title: alkbh1-Anti-OsMORC6b-2

data_processing:
the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15.
The ChIP clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
The DESeq2 method imple_x0002_mented in DiffBind was used to test the differential peak
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: bigWig, broadPeak,narrowPeak (except for Input sample)
The RNA-seq clean data were mapped against the MSU version 7.0 rice genome with the corre_x0002_sponding annotation by hisat2 using default parameters
FeatureCounts (v2.0.0)and DESeq2 (v1.26.0)were used to calculate DEGs.
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: tab-delimited text file include counts for each Sample

extract_protocol:
Genomic DNA was extracted using DNeasy plant mini kit (QIAGEN, Germany) according to the manufacturer’s instructions.
ChIP DNA libraries were prepared using a TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA)
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufac_x0002_turer’s protocol.
RNA-seq library construction using the TruSeq RNA Library Preparation Kit (Illumina, USA), according to the manufac_x0002_turer’s recommendations.

value: ALKBH1 knockout


title: Sample25_Ground.M1.Vitamin_D

status: Public on May 12 2025

type: SRA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Our processing pipeline consists of the following elements: (1) base calls generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 30 using STAR (v2.6.1d).
Gene level expression quantification is generated with RNA-SeQC (v2.3.3) and RSEM (v1.3.1). RPKM and TPM for transcript isoforms are quantitated on the merged lane-level data with RSEM (v1.3.1). Gene-level RPKMs are quantitated with RNA-SeQC (v2.3.3) on a standard collapsed reference annotation.
RSEM transcript abundances were read into R using the Bioconductor tximeta package and summarized at the gene level.
Assembly: Gencode v30 (GRCh38)
Supplementary files format and content: Counts per gene

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: Deidentified human cortical kidney samples were collected through the Northwest Biotrust at the University of Washington Medical Center with local IRB approval (UW IRB Study 1297). Primary human proximal tubule epithelial cells were isolated by mechanical and enzymatic dissociation and cultured as previously described.38,39 Serum-free tubular cell cultures were maintained in PTEC maintenance media consisting of DMEM/F12 (Gibco, 11330-032) supplemented with 1x insulin-transferrin-selenium-sodium pyruvate (ITS-A, Gibco, 51300044), 50 nM hydrocortisone (Sigma, H6909), and 1x Antibiotic-Antimycotic (Gibco, 15240062). Upon reaching 70-80% confluence, PTECs were passaged by enzymatic digestion with 0.05% trypsin EDTA (Gibco, 25200056) and manual cell scraping to obtain a single-cell suspension that was subsequently neutralized with defined trypsin inhibitor (Gibco, R007100). Cells were pelleted by centrifugation at 200 x g for 6 minutes, resuspended in maintenance media, and plated in cell culture-treated flasks at >30% confluency. PTECs were used at passage number 2-3 from all donors in these experiments.

extract_protocol:
RNA was isolated from devices fixed with RNALater by injecting 100 µL of RLT lysis buffer (Qiagen, 79216) into the injection port using a 1 mL syringe outfitted with a 22-gauge needle. The cell lysate was collected at the outlet, 400 µL of RLT lysis buffer was added to each tube, and the samples were stored at -80°C until extraction. RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891). Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA). Sequencing reads were aligned to GRCh38.p12 with reference transcriptome GENCODE human release 30 (with additional ERCC spike-in sequences) using STAR (v2.6.1d).
Total RNA was normalized to 2ng/ul in a total volume of 9ul and then transcribed to cDNA in a dedicated PCR clean workstation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Moutain View, CA).  Sequencing libraries were constructed from cDNA using the SMARTer ThurPLEX DNA-Seq kit (Takara Bio).  Final libraries were quantified and library insert size distribution was checked using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were normalized and pooled prior to treatment to block free adapters in the sequencing reaction.  Final pools were normalized to 10nM prior to sequencing.

treatment_protocol: Triplex microfluidic devices were purchased from Nortis, Inc (Bothell, WA) and prepared as previously described.40 Triplex microfluidic devices contain three fluidic circuits, which enables generation of three PTEC tubules on a single device that can be continuously perfused with media. 19 Maintenance, treatment, and fixation of devices in BioServe perfusion platform: The BioServe perfusion platform was developed to house three Triplex devices in a self-contained, hermetically sealed system to meet the levels of containment required by NASA and reduce the space required to perfuse the Triplex devices. A flow rate of 0.5 µL/min was used for cell maintenance and treatment. The treatments conditions were control (PTEC maintenance media), vitamin D, or 2% human serum.19 To prepare 2% human serum treatment media, normal human serum (Valley Biomedical, HS1021) was diluted in PTEC maintenance media to a final concentration of 2%. Vitamin D treatment media consisted of PTEC maintenance media supplemented with 1.5 µM 25(OH)D3 (Toronto Research Chemicals, C125700) and 3 µM DBP (Athens Research, 16-16-070307). To prepare vitamin D treatment media, stock 25(OH)D3 was solubilized with molecular biology grade ethanol to 5 mM. DBP was reconstituted to 3 µM in PTEC maintenance media to create PTEC-DBP media. 25(OH)D3 was then diluted into PTECDBP media to 1.5 µM. Vitamin D media was allowed to equilibrate at room temperature for 30 minutes prior to filling the treatment cassette to ensure binding of 25(OH)D3 to DBP. The final concentration of ethanol in the vitamin D treatment media was 0.02%. In order to preserve the tubules at the end of treatment for analyses, the devices were fixed for 2 hours with either 10% neutral buffered formalin (Thermo, 5725) or RNALater (ThermoFisher, AM7024) at a flow rate of 10 µL/min

tag: tissue

value: Kidney

tag: cell line

value: Primary cells

tag: Sex

value: Male

tag: environment

value: Ground

tag: treatment

tag: donor


title: ZH11-ATAC-2

city: Wuhan

first: Qingxiao

last: Jia

state: Hubei

address: No.1,Shizishan Street

country: China

institute: HZAU

description: Library name: ZH11-ATAC-2

library_source: genomic

data_processing:
the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15.
The clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
The DESeq2 method imple_x0002_mented in DiffBind was used to test the differential peak
genome assembly: MSU version 7.0 rice genome
processed data files format and content: bigWig

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: seedling

growth_protocol: Seedlings were grown in one-half-strength Murashige and Skoog medium under 16-h light/8-h dark cycles at 30 °C

extract_protocol:
Seedling were cut into small pieces and the nuclei were separated. 1× 105 nuclei were incubated with 50 µL transposition mix containing 2 µL Tn5 transposase (Vazyme, TD711) at 37 °C for 30 min. The mixture was further incubated at 55 °C for 30 min, and the fragmentation products were then subjected to DNA extraction using ATAC DNA Extract Beads.  fragments were sorted using ATAC DNA Clean Beads (Vazyme, TD711), and precipitated by cold ethanol.
Purified genomic DNA was amplified using the universal i5 primer and barcoded i7 primer (Vazyme, TD202) using Vazyme Master Mix (Vazyme, TD711). The library PCR products were cleaned with Agencourt AMPure XP beads (Beckman Coulter, A63881).

value: seedling

tag: genotype

value: WT


title: Female KO MTECs, naïve, biol rep 1

city: Orlando

first: Justine

middle: T.

last: Tigno-Aranjuez

state: FL

address: 6900 Lake Nona Blvd., BSBS Bldg, Rm 370

department: BSBS, Immunity and Pathogenesis Division

institute: University of Central Florida

description: Library name: Sample 13

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an FDR 0.1 and min fold change > 2 were called as differentially expressed genes for each comparison.
For k-means clustering, data was transformed and genes were ranked by standard deviation. Only to the top 2000 are used for clustering (3 clusters were used). Enrichment analysis was performed for each cluster using KEGG pathways. Enrichment p-value are calculated based on one-sided the hypergeometric test, which is then adjusted for multiple testing using the Benjamini-Hochberg procedure and converted to FDR(false discovery rate). FDR tells us how likely to observe the enrichment by chance. Due to increased statistical power, large pathways tend to have smaller FDRs. Fold Enrichment is defined as the percentage of genes in the list belonging to a pathway, divided by the corresponding percentage in the background. As a measure of effect size, Fold Enrichment indicates how drastically genes of a certain pathway is overrepresented. The background genes are filtered genes from the original gene list. The filtered genes are those that are passed a low filter in RNA-seq. A total of 343 gene sets are obtained from KEGG ( Kyoto Encyclopedia of Genes and Genomes ). Dabase version/date is Release 104.0 . For details on this KEGG type of database, please refer to: Kanehisa M, et al. , KEGG: kyoto encyclopedia of genes and genomes , Nucleic Acids Res. 2000 Jan 1;28(1):27-30 ( PubMed ID: 10592173 ). After the analysis is done, pathways are first filtered based on a FDR cutoff (0.05). Then the significant pathways are sorted by. FDR . Only the top 10 pathways are shown.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: *.csv file contains raw counts for each sample

organism: Mus musculus

source_name: Murine tracheal airway epithelium cultures

growth_protocol: Murine tracheal airway epithelial cell cultures were generated as in Lauer et al. J Biol Chem. 2008 Sep 19;283(38):26283-96.

extract_protocol:
Rneasy mini kit as directed by manufacturer (Qiagen)
A. mRNA enrichment, mRNA fragmentation and random priming; B. First and second strand cDNA synthesis; C. End repair, 5' phosphorylation and dA-tailing; D. Adaptor ligation, PCR enrichment and sequencing

treatment_protocol: untreated or treated with 20 ug/ml house dust mite extract overnight

value: Primary

tag: cell type

value: airway epithelial cells

value: LMAN1 KO


title: alkbh1-Anti-OsMORC6b-1

tag: chip antibody


title: Sample24_Ground.F2.Media

value: Female

value: Media


title: 1_1C7

city: madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

description:
patch-seq, pcd112, replicate 1
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

