µl was used for library preparation.

tag: breed

value: Meishan Pig

value: Adipose tissue

tag: age


title: EA.hy926 cells, siNT, poly(I:C) 24 h_rep1

description:
Library name: Sample 13
13_24H_C1_AAGTCGTG-AATTATGC_S5_L001_R1_001.fastq.gz


title: EA.hy926 cells, Mock, poly(I:C) 0 h_rep3

description:
Library name: Sample 3
3_0H_LF3_ACCAACAT-GACGGTCC_S12_L001_R1_001.fastq.gz


title: TERRA_captured_Illumina_RNA-seq_random

description:
TERRA captured Illumina RNA-seq: random group.
TERRA-region_count_Illumina-datasets.txt


title: EA.hy926 cells, siNT, poly(I:C) 0 h_rep1

description:
Library name: Sample 4
4_0H_C1_GTCTGTGC-CTGATGCT_S13_L001_R1_001.fastq.gz


title: EA.hy926 cells, Mock, poly(I:C) 0 h_rep2

description:
Library name: Sample 2
2_0H_LF2_TTGGTGGC-GAGTGCCT_S11_L001_R1_001.fastq.gz


title: ProE_Control_rep1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_ProE_Control_rep1


title: EA.hy926 cells, Mock, poly(I:C) 0 h_rep1

description:
Library name: Sample 1
1_0H_LF1_ACCATATC-TACACGTT


title: CFUE_Kit_low_Mettl3_KO_rep3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_CFUE_Kit_low_Mettl3_KO_rep3

value: Erythroid progenitor cells


title: THP-1, ad, rep.1

city: Puschino

first: Kirill

middle: S

last: Krasnov

state: Moscow region

address: institutskay 3

country: Russia

institute: ITEB RAS

description:
Library name: THP-1ad1
columm name in raw_counts_all_samples.csv: THP-1ad1

data_processing:
Sequencing on HiSeq1500 (Illumina) with ≥10 million 50-nucleotide reads.  Read alignment to the reference genome and quantification performed using STAR (v.2.5.3a). Differential gene expression analysis was performed using limma-trend algorithm
Assembly: GRCh38 (Ensembl v.90)
Supplementary files format and content: csv file includes raw counts for each sample

molecule: polyA RNA

source_name: Peripheral blood

growth_protocol: Human acute myeloid leukemia cells of the THP-1 line obtained from the American Type Cell Culture Collection (ATCC, USA) were used. Cells were cultured in a RPMI-1640 nutrient medium (Sigma, USA) supplemented with 10% fetal bovine serum (Gibco, USA) containing 40 µg/ml gentamicin sulfate (Sigma), at 37°C and 5% CO2 in the gas phase. Cells were seeded in an amount of 5×10^3 in 100 μl of nutrient medium into the wells of a U-shaped 96-well culture plate. The number of cells in a well increased to 1×10^4 (1×10^5 cells/ml) 1 day after seeding, and they were used as low-density cultures (THP-1.LDC). The number of cells in a well increased to 1×10^5 (1×10^6 cells/ml) after 5 days of cultivation without changing the nutrient medium, forming a three-dimensional multicellular aggregate – a high-density cell culture (THP-1.HDC). THP-1ad cells were derived from a subpopulation of THP-1 cells adhered to the surface of culture flasks. For this purpose, THP-1 cells were grown for 7–8 days after seeding at a concentration of 5 × 10^4 cells/mL, until the appearance of cells attached to the surface of the flasks. Then, unattached cells were removed along with the medium, attached cells were washed with medium, and such cells were cultured for about 10 days with replacement of the growth medium with a fresh medium every 3 days until the forming of confluent cell culture of the new subline, THP-1ad. THP-1ad cells were cultured in RPMI/F12 and supplemented with 10% FBS and 40 μg/mL gentamicin sulfate, at 37 °C in a humidified atmosphere of 5% CO2. Accutase cocktail was used to detach THP-1ad cells from surface of culture flasks.

extract_protocol:
Total RNA extraction from cell lysates using Trisol reagent (Thermo Fisher Scientific) and PureLink RNA Micro Kit (Invitrogen).  RNA quality/quantity assessment via BioAnalyzer and RNA 6000 Nano Kit (Agilent Technologies).
PolyA RNA isolation using Dynabeads® Oligo(dT) magnetic beads (Invitrogen).  Library preparation with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB).  Library quantification using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).  Fragment length distribution analysis with Agilent High Sensitivity DNA Kit (Agilent Technologies).

treatment_protocol: No additional treatment was performed

value: Peripheral blood

value: monocyte

value: Macrophage-like cells


title: THP-1, ad, rep.2

description:
Library name: THP-1ad2
columm name in raw_counts_all_samples.csv: THP-1ad2


title: hMM6

city: Thuwal

first: Laura

last: Sudupe

address: King Abdullah University of Science and Technology (KAUST)

country: Saudi Arabia

institute: KAUST

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene epression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger;s default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol: Specified in colums O50 to O64

tag: gender

value: Female

tag: biological replicates

value: Bone marrow

value: Haematopoietic cells

tag: mouse model

tag: genetic changes

tag: cre recomb

tag: reporter

tag: tumor

value: MM

tag: technique

value: Visium CytAssist Spatial Gene Expression_human_V2


title: hMM5

value: Male


title: hMM4


title: CFUE_Kit_low_Mettl3_KO_rep2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_CFUE_Kit_low_Mettl3_KO_rep2


title: CFUE_Kit_low_Mettl3_KO_rep1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_CFUE_Kit_low_Mettl3_KO_rep1


title: hMM3


title: hMM2


title: THP-1, LDC, rep.2

description:
Library name: THP-1.LDC2
columm name in raw_counts_all_samples.csv: THP-1.LDC2

value: Low-density culture


title: hMM1


title: EA.hy926 cells, siELMO1, poly(I:C) 0 h_rep1

description:
Library name: Sample 7
7_0H_E1_ACGCCACT-GTTAACAG_S16_L001_R1_001.fastq.gz

value: human umbilical vein

value: vascular endothelial cells

value: ELMO1 siRNA

value: poly(I:C) 0 h


title: EA.hy926 cells, siNT, poly(I:C) 0 h_rep2

description:
Library name: Sample 5
5_0H_C2_AAGGCAAT-AATTACCA

value: non-targeting siRNA


title: ProE_Control_rep2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_ProE_Control_rep2

value: Erythroid cells


title: hHBM3

value: Not observed


title: THP-1, ad, rep.3

description:
Library name: THP-1ad3
columm name in raw_counts_all_samples.csv: THP-1ad3

value: Peripheral blood


title: CFUE_Control_rep3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_CFUE_Control_rep3

value: Erythroid progenitor cells


title: R403Q EMPA 68695NN

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (v2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, v1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (v0.11.7), and alignment quality was assessed using RSeQC (v3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (v1.32.0).
All analyses were performed using the R environment for statistical computing (v4.1.2).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 21 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 21 matrix of variance-stabilizing-transformed (VST) expression values

source_name: left ventricle

growth_protocol: Mice were housed under standard laboratory conditions with controlled temperature, humidity, and light.

extract_protocol: Frozen left ventricular tissue was homogenized, and mRNA was extracted with the RNeasy Universal Mini Kit (Qiagen)

treatment_protocol: Hypertrophic cardiomyopathy (HCM) is a hereditary cardiac disorder caused by mutations in several sarcomere genes, integral to the heart's contractile machinery. Mice harboring R403Q mutation in cardiac myosin heavy chain (a mouse model of HCM) were used in this study. Mice were randomized by body weight and divided into 3 groups: i) WT-CD; ii) R403Q-CD; and iii) R403Q-EMPA. Nine-to-ten-week-old male mice harboring R403Q mutation in cardiac myosin heavy chain or wild-type littermates (WT) were fed ad libitum a control diet (CD; 10 % kcal lard, 0 % sucrose; product No. D09071703; Research Diets, New Brunswick, NJ, USA) or the same diet enriched with empagliflozin (EMPA, 0.15 mg/g of diet; Boehringer Ingelheim, Ingelheim am Rhein, Germany) for 16 weeks. This dose of empagliflozin is equivalent to approximately 15 mg/kg body weight.

tag: strain

value: left ventricle

tag: cage

tag: notch

value: NN

tag: diet

value: Empagliflozin diet (EMPA)


title: CFUE_Control_rep2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_CFUE_Control_rep2

tag: tissue

value: Bone marrow

tag: cell type


title: THP-1, HDC, rep.3

description:
Library name: THP-1.HDC3
columm name in raw_counts_all_samples.csv: THP-1.HDC3

tag: cell line

value: monocyte

tag: treatment

value: High-density culture


title: hHBM2

value: Male

value: Haematopoietic cells

value: Visium CytAssist Spatial Gene Expression_human_V2


title: R403Q EMPA 68695LN

value: LN

tag: genotype


title: THP-1, LDC, rep.1

description:
Library name: THP-1.LDC1
columm name in raw_counts_all_samples.csv: THP-1.LDC1

value: Low-density culture


title: CFUE_Control_rep1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_CFUE_Control_rep1


title: R403Q EMPA 68692RN

value: RN


title: R403Q EMPA 68692NN


title: THP-1, HDC, rep.1

description:
Library name: THP-1.HDC1
columm name in raw_counts_all_samples.csv: THP-1.HDC1


title: R403Q CD 68666NN

value: Control Diet (CD)


title: R403Q CD 68666RN


title: THP-1, LDC, rep.3

description:
Library name: THP-1.LDC3
columm name in raw_counts_all_samples.csv: THP-1.LDC3


title: R403Q CD 68666BN

value: BN


title: siNFYA-mESC-RAD21-rep3

city: Chapel Hill

first: Alexis

last: Stutzman

address: 250 Bell Tower Drive

description: Library name: siNFYA-mESC-RAD21-rep3

library_source: genomic

data_processing:
ChIP-seq processing and spike-in normalization was performed as previously described (Justice et al. BMC Genomics 2022).
ChIP-seq peaks were called using MACS2 22 with a q value of 0.01; narrow peaks were called for SP1 and NFYA; narrow and broad peaks were called and combined for WDR5.
Assembly: mm10
Supplementary files format and content: Bigwig file for ChIP enrichment visualization in genome browser
Supplementary files format and content: Bed file of called peaks

molecule: genomic DNA

growth_protocol: V6.5 murine embryonic stem cells (mESCs) were a gift from R. Young of the Whitehead Institute for Biomedical Research. V6.5 are male cells derived from a C57BL/6(F) x 129/sv(M) cross. Naive V6.5 mESCs were grown as previously described (Dowen et al. Cell 2022). Briefly, KnockOut DMEM (Thermo Fisher Scientific, 10829-018) was supplemented with 15% fetal bovine serum (VWR, 97068-085, lot 170K19), 1x GlutaMAX (Thermo Fisher Scientific, 35050-061), 1x non-essential amino acids (Thermo Fisher Scientific, 11140-050), 0.1mM beta-mercaptoethanol (Gibco, 21985-023), homemade LIF (1:500), and 100U/ml penicillin and 100ug/ml streptomycin (Thermo Fisher Scientific, 15140-122). Cell counts were obtained on a Countess II FL Automated Cell Counter (Invitrogen). For ChIP-seq spike-in normalization, human embryonic kidney cells (HEK293T, female) were grown in DMEM (Gibco, 11995065) supplemented with 10% Bovine Calf Serum (Seradigm, 2100–500), 100 U/ml penicillin, and 100 ug/ml streptomycin.

