title: ADULT_C57_UI_0h_A57_S90

description:
Library name: A57-C57-UI_S90
8-weeks-old


title: Nanopore #3_2

status: Public on Feb 22 2025

type: SRA

city: Wenzhou

first: Keqing

last: Shi

address: Fanhaixilu

country: China

institute: The First Affiliated Hospital of Wenzou Medical University

description: Library name: Nanopore #3_2

library_source: transcriptomic

data_processing:
Transcriptome sequencing was conducted on the Illumina platform (Illumina NovaSeq 6000)
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were aligned to the reference genome using HISAT2. The FPKM values for each gene were calculated, and the read counts for each gene were obtained using HTSeq-count.
Differential expression analysis was performed using DESeq2. A Q value < 0.05 and fold change > 2 or fold change < 0.5 were set as the criteria for significantly differentially expressed genes (DEGs).
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: NIH-3T3 cells, cultured on Nanopore #3 scaffold

growth_protocol: NIH-3T3 were maintained in DMEM culture medium (Biological Industries, Israel) supplemented with 10% fetal bovine serum (Gemini, USA) and 1% streptomycin and penicillin (Invitrogen Corp., Carlsbad, CA, USA) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from NIH-3T3 cells cultured on plates or scaffolds using TRIzol reagent (catalog #15596026, Invitrogen, Carlsbad, CA, USA).
The libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina according to the manufacture's instructions

treatment_protocol: NIH-3T3 cells cultured on plates or Nanopore #3 scaffolds

tag: tissue

value: embryo

tag: cell line

tag: cell type

value: fibroblast cell

tag: genotype

value: WT

tag: treatment

value: cultured on Nanopore #3 scaffold


title: ADULT_C57_UI_0h_A56_S89

city: Philadelphia

first: Alison

last: Carey

state: PA

address: 245 N 15th Street

country: USA

institute: Drexel University College of Medicine

description:
Library name: A56-C57-UI_S89
8-weeks-old

data_processing:
FastQ generation, including base calling, demultiplexing, and adapter trimming were automatically performed after sequencing on Illumina BaseSpace using BCL Convert.
FastQ reads were pseudoaligned to the indexed mm10/GRCm38 transcriptome reference used Salmon v1.8 in ISR mode. Aggregation of transcript-level counts to gene-level counts used tximport v1.22.
Samples which failed quality control assessments (A1, A2, A3, A4, A5, A6, A38, A39, A40, A48, A49, N57, N69, N78, N79, N81, N83) were dropped from final analyses.
Assembly: mm10
Supplementary files format and content: Processed data files .quant.sf were produced using Salmon v1.8 with mm10 as the reference. The five tab-delimited columns are Name (Ensembl ID), Length (total transcript length), EffectiveLength (computed length accounting for sequencing parameters, TPM (estimate of transcripts per million), NumReads ("count" of reads with multiple mappers fractionally split).

molecule: polyA RNA

source_name: Lung

extract_protocol:
Type II epithelial cells were enriched from homogenized murine lung tissues by filtration for cells <20 microns and antibody depletion of CD45 and CD16/32-expressing cells. Total RNA was isolated using phase-separation with TRIzol following manufacturer recommendations, including DNase treatment. Further purification used RNeasy kits (Qiagen), per manufacturer's instructions. RNA purity was determined by spectrophotometry, concentration by Qbit fluorometry, and quality by Bioanalyzer.
The Illumina TruSeq stranded mRNA kit with selection for polyadenylated trascripts was used to prepare sequencing libraries according to recommended protocols.

treatment_protocol: Adult or neonatal mice of two genotypes (C57/BL6 or an isogenic IFNAR knockout) were infected with flu virus (PR8) or not, and lung tissue was harvested at 1, 2, or 3 days post-infection for isolation of type II epithelial cells.