organism: Macaca mulatta

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

tag: developmental stage

value: cortical cells

value: wild type

value: no treatment


title: Sample23_Ground.F2.Media


title: Female WT MTECs, HDM, biol rep 2

description: Library name: Sample 12

value: Murine tracheal airway epithelium cultures

value: HDM


title: 1_1B6


title: 1_1C6


title: Female WT MTECs, HDM, biol rep 1

description: Library name: Sample 11


title: Female WT MTECs, naïve, biol rep 2

description: Library name: Sample 10


title: NIP-Anti-OsMORC6b-1


title: 2_2H6

description:
patch-seq, pcd106, replicate 1
SMART-seq3


title: Female WT MTECs, naïve, biol rep 1

description: Library name: Sample 9


title: morc-Input

value: MORC1/6a/b knockout


title: Sample22_Ground.F2.Media

value: Kidney

value: Primary cells


title: Sample20_Ground.F1.Media

value: Ground


title: ZH11-Input

value: seedling


title: 1_1A7


title: Male KO MTECs, HDM, biol rep 2

description: Library name: Sample 8


title: Sample21_Ground.F1.Media


title: 2_2H5


title: Sample19_Ground.F1.Media


title: morc-Anti-OsMORC6b-2


title: Male KO MTECs, HDM, biol rep 1

description: Library name: Sample 7


title: 2_2H4


title: Male KO MTECs, naïve, biol rep 2

description: Library name: Sample 6


title: NIP-Anti-OsMORC6b-2

value: WT


title: 2_2H11


title: Sample17_Ground.M1.Media

value: Male


title: ZH11-Anti-OsMORC6b-2


title: Male KO MTECs, naïve, biol rep 1

description: Library name: Sample 5

value: Primary

value: airway epithelial cells


title: 2_2G6


title: ZH11-Anti-OsMORC6b-1


title: Male WT MTECs, HDM, biol rep 2

description: Library name: Sample 4


title: 2_2G5


title: Sample16_Ground.M2.2_human_serum


title: Male WT MTECs, HDM, biol rep 1

description: Library name: Sample 3


title: 2_2F6


title: 2_2G11


title: Sample15_Ground.M2.2_human_serum


title: morc-H3K27me3-2


title: morc-H3K27me3-1


title: Sample14_Ground.F1.2_human_serum

value: Female


title: 2_2F5


title: Sample13_Ground.F1.2_human_serum


title: ZH11-H3K27me3-1


title: Male WT MTECs, naïve, biol rep 1

description: Library name: Sample 1


title: ZH11-H3K27me3-2


title: 2_2F11


title: GMP.dKO.3

city: Columbus

first: Pu

last: Zhang

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

description:
Library name: Sample 12
IonXpress_042

data_processing:
Transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline, and gene set enrichment analysis (GSEA) performed. For transcript-aware analyses, the FASTQ files were aligned with salmon(59) and differentially enriched transcripts were identified using DRIMSeq(60) in a similar workflow to edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes absolute read count values for each Sample

source_name: bone marrow

extract_protocol:
The Clontech SMARTer v4 Kit (Takara Bio USA, Inc.) was used for preamplifying samples prior to library construction with the Nextera XT DNA Library Prep Kit (Illumina, Inc.). Samples were sequenced to a depth of 15–20 million 2 × 150 bp clusters with the Illumina HiSeq 4000 platform.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol.

treatment_protocol: A total of 500 viable GMP cells from WT, single KO or double KO murine bone marrow were sorted directly into SMART-seq lysis buffer with FACSAria Fusion (BD) based on markers, Lin-cKIT+Sca-1-CD16/32+CD34+

value: bone marrow

value: GMP

value: TP53/TET2 KO


title: morc-Anti-OsMORC6b-1


title: Sample18_Ground.M1.Media

value: Media


title: morc-RNA-seq-3

data_processing:
The RNA-seq clean data were mapped against the MSU version 7.0 rice genome with the corre_x0002_sponding annotation by hisat2 using default parameters
FeatureCounts (v2.0.0)and DESeq2 (v1.26.0)were used to calculate DEGs.
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: tab-delimited text file include counts for each Sample
The RNA-seq clean data were mapped against the MSU version 7.0 rice genome with the corre_x0002_sponding annotation by hisat2 using default parameters
FeatureCounts (v2.0.0)and DESeq2 (v1.26.0)were used to calculate DEGs.
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: tab-delimited text file include counts for each Sample

growth_protocol:
Seedlings were grown in one-half-strength Murashige and Skoog medium under 16-h light/8-h dark cycles at 30 °C
Seedlings were grown in one-half-strength Murashige and Skoog medium under 16-h light/8-h dark cycles at 30 °C

extract_protocol:
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufac_x0002_turer’s protocol.
RNA-seq library construction using the TruSeq RNA Library Preparation Kit (Illumina, USA), according to the manufac_x0002_turer’s recommendations.
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufac_x0002_turer’s protocol.
RNA-seq library construction using the TruSeq RNA Library Preparation Kit (Illumina, USA), according to the manufac_x0002_turer’s recommendations.


title: Sample12_Ground.F1.2_human_serum


title: Sample36_Ground.F1.2_human_serum


title: Sample11_Ground.M1.2_human_serum


title: 2_2E6

value: dlPFC

value: cortical cells

value: wild type

value: no treatment


title: morc-RNA-seq-1

value: MORC1/6a/b knockout


title: morc-RNA-seq-2


title: GMP.dKO.1

description:
Library name: Sample 10
IonXpress_040


title: Sample10_Ground.M1.2_human_serum

value: Kidney

value: Primary cells


title: 2_2E5


title: Sample9_Ground.M2.Vitamin_D

value: Ground


title: 2_2D6


title: ZH11-RNA-seq-3

value: seedling

value: WT


title: Sample8_Ground.M2.Vitamin_D

value: Male


title: Sample7_Ground.M2.Vitamin_D


title: GMP.Tet2.1

description:
Library name: Sample 7
IonXpress_037

value: TET2 KO


title: 2_2D5


title: GMP.Tet2.2

description:
Library name: Sample 8
IonXpress_038


title: 2_2C5


title: Sample6_Ground.F1.Vitamin_D

value: Female


title: 2_2C6


title: Sample5_Ground.F1.Vitamin_D


title: GMP.TP53.2

description:
Library name: Sample 5
IonXpress_035

value: bone marrow

value: TP53 KO


title: GMP.dKO.2

description:
Library name: Sample 11
IonXpress_041

value: GMP

value: TP53/TET2 KO


title: 2_2C12

value: dlPFC


title: GMP.TP53.3

description:
Library name: Sample 6
IonXpress_036


title: ERa Antibody ESR1 gRNA EtOH 6hour R2

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Library name: EtOH_6hr_R2

data_processing:
Reads from CUT&RUN were trimmed of adapter sequences using Trim Galore!  Version 0.6.10 with default settings except for specifying Illumina adapter sequences and paired-end validation.
Trimmed sequences were aligned to hg38 and E. coli K-12 MG1655 genomes using bowtie2 (Version 2.5.2) with maximum fragment length 2,000, forward-reverse mate orientation, local read alignment, and no mixed or discordant read alignments
Alignment files were processed using Picard (http://broadinstitute.github.io/picard; Version 3.2.0) for duplicate removal and samtools (Version 1.18) to filter for reads with MAPQ  5
HOMER (Version 5.1) was used to call peaks for each sample with default parameters except mode of operation set to factor and single-end reads. Peak calls for all samples were collapsed to a set of union peaks which were subsequently assigned as positive or negative for ESR1 signal per sample at a threshold of 5x the median IgG signal. Only peaks present in both replicates of a condition were used for downstream analysis.
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: consensus.bed files contain consensus peaks in bed format for each condition.
Supplementary files format and content: bigwig files contain Ecoli spike-in normalized bed files for each sample.
Library strategy: CUT&Run

source_name: THESC

growth_protocol: CRISPR engineered cells were maintained in DMEM/F-12 supplemented with 10% Fetal Bovine Serum and 4ug/mL Blasticidin. Cells were cultured and grown in a 5% CO2 and 37°C incubator. Cell media was changed every three days and cells were passaged before reaching 90% confluency.

extract_protocol:
Targeted DNA amplicons were isolated using the Epicypher CUTANA Cut&Run Kit Version 3.
cells were treated with E2 media or vehicle media for 1, 3, or 6 hours. A total of 550,000 cells per sample were collected in DNA LoBind 1.5mL tubes containing wash buffer. Cells were captured with BioMag Plus Concavalin A beads and incubated with ESR1 antibody (Cell Signaling Technologies, #13258, Danvers, MA, USA; 1:25) or IgG antibody (1:100) supplied by the CUTANA kit overnight at 4°C in antibody incubation buffer. After washing away antibodies, pAG-MNase generated by the NIEHS proteomics core was added and incubated for 30 minutes at room temperature. After washing, CaCl2 was added and incubated for 30 minutes in an aluminum cold block placed in ice. The protein-DNA complexes were released by incubating at 37°C for 10 minutes. DNA was purified using the Qiagen MiniElute PCR Purification Kit. Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina  according to the manufacturer’s instructions, with 14 cycles of PCR amplification. The PCR products were quantified using the Qubit dsDNA HS Assay Kit and quality control was performed with Bioanalyzer DNA Analysis. The libraries were sequenced by the NIEHS sequencing core.

treatment_protocol: Cells were treated with 10nM E2 or 0.01% EtOH (vehicle) in OptiMEM with 2% Charcoal Stripped Serumand 1% Penicillin-Streptomycin for 1, 3, or 6 hours.

value: THESC

value: Endometrial Stromal Cells

value: ESR1 activated

value: Vehicle (0.01% ethanol) 6 hours


title: ZH11-RNA-seq-1


title: ZH11-RNA-seq-2


title: Sample4_Ground.F1.Vitamin_D

value: Kidney


title: GMP.TP53.1

description:
Library name: Sample 4
IonXpress_034


title: IgG Antibody ESR1 gRNA

description: Library name: IgG

value: Vehicle (0.01% ethanol) 1 hour


title: GMP.Tet2.3

description:
Library name: Sample 9
IonXpress_039


title: 2_2B6

value: cortical cells

value: wild type

value: no treatment


title: Sample3_Ground.M1.Vitamin_D

value: Primary cells

value: Male

value: Ground


title: ERa Antibody ESR1 gRNA EtOH 6hour R1

description: Library name: EtOH_6hr_R1


title: 2_2B5


title: Sample2_Ground.M1.Vitamin_D


title: GMP.WT.3

description:
Library name: Sample 3
IonXpress_033

value: bone marrow

value: WT


title: GMP.WT.2

description:
Library name: Sample 2
IonXpress_032

value: GMP


title: ERa Antibody ESR1 gRNA EtOH 3hour R2

description: Library name: EtOH_3hr_R2

value: Vehicle (0.01% ethanol) 3 hours


title: 2_2B12

value: dlPFC


title: ERa Antibody ESR1 gRNA EtOH 3hour R1

description: Library name: EtOH_3hr_R1

value: THESC


title: GMP.WT.1

description:
Library name: Sample 1
IonXpress_031


title: Sample1_Ground.M1.Vitamin_D


title: ERa Antibody ESR1 gRNA EtOH 1hour R2

description: Library name: EtOH_1hr_R2

value: Endometrial Stromal Cells


title: Male WT MTECs, naïve, biol rep 2

description: Library name: Sample 2

value: Murine tracheal airway epithelium cultures

value: Primary

value: airway epithelial cells


title: RUES02, TIRN+iDUX4 (LIF-3i +dox), scRNAseq

city: Baltimore

first: Ludovic

last: Zimmerlin

email: lzimme14@jhmi.edu, ludovicz@gmail.com

state: MD

address: 733 N. Broadway

department: Pediatric Oncology

institute: Johns Hopkins University

description: 10x Genomics Single Cell 3' v3

library_source: transcriptomic single cell

data_processing:
10X libraries were sequenced on an Illumina Novaseq 6000 instrument (28x8x91 run configuration).
A custom hg38 reference genome was built using Cell Ranger v7.0.1 (10X Genomics) to align sequenced reads to Ensembl Id library v109, icnluding the attributes gene_biotype:protein_coding, gene_biotype:lincRNA, gene_biotype:antisense, gene_biotype:processed_transcript, gene_biotype:transcribed_processed_pseudogene.
Alignment and gene counting were made using Cell Ranger Count v7.0.1.
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files

molecule: polyA RNA

growth_protocol: either E8 (primed) or LIF5i -> LIF-3i (TIRN)

extract_protocol:
RUES02 hESC were prepared in E8 (primed) or LIF-3i/MEF (TIRN; TIRN +iDUX4 after 24 hours supplementation with 2mg/mL doxycycline). Cells were gently collected using a mixture 1:1 Versene/Accutase (5 min) and pass through a 70um cell strainer. Viable cells were enriched using the MACS Dead Cell Removal Kit (Miltenyi Biotec) and prepared in PBS, 0.4% BSA. Cell quality check (cell viability >95%, cell diameter) was verified before preparing libraries.
Library preparation was performed according to the manufacturter's instructions (Chromium Next GEM Single Cell 3' Gene expression).