extract_protocol:
mESCs were trypsinized (Gibco, 12604-013) and counted prior to crosslinking. Cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 5 min then quenched with 2.5 M glycine. Crosslinked cells were washed twice with cold PBS then lysed with 10 ml of cold Lysis Buffer 1 (50mM Hepes–KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) by rotating for 10 min at 4°C. After pelleting at 1350xg for 5 min at 4°C, nuclei were lysed in 5 ml Lysis Buffer 2 (10mM Tris–HCl pH 8, 200mM NaCl, 1mM EDTA, and 0.5mM EGTA) by rotating for 20 min at 4°C. After pelleting at 1350 × g for 5 min at 4°C, supernatant was removed and tubes were washed with 1 ml of cold Shearing Buffer (10mM Tris pH 7.5, 1mM EDTA, 0.1% SDS) and spun at 1350 × g for 5 min. Chromatin (pellet) was resuspended in 1 ml of Shearing Buffer and 5% of HEK293T chromatin (extracted using the same protocol) was added prior to sonication to be used later for spike-in normalization. Sonication of chromatin was performed using a Covaris E220 in milliTUBEs (Covaris, 520130) with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 20 min. Following sonication, insoluble material was pelleted and removed by spinning samples for 10 min at 15,000 rpm at 4°C. ChIPs were performed using RAD21 antibody (5ug, Abcam ab992), WDR5 antibody (4uL, CST D9E1I), SP1 antibody (5ug, Millipore 07-645), or Rabbit IgG antibody (5ug, Bethyl P120-101) incubated with 50uL Protein A Dynabeads (Invitrogen 10002D), or using NFYA antibody (2.5ug, Santa Cruz sc-17753) or Mouse IgG (2.5ug, Santa Cruz sc-2025) incubated with 50uL Protein G Dynabeads (Invitrogen 10004D). Antibodies were incubated with beads for 4-6 h prior to the IP. Beads were washed three times with PBS to remove unbound antibody prior to the addition of chromatin. 2% Input was removed, then chromatin from 1 × 107 cells was added to antibody-conjugated beads and incubated in ChIP buffer (20mM Tris pH 8, 2mM EDTA, 0.1% SDS, 225mM NaCl, and 1.5% Triton X-100), rotating overnight at 4°C. The next day, beads were washed with cold Wash Buffer 1 twice (20mM Tris pH 8, 2mM EDTA, 0.1% SDS, 150mM NaCl, and 1% Triton X-100), then with cold High Salt Wash Buffer (20mM Tris–HCl pH 8, 500mM NaCl, 2mM, EDTA, 0.1% SDS, and 1% Triton X-100), cold LiCl Wash Buffer (10mM Tris–HCl pH 8, 250mM LiCl, 1mM EDTA, and 1% NP-40), and cold TE Wash Buffer (10mM Tris pH 8, 1mM EDTA, and 50mM NaCl), each for 5 min rotating at 4°C. All buffers listed above were supplemented with 1X protease inhibitor cocktail (PIC) (Sigma Aldrich, 11697498001) and 1mM PMSF (ThermoFisher 36978). Chromatin was eluted from beads by adding 100uL IP Elution Buffer (50mM Tris pH 8, 10mM EDTA, and 1% SDS) and incubating at 65°C for 1 hour, vortexing every 15 min. Supernatant (and 2% Input chromatin samples) was incubated at 65°C overnight with addition of 5uL Proteinase K (NEB, P8107S) to reverse crosslinks. The next day, DNA was purified using a ChIP DNA Clean and Concentrate kit (Zymo, D5205), per manufacturer’s instructions. Samples were then used for ChIP-qPCR and/or ChIP-seq.
ChIP-Sequencing libraries were prepared using a Hyper Prep kit (Roche/Kapa Biosciences, KK8502) according to manufacturer’s instructions. 50bp paired-end sequencing was performed on NovaSeq 2000 P2, NextSeq 2000 P3, and NovaSeq 6000 S1 platforms using Illumina reagents according to manufacturer’s instructions by the High Throughput Sequencing Facility at UNC Chapel Hill.

treatment_protocol: mES cells were counted and 3-5 × 106 cells were plated per 10cm plate. 50nM of siRNA (pools of 4) or siGLO transfection control was transfected per well using DharmaFECT 1 transfection reagent (Dharmacon, T-2001) following manufacturer’s instructions. siRNA reagents used include siGLO (Horizon Discovery D-001630-01-0), siSMC3 (Horizon Discovery M-064492-01-0005), siWDR5 (Horizon Discovery M-047406-00-0005), siSP1 (Horizon Discovery M-040633-02-0005), and siNFYA (Qiagen 1027416). Cells were harvested after 48 hours for ChIP-qPCR (as explained above) and protein extractions. Protein extraction: 1 million cells per sample were washed with cold PBS then lysed in cold 200uL Kischkel buffer (50mM Tris pH 8.0, 150mM NaCl, 5mM EDTA, 1% Triton X-100, 1X PIC, 1mM PMSF) on ice for 5 min. Samples were spun down at max speed, for 5 min at 4C, then supernatant was saved and protein expression levels were assessed via Western Blot (as explained above).

value: mESC

value: WT

value: siNFYA

tag: chip antibody

value: RAD21 (5ug, Abcam ab992)


title: siGlo-mESC-WDR5-rep5

description:
Library name: siGlo-mESC-WDR5-rep4
siGlo-WDR5-merged.bw
siGlo-WDR5-merged.bed

value: siGlo

value: WDR5 (4uL, CST D9E1I)


title: P14,normal,conventional,RNA-seq

city: Beijing

first: Ying

last: Xu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: Library name: P14-normal-conventional

data_processing:
Trimmed sequencing reads were mapped to hg38 using STAR.
Read counts were extracted with htseq-count.
Assembly: hg38
Supplementary files format and content: text files including raw counts for each sample
Supplementary files format and content: csv file including raw counts for each sample

source_name: epithelial cells

extract_protocol:
To isolate single cells, patient-derived organoids or CRC tissues were incubated with TrypLE Express at 37°C for 20-30 min. The cells were then filtered through a 20 μm cell strainer, after which live cells were counted using a hemocytometer.
According to the manufacture ’ s introduction, Single-cell RNA-seq libraries wereconstructed using Single Cell 3 ’ Library andGel Bead Kit V3.1

value: epithelial cells


title: P7,normal,conventional,RNA-seq

description: Library name: P7-normal-conventional


title: R403Q CD 68664BN

value: left ventricle


title: R403Q CD 68660NN

value: NN


title: R403Q CD 68664RN


title: R403Q CD 68657RN


title: hHBM1

tag: gender

value: Male

tag: biological replicates

value: Bone marrow

value: Not observed


title: WT EMPA 68692LN

value: LN

value: wild-type (WT)

value: Empagliflozin diet (EMPA)


title: WT EMPA 68695RN

value: RN


title: WT EMPA 68691RN


title: shJUND,replicate2,RNA-seq

description: Library name: shJUND-replicate2


title: siGlo-mESC-NFYA-rep3

description: Library name: siGlo-mESC-NFYA-rep3

value: NFYA (2.5ug, Santa Cruz sc-17753)


title: siGlo-mESC-RAD21-rep7

description: Library name: siGlo-mESC-RAD21-rep7

value: mESC


title: WT EMPA 68691NN


title: siNFYA-mESC-NFYA-rep3

description: Library name: siNFYA-mESC-NFYA-rep3

value: WT


title: shJUND,replicate3,RNA-seq

description: Library name: shJUND-replicate3


title: WT CD 68666LN

value: Control Diet (CD)


title: siWDR5-mESC-WDR5-rep3

description: Library name: siWDR5-mESC-WDR5-rep5


title: THP-1, HDC, rep.2

description:
Library name: THP-1.HDC2
columm name in raw_counts_all_samples.csv: THP-1.HDC2

value: Peripheral blood

value: monocyte

value: High-density culture


title: shFOS,replicate3,RNA-seq

description: Library name: shFOS-replicate3

value: epithelial cells


title: siNFYA-mESC-RAD21-rep2

description: Library name: siNFYA-mESC-RAD21-rep2

value: siNFYA

value: RAD21 (5ug, Abcam ab992)


title: shJUND,replicate1,RNA-seq

description: Library name: shJUND-replicate1


title: shFOS,replicate2,RNA-seq

description: Library name: shFOS-replicate2


title: siWDR5-mESC-RAD21-rep3

description: Library name: siWDR5-mESC-RAD21-rep5


title: WT CD 68660LN

value: left ventricle


title: WT CD 68657NN

value: NN


title: shFOS,replicate1,RNA-seq

description: Library name: shFOS-replicate1


title: siGlo-mESC-RAD21-rep6

description: Library name: siGlo-mESC-RAD21-rep6

value: siGlo


title: shControl,RNA-seq

description: Library name: shControl


title: MM4

value: Female

value: Bone marrow

value: Haematopoietic cells

tag: mouse model

tag: genetic changes

value: MYCstopF/WT Ikk2stopF/stopF

value: GFP

value: MM

value: Visium Spatial Gene Expression for FFPE_mouse_V1


title: MM2

tag: cre recomb

tag: reporter


title: siNFYA-mESC-NFYA-rep2

description: Library name: siNFYA-mESC-NFYA-rep2

value: mESC

value: WT

value: NFYA (2.5ug, Santa Cruz sc-17753)


title: MM3

tag: tumor

tag: technique


title: WT EMPA 68691LN

tag: strain

tag: cage

value: LN

value: wild-type (WT)

value: Empagliflozin diet (EMPA)


title: P14,3C,RNA-seq

description: Library name: P14-3C

value: epithelial cells


title: MM1


title: siWDR5-mESC-WDR5-rep4

description: Library name: siWDR5-mESC-WDR5-rep4

value: WDR5 (4uL, CST D9E1I)


title: U2OS, polyA-TERRA

address: No. 1 Sec4 Roosevelt Rd.