value: Lung

value: Type II alveolar epithelial cell


title: ADULT_IFNAR_UI_0h_A60_S95

description:
Library name: A60-IFNAR-UI_S95
8-weeks-old


title: ADULT_IFNAR_FLU_72h_A17_S84

description:
Library name: A17-IFNAR-72h_S84
8-weeks-old

value: FLU


title: ADULT_IFNAR_UI_0h_A63_S93

description:
Library name: A63-IFNAR-UI_S93
8-weeks-old


city: Nanjing

first: Hao

last: Zhang

address: Dingjiaqiao 87#, Southeast University, Gulou District, Nanjing, Jiangsu Province, China

institute: Southeast University

description:
Library name: p53KO_TAC_1
p53 knockout mice undergoing TAC surgery

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger, with alignment to the Mus musculus reference genome.
Quality control and filtering of low-quality cells were performed using the Seurat R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Total RNA was extracted from the hypertrophied left ventricle of mice using a commercial RNA extraction kit.
Single-cell RNA sequencing libraries were constructed using the 10x Genomics Chromium Single Cell 3’ Reagent Kit, following the manufacturer’s instructions.

value: Heart

value: Cardiomyocytes


title: ADULT_C57_FLU_72h_A49_S82

description:
Library name: A49-C57-72h_S82
8-weeks-old -- QC Fail


title: ADULT_IFNAR_FLU_72h_A53_S87

description:
Library name: A53-IFNAR-72h_S87
8-weeks-old


title: ADULT_IFNAR_FLU_72h_A55_S86

description:
Library name: A55-IFNAR-72h_S86
8-weeks-old


title: ADULT_C57_FLU_72h_A13_S83

description:
Library name: A13-C57-72h_S83
8-weeks-old


title: ADULT_IFNAR_FLU_72h_A54_S85

description:
Library name: A54-IFNAR-72h_S85
8-weeks-old


title: ADULT_IFNAR_FLU_72h_A52_S88

description:
Library name: A52-IFNAR-72h_S88
8-weeks-old


title: ADULT_IFNAR_FLU_48h_A48_S77

description:
Library name: A48-IFNAR-48h_S77
8-weeks-old -- QC Fail


title: ADULT_IFNAR_FLU_48h_A45_S76

description:
Library name: A45-IFNAR-48h_S76
8-weeks-old


title: ADULT_IFNAR_FLU_48h_A11_S78

description:
Library name: A11-IFNAR-48h_S78
8-weeks-old


title: ADULT_C57_FLU_72h_A51_S80

description:
Library name: A51-C57-72h_S80
8-weeks-old


title: ADULT_IFNAR_FLU_48h_A46_S79

description:
Library name: A46-IFNAR-48h_S79
8-weeks-old


title: ADULT_C57_FLU_48h_A44_S73

description:
Library name: A44-C57-48h_S73
8-weeks-old


title: ADULT_C57_FLU_48h_A43_S71

description:
Library name: A43-C57-48h_S71
8-weeks-old


title: MM.1S cells EGCG 80μM 3

status: Public on Feb 23 2025

city: Jinan

first: xunqi

last: zhang

address: Bei yuan street N0.247

department: hematology

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fq.gz) were mapped to the reference genome GRCh38.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCh38.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Homo sapiens

source_name: MM.1S cells multiple myeloma

growth_protocol: MM.1S cells were cultured in RPMI 1640 medium  containing 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured in an incubator with 5% CO2, 37℃ and constant humidity. The medium was changed every other day.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MM.1S cells were treated with EGCG (0、40μM、80μM ) for 24h