treatment_protocol: For the TIRN+iDUX4 condition, transgenic RUES02 hESC were treated for 24 hours with doxycycline to activate DUX4 expression.

value: human embryonic stem cells (hESC)

tag: lentiviral transduction

tag: condition

tag: culture method

value: LIF5i -> LIF-3i

value: 24 hours 2ug/mL doxycycline

tag: passage


title: RUES02, TIRN (LIF-3i), scRNAseq

description: 10x Genomics Single Cell 3' v3

value: TIRN


title: 2_2A12

value: cortical cells

value: wild type

value: no treatment


title: ERa Antibody ESR1 gRNA EtOH 1hour R1

description: Library name: EtOH_1hr_R1

value: ESR1 activated

value: Vehicle (0.01% ethanol) 1 hour


title: ERa Antibody ESR1 gRNA E2 6hour R2

description: Library name: E2_6hr_R2

value: 10nM estradiol (E2) 6 hours


title: Spleen.TP53.TET2.LK.2.BAM

data_processing:
Transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline, and gene set enrichment analysis (GSEA) performed. For transcript-aware analyses, the FASTQ files were aligned with salmon(59) and differentially enriched transcripts were identified using DRIMSeq(60) in a similar workflow to edgeR.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
The Clontech SMARTer v4 Kit (Takara Bio USA, Inc.) was used for preamplifying samples prior to library construction with the Nextera XT DNA Library Prep Kit (Illumina, Inc.). Samples were sequenced to a depth of 15–20 million 2 × 150 bp clusters with the Illumina HiSeq 4000 platform.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol.

treatment_protocol: A total of 500 viable LK or LSK cells from WT, single KO or double KO murine bone marrow were sorted directly into SMART-seq lysis buffer with FACSAria Fusion (BD) based on markers, Lin-cKIT+Sca-1-(LK), and Lin-cKIT+Sca-1+(LSK).

value: spleen

value: bone marrow cells

value: TP53/TET2 KO


title: Spleen.TP53.TET2.LK.3.BAM


title: 2_2A5

value: dlPFC


title: Spleen.TP53.TET2.LK.1.BAM


title: RUES02, primed (E8), scRNAseq

description: 10x Genomics Single Cell 3' v3

value: primed


title: 4_1H5

description:
patch-seq, pcd104, replicate 1
SMART-seq3


title: CD8T,SCA,Donor7

city: Houston

first: Benxia

last: Hu

state: Texas

address: 431 Fannin

institute: University of Texas Health Science Center at Houston

data_processing:
Basecalls were performed using bcl2fastq v2.19.0.316 for Novaseq output.
Hi-C reads were aligned to USCS hg38 genome using HiC-Pro (v2.11.1) using parameters ‘ligation_site’ = GATCGATC and ‘genome_fragment’ generated for the MboI restriction enzyme, keeping other parameters as default to analyze Hi-C datasets.
Cooltools (v.0.5.4) with default parameters was used to call compartments from genome-wide chromatin contact matrices at 100kb resolution.
We used matrix2insulation (v1.0.0)97 with default parameters to calculate insulation scores from the ICE normalized 40kb contact matrices.
To calculate the DLR, the ICE normalized Hi-C interaction frequencies generated by HiC-Pro were used to calculate the total number of interactions interacting with the 100kb region of interest to regions located either greater than 3Mb (i.e.,distal) versus those less than 3Mb away (i.e.,local). For ICF analysis, the total number of the ICE normalized Hi-C interactions between the 100kb regions of interest and other chromosomes were compared to the total number of normalized interactions at that locus. We then calculated the difference in the DLR or ICF between conditions (ΔDLR and ΔICF).
Assembly: hg38
Supplementary files format and content: bedGraph
Supplementary files format and content: mcool

source_name: No

growth_protocol: The cryopreserved PBMCs were thawed and activated with ImmunoCult Human CD3/CD28/CD2 T Cell Activator (STEMCELL) plus human IL-2 (10 ng/ml). CD8+ T cells were isolated from PBMCs using a positive selection kit (Miltenyi Biotec, Inc.)

extract_protocol:
Briefly, 5 million cells were cross-linked using 1% formaldehyde for 10 min at room temperature, quenched with 0.125M glycine for 10 min, and were washed with cold PBS. Cross-linked cells were resuspended in 1mL iced-cold Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10mM NaCl, 0.2% NP-40 and protease inhibitor cocktail), and rotated at 4°C for 30 min. The nuclei were resuspended and permeabilized in 0.5% SDS at 62°C for 10 min, quenched by Triton X-100. Subsequently, chromatin was digested by MboI at 37°C overnight (NEB, R0147M). DNA ends were filled by DNA polymerase I (Klenow, NEB, M0210) to incorporate biotin-14-dATP (Jeana Bioscience). Then, blunt end Hi-C DNA ligation was performed using NEB T4 DNA ligase at room temperature for four hours with rotation. After ligation, nuclei were pelleted down and resuspended with Hi-C nuclear lysis buffer (50mM Tris-HCl pH7.5; 10mM EDTA, 1% SDS and protease inhibitor cocktail), and sheared using the parameter of 10/20 s ON/OFF cycle, 25% Amp, 5mins by a QSonica 800R sonicator. We de-crosslinked ~10% of sonicated DNA by heating overnight at 65°C in 1% SDS and 10mM Tris-HCl pH7.5, then treated this with proteinase K, purify biotin-incorporated DNA by C1 streptavidin beads (ThermoFisher).
We generated illumina sequencing library using NEB Ultra DNA library kit by following the manufacturer's protocol. Hi-C library was first run on a NextSeq 550 platform with 40nt/40nt mode at a shallow sequencing depth, and then sequenced deeper by a NovaSeq 6000 platform with 150nt/150nt model.

treatment_protocol: CD8+ T cells were isolated from PBMC and cultured in T Cell expansion medium and then subjected to Hi-C.

value: No

value: CD8+ T cells

tag: disease state

value: sickle cell disease


title: ERa Antibody ESR1 gRNA E2 6hour R1

description: Library name: E2_6hr_R1

value: THESC

value: Endometrial Stromal Cells


title: Spleen.TET2.LK.8.BAM

value: TET2 KO


title: ERa Antibody ESR1 gRNA E2 3hour R2

description: Library name: E2_3hr_R2

value: 10nM estradiol (E2) 3 hours


title: CD8T,SCA,Donor5


title: 4_1H4

value: cortical cells

value: wild type


title: 4_1G5

value: no treatment


title: ERa Antibody ESR1 gRNA E2 3hour R1

description: Library name: E2_3hr_R1

value: ESR1 activated


title: CD8T,Health,Donor2

value: healthy


title: Spleen.TET2.LK.4.BAM

value: spleen


title: 4_1G4


title: 2_2A6


title: 4_1F5


title: Spleen.TET2.LK.3.BAM

value: bone marrow cells


title: CD8T,Health,Donor1


title: 4_1F4


title: Spleen.TP53.LK.2.BAM

value: TP53 KO


title: 4_1G12

description:
patch-seq, pcd132, virus-infected replicate 86
SMART-seq3

value: dlPFC

value: organotypic dlPFC slice cells

value: lentivirus infected

value: shNC


title: 4_1E5


title: RUES02, TIRN (LIF-3i), SOX2 ChIPseq, replicate 001

description: Library name: RUES02_L3i_SOX2_ChIP_rep1

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the BWA algorithm (“bwa aln/samse” with default settings). Only reads containing Illumina chastity-filtered reads with phred+33 quality scores were retained. Uniquely mapped reads were filtered and PCR duplicates were eliminated using samtools. .
Initial set of peaks were called using MACS2.2.7.1 with low stringent p-values (narrowPeaks with p=0.05: PARP1; p=0.01: NANOG, POU5F1, phosphoSTAT3; p=0.001: SOX2, H3K4me3;  broad peaks with p=0.0001: BRD4, H3K27me3, H3K27ac).
Replicates were consolidated using the Irreproducible Discovery Rate (IDR v2.0.4.2) program (narrowPeaks) or bedtools -intersect (broadPeaks). For differential analysis of NANOG, SOX2 and POU5F1 binding sites, peaks were recentered at a uniform length of 400bp using the Diffbind R package.
bigWig files were created using deeptools 3.5.4 from the filtered bam files using the bamCoverage tool with the following parameters: --binSize 10, --normalizeUsing RPGC, --smoothLength 60, --extendReads 75, centerReads.
a second set of bigWig files is provided for input-subtracted averaged replicates. (using bigwigCompare --operation subtract and bigwigAverage commands from deeptools.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak, broadPeak, annotated differential analysis of NANOG-SOX2-POU5F1 bound sites

growth_protocol: RUES02 hESC were maintained in either E8 (primed) or LIF5i -> LIF-3i (TIRN)

extract_protocol:
Cells were gently collected using a mixture 1:1 Versene/Accutase (5 min) and pass through a 70um cell strainer. Cells were fixed with freshly prepared 11% formaldehyde, 5M NaCl, 0.5M EDTA ph8.0, 1M HEPES ph7.9 for 15 minutes at room temperature. After quenching  with 1/20 volume pf 2.5M glycine solution), cells were washed with PBS, 0.5% Igepal. The protease inhibitor PMSF  was added (1mM) prior to preparing snapfrozen cell pellets for Active Motif’s FactorPath and HistonePath services.
40 ug chromatin was used as starting material for input and ChIP samples (4-10uL antibody per ChIP).