institute: NATONAL TAIWAN UNIVERSITY

description: Library name: U2OS-polyA-TERRA

data_processing:
The fastq files obtained from TERRA-capture Illumina RNA-seq were subjected to a quality filter (Q > 30), and Illumina adaptor sequences were trimmed using Trimgalore v0.6.7. The reads that passed the quality filter were aligned to the T2T-CHM13 genome using the STAR aligner v2.7.9a. (star --runMode alignReads --genomeDir /path/to/T2T-CHM13 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix output_path/id --readFilesIn trimmed_Read1.fastq trimmed_Read2.fastq). To quantify TERRA read counts, the alignments were extracted from the BAM files using samtools v1.17 (samtools view -b -h -q 30)
Assembly: CHM13
Supplementary files format and content: Gene counts for each sample

growth_protocol: U2OS and HeLa cells were cultured using Gibco Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum, L-glutamine, and 1% penicillin/streptomycin in a 37℃, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from 1 x 10^7 cells using TRIzol™ Reagent (Invitrogen™, Cat:15596018) following the manufacturer's protocol. For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010),  using 1 μM of telomeric C-rich primer. The rest steps were performed as the protocol provided by manufactory.
For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010).

value: Osteosarcoma


title: YFP2

value: biol rep 2

value: YFPstopF/WT

value: YFP

value: Not observed


title: YFP1

value: Female

value: biol rep 1

value: Bone marrow

value: Haematopoietic cells


title: U2OS, non-polyA-TERRA

description: Library name: U2OS-non-polyA-TERRA


title: siGlo-mESC-NFYA-rep2

description: Library name: siGlo-mESC-NFYA-rep2

value: mESC

value: siGlo


title: P13,3C,RNA-seq

description: Library name: P13-3C


title: P10,3C,RNA-seq

description: Library name: P10-3C


title: WT CD 68664DR

value: left ventricle

tag: notch

value: DR

tag: diet

value: Control Diet (CD)


title: HeLa, polyA-TERRA

description: Library name: HeLa-polyA-TERRA

source_name: HeLa

value: HeLa

tag: cell type

value: epithelial cell


title: siGlo-mESC-WDR5-rep4

description: Library name: siGlo-mESC-WDR5-rep4

tag: cell line

value: WT

value: WDR5 (4uL, CST D9E1I)


title: WT CD 68660RN

tag: tissue

value: RN

value: wild-type (WT)


title: HEK293FT, NAT10 knockdown, 1.5 hour Thapsigargin, Heavy fraction, replicate 2

library_source: other

data_processing:
sequence reads were trimmed for adapter sequence/ low quality sequences using cutadapt version 4.1 with python 3.9.13 with the options -n 1 -e 0.15.
Trimmed sequence reads were mapped to hg38 using STAR aligner version 2.7.0d and UCSC gene transfer format for annotations.
Read counts table extraction using CLIPSEQTOOLS with the option count_reads_on_genic_elements.
Normalization and other data processing for the count reads tables were performed using custom python scripts which can be found in the following GitHub page: https://github.com/Abdelmonsif/DDX3X.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing raw counts for each sample
Supplementary files format and content: Tab-delimited file containing TPM values for each sample

molecule: other

growth_protocol: Human embryonic  kidney  were maintained in DMEM supplemented with 10% defined FBS, 1X Glutamax, 1X MEM non-essential amino acids,   and 1 mM sodium Pyruvate in humidified atmosphere with 5% CO2  at 37C.

extract_protocol:
Cells were seeded in 3 dishes of 100-mm culture dishes and grown to 80% confluency. 1.5 h prior to collection, cell culture media was replaced with full media containing DMSO (rest) or 400 nM Thapsigargin (ER stress). Cells were incubated for the last 5 min of the treatment with cycloheximide (CHX) at a final concentration of 100 μg/mL. Cells were then washed twice with ice cold phosphate-buffered saline supplemented with CHX and centrifuged at 4,500 X g for 5 min at 4° C. Cell pellets were lysed in 800 μL of Hypotonic buffer (5 mM Tris HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 0.5% Triton X, 0.5% sodium deoxycholate, 100 μg/mL CHX, 2 mM DTT, 200 units/mL RNase inhibitor, 1X protease inhibitor cocktail). Cells were resuspended in the hypotonic buffer either by pipetting or vortexing for 5 sec followed by centrifugation at 17,000 xg for 7 min at 4° C. The supernatant (post-nuclear lysate) OD was measured at 260 nm to determine the amount of lysate needed to be added to sucrose gradient. Samples of the post-nuclear lysates were also kept for western blots and input RNA extraction 500 mL from the top of the sucrose gradient was removed and the lysate volume per condition was adjusted so they contain the same OD between 10 to 20 at 260 nm and added to the top of the sucrose gradient. Each gradient was weighed and balanced before ultracentrifugation at 222,222 xg for 2 hours at 4° C while using low brake option. 14 fractions of 800 μL were collected. RNA was extracted from total RNA and heavy fractions using TRIZOL LS and kept at -80C.
RNA  libraries  for RNA-seq were prepared using Illumina Stranded mRNAs prep Ligation Reference Guide, Document # 1000000124518 V03 protocol without changes.

treatment_protocol: ER stress was induced  by treating cells with 400 nM Thapsigargin for 1.5 hours

value: Human embryonic kidney

tag: genotype

tag: treatment

value: Thapsigargin


title: HeLa, non-polyA-TERRA

description: Library name: HeLa-non-polyA-TERRA


title: siWDR5-mESC-RAD21-rep4

description: Library name: siWDR5-mESC-RAD21-rep4

tag: chip antibody

value: RAD21 (5ug, Abcam ab992)


title: siNFYA-mESC-RAD21-rep1

description: Library name: siNFYA-mESC-RAD21-rep1

value: siNFYA


title: P15,normal,4C,RNA-seq

description: Library name: P15-normal-4C

value: epithelial cells


title: HEK293FT, NAT10 knockdown, 1.5 hour Thapsigargin, Total RNA, replicate 2


title: siSP1-mESC-RAD21-rep4

description: Library name: siSP1-mESC-RAD21-rep4


title: HEK293FT, NAT10 knockdown, 1.5 hour Thapsigargin, Total RNA, replicate 1


title: P1,normal,4C,RNA-seq

description: Library name: P1-normal-4C


title: HEK293FT, NAT10 knockdown, Rest, Total RNA, replicate 2

value: DMSO


title: P14,normal,4C,RNA-seq

description: Library name: P14-normal-4C


title: siGlo-mESC-RAD21-rep5

description: Library name: siGlo-mESC-RAD21-rep5

value: mESC


title: siNFYA-mESC-NFYA-rep1

description: Library name: siNFYA-mESC-NFYA-rep1

value: NFYA (2.5ug, Santa Cruz sc-17753)


title: HEK293FT, NAT10 knockdown, Rest, Heavy fraction, replicate 1


title: HEK293FT, NAT10 knockdown, Rest, Total RNA, replicate 1


title: P3,normal,4C,RNA-seq

description: Library name: P3-normal-4C


title: HEK293FT, Mock knockdown, 1.5 hour Thapsigargin, Heavy fraction, replicate 2

value: Mock-KD


title: HEK293FT, Mock knockdown, 1.5 hour Thapsigargin, Total RNA, replicate 1


title: siSP1-mESC-SP1-rep4

description: Library name: siSP1-mESC-SP1-rep4

value: SP1 (5ug, Millipore 07-645)


title: HEK293FT, Mock knockdown, Rest, Total RNA, replicate 2


title: HEK293FT, NAT10 knockdown, 1.5 hour Thapsigargin, Heavy fraction, replicate 1


title: HEK293FT, Mock knockdown, 1.5 hour Thapsigargin, Total RNA, replicate 2


title: siGlo-mESC-NFYA-rep1

description: Library name: siGlo-mESC-NFYA-rep1

value: siGlo


title: HEK293FT, Mock knockdown, Rest, Total RNA, replicate 1


title: siGlo-mESC-RAD21-rep4

description: Library name: siGlo-mESC-RAD21-rep4


title: P1,tumor,conventional,RNA-seq

description: Library name: P1-tumor-conventional


title: P7,normal,4C,RNA-seq

description: Library name: P7-normal-4C


title: HEK293FT, Mock knockdown, 1.5 hour Thapsigargin, Heavy fraction, replicate 1


title: P14,tumor,conventional,RNA-seq

description: Library name: P14-tumor-conventional


title: HEK293FT, Mock knockdown, Rest, Heavy fraction, replicate 2


title: P7,tumor,conventional,RNA-seq

description: Library name: P7-tumor-conventional


title: siGlo-mESC-SP1-rep4

description: Library name: siGlo-mESC-SP1-rep4


title: HEK293FT, DDX3X knockdown, 1.5 hour Thapsigargin, Heavy fraction, replicate 2


title: P1,3C,RNA-seq

description: Library name: P1-3C


title: HEK293FT, NAT10 knockdown, Rest, Heavy fraction, replicate 2


title: HEK293FT, Mock knockdown, Rest, Heavy fraction, replicate 1


title: HEK293FT, DDX3X knockdown, 1.5 hour Thapsigargin, Total RNA, replicate 2


title: HEK293FT, DDX3X knockdown, 1.5 hour Thapsigargin, Heavy fraction, replicate 1