value: MM.1S cells multiple myeloma

value: tumor cells

value: EGCG 80 microM 24h


title: ADULT_IFNAR_FLU_24h_A4_S69

description:
Library name: A4-IFNAR-24h_S69
8-weeks-old -- QC Fail


title: ADULT_C57_FLU_48h_A41_S74

description:
Library name: A41-C57-48h_S74
8-weeks-old


title: ADULT_C57_FLU_48h_A42_S72

description:
Library name: A42-C57-48h_S72
8-weeks-old


title: ADULT_IFNAR_FLU_24h_A40_S67

description:
Library name: A40-IFNAR-24h_S67
8-weeks-old -- QC Fail


title: ADULT_C57_FLU_24h_A2_S65

description:
Library name: A2-C57-24h_S65
8-weeks-old -- QC Fail


title: ADULT_C57_FLU_24h_A1_S66

description:
Library name: A1-C57-24h_S66
8-weeks-old -- QC Fail


title: ADULT_IFNAR_FLU_24h_A6_S68

description:
Library name: A6-IFNAR-24h_S68
8-weeks-old -- QC Fail


title: ADULT_C57_FLU_24h_A38_S64

description:
Library name: A38-C57-24h_S64
8-weeks-old -- QC Fail


title: ADULT_C57_FLU_24h_A3_S62

description:
Library name: A3-C57-24h_S62
8-weeks-old -- QC Fail


title: NEO_IFNAR_UI_72h_N55_S61

description:
Library name: N55-IFNAR-UI72h_S61
6-days-old


title: ADULT_C57_FLU_24h_A39_S63

description:
Library name: A39-C57-24h_S63
8-weeks-old -- QC Fail


title: NEO_IFNAR_UI_72h_N54_S60

description:
Library name: N54-IFNAR-UI72h_S60
6-days-old


title: NEO_C57_UI_72h_N49_S57

description:
Library name: N49-C57-UI72h_S57
6-days-old


title: NEO_IFNAR_UI_72h_N53_S59

description:
Library name: N53-IFNAR-UI72h_S59
6-days-old


title: NEO_C57_UI_72h_N86_S54

description:
Library name: N86-C57-UI72h_S54
6-days-old


title: NEO_IFNAR_UI_72h_N52_S58

description:
Library name: N52-IFNAR-UI72h_S58
6-days-old


title: NEO_C57_UI_72h_N51_S56

description:
Library name: N51-C57-UI72h_S56
6-days-old


title: ADULT_IFNAR_FLU_48h_A47_S75

description:
Library name: A47-IFNAR-48h_S75
8-weeks-old


title: NEO_C57_UI_72h_N50_S55

description:
Library name: N50-C57-UI72h_S55
6-days-old


title: NEO_IFANR_UI_48h_N47_S52

description:
Library name: N47-IFANR-UI48h_S52
5-days-old


title: NEO_IFNAR_UI_48h_N48_S53

description:
Library name: N48-IFNAR-UI48h_S53
5-days-old


title: ADULT_IFNAR_FLU_24h_A5_S70

description:
Library name: A5-IFNAR-24h_S70
8-weeks-old -- QC Fail


title: NEO_IFNAR_UI_48h_N46_S51

description:
Library name: N46-IFNAR-UI48h_S51
5-days-old


title: ADULT_C57_FLU_72h_A50_S81

description:
Library name: A50-C57-72h_S81
8-weeks-old


title: NEO_C57_UI_48h_N41_S49

description:
Library name: N41-C57-UI48h_S49
5-days-old


title: NEO_C57_UI_48h_N43_S48

description:
Library name: N43-C57-UI48h_S48
5-days-old


title: NEO_IFNAR_UI_48h_N45_S50

description:
Library name: N45-IFNAR-UI48h_S50
5-days-old


title: NEO_C57_UI_48h_N42_S47

description:
Library name: N42-C57-UI48h_S47
5-days-old


title: NEO_C57_UI_48h_N84_S46

description:
Library name: N84-C57-UI48h_S46
5-days-old


title: NEO_IFNAR_UI_24h_N40_S44

description:
Library name: N40-IFNAR-UI24h_S44
4-days-old


title: NEO_IFNAR_UI_24h_N36_S41

description:
Library name: N36-IFNAR-UI24h_S41
4-days-old


title: NEO_IFNAR_UI_24h_N37_S42

description:
Library name: N37-IFNAR-UI24h_S42
4-days-old


title: NEO_IFNAR_UI_24h_N39_S43

description:
Library name: N39-IFNAR-UI24h_S43
4-days-old


title: VU_ILD_94_more_fibrotic

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

description: Library name: 5465_1

data_processing:
Cellranger multiple versions. 4859_2: v3.1; 6281: 6.0.1; 7539: 6.1.2; 8981: 7.0.1; 9367: 7.0.1; 9564: 7.0.1
Assembly: 4859_2: GRCh38-3.0.0; all others GRCh38-2020-A
Supplementary files format and content: CellRanger filtered_feature_bc_matrix.h5 files