value: human embryonic stem cells (hESC)

value: SOX2 (Active Motif #39823)

value: TIRN

value: LIF5i -> LIF-3i


title: Spleen.TP53.LK.1.BAM


title: 4_1H11

description:
patch-seq, pcd132, virus-infected replicate 87
SMART-seq3


title: RUES02, primed (E8), SOX2 ChIPseq, replicate 002

description: Library name: RUES02_E8_SOX2_ChIP_rep2

value: primed


title: 4_1F11

description:
patch-seq, pcd132, virus-infected replicate 84
SMART-seq3


title: 4_1E4

value: cortical cells


title: 4_1D5

value: wild type


title: Spleen.TET2.LK.7.BAM

value: TET2 KO


title: Spleen.TP53.LK.3.BAM


title: 4_1D4

value: no treatment


title: 4_1G10

description:
patch-seq, pcd132, virus-infected replicate 85
SMART-seq3


title: RUES02, primed (E8), SOX2 ChIPseq, replicate 001

description: Library name: RUES02_E8_SOX2_ChIP_rep1


title: RUES02, TIRN (LIF-3i), SOX2 ChIPseq, replicate 002

description: Library name: RUES02_L3i_SOX2_ChIP_rep2


title: 4_1F10

description:
patch-seq, pcd132, virus-infected replicate 83
SMART-seq3


title: RUES02, TIRN (LIF-3i), OCT4 ChIPseq, replicate 002

description: Library name: RUES02_L3i_OCT4_ChIP_rep2

value: POU5F1 (Active Motif #39811)


title: 4_1E12

description:
patch-seq, pcd132, virus-infected replicate 82
SMART-seq3


title: 4_1B5


title: ERa Antibody ESR1 gRNA E2 1hour R2

description: Library name: E2_1hr_R2

value: THESC

value: Endometrial Stromal Cells

value: ESR1 activated

value: 10nM estradiol (E2) 1 hour


title: Spleen.WT.LK.1.BAM

value: spleen

value: bone marrow cells

value: WT


title: Spleen.WT.LK.2.BAM


title: ERa Antibody ESR1 gRNA E2 1hour R1

description: Library name: E2_1hr_R1


title: 4_1E11

description:
patch-seq, pcd132, virus-infected replicate 81
SMART-seq3

value: dlPFC

value: organotypic dlPFC slice cells

value: lentivirus infected

value: shNC


title: RUES02, TIRN (LIF-3i), OCT4 ChIPseq, replicate 001

description: Library name: RUES02_L3i_OCT4_ChIP_rep1

value: human embryonic stem cells (hESC)

value: TIRN

value: LIF5i -> LIF-3i


title: BM.TP53.TET2.LSK.4.BAM

value: bone marrow

value: TP53/TET2 KO


title: 4_1A6

value: cortical cells

value: wild type

value: no treatment


title: RUES02, primed (E8), OCT4 ChIPseq, replicate 002

description: Library name: RUES02_E8_OCT4_ChIP_rep2

value: POU5F1 (Active Motif #39811)

value: primed


title: 4_1E10

description:
patch-seq, pcd132, virus-infected replicate 80
SMART-seq3


title: BM.TP53.TET2.LSK.3.BAM


title: Spleen.WT.LK.3.BAM

value: spleen


title: RUES02, primed (E8), OCT4 ChIPseq, replicate 001

description: Library name: RUES02_E8_OCT4_ChIP_rep1


title: 4_1A5


title: 4_1C12

description:
patch-seq, pcd132, virus-infected replicate 79
SMART-seq3


title: BM.TP53.TET2.LSK.2.BAM

value: bone marrow cells


title: RUES02, TIRN (LIF-3i), pSTAT3 ChIPseq, replicate 002

description: Library name: RUES02_L3i_pSTAT3_ChIP_rep2

value: STAT3-phosp (Cell Signaling #9145)


title: 4_1C11

description:
patch-seq, pcd132, virus-infected replicate 78
SMART-seq3

value: dlPFC


title: BM.TP53.TET2.LSK.1.BAM


title: RUES02, TIRN (LIF-3i), pSTAT3 ChIPseq, replicate 001

description: Library name: RUES02_L3i_pSTAT3_ChIP_rep1


title: 3_3F9

description:
patch-seq, pcd101, replicate 1
SMART-seq3


title: BM.TET2.LSK.3.BAM

value: TET2 KO


title: 3_3E10


title: 4_1A12

description:
patch-seq, pcd132, virus-infected replicate 77
SMART-seq3

value: organotypic dlPFC slice cells

value: lentivirus infected


title: 4_1A11

description:
patch-seq, pcd132, virus-infected replicate 76
SMART-seq3

value: shNC


title: RUES02, TIRN (LIF-3i), H3K27me3 ChIPseq, replicate 002

description: Library name: RUES02_L3i_H3K27me3_ChIP_rep2

value: human embryonic stem cells (hESC)

value: H3K27me3 (Active Motif #39155)

value: TIRN


title: 3_1H5

description:
patch-seq, pcd132, virus-infected replicate 75
SMART-seq3


title: 3_3C10


title: BM.TET2.LSK.1.BAM

value: bone marrow


title: BM.TET2.LSK.2.BAM


title: 3_3D10

value: cortical cells


title: RUES02, TIRN (LIF-3i), H3K27me3 ChIPseq, replicate 001

description: Library name: RUES02_L3i_H3K27me3_ChIP_rep1

value: LIF5i -> LIF-3i


title: BM.TP53.LSK.1.BAM

value: TP53 KO


title: RUES02, primed (E8), H3K27me3 ChIPseq, replicate 002

description: Library name: RUES02_E8_H3K27me3_ChIP_rep2


title: RUES02, primed (E8), H3K27me3 ChIPseq, replicate 001

description: Library name: RUES02_E8_H3K27me3_ChIP_rep1


title: 3_1H3

description:
patch-seq, pcd132, virus-infected replicate 73
SMART-seq3


title: 3_3G9

value: wild type

value: no treatment


title: 3_3A10


title: RUES02, TIRN (LIF-3i), H3K4me3 ChIPseq, replicate 002

description: Library name: RUES02_L3i_H3K4me3_ChIP_rep2

value: H3K4me3 (Active Motif #39159)


title: BM.WT.LSK.1.BAM

value: bone marrow cells

value: WT


title: 3_1G6

description:
patch-seq, pcd132, virus-infected replicate 72
SMART-seq3

value: dlPFC


title: 3_3H8

description:
patch-seq, pcd100, replicate 2
SMART-seq3


title: 3_1G5

description:
patch-seq, pcd132, virus-infected replicate 71
SMART-seq3


title: RUES02, primed (E8), H3K4me3 ChIPseq, replicate 002

description: Library name: RUES02_E8_H3K4me3_ChIP_rep2

value: primed


title: 3_3H7


title: 3_1G4

description:
patch-seq, pcd132, virus-infected replicate 70
SMART-seq3

value: organotypic dlPFC slice cells


title: 3_1H4

description:
patch-seq, pcd132, virus-infected replicate 74
SMART-seq3

value: lentivirus infected


title: BM.WT.LSK.3.BAM


title: 3_3G8


title: 3_1F6

description:
patch-seq, pcd132, virus-infected replicate 69
SMART-seq3


title: RUES02, TIRN (LIF-3i), H3K27ac ChIPseq, replicate 002

description: Library name: RUES02_L3i_H3K27ac_ChIP_rep2

value: H3K27ac (Active Motif #39133)


title: 3_3H6


title: VGD1 replicate 1

city: Tübingen

first: Sebastian

last: Wolf

state: Baden-Württemberg

address: Auf der Morgenstelle 32, ZMBP, ZMBP

country: Germany

institute: ZMBP, Universität Tübingen

description: Library name: sample 4

data_processing:
RNAstar
feautureCounts
Deseq2
Assembly: Tair10
Supplementary files format and content: normalized read counts
Supplementary files format and content: DEseq2 results file

organism: Arabidopsis thaliana

source_name: shoot apical meristem

growth_protocol: For SAM imaging, plants were grown in long day conditions (16h light, 8h dark, 22°C, 60-70 % humidity, 100-125 μmol·m-2·s-1 light intensitiy) for 7 days on half-strength MS plates with 0.9% agar and 1 sucrose before being transferred to soil. Imaging was performed on inflorescence meristems of 15 cm tall stems.

extract_protocol:
Shoot apices of 15 cm tall stems were DEX-treated in staggered fashion and dissected and frozen in liquid nitrogen after 48 hours. RNA was extracted using GeneMATRIX Universal RNA/ miRNA Purification Kit (Cat. No. E3599 Distributor Roboklon GmbH).
commercial (EurofinsGenomic) polyA-selected

treatment_protocol: Induction of GR-LhG4-mediated expression was performed by spraying shoot apices with 30 µM dexamethasone solution. Inflorescence meristems were dissected by cutting the stem with and primordia were removed by forceps or a canula up to flower stage 3-4.

value: shoot apical meristem

value: meristem

value: pCLV3>>erTurquoise, >>VGD1

value: 30 mM Dexamethasone


title: 3_1F5

description:
patch-seq, pcd132, virus-infected replicate 68
SMART-seq3

value: shNC


title: 3_3B10

description:
patch-seq, pcd101, replicate 1
SMART-seq3

value: cortical cells


title: 3_1F4

description:
patch-seq, pcd132, virus-infected replicate 67
SMART-seq3


title: RUES02, TIRN (LIF-3i), H3K27ac ChIPseq, replicate 001

description: Library name: RUES02_L3i_H3K27ac_ChIP_rep1

value: human embryonic stem cells (hESC)

value: TIRN

value: LIF5i -> LIF-3i


title: Control replicate 3

description: Library name: sample 3


title: 3_3G7

value: wild type

value: no treatment


title: VGD1 replicate 2

description: Library name: sample 5


title: RUES02, primed (E8), H3K27ac ChIPseq, replicate 002

description: Library name: RUES02_E8_H3K27ac_ChIP_rep2


title: Control replicate 2

description: Library name: sample 2


title: RUES02, TIRN (LIF-3i), H3K4me3 ChIPseq, replicate 001

description: Library name: RUES02_L3i_H3K4me3_ChIP_rep1

value: H3K4me3 (Active Motif #39159)


title: BM.TP53.LSK.2.BAM

value: bone marrow

value: bone marrow cells

value: TP53 KO


title: 3_1E6

description:
patch-seq, pcd132, virus-infected replicate 66
SMART-seq3

value: dlPFC

value: organotypic dlPFC slice cells

value: lentivirus infected


title: 3_3F7


title: RUES02, primed (E8), H3K27ac ChIPseq, replicate 001

description: Library name: RUES02_E8_H3K27ac_ChIP_rep1

value: H3K27ac (Active Motif #39133)

value: primed


title: 3_1E5

description:
patch-seq, pcd132, virus-infected replicate 65
SMART-seq3


title: Control replicate 1

description: Library name: sample 1

value: shoot apical meristem

value: meristem

value: 30 mM Dexamethasone


title: VGD1 replicate 3

description: Library name: sample 6

value: pCLV3>>erTurquoise, >>VGD1


title: 3_3E9

value: cortical cells


title: RUES02, primed (E8), H3K4me3 ChIPseq, replicate 001

description: Library name: RUES02_E8_H3K4me3_ChIP_rep1

value: human embryonic stem cells (hESC)