title: HEK293FT, DDX3X knockdown, Rest, Heavy fraction, replicate 2


title: HEK293FT, DDX3X knockdown, 1.5 hour Thapsigargin, Total RNA, replicate 1


title: siSP1-mESC-RAD21-rep3

description: Library name: siSP1-mESC-RAD21-rep3


title: HEK293FT, DDX3X knockdown, Rest, Total RNA, replicate 2


title: siGlo-mESC-RAD21-rep3

description: Library name: siGlo-mESC-RAD21-rep3


title: HEK293FT, DDX3X knockdown, Rest, Heavy fraction, replicate 1


title: Control-2

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

institute: China Medical University

description: Library name: Sample 2

data_processing:
Quality control: in order to remove technical sequences pass filter data of fastq format were processed by trmmomatic (v0.30) to be high quality data. Data processing include the folloeing steps: 1. remove the adapter sequences 2. remove the 5' or 3' end bases that contains N's or of quality values below 20 3. remove bases with avaerage quality score below 20 using the sliding window of 4bp 4. remove reads that are less than 18bp long after trimming
MicroRNA identify: according to miRDeep2[2], a software tha discivering known and novel miRNA from deep sequencing, we can get all identified microRNA and their expression data
Differential Expression Analysis: Differential expression analysis was conducted using the DESeq2 package from Bioconductor. Genes or microRNAs with a fold change ≥ 2 were considered differentially expressed.
GO and KEGG enrichment analysis: GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of microRNA target genes with a significant padj less than 0.05. And topGO was used to plot DAG.
Assembly: miRbase (V22)
Supplementary files format and content: miRNA_expression.xls
Supplementary files format and content: all.TPM.xls

source_name: Esophagus

growth_protocol: The KYSE410 cells were grown in RPMI medium with 10% fetal bovine serum and antibiotics, and kept in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNA was collected using TRIzol reagent
1μg total RNA or 10ng small RNA was used for library preparation. 3 ´SR Adaptor for Illumina was ligated to the small RNA using 3´ Ligation Enzyme. To prevent adaptor-dimer, the excess of 3 ´SR Adaptor were hybrid with SR RT Primer for Illumina. 5 ´SR Adaptor for Illumina was ligated to the small RNA using 5´ Ligation Enzyme and first strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was then amplified by PCR using P5 and P7 primers, the PCR product were purified by DNA clean beads. The purified products of 140- 160bp were recovered and cleaned up using PAGE, validated using an Agilent 2100 Bioanalyzer.

treatment_protocol: The KYSE410 esophagus cancer cell line was treated with 30 ng/ml of Visfatin for 24 hours in culture medium.

value: Esophagus

value: cancer cell

value: non


title: Visfatin-30ng-mL-1

description: Library name: Sample 3

value: WT

value: Visfatin


title: Visfatin-30ng-mL-2

description: Library name: Sample 4


title: siSP1-mESC-SP1-rep3

description: Library name: siSP1-mESC-SP1-rep3


title: HEK293FT, DDX3X knockdown, Rest, Total RNA, replicate 1


title: siGlo-mESC-SP1-rep3

description: Library name: siGlo-mESC-SP1-rep3


title: siGlo-mESC-WDR5-rep3

description: Library name: siGlo-mESC-WDR5-rep3

value: WDR5 (4uL, CST D9E1I)


title: Control-1

description: Library name: Sample 1


title: TERRAPCR_pBJ_hg38_17q

description: TERRA PCR product amplified by primer hg38_17q in pBJ

data_processing:
The FASTQ reads derived from TERRA PCR products underwent quality filtration (Q > 30) and adapters pruning using TrimGalore (v0.6.3) (https://github.com/FelixKrueger/ TrimGalore). Trimmed reads were aligned to CHM13 genome using Bowtie2 aligner (v2.4.2) with the default setting. SAM files were transformed to BAM files, and were deduplicated using SAMTools (v.1.18). Bigwig files were generated by DeepTools (v.3.3.1) bamCoverage, with parameters: --normalizeUsing CPM, --centerReads, and --extendReads 150.
To assess the proportion of PCR products at the TERRA-enriched regions where supposedly be targeted by the designed primers in this study, we calculated the read counts of PCR products on TERRA regions using SAMTools (v.1.13) view with parameters: --fetch-pairs, -h, -b, -M (--use-index), and -L (--target-file) with TERRA-enriched regions files, and finally generated the heatmaps of TERRA PCR products raw read count on CHM13 chromosomes ends.
Assembly: CHM13
Supplementary files format and content: bigwig formats is read coverage files (Illumina dataset)
Library strategy: DNA-seq

source_name: pBJ

extract_protocol:
Total RNA was extracted from 1 x 10^7 cells using TRIzol™ Reagent (Invitrogen™, Cat:15596018) following the manufacturer's protocol. For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010).
For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010).

value: pBJ

value: primary fibroblast


title: TERRAPCR_pBJ_hg38_10q_2

description: TERRA PCR product amplified by primer hg38_10q-2 in pBJ


title: U2OS, FOXK1_2, ATACseq

city: Montreal

first: Louis

last: Masclef

state: QC

address: 5415 Boulevard de l'Assomption

department: Biochemistry

country: Canada

institute: University of Montreal

description: Library name: U2OS_RFP_FOXK1_siK1_2

data_processing:
For ChIP-seq and ATAC-seq reads were aligned on UCSC hg38 genome using bowtie2 v2.3.1 using per-end settings. Optical and PCR duplicates reads were removed using picard v2.9.0. Peak calling was performed with MACS2 v2.1.1. ChIP-seq and ATAC-seq coverage were generated with deeptools bamcoverage using CPM normalization. ChIPseq coverage for K562 were generated using deeptools using bamcoverage FPKM normalization. Cut&Run were analyzed using nf-core/cutandrun (v3.2.2). Highly correlated technical replicates were merged. Normalization was performed with spike-in mode using aligned reads from E.Coli (K-12), expect for the analysis of FOXK1 and FOXK2 recruitment following U2OS cell synchronization, CPM normalization was applied.
For RNA-seq, the quality of the raw reads was assessed with FASTQC v0.11.8. After examining the quality of the raw reads, no trimming was deemed necessary. The human samples were spiked-in with drosophila S2 cells. A hybrid reference genome and annotation concatenating both species were used for the alignment. The GRCh38 (release 102) reference genome and BDGP6.32 (release 107) reference genome were used and downloaded from Ensembl. The reads were aligned to the hybrid reference genome with STAR v2.7.6a. The raw counts were calculated with HTseq v0.11.2 based on the hybrid reference genome. Differential expression was performed using DESeq2 v1.30.0 R package.
Assembly: hg38
Supplementary files format and content: gene counts, narrowPeaks

growth_protocol: IMR90 cells were grown in DMEM supplemented with 10% FBS, 4mM glutamine and penicilin streptomycin. U2OS were grown in DMEM supplemented with 5% NBS + 2% FBS, 4mM glutamine and penicilin streptomycin. K562 cells were grow in RPMI 1640 supplemented with 5% NBS, 4mM glutamine and penicilin streptomycin. Cells were cultured at 37C in 5% CO2.

extract_protocol:
For ChIPseq, cells were fixed in 1% formaldehyde for 10 min at room temperature. Cells were quenched in ice cold PBS with 125 mM glycine. Chromatin was then sonicated using probe sonicator. Samples preparation for Cut&Run were done following manufacturer (Epycipher CUTANA™). For RNAseq, IMR90 cells were infected with retroviruses coding for empty vector, FOXK1 or FOXK2. 48h following the end of antibiotic selection, cells were harvested in TRIzol and RNA was extracted. For ATAC-seq, transposition was performed directly on nuclei following manufacturer recommendations (Tn5 Illumina).
For ChIP-Seq samples, size distribution and molarity of immunoprecipitated and input samples were evaluated on a 2100 bioanalyzer (Agilent Technologies). ChIP-seq libraries and CUT&RUN librairies were prepared using the KAPA hyperprep library kit (Roche Diagnostics). The number of PCR cycles was calculated based on the quantification of the ligation products (Illumina adapters) by qPCR. Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired end reads (PE100), on a Novaseq 6000 system or HiSeq 4000 for K562 ChIP-Seq (Illumina), with a S4 flowcell and a coverage of 50M for ChIP-Seq and H2AUb Cut&Run library. 10M fragments were sequenced for BAP1 and H3K4me1 Cut&Run per library. For RNAseq, libraries were prepared using ribosomal RNA depletion (KAPA RNA HyperPrep kit) with a sequencing depth of a minimum of 50 million reads.

treatment_protocol: For Cut&Run and ATACseq, cells were treated twice with siRNA against FOXK1. 72h after the first transfection cells were harvested for Cut&Run or ATACseq. For FOXK1 and FOXK2 Cut&Run following realse into the cell cycle, fibroblasts were grown to confluence and further cultured for 3 days. The cells were then serum starved for two days, trypsinized and replated in fresh medium before being harvested. For RNAseq, IMR90 cells were infected with retroviruses coding for empty vector, FOXK1 or FOXK2. 48h following the end of antibiotic selection, cells were harvested in TRIzol and RNA was extracted.