source_name: lung

extract_protocol:
Single cell suspensions were generated using collagenase/dispase digest (1 mg/ml each) using a Gentlemacs Auto-dissociator. After serial filtering, column-based sorting of CD45+ cells (Miltenyi Microbeads) was performed, and CD45+ and CD45- fractions were mixed 1:2 for scRNA-seq library preparation.
10X Genomics 5' v1

value: lung


title: NEO_C57_UI_24h_N33_S40

description:
Library name: N33-C57-UI24h_S40
4-days-old


title: CircRBM39 OE 1

city: Hefei City

first: Dun

last: Liu

state: Anhui Province

address: Division of Life Sciences and Medicine, 443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: Sample 7

data_processing:
For data processing, the adapters were trimmed from raw data with Cutadapt (-e 0.1 -O 5) to obtain clean reads, which were subsequently aligned to the human genome (hg19) with BWA-MEM or Bowtie2 allowing one mismatch. For circRNA prediction, two published pipelines CIRI2 and Find_circ were applied to identify high-confidence BSJs. Overlapped circRNAs annotated by both pipelines were used for further analysis and CIRI2-identified BSJ Reads Per Million (BRPM) were used to calculate circRNA levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA from frozen specimen or cultured cells was extracted with the TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
For ribosomal RNA-depleted (Ribo-) RNA-seq for two-paired breast cancer specimen and NT tissues, total RNA was depleted rRNA with the Illumina Rio-Zero Gold Kit (Illumina) and subjected to library preparation with the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer’s instructions. For polyadenylated (poly(A)+) RNA-seq for MDA-231 cells with or without circRBM39 OE, total RNA was polyadenylated and subjected to library preparation.

value: MDA-MB-231 cells

value: Transfected with circRBM39 OE constructs


title: Con 2

description: Library name: Sample 6

value: Transfected with control constructs


title: CircRBM39 OE 2

description: Library name: Sample 8


title: Con 1

description: Library name: Sample 5


title: Non-tumor tissue 2

description: Library name: Sample 2

source_name: Adjacent non-tumor tissues

value: Adjacent non-tumor tissues


title: Breast cancer specimen 2

description: Library name: Sample 4

source_name: Breast cancer tumors

value: Breast cancer tumors


title: NEO_C57_UI_24h_N34_S38

description:
Library name: N34-C57-UI24h_S38
4-days-old


title: Breast cancer specimen 1

description: Library name: Sample 3


title: NEO_IFNAR_FLU_72h_N70_S34

description:
Library name: N70-IFNAR-72h_S34
6-days-old


title: NEO_C57_UI_24h_N83_S37

description:
Library name: N83-C57-UI24h_S37
4-days-old -- QC Fail


title: VU_ILD_94_less_fibrotic

description: Library name: 5465_2


title: WT Hela cells, target PCNA, biol rep 2

city: Beijing

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

description: Library name: PCNA_WT_2

library_source: genomic

data_processing:
Sequencing reads were aligned to the reference genome hg19. Peak calling was performed using MACS2 (v2.2.7.1). Differential peak analysis between groups was performed using Bedtools.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Hela

growth_protocol: HeLa cells were cultured in 10 cm plastic dishes (Corning, 430167) or 35 mm glass-bottom dishes (Cellvis, D35-20-1.5-N) to facilitate monitoring and imaging. The cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, 11965-092) supplemented with 10% fetal bovine serum (Gibco, 10099-141) and 100 U/mL penicillin-streptomycin (Gibco, 15140-122). Cultures were incubated at 37°C in a humidified atmosphere containing 5% CO₂ (Thermo Scientific, Forma Series II). Cell growth was monitored regularly, and subculturing was performed every 2-3 days when confluency reached approximately 80%, using 0.25% trypsin (Gibco, 25200-056).