title: 3_1E4

description:
patch-seq, pcd132, virus-infected replicate 64
SMART-seq3

value: shNC


title: RUES02, TIRN (LIF-3i), BRD4 ChIPseq, replicate 002

description: Library name: RUES02_L3i_BRD4_ChIP_rep2

value: BRD4 (Active Motif #91301)

value: TIRN

value: LIF5i -> LIF-3i


title: 3_3F8

description:
patch-seq, pcd100, replicate 2
SMART-seq3

value: wild type

value: no treatment


title: 3_3E8

value: dlPFC


title: 3_1D6

description:
patch-seq, pcd132, virus-infected replicate 63
SMART-seq3

value: organotypic dlPFC slice cells


title: RUES02, TIRN (LIF-3i), BRD4 ChIPseq, replicate 001

description: Library name: RUES02_L3i_BRD4_ChIP_rep1


title: 3_3E7


title: mCherry cells, rag1 crispant, R848 treated

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Library name: rag1 crispant + R848 treated at 8 dpf

data_processing:
For experiments (1) lineage tracing and (2) runx1 mutants, CellRanger 7.0.1 was used. For experiment (3) slc24a5/rag1/R848, CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples.
Assembly: Danie rerio GRCz11
Supplementary files format and content: Matrix files (CellRanger output filtered_feature_bc_matrix)

organism: Danio rerio

source_name: Hematopoietic & Immune Cells

growth_protocol: Larvae were maintained in standard conditions, at 28C

extract_protocol:
Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS.
Libraries were prepared according to manufacturer's instructions of the kits. For experiments (1) lineage tracing & (2) runx1 mutants, the Chromium Next GEM Single Cell 3' Kit v3.1 was used. For experiment (3) slc24a5/rag1/R848, the Chromium Next GEM Single Cell 3' Kit v4 was used.

treatment_protocol: The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod (R848) at 6 dpf

value: Hematopoietic & Immune Cells

value: rag1 mosaic mutant

value: Resiquimod (R848) treated


title: mCherry cells, slc24a5 crispant, R848 treated

description: Library name: slc24a5 crispant + R848 treated at 8 dpf

value: slc24a5 mosaic mutant


title: 3_3E6


title: RUES02, primed (E8), BRD4 ChIPseq, replicate 001

description: Library name: RUES02_E8_BRD4_ChIP_rep1

value: primed


title: mCherry cells, slc24a5 crispant

description: Library name: slc24a5 crispant control at 8 dpf


title: 3_1C6

description:
patch-seq, pcd132, virus-infected replicate 60
SMART-seq3

value: lentivirus infected


title: RUES02, TIRN (LIF-3i), NANOG ChIPseq, replicate 002

description: Library name: RUES02_L3i_NANOG_ChIP_rep2

value: NANOG (Active Motif #61419)


title: 3_3D6

value: cortical cells


title: 3_1C5

description:
patch-seq, pcd132, virus-infected replicate 59
SMART-seq3


title: RUES02, primed (E8), BRD4 ChIPseq, replicate 002

description: Library name: RUES02_E8_BRD4_ChIP_rep2

value: human embryonic stem cells (hESC)


title: RUES02, TIRN (LIF-3i), NANOG ChIPseq, replicate 001

description: Library name: RUES02_L3i_NANOG_ChIP_rep1


title: mCherry cells, runx1 homozygous mutants

description: Library name: Runx1 homozygous mutants at 6 dpf

value: runx1 homozygous


title: 3_3C9


title: mCherry cells, sibling controls

description: Library name: Sibling Controls at 6 dpf

value: wild-type or runx1 heterozygous


title: 3_3C8


title: mCherry cells, late-HSPCs_10 dpf

description: Library name: late-HSPCs at 10 dpf


title: 3_1B6

description:
patch-seq, pcd132, virus-infected replicate 57
SMART-seq3

value: shNC


title: RUES02, primed (E8), NANOG ChIPseq, replicate 001

description: Library name: RUES02_E8_NANOG_ChIP_rep1


title: RUES02, TIRN (LIF-3i), PARP1 ChIPseq, replicate 002

description: Library name: RUES02_L3i_PARP1_ChIP_rep2

value: PARP1 (Active Motif #39561)

value: TIRN

value: LIF5i -> LIF-3i


title: mCherry cells, late-HSPCs_6 dpf

description: Library name: lateHSPCs at 6 dpf


title: 3_1B5

description:
patch-seq, pcd132, virus-infected replicate 56
SMART-seq3

value: dlPFC


title: 3_3C7

value: wild type

value: no treatment


title: mCherry cells, late-HSPCs_4 dpf

description: Library name: late-HSPCs one-day-post labelling

value: Hematopoietic & Immune Cells


title: 3_1D4

description:
patch-seq, pcd132, virus-infected replicate 61
SMART-seq3

value: organotypic dlPFC slice cells


title: mCherry cells, rag1 crispant

description: Library name: rag1 crispant control at 8 dpf

value: rag1 mosaic mutant


title: RUES02, TIRN (LIF-3i), PARP1 ChIPseq, replicate 001

description: Library name: RUES02_L3i_PARP1_ChIP_rep1


title: 3_1D5

description:
patch-seq, pcd132, virus-infected replicate 62
SMART-seq3


title: mCherry cells, mid-HSPCs_10 dpf

description: Library name: mid-HSPCs at 10 dpf


title: 3_3B7

description:
patch-seq, pcd100, replicate 2
SMART-seq3


title: 3_3D9


title: 3_1A6

description:
patch-seq, pcd132, virus-infected replicate 54
SMART-seq3


title: RUES02, primed (E8), PARP1 ChIPseq, replicate 002

description: Library name: RUES02_E8_PARP1_ChIP_rep2

value: primed


title: 3_3B8


title: RUES02, primed (E8), NANOG ChIPseq, replicate 002

description: Library name: RUES02_E8_NANOG_ChIP_rep2


title: RUES02, primed (E8), PARP1 ChIPseq, replicate 001

description: Library name: RUES02_E8_PARP1_ChIP_rep1


title: 3_3A9


title: mCherry cells, mid-HSPCs_3 dpf

description: Library name: mid-HSPCs one-day-post labelling


title: 3_1A5

description:
patch-seq, pcd132, virus-infected replicate 53
SMART-seq3

value: lentivirus infected


title: mCherry cells, mid-HSPCs_6 dpf

description: Library name: mid-HSPCs at 6 dpf


title: 3_1C4

description:
patch-seq, pcd132, virus-infected replicate 58
SMART-seq3


title: 3_1A4

description:
patch-seq, pcd132, virus-infected replicate 52
SMART-seq3


title: RUES02, pooled, input

description: Library name: RUES02_input

value: E8 and LIF5i -> LIF-3i


title: mCherry cells, early-HSPCs_10 dpf

description: Library name: early-HSPCs at 10 dpf


title: 3_3A8

value: cortical cells


title: 3_3A7


title: 2_2H10

description:
patch-seq, pcd132, virus-infected replicate 51
SMART-seq3


title: mCherry cells, early-HSPCs_6 dpf

description: Library name: early-HSPCs at 6 dpf


title: 3_1B4

description:
patch-seq, pcd132, virus-infected replicate 55
SMART-seq3


title: 2_2G10

description:
patch-seq, pcd132, virus-infected replicate 50
SMART-seq3


title: CD8+ TIL, pt #5, aPD1

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Library name: GBM__23

data_processing:
FASTQ files were mapped to the human genomic DNA reference (GRCh38/hg38) using Hisat2
StringTie was used to quantify gene expression based on the aligned reads.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: primary

extract_protocol:
Total RNA was extracted from the sorted cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).

value: CD8+ tumor-infiltrating T cells

value: CD8+ T cell


title: 2_2G1

description:
patch-seq, pcd100, replicate 1
SMART-seq3


title: CD8+ TIL, pt #5, galunisertib

description: Library name: GBM__22

value: galunisertib


title: 2_2F10

description:
patch-seq, pcd132, virus-infected replicate 49
SMART-seq3


title: Human_A549, 8 hours post infection, rep2

city: Guangzhou

first: Alvaro

last: Castells-Garcia

state: Guandong

address: 106 Zhongshan Er Road, Yuexiu district

department: Medical Research Department

institute: Guandong Peoples Hospital

data_processing:
Fragment pairs were filtered for non-digested fragments, non-ligated fragments, self-circles and random breaks. Filtered valid pairs were used to generate Hi-C contact matrices (adjusted to chromosome 1 to chromosome X and virus) at several resolutions (10 kb, 50 kb, 100 kb and 500 kb). Matrices were normalized and corrected for intrinsic biases using Knight-Ruiz correction (hicCorrectMatrix; HiCExplorer1) prior to further analysis. Normalized contact matrices were plotted using hicPlotMatrix.(1.- Wolff, J., et al., Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res, 2018. 46(W1): p. W11-W16.)
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data is in .hic file format. Hic format is an indexed binary format designed to permit fast random access to contact matrix heatmaps. We provide the .hic track for each one of the biological replicates of each one of our conditions.

growth_protocol: A549 cells (Lung Carcinoma, American Type Culture Collection, ATCC CRL-185) were cultured in F-12K (Kaighn's) Medium (Gibco, Thermo Fisher Scientific, #21127022) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #10270106), 1% Penicillin–Streptomycin (Thermo Fisher Scientific, #15140122). Cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Samples were cross-linked with 2% formaldehyde (wt/vol) and intact nuclei were submitted to DNA digestion with MboI. After filling with biotinylated dATP, ligation and reversion of the cross-link, purified DNA was sheared using a Covaris ultrasonicator (Covaris, LE220). Biotinylated fragments were pulled down using streptavidin beads.
Hi-C libraries were paired-end sequenced (2x75 nt) on a MGISEQ-2000 (MGI), on the BGI sequencing service (BGI-Shenzhen, China). The resulting sequencing data were mapped against a chimeric genome based on the GRCh38/hg38 (GRCh38.p13) human genome assembly and the HSV-1 genome assembly (Human herpesvirus 1 strain, Herpes Simplex Virus (HSV), KOS, JQ673480.1). Fragment pairs were filtered for non-digested fragments, non-ligated fragments, self-circles and random breaks.

treatment_protocol: After media wash, cells were infected with HSV-1 (KOS strain, JQ673480.1) at a multiplicity of infection (MOI) of 3 for 1 h at 37°C in a humidified incubator with 5% CO2, then, the medium was removed and replaced by fresh DMEM medium (supplemented with 2% FBS). At 1, 3 and 8 hours post infection, cells  Cells were gently scraped and pelleted at low-speed centrifugation to maintain cellular and nuclear integrity. We generated 2 biological replicates for mock, 1, 3 and 8 hpi of approximately 10 million cells each.  Non infected cells had their media replaced by fresh DMEM+2% FBS media, without HSV-1 infection.