value: Human osteosarcoma


title: TERRAPCR_pBJ_hg38_XqYq_2

description: TERRA PCR product amplified by primer hg38_XqYq-2 in pBJ


title: U2OS, FOXK1_7A_1, ATACseq

description: Library name: U2OS_RFP_FOXK1_7A_siK1_1


title: U2OS, FOXK1_7A_2, ATACseq

description: Library name: U2OS_RFP_FOXK1_7A_siK1_2


title: TERRAPCR_pBJ_hg38_15q_2

description: TERRA PCR product amplified by primer hg38_15q-2 in pBJ


title: TERRAPCR_pBJ_hg38_10q_1

description: TERRA PCR product amplified by primer hg38_10q-1 in pBJ


title: siSP1-mESC-RAD21-rep2

description: Library name: siSP1-mESC-RAD21-rep2

value: RAD21 (5ug, Abcam ab992)


title: TERRAPCR_pBJ_hg38_15q_1

description: TERRA PCR product amplified by primer hg38_15q-1 in pBJ


title: TERRAPCR_pBJ_hg38_2q

description: TERRA PCR product amplified by primer hg38_2q in pBJ


title: siGlo-mESC-SP1-rep2

description: Library name: siGlo-mESC-SP1-rep2


title: U2OS, FOXK1_1, ATACseq

description: Library name: U2OS_RFP_FOXK1_siK1_1


title: siSP1-mESC-RAD21-rep1

description: Library name: siSP1-mESC-RAD21-rep1


title: IMR90, FOXK2_3, RNAseq

description: Library name: IMR90_FOXK2_3

value: Human lung fibroblast


title: TERRAPCR_pBJ_CHM13_15q

description: TERRA PCR product amplified by primer CHM13_15q in pBJ


title: TERRAPCR_pBJ_hg38_XqYq_1

description: TERRA PCR product amplified by primer hg38_XqYq-1 in pBJ


title: TERRAPCR_pBJ_CHM13_13q

description: TERRA PCR product amplified by primer CHM13_13q in pBJ


title: siSP1-mESC-SP1-rep1

description: Library name: siSP1-mESC-SP1-rep1


title: TERRAPCR_pBJ_CHM13_3q

description: TERRA PCR product amplified by primer CHM13_3q in pBJ


title: TERRAPCR_pBJ_CHM13_8p

description: TERRA PCR product amplified by primer CHM13_8p in pBJ


title: TERRAPCR_pBJ_CHM13_22q

description: TERRA PCR product amplified by primer CHM13_22q in pBJ


title: siWDR5-mESC-RAD21-rep2

description: Library name: siWDR5-mESC-RAD21-rep2


title: TERRAPCR_pBJ_CHM13_1q

description: TERRA PCR product amplified by primer CHM13_1q in pBJ


title: siSP1-mESC-SP1-rep2

description: Library name: siSP1-mESC-SP1-rep2


title: TERRAPCR_pBJ_CHM13_4q

description: TERRA PCR product amplified by primer CHM13_4q in pBJ


title: TERRAPCR_HeLa_hg38_XqYq_2

description: TERRA PCR product amplified by primer hg38_XqYq-2 in HeLa

value: HeLa

value: epithelial cell


title: IMR90, FOXK2_2, RNAseq

description: Library name: IMR90_FOXK2_2


title: siGlo-mESC-SP1-rep1

description: Library name: siGlo-mESC-SP1-rep1

value: mESC


title: IMR90, FOXK1_3, RNAseq

description: Library name: IMR90_FOXK1_3


title: TERRAPCR_HeLa_hg38_15q_2

description: TERRA PCR product amplified by primer hg38_15q-2 in HeLa


title: siGlo-mESC-RAD21-rep2

description: Library name: siGlo-mESC-RAD21-rep2


title: IMR90, FOXK2_1, RNAseq

description: Library name: IMR90_FOXK2_1


title: TERRAPCR_HeLa_hg38_10q_2

description: TERRA PCR product amplified by primer hg38_10q-2 in HeLa


title: TERRAPCR_HeLa_hg38_17q

description: TERRA PCR product amplified by primer hg38_17q in HeLa


title: TERRAPCR_HeLa_hg38_XqYq_1

description: TERRA PCR product amplified by primer hg38_XqYq-1 in HeLa


title: IMR90, FOXK1_2, RNAseq

description: Library name: IMR90_FOXK1_2


title: siGlo-mESC-WDR5-rep2

description: Library name: siGlo-mESC-WDR5-rep2


title: IMR90, FOXK1_1, RNAseq

description: Library name: IMR90_FOXK1_1


title: TERRAPCR_HeLa_hg38_15q_1

description: TERRA PCR product amplified by primer hg38_15q-1 in HeLa


title: IMR90, vector_3, RNAseq

description: Library name: IMR90_vector_3


title: NOD.CB17-Prkdcscid/NCrCrl control brain, 18 weeks, Section 2

city: London

first: Simona

last: Parrinello

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
Reads from PDX experiments were aligned to reference genomes GRCh38-2020-A (human) and mm10-2020-A (mouse) using10x Genomics Space Ranger 2.0.1. To assign reads to either species, they were mapped three times: i) to the human genome, ii) to the mouse genome, iii) to a combination of both genomes. Reads mapping consistently to a single species using this procedure were selected and remapped to the combined genome as in point iii) to form the final dataset. Reads from normal mouse brain were filtered as above and remapped to mouse genome for downstream analysis.
Assembly: GRCh38-2020-A; mm10-2020-A
Supplementary files format and content: *tar.gz: output from spaceranger
Library strategy: Spatial transcriptomics

source_name: Brain

growth_protocol: Human glioblastoma PDX cell lines were implanted into the striatum of 8-12 week NOD.CB17-Prkdcscid/NCrCrl mice.

extract_protocol:
Fresh frozen tissue were OCT embedded and 10mm sections cut on a cryostat onto 10xGenomics Visium Spatial Gene Expression Slides
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent Kit according to manufacturer's instructions

treatment_protocol: Brains were collected when mice showed evidence of disease, snap frozen in methylbutane cooled in a bath of dry ice and liquid nitrogen.

value: Brain

tag: model

value: NOD.CB17-Prkdcscid/NCrCrl control brain

tag: tumour stage

value: No tumour control


title: NOD.CB17-Prkdcscid/NCrCrl control brain, 18 weeks, Section 1


title: siWDR5-mESC-WDR5-rep2

description: Library name: siWDR5-mESC-WDR5-rep2


title: siWDR5-mESC-RAD21-rep1

description: Library name: siWDR5-mESC-RAD21-rep1


title: TERRAPCR_HeLa_hg38_10q_1

description: TERRA PCR product amplified by primer hg38_10q-1 in HeLa


title: IMR90, vector_2, RNAseq

description: Library name: IMR90_vector_2


title: siGlo-mESC-RAD21-rep1

description: Library name: siGlo-mESC-RAD21-rep1

value: siGlo


title: TERRAPCR_HeLa_hg38_2q

description: TERRA PCR product amplified by primer hg38_2q in HeLa


title: IMR90, vector_1, RNAseq

description: Library name: IMR90_vector_1


title: NPB-RSV4

city: Fuzhou

first: Jing

last: Zou

address: 15 shangxiadian road

institute: Fujian Agriculture and Forestry University

description: Library name: R4

data_processing:
SmallRNA-seq step 1, After the original data was examined by FastQC, the joint sequence and reads containing more than one base "N" were removed by Cutadapt to obtain Clean data
SmallRNA-seq step 2, The Clean data data is converted by a Python program commonly used in the laboratory into a fasta format file that removes redundant sequences and contains sequence number and length information in the header
SmallRNA-seq step 3, The obtained fasta files were compared to the tRNA, rRNA, chloroplast and mitochondrial sequences of rice using the short sequence alignment software bowtie. The parameters were set as no mismatch was allowed, and the sequences that were not matched were retained. All sequences were counted
SmallRNA-seq step 4, The obtained sequence is then compared to the rice reference genome, and the mismatch is not allowed, and the matched and unmatched sequences are obtained
SmallRNA-seq step 5, The precursor and mature miRNA sequences of rice miRNA were downloaded from the miRbase database. Then, according to the position of the mature sequence in the precursor, the number of reads near the position was counted by using the commonly used scripts in the laboratory, and the sequences with a length of 20-24 nt were retained. The expression level of sRNA was homogenized using Reads of exon model per million mapped reads
Assembly: (IRGSP 1.0) (http://rapdb.dna.affrc.go.jp/)
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Oryza sativa

source_name: leaf

extract_protocol:
RSV were inoculated on rice seedlings after 14 days of germination, and the inoculation process lasted for 3 days
Using 500 ng total RNA or enriched small RNA200ng, the 3' splices and 5' splices were connected respectively and then reverse-transcribed using RT primer as primer, using the small RNAs attached to the 5' and 3' splices as templates, cDNA was synthesized under the action of reverse transcriptase. Universal Primer and PCR Primer were used as primers of the two strands respectively, and the first strand of reverse transcriptional cDNA was used as a template to amplify and enrich the fragments. Finally, the glue was cut to recover the small RNA fragments.

value: leaf

value: NPB

value: wt

value: RSV


title: NPB-RSV3

description: Library name: R3


title: TERRAPCR_HeLa_CHM13_22q

description: TERRA PCR product amplified by primer CHM13_22q in HeLa


title: siWDR5-mESC-WDR5-rep1

description: Library name: siWDR5-mESC-WDR5-rep1

value: WT

value: WDR5 (4uL, CST D9E1I)


title: RUNXi_3

first: Charlotte

last: Kuperwasser

address: 150 Harrison Ave

department: Developmental, Molecular and Chemical Biology

institute: Tufts School of Medicine

description: Library name: RUNXi_696

data_processing:
Read Alignment to the human genome was performed using STAR (Dobin et al., 2013)
Assembly: GRCh38.p14 Assembly
Supplementary files format and content: CSV file containing the the Normalized counts of all samples

source_name: Breast

extract_protocol:
RNA was harvested using Rneasy minikit
Standard Illumina Primer Library used

value: Breast

value: Primary

value: Epithelial Cell

value: Diploid

value: RUNXi


title: siGlo-mESC-WDR5-rep1

description: Library name: siGlo-mESC-WDR5-rep1


title: NPB-RSV2

description: Library name: R2


title: NPB-RSV1

description: Library name: R1


title: DDR1i_3

description: Library name: DDR1i_696


title: TERRAPCR_HeLa_CHM13_15q

description: TERRA PCR product amplified by primer CHM13_15q in HeLa

value: HeLa

value: epithelial cell


title: WT-mESC-NFYA-rep2

description: Library name: WT-mESC-NFYA-rep2

value: mESC

value: NFYA (2.5ug, Santa Cruz sc-17753)