extract_protocol:
Approximately 100,000 Hela cells were harvested and permeabilized with digitonin in wash buffer. ConA beads were activated and incubated with cells at room temperature for 10 minutes. Primary antibodies（PCNA） against the target protein were added, and the reaction was incubated overnight at 4°C.
Cut&Tag was performed using the Vazyme CUT&Tag kit (#TD904) according to the manufacturer’s instructions, with minor modifications. Briefly, approximately 100,000 Hela cells were harvested and permeabilized with digitonin in wash buffer. ConA beads were activated and incubated with cells at room temperature for 10 minutes. Primary antibodies（PCNA） against the target protein were added, and the reaction was incubated overnight at 4°C. The next day, samples were washed and incubated with a secondary antibody conjugated to Protein A-Tn5 transposase. Following tagmentation, DNA was extracted using DNA Clean Beads (Vazyme #N411) and purified. The libraries were amplified using the Vazyme library amplification primers (#TD202/TD203) and sequenced on an Illumina platform.

value: Hela


title: WT Hela cells, target PCNA, biol rep 1

description: Library name: PCNA_WT_1

value: WT


title: Non-tumor tissue 1

description: Library name: Sample 1


title: NEO_IFNAR_FLU_72h_N31_S36

description:
Library name: N31-IFNAR-72h_S36
6-days-old


title: Lamin A/C knockout Hela cells, target PCNA, biol rep 2

description: Library name: PCNA_KO_2

value: Lamin A/C knockout


title: Lamin A/C knockout Hela cells, target PCNA, biol rep 1

description: Library name: PCNA_KO_1


title: NEO_IFNAR_FLU_72h_N29_S33

description:
Library name: N29-IFNAR-72h_S33
6-days-old

value: Lung


title: WT Hela cells, BrdU-seq, input

description: Library name: brdu_WT_input

data_processing:
Sequencing data were preprocessed to remove low-quality reads, and adapter sequences were trimmed using Trim Galore. Processed reads were aligned to the human reference genome (hg19) using Bowtie2. Peak calling was performed using MACS2 to identify BrdU-enriched regions. Visualization of BrdU-labeled regions was done using the Integrative Genomics Viewer (IGV). Differential analysis between wild-type and Lamin A/C knockout cell lines was conducted using DiffBind and DESeq2, with significant peaks identified by thresholds of p < 0.05 and log2FoldChange > 1 or < -1. When considering the reported fork speed (~1 Kbp /min), an estimated 10-min replication peak length of ~10 Kbp was chosen to select the peak containing at least one replication origin.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: BRU-Seq