value: Human Herpesvirus Simplex Type 1 (HSV-1) infection, 8 hour post infection

value: 8 hpi, HSV-1


title: CD8+ TIL, pt #5, control

description: Library name: GBM__21

value: control


title: 1_4D6


title: 2_2E4

description:
patch-seq, pcd132, virus-infected replicate 48
SMART-seq3


title: Human_A549, 8 hours post infection, rep1


title: CD8+ TIL, pt #4, combi

description: Library name: GBM__20


title: 2_2E10

description:
patch-seq, pcd132, virus-infected replicate 47
SMART-seq3


title: CD8+ TIL, pt #4, aPD1

description: Library name: GBM__19


title: 1_1H11


title: 1_4C6


title: Human_A549, 3 hours post infection, rep1

value: Human Herpesvirus Simplex Type 1 (HSV-1) infection, 3 hour post infection

value: 3 hpi, HSV-1


title: 1_1G11

value: dlPFC

value: wild type


title: Human_A549, 3 hours post infection, rep2


title: CD8+ TIL, pt #4, galunisertib

description: Library name: GBM__18


title: CD8+ TIL, pt #4, control

description: Library name: GBM__17


title: Human_A549, 1 hour post infection, rep2

value: Human Herpesvirus Simplex Type 1 (HSV-1) infection, 1 hour post infection

value: 1 hpi, HSV-1


title: 2_2C4

description:
patch-seq, pcd132, virus-infected replicate 45
SMART-seq3

value: organotypic dlPFC slice cells


title: 1_1F11

value: no treatment


title: 2_2H1


title: 2_2C10

description:
patch-seq, pcd132, virus-infected replicate 44
SMART-seq3

value: lentivirus infected

value: shNC


title: CD8+ TIL, pt #5, combi

description: Library name: GBM__24


title: Human_A549, 1 hour post infection, rep1


title: mCherry cells, early-HSPCs_2 dpf

description: Library name: early-HSPCs one-day-post labelling

value: Hematopoietic & Immune Cells


title: 1_1E12

value: cortical cells


title: CD8+ TIL, pt #3, combi

description: Library name: GBM__16

value: CD8+ tumor-infiltrating T cells

value: CD8+ T cell


title: CD8+ TIL, pt #3, aPD1

description: Library name: GBM__15


title: 2_2A11

description:
patch-seq, pcd132, virus-infected replicate 43
SMART-seq3


title: Human_A549, non infected, rep2


title: 1_4H10

description:
patch-seq, pcd132, virus-infected replicate 42
SMART-seq3


title: CD8+ TIL, pt #3, galunisertib

description: Library name: GBM__14

value: galunisertib


title: Human_A549, non infected, rep1


title: 1_1D12


title: 1_1E11


title: 1_1D11


title: 2_2D4

description:
patch-seq, pcd132, virus-infected replicate 46
SMART-seq3


title: CD8+ TIL, pt #3, control

description: Library name: GBM__13


title: 1_4G10

description:
patch-seq, pcd132, virus-infected replicate 41
SMART-seq3


title: 1_4F11

description:
patch-seq, pcd132, virus-infected replicate 40
SMART-seq3


title: CD8+ TIL, pt #2, combi

description: Library name: GBM__12


title: 1_4E11

description:
patch-seq, pcd132, virus-infected replicate 39
SMART-seq3


title: ACD_E_T_8_L_1

city: Kaifeng

first: Zhu

last: Renkai

state: Henan

address: Dongjing avenue

institute: Henan  university

data_processing:
Base calling and the quality score of each base are calculated based on the phred-33 quality score standard by the sub-Pixel Registration algorithm according to the optical signal intensity of each lane
This project uses the filtering software SOAPnuke (Versionv1.5.2) developed by BGI independently for filtering. SOAPnuke   Official Websitehttps://github.com/BGI-flexlab/SOAPnuke The specific steps are as follows: 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software information:HISAT2 (Version：v2.0.4) ,Official Website：http://www.ccb.jhu.edu/software/hisat
Bowtie2 (v2.2.5) was used to compare clean reads to reference sequences for gene alignment with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200. And then RSEM (v1.2.8) was used to calculate gene and transcript expression levels with -p 8 --forward-prob 0.5 --paired-end.
Assembly: GCF_000001635.26_GRCm38.p6 for Mus musculus GCF_000001405.39_GRCh38.p13 for Homo sapiens
Supplementary files format and content: Excel files include FPKM values, Reads Count for each Sample

source_name: mouse tissue samples

growth_protocol: Healthy C57BL/6 mice (6-7 weeks, weight between 16-18 g) were selected and bred in Specific pathogen-free (SPF) animal chambers in separate cages. The room temperature was maintained at 20-27℃ and the normal day and night alternated, during which the normal diet was guaranteed.

extract_protocol:
Mouse ear tissue samples were ground in liquid ammonia, and RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

treatment_protocol: SB415286 (0.7mg/kg) was injected into the abdominal cavity of AD mouse model mice,SB415286 (2mg/kg) was injected into the abdominal cavity of AD mouse model mice ,and ear samples were taken 4 hours later for RNA extraction.

value: ear tissue

value: SB415286(2mg/kg) treated


title: ACD_E_C_6_L_1

value: untreated


title: 1_1C11


title: ACD_E_C_5_L_1


title: 1_4E1

description:
patch-seq, pcd132, virus-infected replicate 38
SMART-seq3


title: ACD_E_T_7_L_1


title: 1_4D11

description:
patch-seq, pcd132, virus-infected replicate 37
SMART-seq3


title: 1_1B11


title: CD8+ TIL, pt #2, galunisertib

description: Library name: GBM__10


title: CD8+ TIL, pt #2, control

description: Library name: GBM__9

value: control


title: ACD_E_C_4_L_1


title: 1_4C11

description:
patch-seq, pcd132, virus-infected replicate 36
SMART-seq3

value: dlPFC


title: ACD_E_T_5_L_1


title: 1_4B11

description:
patch-seq, pcd132, virus-infected replicate 35
SMART-seq3


title: 1_1A12

description:
patch-seq, pcd100, replicate 1
SMART-seq3

value: wild type


title: ACD_E_C_3_L_1


title: 1_1A11


title: CD8+ TIL, pt #1, aPD1

description: Library name: GBM__7


title: 1_1C12


title: 1_4A11

description:
patch-seq, pcd132, virus-infected replicate 34
SMART-seq3


title: multiome snRNA-seq 7

description:
snRNA-seq, pcd155, replicate 2
10X genomics


title: CD8+ TIL, pt #1, combi

description: Library name: GBM__8


title: CD8+ TIL, pt #2, aPD1

description: Library name: GBM__11


title: multiome snRNA-seq 6

description:
snRNA-seq, pcd155, replicate 1
10X genomics


title: CD8+ TIL, pt #1, galunisertib

description: Library name: GBM__6


title: ACD_E_T_4_L_1


title: ACD_E_C_1_L_1


title: multiome snRNA-seq 5

description:
snRNA-seq, pcd112, replicate 1
10X genomics


title: 1_3H8

description:
patch-seq, pcd132, virus-infected replicate 32
SMART-seq3


title: CD8+ TIL, pt #1, control

description: Library name: GBM__5


title: multiome snRNA-seq 4

description:
snRNA-seq, pcd104, replicate 1
10X genomics


title: PfSIP2-GFP - input 1

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

description: Library name: ChIP_SIP2_input

data_processing:
Reads were mapped against the P. falciparum 3D7 reference genome from PlasmoDB v24 (www.plasmodb.org) using the Burrow-Wheeler Aligner (BWA) tool. Only uniquely mapping reads, not mapping to the mitochondrial or apicoplast genome, with mapping quality ≥15 (SAM tools v1.21) were used for further analysis. The bam-files generated were merged and deeptools bamCompare function was used to produce ChIP-over-input log2 ratio tracks for all samples, provided as bedgraph format.
Assembly: P.falciparum 3D7 reference genome v24 (plasmodb.org)
Supplementary files format and content: Sequencing was performed twice for both the ChIP-SIP2 and ChIP-SIP2-input sample processed as described above and the bam-files were merged. After merging bam-files from the separate sequencing runs, deeptools bamCompare was done to produce a combined log2 ratio track of ChIP-over-input. This log2 ratio track is provided as a bedgraph file.

organism: Plasmodium falciparum

source_name: Infected red blood cells

growth_protocol: Standard culture conditions for Plasmodium falciparum asexual parasites.

extract_protocol:
RBC culture pellets were crosslinked with 1% formaldehyde for 10 min at 37ºC followed by quenching with 0.125 M glycine. Parasites were isolated by RBC lysis in 0.05% saponin and preserved at -80°C . Nuclei were obtained by lysing the parasites in cytoplasmic lysis buffer. Chromatin was sheared to 100-600 bp fragment size range by sonication for 20 cycles of 30 sec ON/30 sec OFF in sonication buffer. ChIPs were performed under rotation overnight at 4°C in incubation buffer containing sonicated chromatin and  α-GFP antibody (Roche 11 814 460 001)  in the presence of 10 μl Dynabeads Protein A and Dynabeads Protein G. Magnetic beads were washed six times and immunoprecipitated chromatin was eluted with 1% SDS, 0.1 M NaHCO3. After de-crosslinking at 45°C in a shaking heat block overnight, DNA fragments were purified using QIAquick MinElute PCR columns.
The purified DNA fragments were end-repaired, extended with 3′ A-overhangs and ligated to barcoded NextFlex adapters. Libraries were amplified using KAPA HiFi HotStart ready mix, NextFlex primer mix and the following PCR program: 98°C for 2 min; four cycles of 98°C for 20 sec, 62°C for 3 min; 62°C for 5 min. Amplified libraries were size-selected for 225-325 bp (mono-nucleosomes + 125 bp NextFlex adapter) using 2% E-Gel Size Select agarose gels and amplified by PCR for ten cycles using the same PCR program. Libraries were purified by Agencourt AMPure XP beads purification using a 1:1 library:beads ratio.