title: CTRL_3

description: Library name: Control_696

value: Vehicle


title: TERRAPCR_HeLa_CHM13_13q

description: TERRA PCR product amplified by primer CHM13_13q in HeLa


title: NPB-Mock4

description: Library name: M4

value: mock


title: WT-mESC-NFYA-rep1

description: Library name: WT-mESC-NFYA-rep1


title: NPB-Mock3

description: Library name: M3

value: leaf


title: RUNXi_2

description: Library name: RUNXi_686


title: WT-mESC-SP1-rep2

description: Library name: WT-mESC-SP1-rep2

value: SP1 (5ug, Millipore 07-645)


title: TERRAPCR_HeLa_CHM13_4q

description: TERRA PCR product amplified by primer CHM13_4q in HeLa


title: NPB-Mock2

description: Library name: M2

value: NPB

value: wt


title: WT-mESC-SP1-rep1

description: Library name: WT-mESC-SP1-rep1

value: WT


title: NPB-Mock1

description: Library name: M1


title: CTRL_2

description: Library name: Control_686


title: TERRAPCR_HeLa_CHM13_8p

description: TERRA PCR product amplified by primer CHM13_8p in HeLa


title: DDR1i_2

description: Library name: DDR1i_686


title: WT-mESC-WDR5-rep2

description: Library name: WT-mESC-WDR5-rep2

value: WDR5 (4uL, CST D9E1I)


title: TERRAPCR_HeLa_CHM13_3q

description: TERRA PCR product amplified by primer CHM13_3q in HeLa


title: TERRAPCR_HeLa_CHM13_1q

description: TERRA PCR product amplified by primer CHM13_1q in HeLa


title: RUNXi_1

description: Library name: RUNXi_683

value: Breast


title: WT-mESC-WDR5-rep1

description: Library name: WT-mESC-WDR5-rep1


title: TERRAPCR_U2OS_hg38_XqYq_2

description: TERRA PCR product amplified by primer hg38_XqYq-2 in U2OS

value: Osteosarcoma


title: DDR1i_1

description: Library name: DDR1i_683

value: Primary

value: Epithelial Cell


title: Total_RNAseq_MCF7_sgNONO_6hours_S-SKBG-1_Replicate_2

city: La Jolla

first: Garrett

middle: Lee

last: Lindsey

state: CA

address: 10650 N Torrey Pines Rd

department: Chemistry

institute: Scripps Research

description: Library name: Sample 29

data_processing:
Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
Gene level quantification was performed using tximeta [v1.8.4].
Differential gene expression was analyzed by DESeq2 [v1.30.1]
Assembly: HG19
Supplementary files format and content: Feature counts for differential expression

growth_protocol: Cells were grown in vitro under standard culture conditions

extract_protocol:
QIAGEN Rneasy Plus mini
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Samples were treated in biological triplicate in the presence of small molecules, as indicated, for 6 hours prior to collection.

value: Breast carcinoma

value: single guide - NONO_KO

value: (S)-SKBG-1, 20µM , 6 hours


title: TERRAPCR_U2OS_hg38_15q_2

description: TERRA PCR product amplified by primer hg38_15q-2 in U2OS


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep2, anti-IgG

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

data_processing:
All raw sequence data were quality trimmed using fastp (version0.19.7)
Aligned to the mm10 mouse genome using Bowtie2 (version 2.3.5.1) with options' –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700'.
PCR duplicates were removed using Picard MarkDuplicates (version 2.25.0).
Peaks were called using MACS2 (version 2.2.7.1) with options 'q 0.05'. DeepTools2 software (version 3.5.1) was used to create the peaks density plot and heatmap graph.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV.
Genomic annotation was assigned using ChIPSeeker (version 1.28.3). Promoters were defined as follows: within 3000bp around the transcriptional start site (TSS).
Assembly: mm10
Supplementary files format and content: bigWig, peaks.narrowPeak(except for Input sample)
Library strategy: CUT&Tag

source_name: small intestine

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Small intestinal ILC3s were sorted from siLP of aged  and young mice.  H3K4me3 Chip of three subsets of ILC3s were both performed on 100,000 cells  with modifications according to the protocol of Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD 901, Vazyme)
Briefly, sorted CCR6+ ILC3s，NKp46+ ILC3s and DN ILC3s were washed with 500 μl of wash buffer containing 1× protease inhibitor cocktail (5056489001, Sigma-Aldrich). Cell pellets were resuspended in wash buffer. After two washes with binding buffer, Concanavalin A-coated magnetic beads were added and incubated at room temperature. Bead-bound cells were resuspended in 50 μl of antibody buffer.

value: small intestine

value: Group 3 innate lymphoid cell

value: IgG (Normal Rabbit IgG (2729),Cell Signaling,Cat# 2729S)

tag: age

value: 6-8 weeks-old


title: CTRL_1

description: Library name: Control_683

value: Diploid

value: Vehicle


title: TERRAPCR_U2OS_hg38_10q_2

description: TERRA PCR product amplified by primer hg38_10q-2 in U2OS


title: Group 3 innate lymphoid cell, WT DN ILC3s rep2, anti-IgG


title: MatsuiWTA1

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

country: Japan

institute: ImmunoGeneTeqs

description:
Library name: Sample1
BD Rhapsody

data_processing:
Paired-end Fastq files underwent adapter trimming, quality filtering, and phase-shift base removal using Cutadapt (4.1). The processed cell barcode and cDNA reads were annotated and aligned to the GRCh38 (release-107) reference genome with STARsolo (2.7.10b), using known BD Rhapsody cell barcodes. The resulting count data were transformed into a genes-by-cells matrix, and the inflection threshold in the barcode rank plot was identified with the DropletUtils package in R (4.3.1). Valid cell barcodes and background noise were isolated within the threshold range (0.9–1.1 of the inflection threshold) using the Dropkick package. Small RNA annotations were removed from the Gencode v41 GTF file for STAR index construction.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw count values

extract_protocol:
Mononuclear cells were obtained from freshly collected bone marrow cells. CD34-positive HSPCs were isolated using the EasySep Human CD34 Positive Selection Kit II (STEMCELL Technologies). Subsequently, 40,000 cells were immediately loaded into the BD Rhapsody Express Single-Cell Analysis System (BD Biosciences).
scRNA-seq library was prepared using the TAS-Seq method (PMID: 35760847). Briefly, first-strand cDNA synthesis was performed on the BD Rhapsody Enhanced magnetic beads (BD Biosciences). Following exonuclease I treatment, a dC-tailing reaction was carried out at the 3' end of the cDNA using terminal deoxynucleotidyl transferase/RNase H enzymes. A mixture of dideoxycytidine 5′-triphosphate (ddCTP) and deoxycytidine triphosphate (dCTP) at a specific ratio was used to terminate the elongation reaction once ddCTP was incorporated. For the second-strand synthesis, a 5' universal-dG12 primer was employed instead of the 5' universal-dG9 primer described in the original protocol to enhance gene-detection sensitivity. After performing the first PCR with universal primers, size selection, and amplification via a second PCR, the library was ligated with Illumina TruSeq i7 adaptors (Illumina) and further amplified through PCR to add Illumina P5/P7 sequencing adapters.

value: Bone marrow

tag: disease state

value: Myelodysplastic neoplasms (MDS-IB2)

value: CD34-positive hematopoietic stem/progenitor cells

value: DDX41 p.R525H variant (somatic).


title: Total_RNAseq_MCF7_sgNONO_6hours_R-SKBG-1_Replicate_3

description: Library name: Sample 27

value: Breast

value: (R)-SKBG-1, 20µM, 6 hours


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep2, anti-IgG


title: Total_RNAseq_MCF7_sgNONO_6hours_R-SKBG-1_Replicate_2

description: Library name: Sample 26


title: MP411 fibroid/leiomyoma rep1

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

data_processing:
HiC reads were aligned with BWA
ATAC-seq reads were aligned with MACS2
Assembly: HiC reads were aligned to GRCh38
Assembly: ATAC-seq reads were aligned to GRCh38
Supplementary files format and content: Processed data files for HiC include HiCExplorer feature matrix files (.h5).
Supplementary files format and content: Processed data files for ATAC-seq are peak calls (*.*broadPeak) using  MACS2

source_name: uterus

extract_protocol:
Chromatin was prepared from flash frozen tissue samples using Corces et al doi.org/10.1038/nmeth.4396 methods.
HiC libraries were made with a kit from Arima; ATAC libraries were made using Corces et al doi.org/10.1038/nmeth.4396 methods.

value: uterus

tag: patient id

value: fibroid smooth muscle

tag: fibroid subtype

value: MED12 mutant

tag: biological replicate


title: Total_RNAseq_MCF7_sgNONO_6hours_R-SKBG-1_Replicate_1

description: Library name: Sample 25

value: Breast carcinoma

value: single guide - NONO_KO


title: TERRAPCR_U2OS_hg38_15q_1

first: Hsueh-Ping

last: Chu

address: No. 1 Sec. 4 Roosevelt Road

institute: National Taiwan University

description: TERRA PCR product amplified by primer hg38_15q-1 in U2OS

value: Osteosarcoma


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep2, anti-IRF4

value: small intestine

value: Group 3 innate lymphoid cell

value: IRF4 antibody (IRF-4 Rabbit mAb (D9P5H),Cell Signaling, Cat# 15106T)


title: Total_RNAseq_MCF7_sgNONO_6hours_DMSO_Replicate_3

description: Library name: Sample 24

value: DMSO


title: MP411 fibroid/leiomyoma rep2


title: Group 3 innate lymphoid cell, WT DN ILC3s rep2, anti-IRF4

value: 6-8 weeks-old


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep2, anti-IRF4


title: TERRAPCR_U2OS_hg38_17q

description: TERRA PCR product amplified by primer hg38_17q in U2OS


title: MP411 matched myometrium rep2

value: myometrial smooth muscle

value: Not applicable


title: MP411 matched myometrium rep1


title: TERRAPCR_U2OS_hg38_10q_1

description: TERRA PCR product amplified by primer hg38_10q-1 in U2OS


title: Total_RNAseq_MCF7_sgNONO_6hours_S-SKBG-1_Replicate_3

description: Library name: Sample 30

value: (S)-SKBG-1, 20µM, 6 hours


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep1, anti-IgG

value: IgG (Normal Rabbit IgG (2729),Cell Signaling,Cat# 2729S)