extract_protocol:
Hela cells were cultured in 10 cm dishes at a density of ~20%, then synchronized at either the G1/S boundary or specific points in S phase. After synchronization, cells were washed three times with PBS. BrdU (Sigma-Aldrich, B5002) was added to the medium to label replicating DNA for specific durations. Following labeling, cells were washed with PBS, and lysed in RIPA buffer (Yeasen, 20101ES60) containing RNase A (Qiagen, 19101) and Proteinase K (Thermo Fisher Scientific, EO0491) at final concentrations of 0.1 mg/mL and 0.2 mg/mL, respectively. Lysis was carried out in a thermomixer first at 37°C for 2 hours, followed by 55°C for 5 hours to ensure complete cell lysis and DNA release.
Genomic DNA was extracted from the lysate using phenol-chloroform extraction to ensure purity. DNA was mixed with phenol-chloroform-isoamyl alcohol (24:25:1) at a 1:1 ratio, shaken for 5 minutes, and allowed to settle for phase separation. After centrifugation (15,000 g, 10 minutes), the upper aqueous phase containing the DNA was collected. The extraction was repeated, and the DNA was precipitated with ethanol and 3 M sodium acetate (pH 5.5). DNA was pelleted by centrifugation (16,000 g, 30 minutes at 4°C), washed with 75% ethanol, air-dried, and resuspended in ultrapure water. The extracted DNA was fragmented into ~200 bp fragments using a Covaris sonicator (175 W, 10% duty cycle, 200 cycles per burst). Fragmented DNA was then purified using Vazyme magnetic beads (Vazyme, N401-01). Following DNA fragmentation, BrdU-labeled DNA was denatured to single-stranded DNA by heat treatment. The denatured DNA was incubated with BrdU-specific antibodies (BD, 555627) in an immunoprecipitation buffer. Protein G-Dynabeads (Invitrogen, 10004D) were used to capture the antibody-DNA complexes. The immunoprecipitated DNA was washed extensively, and DNA was eluted with TE buffer. The recovered DNA fragments were used to generate sequencing libraries with the Vazyme single-strand DNA library preparation kit (Vazyme, NE103). Libraries were sequenced on an Illumina platform.


title: NEO_IFNAR_FLU_72h_N71_S31

description:
Library name: N71-IFNAR-72h_S31
6-days-old

value: Type II alveolar epithelial cell


title: NEO_IFNAR_UI_24h_N38_S45

description:
Library name: N38-IFNAR-UI24h_S45
4-days-old


title: WT Hela cells, BrdU-seq, biol rep 2

description: Library name: brdu_WT_2


title: NEO_C57_UI_24h_N32_S39

description:
Library name: N32-C57-UI24h_S39
4-days-old


title: Lamin A/C knockout Hela cells, BrdU-seq, input

description: Library name: brdu_KO_input


title: NEO_IFNAR_FLU_72h_N30_S35

description:
Library name: N30-IFNAR-72h_S35
6-days-old

value: FLU


title: NEO_C57_FLU_72h_N78_S27

description:
Library name: N78-C57-72h_S27
6-days-old -- QC Fail


title: Lamin A/C knockout Hela cells, BrdU-seq, biol rep 2

description: Library name: brdu_KO_2


title: NEO_IFNAR_FLU_72h_N12_S32

description:
Library name: N12-IFNAR-72h_S32
6-days-old


title: donor 4, patient ID 7042, CD264 positive

city: New Orleans

first: Kim

last: OConnor

state: LA

address: 6823 St. Charles Ave

institute: Tulane University

data_processing:
The FastQC program was employed to check the overall quality of the paired-end reads.
Salmon v 1.9.0 and GRCh38 assembly of the human genome were used for transcript quantification. Default parameters were used.
Bioconductor's tximport package was used to generate raw count matrix of gene expression.
Assembly: GRCh38
Supplementary files format and content: csv file contains raw counts for each sample

source_name: bone marrow

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). Extracted RNA was treated with the RNase-Free DNase Set (Qiagen) and purified with RNAClean XP beads on the SPRIStand magnetic tube stand (Beckman Coulter).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used to purify polyA RNA mRNA and then to convert fragmented mRNA into cDNA libraries.

value: bone marrow

value: mesenchymal stem cell

tag: donor

tag: patient id

tag: cell subtype

value: CD264 positive

tag: age

tag: Sex

value: female

tag: passage


title: NEO_C57_FLU_72h_N27_S30

description:
Library name: N27-C57-72h_S30
6-days-old


title: WT Hela cells, ATAC-seq, biol rep 3

description: Library name: ATAC_WT_3

data_processing:
Sequencing reads were aligned to the reference genome hg19. Peak calling was performed using MACS2. Data visualization was performed using IGV and Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
The nuclei were extracted from G1/S-transition synchronized cells using lysis buffer and centrifuged at 500×g for 5 minutes at 4°C.
ATAC-seq was performed using the Vazyme Hyperactive ATAC-Seq Library Prep Kit for Illumina (#TD711) according to the manufacturer’s instructions.The nuclei were extracted from G1/S-transition synchronized cells using lysis buffer and centrifuged at 500×g for 5 minutes at 4°C. Nuclei pellets were resuspended in the Tn5 transposase reaction mix and incubated at 37°C for 30 minutes. Following transposition, equimolar adapters were ligated, and the resulting libraries were amplified by PCR. Libraries were purified using AMPure beads and quantified using a Qubit fluorometer. Sequencing was conducted on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: WT Hela cells, BrdU-seq, biol rep 1