value: Infected red blood cells

value: schizonts (38-46 hpi)

tag: antibody


title: ACD_E_T_3_L_1


title: 1_3H12

description:
patch-seq, pcd132, virus-infected replicate 31
SMART-seq3

value: organotypic dlPFC slice cells


title: multiome snRNA-seq 3

description:
snRNA-seq, pcd101, replicate 1
10X genomics

value: no treatment


title: 1_3H10

description:
patch-seq, pcd132, virus-infected replicate 30
SMART-seq3

value: lentivirus infected


title: PfSIP2-GFP - ChIP-seq 1

description: Library name: ChIP_SIP2

value: α-GFP antibody (Roche 11 814 460 001)


title: AD_T_7_E_L_1

value: SB415286(0.7mg/kg) treated


title: multiome snRNA-seq 2

description:
snRNA-seq, pcd96, replicate 1
10X genomics

value: cortical cells


title: 1_3G9

description:
patch-seq, pcd132, virus-infected replicate 29
SMART-seq3

value: shNC


title: MFG_9-8122-A1A1

city: Pamplona

first: Olaia

last: Urrutia

state: Navarra

address: Campus Arrosadia S/N

department: Agronomy, Biotechnology and Nutrition

country: Spain

institute: Public University of Navarre

data_processing:
Quality control analysis of the raw sequencing data was performed using the FastQC tool version 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequencing reads were trimmed for adaptor sequence/low quality sequence using Cutadapt 4.0 software.
RNAseq reads were aligned to the bovine reference genome, UCD1.3 (Ensembl release 112) using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.7.11b).
Read count normalization (per million mapped reads, adjusted for sample library size) was performed calculating fragments per kilobase per million mapped fragments (FPKM) for each gene using the rpkm function of EdgeR (version 4.0.16) in Rstudio (version 4.3.2)
Assembly: ARS.UCD1.3 (Ensembl release 112)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file includes FPKM values for each sample

organism: Bos taurus

source_name: Milk fat globules

growth_protocol: Purebred Holstein cows belonged to a commercial farm (n=14) were assigned to one of two experimental groups: (1) A1A1 genotype for β-casein and (2) A2A2 genotype for β-casein. All cows were fed with the same rations, had no water restrictions and were kept under same management conditions.

extract_protocol:
Total RNA was extracted from frozen milk samples using Trizol LS reagent (Invitrogen, Waltham, MA, USA) and a GenElute mammalian RNA isolation kit (Sigma-Aldrich, CA, USA).
Paired-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

value: Milk fat globules


title: 1_3G8

description:
patch-seq, pcd132, virus-infected replicate 28
SMART-seq3


title: AD_T_6_E_L_1


title: AD_C_5_E_L_1


title: multiome snRNA-seq 1

description:
snRNA-seq, pcd87, replicate 1
10X genomics


title: MFG_8-8039-A1A1


title: 1_3H9

description:
patch-seq, pcd132, virus-infected replicate 33
SMART-seq3


title: 1_3G12

description:
patch-seq, pcd132, virus-infected replicate 27
SMART-seq3


title: MFG_7-8183-A1A1


title: multiome snATAC-seq 7

description:
snATAC-seq, pcd155, replicate 2
10X genomics


title: 1_3G11

description:
patch-seq, pcd132, virus-infected replicate 26
SMART-seq3


title: AD_T_4_E_L_1


title: MFG_6-8217-A2A2


title: multiome snATAC-seq 5

description:
snATAC-seq, pcd112, replicate 1
10X genomics


title: AD_C_4_E_L_1


title: 1_3G10

description:
patch-seq, pcd132, virus-infected replicate 25
SMART-seq3


title: multiome snATAC-seq 6

description:
snATAC-seq, pcd155, replicate 1
10X genomics


title: MFG_5-8115-A2A2


title: multiome snATAC-seq 4

description:
snATAC-seq, pcd104, replicate 1
10X genomics


title: MFG_4-8175-A2A2


title: AD_C_2_E_L_1


title: 1_3F9

description:
patch-seq, pcd132, virus-infected replicate 24
SMART-seq3


title: AD_C_6_E_L_1


title: multiome snATAC-seq 3

description:
snATAC-seq, pcd101, replicate 1
10X genomics


title: MFG_3-8125-A1A1


title: AD_C_1_E_L_1


title: multiome snATAC-seq 2

description:
snATAC-seq, pcd96, replicate 1
10X genomics


title: 1_3F8

description:
patch-seq, pcd132, virus-infected replicate 23
SMART-seq3


title: 1_3F12

description:
patch-seq, pcd132, virus-infected replicate 22
SMART-seq3


title: MFG_2-7220-A1A1


title: AD_T_2_E_L_1


title: MFG_17-8228-A2A2


title: multiome snATAC-seq 1

description:
snATAC-seq, pcd87, replicate 1
10X genomics


title: 1_3F11

description:
patch-seq, pcd132, virus-infected replicate 21
SMART-seq3


title: Female pedicel 5

city: Nagoya

first: Takuro

middle: S

last: OHASHI

address: E-324, Science building, Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

description:
Library name: Female_pedicel_5
Column name in RNAseq_raw_counts.xlsx: female_JO_5

data_processing:
Quality of sequenced reads was checked using FastQC and no sequence flagged as poor quality was detected.
Single-end reads were aligned using HISAT2, with more than 90% of reads aligned and used for analysis.
The number of reads mapped to each gene of a gene transfer format (GTF) file of the AaegL5.0 genome was counted with featureCounts.
Assembly: AaegL5.0 genome
Supplementary files format and content: .csv file includes raw counts for each sample

organism: Aedes aegypti

source_name: Pedicel

extract_protocol:
RNA was extracted from mosquito tissues using the phenol-chloroform protocol.
Library construction was conducted by the Center for Gene Research at Nagoya University

value: Pedicel

value: Liverpool


title: MFG_15-8165-A1A1


title: 1_3F10

description:
patch-seq, pcd132, virus-infected replicate 20
SMART-seq3


title: AD_T_3_E_L_1

value: ear tissue


title: 50 weeks shell gland breeder # 42 egg in shell gland (active calcification)

city: Honolulu

first: Birendra

last: Mishra

state: HI

address: 1955 East west road

department: Department of Human Nutrition Food and Animal Sciences

institute: University of Hawaii at Manoa

description:
Library name: Sample 11
U42

data_processing:
Miniconda 3 was used for the analysis
Adapter sequences and low-quality reads with a Phred score of less than 30 were removed with the help of the Trimmomatic function in miniconda3 (var. 27.7.3.dev31)
Clean reads were aligned with the reference genome sequence Gallus gallus (assembly bGalGal.mat.broiler.GRCg7b) in HISAT2 (var. 2.1.0).
Transcript assembly and quantification were performed with cufflinks (var. 1.5.1), available in miniconda3.
Differentially Expressed Genes (DEGs) were calculated for young broiler breeder hens about aged hens in DESeq2 (var.1.14.1) in RStudio (var.4.2.3)
Assembly: bGalGal.mat.broiler.GRCg7b
Supplementary files format and content: excel file, .xlsx file with raw count, normalized data for each samples, and DEGs in different excel sheets

organism: Gallus gallus

source_name: Shell gland

extract_protocol:
RNA was extracted using TRIzol, followong standard company protocol for animal tissue
RNA concentration was measured by Qubit 3.0 using RNA BR Assay Kit (Thermo Fisher Scientific). RNA quality was determined with the Agilent Bioanalyzer Agilent 2100 Bioanalyzer (Agilent Technologies) and only samples with an RNA integrity number (RIN) of >7 were further used for RNA-sequencing. mRNA NGS libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol without further modifications.

value: Shell gland

value: 50 weeks (Aged)


title: 50 weeks shell gland breeder # 44 egg in shell gland (active calcification)

description:
Library name: Sample 12
U44


title: MFG_13-8253-A2A2


title: Female pedicel 3

description:
Library name: Female_pedicel_3
Column name in RNAseq_raw_counts.xlsx: female_JO_3


title: 50 weeks shell gland breeder # 39 egg in shell gland (active calcification)

description:
Library name: Sample 10
U39


title: MFG_11-8047-A2A2


title: Female pedicel 4

description:
Library name: Female_pedicel_4
Column name in RNAseq_raw_counts.xlsx: female_JO_4


title: 50 weeks shell gland breeder # 34 egg in shell gland (active calcification)

description:
Library name: Sample 9
U34


title: Female pedicel 2

description:
Library name: Female_pedicel_2
Column name in RNAseq_raw_counts.xlsx: female_JO_2


title: 1_3E11

description:
patch-seq, pcd132, virus-infected replicate 18
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.

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


title: 1_3E10

description:
patch-seq, pcd132, virus-infected replicate 17
SMART-seq3


title: 1_3E12

description:
patch-seq, pcd132, virus-infected replicate 19
SMART-seq3


title: 1_3D9

description:
patch-seq, pcd132, virus-infected replicate 16
SMART-seq3


title: MFG_1-8181-A2A2


title: Male pedicel 5

description:
Library name: Male_pedicel_5
Column name in RNAseq_raw_counts.xlsx: male_JO_5


title: 50 weeks shell gland breeder # 32 egg in shell gland (active calcification)

description:
Library name: Sample 7
U32


title: MFG_10-8130-A1A1


title: 50 weeks shell gland breeder # 33 egg in shell gland (active calcification)

description:
Library name: Sample 8
U33


title: 1_3D11

description:
patch-seq, pcd132, virus-infected replicate 15
SMART-seq3


title: Male pedicel 4

description:
Library name: Male_pedicel_4
Column name in RNAseq_raw_counts.xlsx: male_JO_4


title: Losartan treated , 7 Days , rep 3

city: SEOUL

first: JIN SU

last: KIM

address: 75 Nowon-ro, Nowon-gu, Seoul, 01812, Republic of Korea

institute: Korea Institute of Radiological & Medical Sciences

description: Library name: W3

data_processing:
BowTie, Langmead and Salzberg, 2012
Differentially expressed genes were determined based on counts from unique and multiple alignments, using coverage in Bedtools. The read count data were processed based on the quantile normalization method using EdgeR within R (R Development Core Team, 2016) and Bioconductor (Gentleman et al., 2004).
Assembly: UCSC hg19 (Human)
Supplementary files format and content: excel file .xlsx , Foldchange/P value/normalised data/ gene annotation/raw data counts

source_name: gastric cancer tumor

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen). RNA quality was assessed using an Agilent 2100 bioanalyzer and an RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands) and RNA quantification was performed using an ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, library construction was performed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions.