title: TERRAPCR_U2OS_hg38_2q

description: TERRA PCR product amplified by primer hg38_2q in U2OS


title: MP411 fibroid/leiomyoma


title: Total_RNAseq_MCF7_sgNONO_6hours_S-SKBG-1_Replicate_1

description: Library name: Sample 28

value: Breast


title: Total_RNAseq_MCF7_sgNONO_6hours_DMSO_Replicate_1

description: Library name: Sample 22


title: Group 3 innate lymphoid cell, WT DN ILC3s rep1, anti-IgG


title: TERRAPCR_U2OS_CHM13_22q

description: TERRA PCR product amplified by primer CHM13_22q in U2OS


title: Total_RNAseq_MCF7_sgNONO_6hours_S,S-GL-373_Replicate_3

description: Library name: Sample 21


title: MP411 matched myometrium


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep1, anti-IgG


title: TERRAPCR_U2OS_CHM13_15q

description: TERRA PCR product amplified by primer CHM13_15q in U2OS


title: TERRAPCR_U2OS_hg38_XqYq_1

description: TERRA PCR product amplified by primer hg38_XqYq-1 in U2OS


title: Total_RNAseq_MCF7_sgNONO_6hours_S,S-GL-373_Replicate_2

description: Library name: Sample 20


title: TERRAPCR_U2OS_CHM13_13q

description: TERRA PCR product amplified by primer CHM13_13q in U2OS


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep1, anti-IRF4


title: patch-seq, virus-infected, replicate 154

city: madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

description:
Library name: 5_3H10
SMART-seq3

data_processing:
snATAC/RNA-seq: The 10x Multiome ATAC(snATAC-seq) + Gene Expression(snRNA-seq) dataset was processed using the Cell Ranger ARC pipeline. To analyze the macaque data, we used the Cell Ranger ARC mkref to create a rheMac10 reference. Subsequently, we performed a quality check on the output of the Cell Ranger ARC pipeline, and then used it for downstream analysis.
SMART-seq:The SMART-seq3 RNA-seq reads from human were aligned to reference genome GRCh38 and the reads from rhesus macaque were aligned to reference genome rheMac10. Trim Galore was used for the adaptor trimming. We used STAR (v2.7.2b) (69) in two pass Mode for the alignment and removed PCR duplicates. STAR quantMode was used for gene counts on uniquely aligned reads, and the intergenic regions were excluded.
Assembly: rheMac10; GRCh38
Supplementary files format and content: snATAC-seq: fragments files are generated from Cell Ranger ARC pipeline. ; snRNA-seq: barcodes, features and matrix files are generated from Cell Ranger ARC pipeline. SMART-seq3: "AcuteRhesusPatchseq.csv" and "OrganotypicCHD8Patchseq.csv" are normalized gene expression data files.

molecule: nuclear RNA

source_name: dlPFC

extract_protocol:
Macaque brain specimens were collected from postconceptional day (PCD) 87 to PCD155. All experiments using non-human primates were carried out in accordance with a protocol approved by the University of Wisconsin’s Institutional Animal Care and Use Committee and NIH guidelines.
snMultiomes:The libraries were constructed in accordance with the guidelines provided in the "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide" (10x Genomics, CG000338); SMART-seq3: follow the protocol according to publication "Single-cell RNA counting at allele and isoform resolution using Smart-seq3" (PMID: 32518404).

value: dlPFC

value: tissue

value: organotypic dlPFC slice cells

value: lentivirus infected

value: shNC

tag: batch

value: patch-seq, virus-infected


title: patch-seq, virus-infected, replicate 155

description:
Library name: 5_3H11
SMART-seq3


title: TERRAPCR_U2OS_CHM13_8p

city: Taipei

description: TERRA PCR product amplified by primer CHM13_8p in U2OS

value: Osteosarcoma


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep1, anti-IRF4

value: small intestine


title: Total_RNAseq_MCF7_sgNONO_6hours_R,R-GL-373_Replicate_3

description: Library name: Sample 18

value: Breast carcinoma

value: single guide - NONO_KO


title: patch-seq, virus-infected, replicate 153

description:
Library name: 5_3G11
SMART-seq3


title: Total_RNAseq_MCF7_sgNONO_6hours_DMSO_Replicate_2

description: Library name: Sample 23

value: DMSO


title: Total_RNAseq_MCF7_sgNONO_6hours_S,S-GL-373_Replicate_1

description: Library name: Sample 19


title: patch-seq, virus-infected, replicate 152

description:
Library name: 5_3E12
SMART-seq3


title: TERRAPCR_U2OS_CHM13_3q

description: TERRA PCR product amplified by primer CHM13_3q in U2OS


title: Total_RNAseq_MCF7_sgNONO_6hours_R,R-GL-373_Replicate_2

description: Library name: Sample 17


title: Hippocampus, Li deficient, rep 5

first: Chenxi

last: Qiu

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
We aligned the demultiplexed raw sequencing reads to the mouse genome (mm10 from 10X genomics) using Cell Ranger (6.1.2), with –include-introns option. The generated counts table were loaded to Seurat (v4) to generate Seurat objects. Cells with more than 10 percent of reads being attributed to mitochondrial transcripts were filtered. Cells that express less than 200 genes (low quality cells) or higher than 8000 genes (apparent doublets) were also filtered.
The cells that pass quality controls are log normalized using NormalizeData function from Seurat with a scale.factor of 10,000. Variable features are identified using FindVariableFeatures function from Seurat with vst selection method and 2000 features. Data are scaled using ScaleData, and PCA is performed using RunPCA with the identified variable features using Seurat. Nearest neighbors are found using FindNeighbors using dimension 1:30, which was determined by ElbowPlot following Seurat’s manual.
The number of clusters were determined by FindClusters function using Seurat v4. UMAP and TSNE were performed using RunUMAP or RunTSNE using Seurat with dimensions 1:30 and do.fast=TRUE parameter. Potential doubets were removed using DoubletFinder (v3) following the default parameters. The vast majority of the cells passed these quality controls, and the number of cells before and after filtration are documented. After filtration, cluster specific markers are determined by FindAllMarkers function (Seurat v4), with parameters only.pos = F, min.pct = 0.25 and max.cell.per.ident = 500.
Cell types were identified by cross-referencing the transcriptome of each individual cell to the Mouse Cell Atlas and independently validated by checking expression of established cell type-specific markers. Violin and heat scatter plots to demonstrate the expression distribution of established markers are plotted using VlnPlot and FeaturePlot functions from Seurat.
Cell type-specific abundance and differential gene expression analyses were performed on the major cell types (excitatory neurons, inhibitory neurons, granule cells, microglia, astrocytes, oligodendrocytes, oligodendrocyte precursor cells and endothelial cells). Clusters of the same cell types were combined to increase the statistical power, and clusters with mixed cell types (<80% homogenous) were removed for cell type-specific analyses. Relative abundance of each cell type was computed by dividing the number of cells of the particular cell type by the total number of cells. Students’ t test was performed to test if the relative abundance of each cell type between the control and lithium deficient conditions. Differentially expressed genes (DEGs) were computed by the MAST61 test in Seurat. Genes expressed in less than 1% of the cells in each cell type were filtered out. All the differentially expressed genes are reported in the Supplemental Table 2. DEGs with FDR<0.05 were used for gene ontology analyses using Metascape62 v3.5.20240101. Heat scatter plots for differentially expressed genes were generated using the FeaturePlot function from Seurat.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Mouse hippocampus

growth_protocol: 3xTg mice have been bred, genotyped and maintained at HMS HCCM facility for 15 months prior to the treatment.

extract_protocol:
Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation.
The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual.

treatment_protocol: We treated 3xTg mice (n=4) with regular diet and or lithium deficient diet (n=5) for 1 month.

value: Mouse hippocampus

value: Li deficient diet, 1 month


title: Group 3 innate lymphoid cell, WT DN ILC3s rep1, anti-IRF4

value: Group 3 innate lymphoid cell

value: IRF4 antibody (IRF-4 Rabbit mAb (D9P5H),Cell Signaling, Cat# 15106T)

value: 6-8 weeks-old


title: Hippocampus, Li deficient, rep 4


title: Total_RNAseq_MCF7_sgNONO_6hours_R,R-GL-373_Replicate_1

description: Library name: Sample 16

value: Breast


title: Total_RNAseq_MCF7_sgControl_6hours_S-SKBG-1_Replicate_3

description: Library name: Sample 15

value: single guide - Control

value: (S)-SKBG-1, 20µM, 6 hours


title: patch-seq, virus-infected, replicate 151

description:
Library name: 5_3E11
SMART-seq3

value: dlPFC

value: tissue

value: organotypic dlPFC slice cells


title: TERRAPCR_U2OS_CHM13_1q

description: TERRA PCR product amplified by primer CHM13_1q in U2OS


title: Hippocampus, Li deficient, rep 3


title: TERRA_CaptureSeq_HeLa_specific

description: TERRA captured Illumina RNA-seq: specific group in HeLa

data_processing:
The FASTQ reads derived from TERRA PCR products underwent quality filtration (Q > 30) and adapters pruning using TrimGalore (v0.6.3) (https://github.com/FelixKrueger/ TrimGalore). Trimmed reads were aligned to CHM13 genome using Bowtie2 aligner (v2.4.2) with the default setting. SAM files were transformed to BAM files, and were deduplicated using SAMTools (v.1.18). Bigwig files were generated by DeepTools (v.3.3.1) bamCoverage, with parameters: --normalizeUsing CPM, --centerReads, and --extendReads 150.
For TERRA capture-seq, trimmed reads were aligned to Homo sapiens T2T-CHM13 reference genome by STAR aligner (v2.7.9a) with default parameters.
Assembly: CHM13
Supplementary files format and content: bigwig formats is read coverage files (Illumina dataset)

extract_protocol:
Total RNA was extracted from 1 x 10^7 cells using TRIzol™ Reagent (Invitrogen™, Cat:15596018) following the manufacturer's protocol. For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010). The TERRA-captured RNA sample was divided into two equal halves for the reverse transcription reaction. Half of the TERRA-captured sample was reverse transcribed using 2 μM random hexamers (Thermo Fisher Scientific, 48190011), while the other half using 1 μM of telomeric C-rich primer. These two groups are referred to as the random and specific groups, respectively. The rest steps were performed as the protocol provided by manufactory.
For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010).