description: Library name: brdu_WT_1


title: NEO_C57_FLU_72h_N26_S29

description:
Library name: N26-C57-72h_S29
6-days-old


title: donor 4, patient ID 7042, CD264 negative

value: CD264 negative


title: donor 5, patient ID 7068, CD264 positive

value: male


title: donor 5, patient ID 7068, CD264 negative


title: donor 3, patient ID 7015, CD264 positive


title: NEO_C57_FLU_72h_N69_S28

description:
Library name: N69-C57-72h_S28
6-days-old -- QC Fail


title: NEO_IFNAR_FLU_48h_N65_S24

description:
Library name: N65-IFNAR-48h_S24
5-days-old


title: NEO_C57_FLU_72h_N28_S26

description:
Library name: N28-C57-72h_S26
6-days-old


title: Lamin A/C knockout Hela cells, BrdU-seq, biol rep 1

description: Library name: brdu_KO_1


title: NEO_C57_FLU_72h_N77_S25

description:
Library name: N77-C57-72h_S25
6-days-old


title: WT Hela cells, ATAC-seq, biol rep 1

description: Library name: ATAC_WT_1


title: WT Hela cells, ATAC-seq, biol rep 2

description: Library name: ATAC_WT_2


title: donor 2, patient ID 7038, CD264 postive


title: donor 3, patient ID 7015, CD264 negative


title: donor 2, patient ID 7038, CD264 negative


title: NEO_IFNAR_FLU_48h_N24_S23

description:
Library name: N24-IFNAR-48h_S23
5-days-old


title: NEO_IFNAR_FLU_48h_N66_S22

description:
Library name: N66-IFNAR-48h_S22
5-days-old


title: donor 1, patient ID 7043, CD264 positive


title: donor 1, patient ID 7043, CD264 negative


title: Lamin A/C knockout Hela cells, ATAC-seq, biol rep 3

description: Library name: ATAC_KO_3


title: K562 cells, shMETTL14-2

city: 成都

first: Yuqian

last: Tang

state: 四川

address: 玉林街道

institute: Sichuan university

description: Library name: sample 6

data_processing:
The gene expression levels of each sample were analyzed using HTSeq software version 0.6.1, with the model set to union.
Assembly: hg38
Supplementary files format and content: Excel file contains gene expression counts for six samples, including gene IDs and their corresponding counts.

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from cells using the TRIzol method. Cells were collected and resuspended in 1 ml of TRIzol and incubated at room temperature for 5 minutes for complete lysis. Following this, 200 μl of chloroform per ml of TRIzol was added, mixed vigorously, and incubated for 3 minutes. The samples were centrifuged at 12,000×g for 15 minutes at 4°C, resulting in three layers. The upper aqueous phase, containing RNA, was transferred to a new RNase-free tube. Isopropanol was added (0.5 ml per ml of TRIzol), mixed, and incubated for 10 minutes before centrifugation. The RNA pellet was washed with 75% ethanol, dried, and dissolved in RNase-free water. RNA concentration was measured using a Nanodrop 2000.
After sample assessment, mRNA from eukaryotic cells was enriched using magnetic beads with Oligo(dT), which bind to the polyA tails of mRNA through A-T complementary pairing. Fragmentation buffer was then added to break the mRNA into short fragments. Using these fragments as templates, first-strand cDNA was synthesized with six-base random primers, followed by the addition of buffer, dNTPs, and DNA polymerase I to create double-stranded cDNA. The double-stranded cDNA was purified using AMPure XP beads. The purified cDNA underwent end repair, A-tailing, and adapter ligation, followed by size selection with AMPure XP beads. Finally, PCR enrichment was performed to obtain the final cDNA library.