value: gastric cancer tumor

value: NCI-N87 HER2-positive gastric cancer


title: 35 weeks shell gland breeder # 30 egg in shell gland (active calcification)

description:
Library name: Sample 6
U30

value: 35 weeks (Young)


title: Losartan treated , 7 Days , rep 2

description: Library name: W2


title: Male pedicel 3

description:
Library name: Male_pedicel_3
Column name in RNAseq_raw_counts.xlsx: male_JO_3


title: 1_3C9

description:
patch-seq, pcd132, virus-infected replicate 14
SMART-seq3

value: organotypic dlPFC slice cells


title: 35 weeks shell gland breeder # 29 egg in shell gland (active calcification)

description:
Library name: Sample 5
U29


title: 1_3C8

description:
patch-seq, pcd132, virus-infected replicate 13
SMART-seq3


title: 1_3C12

description:
patch-seq, pcd132, virus-infected replicate 12
SMART-seq3


title: 35 weeks shell gland breeder # 27 egg in shell gland (active calcification)

description:
Library name: Sample 4
U27


title: Male pedicel 1

description:
Library name: Male_pedicel_1
Column name in RNAseq_raw_counts.xlsx: male_JO_1


title: 35 weeks shell gland breeder # 16 egg in shell gland (active calcification)

description:
Library name: Sample 3
U16


title: Male pedicel 2

description:
Library name: Male_pedicel_2
Column name in RNAseq_raw_counts.xlsx: male_JO_2


title: 1_3C11

description:
patch-seq, pcd132, virus-infected replicate 11
SMART-seq3


title: Female head 5

description:
Library name: Female_head_5
Column name in RNAseq_raw_counts.xlsx: female_brain_5

source_name: Head

value: Head


title: Female pedicel 1

description:
Library name: Female_pedicel_1
Column name in RNAseq_raw_counts.xlsx: female_JO_1


title: 35 weeks shell gland breeder # 3 egg in shell gland (active calcification)

description:
Library name: Sample 2
U3


title: Losartan treated , 1 Day , rep 2

description: Library name: D2


title: Female head 4

description:
Library name: Female_head_4
Column name in RNAseq_raw_counts.xlsx: female_brain_4


title: Losartan treated , 1 Day , rep 3

description: Library name: D3


title: 1_3C10

description:
patch-seq, pcd132, virus-infected replicate 10
SMART-seq3

value: lentivirus infected


title: 35 weeks shell gland breeder # 2 egg in shell gland (active calcification)

description:
Library name: Sample 1
U2


title: 1_3B8

description:
patch-seq, pcd132, virus-infected replicate 9
SMART-seq3


title: Control, rep 3

description: Library name: C3


title: Female head 3

description:
Library name: Female_head_3
Column name in RNAseq_raw_counts.xlsx: female_brain_3


title: RENCA cells with NDUFA4L2 stably re-expressed (rescue), replicate 3

city: Nashville

first: w. Kimryn

middle: N.

last: Rathmell

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

description: Library name: RES_3

data_processing:
Nextera adaptor sequences were firstly trimmed form the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Assembly: mm10
Supplementary files format and content: BigWig (bw) files were generated using deepTools

source_name: Kidney Tumor

growth_protocol: RENCA cells (ATCC CRL-2947) were grown in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin, 1% l-glutamine, 1% HEPES, 1% sodium pyruvate, and 1% MEM amino acid.

extract_protocol:
ATAC-seq was performed as previously reported (Buenrostro et al. 2013;Corces et al. 2017; Bajic M et al. 2018). Briefly, nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The following CRISPR guides were used for single-guide scaffold PX458. For NDUFA4L2: forward, CACCGAGATGGCAGGAACTAGTCTA; for reverse, aaacTAGACTAGTTCCTGCCATCTC. NDUFA4L2 KO clones were grown from single-cell colonies and screened for effective KO using qPCR. For re-expression, an NDUFA4L2 3rd-generation lentiviral expression vector were designed with a puromycin resistance cassette and purchased from Vectorbuilder Inc. Lentiviral supernatants were used immediately to infect target cells. 48-72hrs after transduction, cells were selected using 1.5ug/mL puromycin.

value: Kidney Tumor

value: RENCA

value: Cancer Cell

value: NDUFA4L2 +/+

value: NDUFA4L2 expressed via Lentivirus


title: Control, rep 2

description: Library name: C2


title: Losartan treated , 1 Day , rep 1

description: Library name: D1


title: RENCA cells with NDUFA4L2 stably re-expressed (rescue), replicate 2

description: Library name: RES_2


title: Losartan treated , 7 Days , rep 1

description: Library name: W1


title: 1_3B11

description:
patch-seq, pcd132, virus-infected replicate 7
SMART-seq3


title: 1_3B12

description:
patch-seq, pcd132, virus-infected replicate 8
SMART-seq3


title: Female head 1

description:
Library name: Female_head_1
Column name in RNAseq_raw_counts.xlsx: female_brain_1


title: RENCA cells with NDUFA4L2 stably re-expressed (rescue), replicate 1

description: Library name: RES_1


title: Cγ1ATG7fl/fl  (Exp), 21d.p.i, Replicate 1

city: London

first: Marta

last: Crespi-Sallan

address: Charterhouse Square

department: Haemato-Oncology

country: United Kingdom

institute: Barts Cancer Institute

description:
10X Genomics
E21

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger-6.0.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Freshly collected total splenic cells were isolated from spleens of 10- or 21-days immunized mice by tissue homogenization. Cells were resuspended in staining buffer (5% FBS in PBS 1X) and preserved at 4C during all process. Red blood cells were lysed using RBC lysis buffer (Biolegend).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3'Kit v3.1, 10x Genomics). Briefly, splenocytes were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Intraperitonally administered NP-CGG (1mg/mL) in a final volume of 100uL mixed with 100uL Imject™ Alum Adjuvant

value: Spleen

value: Splenocytes

value: NP-CGG immunisation to 8-12 weeks old


title: 1_3B10

city: madison

first: Xinyu

last: Zhao

address: 1500 Highland Ave

institute: University of Wisconsin-Madison

description:
patch-seq, pcd132, virus-infected replicate 6
SMART-seq3

source_name: dlPFC


title: Male head 5

description:
Library name: Male_head_5
Column name in RNAseq_raw_counts.xlsx: male_brain_5

value: Liverpool


title: Male head 4

description:
Library name: Male_head_4
Column name in RNAseq_raw_counts.xlsx: male_brain_4


title: RENCA cells with NDUFA4L2 knocked out, replicate 1

description: Library name: KO_1

value: NDUFA4L2 -/-

value: NDUFA4L2 knocked out


title: RENCA cells with NDUFA4L2 knocked out, replicate 2

description: Library name: KO_2


title: 1_3A9

description:
patch-seq, pcd132, virus-infected replicate 5
SMART-seq3

value: dlPFC


title: Cγ1Cre+/- (Control), 21d.p.i, Replicate 1

description:
10X Genomics
C21

value: Cgamma1-cre (Ighg1tm1(cre)Cgn)


title: Male head 3

description:
Library name: Male_head_3
Column name in RNAseq_raw_counts.xlsx: male_brain_3


title: Cγ1ATG7fl/fl  (Exp), 10d.p.i, Replicate 1

description:
10X Genomics
Exp


title: 1_3A8

description:
patch-seq, pcd132, virus-infected replicate 4
SMART-seq3


title: Female head 2

description:
Library name: Female_head_2
Column name in RNAseq_raw_counts.xlsx: female_brain_2


title: Cγ1Cre+/- (Control), 10d.p.i, Replicate 1

description:
10X Genomics
Control

value: splenocytes


title: Male head 2

description:
Library name: Male_head_2
Column name in RNAseq_raw_counts.xlsx: male_brain_2


title: 1_3A12

description:
patch-seq, pcd132, virus-infected replicate 3
SMART-seq3

value: organotypic dlPFC slice cells

value: shNC


title: RENCA cells expressing empty vector, replicate 2

description: Library name: EVP_2

value: WT

value: Empty Vector


title: 1_3A11

description:
patch-seq, pcd132, virus-infected replicate 2
SMART-seq3

value: lentivirus infected


title: Cγ1ATG7fl/fl  (Exp), 10d.p.i_scATAC-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger-6.0.1 using "--chemistry=ARC-v1" (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Freshly collected total splenic cells were isolated from spleens of 10- or 21-days immunized mice by tissue homogenization. Cells were resuspended in staining buffer (5% FBS in PBS 1X) and preserved at 4C during all process. Red blood cells were lysed using RBC lysis buffer (Biolegend).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell ATAC v1.1, 10x Genomics). Briefly,  Nulcei from splenocytes were obeined after incubation 2 mins in 0.1X lysis buffer.  Nuclei were resuspended in DIluted Nuclei Buffer to get the corresponding Nuclei Stock solution. Nuclei suspensions are incubated in a Transposition Mix that includes a Transposase. Simultaneously, adapter sequences are added to the ends of  the DNA fragments. GEMs are generated by combining  barcoded Gel Beads, transposed  nuclei, a Master Mix, and  Partitioning Oil on a Chromium  Next GEM Chip.  Upon GEM generation, the Gel  Bead is dissolved. Oligonucleotides  containing (i) an Illumina® P5  sequence, (ii) a 16 nt 10x Barcode  and (iii) a Read  1 (Read 1N)  sequence are released and mixed  with DNA fragments and Master  Mix. Thermal cycling of the GEMs  produces 10x barcoded singlestranded DNA. After incubation,  the GEMs are broken and pooled  fractions are recovered.  Solid Phase Reversible Immobilization (SPRI) beads are  used to eliminate unused barcodes from the sample. P7 and a sample index  are added during library  construction via PCR. The  final libraries contain the  P5 and P7 sequences  used in Illumina® bridge  amplification.  corresponding Nuclei Stock Concentrations  corresponding Nuclei Stock Concentrationssplenocytes were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: Cγ1Cre+/- (Control), 10d.p.i_scATAC-seq

description: 10x Genomics


title: Control, rep 1

description: Library name: C1

value: gastric cancer tumor

value: NCI-N87 HER2-positive gastric cancer


title: 1_3A10

description:
patch-seq, pcd132, virus-infected replicate 1
SMART-seq3


title: Male head 1

description:
Library name: Male_head_1
Column name in RNAseq_raw_counts.xlsx: male_brain_1

value: Head


title: shJARID2_2

status: Public on May 11 2025

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Trimmomatic (version: v0.39) was used for filter reads, parameters: -ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Hisat2 (version: v2.0.4) was used to map clean reads to reference gene with the default parameter.
Samtools (version: v1.7) was used to build index to bam file.
FPKM method was used in calculated expression level with featureCounts (version: v2.0.1).
Assembly: hg 38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from the MDA-MB-231 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard capitalbiotech protocols

treatment_protocol: Corresponding shRNA was infected into MDA-MB-231 cells using Polybrene (Sigma-Aldrich).

value: breast cancer cell

value: JARID2 knockdown


title: shSCR_2

value: shSCR


title: shSCR_1


title: JARID2-ChIPseq

data_processing:
Basecalls performed using Illumina BCL2fastq version v1.8.4
Data were filtered using NGS QC Toolkit version v2.3.3. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed."
The high quality reads were mapped to the Human genome of Ensembl by using Bowtie(version 0.12.8) with parameter: mismatch=2, special parameter: -m 1 and –best.
The expression peaks were detected by MACS (Model-based Analysis for ChIP-Seq) with the default parameter.
Assembly: hg19
Supplementary files format and content: tab-delimited text files were generated using MACS2 and The R programming language-ChIPseeker

extract_protocol:
Approximately 4 x 10^7 cells were used for each ChIP-Seq assay. Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and the chromatin DNA precipitated by polyclonal antibody against JARID2. The DNA was purified with a Qiagen PCR purification kit.
A Vazyme TruePrep DNA Library Prep Kit V2 for Illumina ® (Vazyme Biotech) was used for DNA library construction. Briefly,the kit uses a new-type transposasea for DNA fragmentation and ligation  of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: MDA-MB-231 cells

value: JARID2(Novus Biologicals, NB100-2214)

value: untreated


title: Input DNA for JARID2

source_name: input


title: shJARID2_1