value: HeLa

value: epithelial cell


title: Total_RNAseq_MCF7_sgControl_6hours_S-SKBG-1_Replicate_2

description: Library name: Sample 14


title: patch-seq, virus-infected, replicate 150

description:
Library name: 5_3E10
SMART-seq3

value: lentivirus infected

value: shNC

value: patch-seq, virus-infected


title: Hippocampus, Li deficient, rep 2


title: patch-seq, virus-infected, replicate 149

description:
Library name: 5_3D12
SMART-seq3


title: Total_RNAseq_MCF7_sgControl_6hours_S-SKBG-1_Replicate_1

description: Library name: Sample 13

value: Breast carcinoma


title: patch-seq, virus-infected, replicate 156

description:
Library name: 5_3H12
SMART-seq3


title: TERRAPCR_U2OS_CHM13_4q

description: TERRA PCR product amplified by primer CHM13_4q in U2OS

value: Osteosarcoma


title: Synchronized culture - sample 6h_21_S60_R1_001

city: paris

first: yuping

last: dia

address: 4 pl.jussieu

country: France

institute: sorbonne university

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_21_S60_R1_001

data_processing:
The amount of reads per gene was counted with featureCounts91 with default parameters. Data was then processed using R and the EdgeR library92. Read counts per gene were standardized to counts per million and filtered to eliminate all of the genes which did not have at least one read per million in all 15 samples.
Assembly: S. islandicus REY15A genome (RefSeq accession number: NC_017276)
Supplementary files format and content: Comma-delimited text file includes raw counts for each sample

organism: Saccharolobus islandicus

source_name: archaeal cell

growth_protocol: Saccharolobus islandicus strain REY15A was grown aerobically at 76ºC with shaking in 25 ml of MTSV medium containing mineral salts (M), 0.2% (wt/vol) tryptone (T), 0.2% (wt/vol) sucrose (S) and a mixed vitamin solution (V); the pH was adjusted to 3.5 with sulfuric acid, as described previously

extract_protocol:
RNA was then isolated from each batch on different days, no variance between batches was found using principal component analysis. The total RNA was extracted from the 15 biological replicates at three different time-points after synchronization: 2h30, 4h and 6h. The time points were selected based on the results of the flow cytometry analysis which showed that samples at these three time points are enriched in cells in the M-G1, S and G2 phases, respectively. Total RNA was extracted using TRI Reagent (SIGMA-Aldrich), following the manufacturer’s protocol, and treated with DNase (TURBO DNA-free kit; Invitrogen) following the manufacturer’s instructions. DNase treated samples were further purified with RNeasy Mini Kit (Qiagen). RNA samples were quantified using a Qubit Fluorometer (Thermo Fischer Scientific) and assessed for quality with a BioAnalyzer (Agilent)
Analyzer (Agilent). Sequencing was performed on an Illumina NextSeq 2000 sequencer with a P3 50-cycle kit and a target of 30 to 40 million reads per sample. The reads obtained were mapped to the reference S. islandicus REY15A genome (RefSeq accession number: NC_017276) with Bowtie-290 using default parameters.

treatment_protocol: Cells were plated on solid media and 15 single colonies were inoculated in liquid media. forming 15 cultures that represent completely independent biological replicates. The 15 biological replicates were grown in 3 different batches (5 cultures per batch), each batch was grown and synchronized at a different time (5 cultures at a time). RNA was then isolated from each batch on different days, no variance between batches was found using principal component analysis (see supplementary table S1 for batch number for each sample). The total RNA was extracted from the 15 biological replicates at three different time-points after synchronization: 2h30, 4h and 6h (Fig. 1B). The time points were selected based on the results of the flow cytometry analysis which showed that samples at these three time points are enriched in cells in the M-G1, S and G2 phases, respectively (Figure 1C). Total RNA was extracted using TRI Reagent (SIGMA-Aldrich), following the manufacturers protocol, and treated with DNase (TURBO DNA-free kit; Invitrogen) following the manufacturers instructions. DNase treated samples were further purified with RNeasy Mini Kit (Qiagen). RNA samples were quantified using a Qubit Fluorometer (Thermo Fischer Scientific) and assessed for quality with a BioAnalyzer (Agilent) (see supplementary table S1 for quality control parameters for each sample).  Libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Illumina Ribo-Zero Plus kit, with custom ribodepletion. Following PCR amplification, all samples underwent two rounds of purification with AMPure beads (Beckman Coulter) to remove small fragments. Libraries were subsequently validated using both the Qubit Fluorometer and the Fragment Analyzer (Agilent). Sequencing was performed on an Illumina NextSeq 2000 sequencer with a P3 50-cycle kit and a target of 30 to 40 million reads per sample. The reads obtained were mapped to the reference S. islandicus REY15A genome (RefSeq accession number: NC_017276) with Bowtie-290 using default parameters.

tag: strain

value: archaeal cell

tag: time


title: patch-seq, virus-infected, replicate 148

description:
Library name: 5_3C11
SMART-seq3


title: Hippocampus, Control, rep 4

value: Mouse hippocampus

value: Control diet, 1 month


title: patch-seq, virus-infected, replicate 147

description:
Library name: 5_3C10
SMART-seq3


title: Synchronized culture - sample 6h_19_S58_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_19_S58_R1_001


title: Total_RNAseq_MCF7_sgControl_6hours_R-SKBG-1_Replicate_3

description: Library name: Sample 12

value: (R)-SKBG-1, 20µM, 6 hours


title: Synchronized culture - sample 6h_20_S59_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_20_S59_R1_001


title: patch-seq, virus-infected, replicate 146

description:
Library name: 5_3B12
SMART-seq3


title: Total_RNAseq_MCF7_sgControl_6hours_R-SKBG-1_Replicate_2

description: Library name: Sample 11

value: Breast


title: Synchronized culture - sample 6h_17_S57_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_17_S57_R1_001


title: Total_RNAseq_MCF7_sgControl_6hours_DMSO_Replicate_3

description: Library name: Sample 9

value: single guide - Control

value: DMSO, 6 hours


title: TERRA_CaptureSeq_HeLa_random

description: TERRA captured Illumina RNA-seq: random group in HeLa


title: Total_RNAseq_MCF7_sgControl_6hours_R-SKBG-1_Replicate_1

description: Library name: Sample 10


title: Hippocampus, Control, rep 3


title: patch-seq, virus-infected, replicate 145

description:
Library name: 5_3B10
SMART-seq3

value: dlPFC


title: Total_RNAseq_MCF7_sgControl_6hours_DMSO_Replicate_2

description: Library name: Sample 8


title: patch-seq, virus-infected, replicate 144

description:
Library name: 5_3A12
SMART-seq3

value: tissue


title: Hippocampus, Control, rep 1


title: Synchronized culture - sample 6h_11_S54_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_11_S54_R1_001


title: patch-seq, virus-infected, replicate 142

description:
Library name: 5_2E1
SMART-seq3

value: organotypic dlPFC slice cells


title: Total_RNAseq_MCF7_sgControl_6hours_S,S-GL-373_Replicate_3

description: Library name: Sample 6


title: patch-seq, virus-infected, replicate 143

description:
Library name: 5_2F1
SMART-seq3


title: Hippocampus, Li deficient, rep 1

value: Li deficient diet, 1 month


title: Synchronized culture - sample 6h_12_S55_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_12_S55_R1_001


title: Synchronized culture - sample 6h_10_S53_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_10_S53_R1_001


title: BM_NCF2-/-_CL

city: Tianjin

first: Hanzhi

last: Yu

address: 22 Meteorology Station Road, Heping District, Tianjin

institute: Tianjin Medical University

description: EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit(STEMCELL, 19856A) was used to enrich Lin- cells

data_processing:
After sequencing, raw data were processed with the SeekSpace tools (v1.0.0, Seekgene) to align reads to the mouse reference genome (mm10) and generate a gene-cell expression matrix for subsequent analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

source_name: bone marrow

extract_protocol:
After harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Tissue Dissociation Reagent A (Seekone K01301-30) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate.
The SeekOne® Digital Droplet Single Cell 3’ Library Preparation Kit (SeekGene, No.K00202) was used to prepare the single-cell RNA-Seq library.

value: bone marrow

value: CL


title: COLON_NCF2-/-_CL

source_name: colon

value: colon


title: Synchronized culture - sample 6h_9_S52_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_9_S52_R1_001


title: Total_RNAseq_MCF7_sgControl_6hours_S,S-GL-373_Replicate_2

description: Library name: Sample 5


title: Hippocampus, Control, rep 2


title: patch-seq, virus-infected, replicate 140

description:
Library name: 5_2C1
SMART-seq3

value: lentivirus infected

value: shNC

value: patch-seq, virus-infected


title: Total_RNAseq_MCF7_sgControl_6hours_S,S-GL-373_Replicate_1

description: Library name: Sample 4

value: Breast carcinoma


title: Synchronized culture - sample 6h_8_S51_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_8_S51_R1_001

value: archaeal cell


title: patch-seq, virus-infected, replicate 141

description:
Library name: 5_2D1
SMART-seq3


title: patch-seq, virus-infected, replicate 139

description:
Library name: 5_2B1
SMART-seq3


title: Synchronized culture - sample 6h_13_S56_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_13_S56_R1_001


title: BM_WT_CL

value: WT


title: LUNG_NCF2-/-_CL

source_name: Lung

value: Lung


title: LUNG_WT_CL


title: patch-seq, virus-infected, replicate 138

description:
Library name: 5_2A1
SMART-seq3


title: Total_RNAseq_MCF7_sgControl_6hours_DMSO_Replicate_1

description: Library name: Sample 7

value: Breast


title: COLON_WT_CL


title: Synchronized culture - sample 6h_5_S49_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_5_S49_R1_001


title: LUNG_NCF2-/-_SPF

value: SPF


title: patch-seq, virus-infected, replicate 136

description:
Library name: 5_1H8
SMART-seq3