treatment_protocol: Cells cultured to logarithmic growth stage were collected to extract total RNA

value: chronic myeloid leukemia cells in acute myeloid blast phase

value: METTL14 knockdown


title: K562 cells, shMETTL3-1

description: Library name: sample 3

value: METTL3 knockdown


title: THP1, 4 hr nigericin, replicate 3

city: Cleveland

first: Meghan

middle: Elizabeth

last: O'Keefe

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University School of Medicine

description:
Library name: Sample_9
NT_4H_Rep3

data_processing:
The sequence data  was checked using FastQC (v0.12.1) for QC analysis.
Multiqc (v1.15) was used to summarize the QC report for all samples.
The reads were aligned to hg38/GRCh38 (NCBI RefSeq assembly: GCA_000001405.15) using STAR (v2.5.2b).
RSEM (v1.2.28) was performed to generate gene expression values.
DESeq2 (v1.42.0) was applied for DE analysis according to the target features.
Assembly: hg38
Supplementary files format and content: Excel file containing normalize counts for each sample

growth_protocol: THP-1 monocytes were cultured in RPMI supplemented with 10% fetal bovine serum and 1% antibiotics/antimycotics in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using QIAshredder and RNeasy Plus Kits (Qiagen).
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations

treatment_protocol: Differentiation was induced by treatment with 100 ng/ml phorbol 12-myristate-13-acetate (PMA) for 18 hours. After 18 hours, differentiation media was replaced with complete RPMI. Cells were stimulated with 10 μM nigericin or ethanol vehicle control. Cells were harvested for RNA collection after 0, 2, or 4 hours of nigericin stimulation.

value: monocyte

value: 18 hr PMA differentiation, 4 hr nigericin


title: K562 cells, shCTR-2

description: Library name: sample 2


title: E15.5 Six2creTGC paired kidneys_biol rep 2

city: Dallas

first: Keri

last: Drake

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatric Nephrology

institute: UTSW

description:
Library name: Sample 3
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cell Ranger software (Version 5.0.1).
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

source_name: embryonic kidney

extract_protocol:
Nuclei were isolated as previously reported from paired kidneys with Nuclei EZ Lysis buffer supplemented with protease inhibitor and RNase inhibitor. Samples were homogenized using a Dounce homogenizer in 2ml of ice-cold Nuclei EZ Lysis buffer first with a loose pestle, then passed through a 200 µm strainer into 50 ml conical tube and followed by homogenization with a tight pestle which was then filtered through a 40-µm cell strainer and incubated on ice for 5 minutes. The suspension was centrifuged at 500 g x for 5 min at 4 ºC with the pellet resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor) and filtered through a 5-µm cell strainer into a conical tube. The nuclei were counted with a disposable hemacytometer and diluted to a concentration of 700-1200 cells per µL.
Library was performed according to the manufacturer’s instructions (single cell 3’ GEX kit).

value: embryonic kidney


title: Human9_p65ChIPseq_ZIKVPos

city: La Jolla

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

description: NF-kB p65 ChIP-seq

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq reads aligned to the GRCh38/hg38 assembly using STAR were used to generate gene expression FPKM values using HOMER. Gene expression (RNA-seq) was measured using HOMER with the following parameters: analyzeRepeats.pl rna hg38 -count exons -raw -pc 3 -strand - -condenseGenes followed by DESeq normalized regularized logarithm (rlog) normalization values while accounting for individual donors in the design matrix. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific (RNA-seq = exonic reads) reads for each transcript.
ChIP-seq reads were aligned to the human genome (hg38) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called from two biologic replicates of DENV- or ZIKV-infected samples with mock-infected conditions as the background (-b) and input DNA as input (-i) using HOMER’s getDifferentialPeaksReplicates.pl with the “-style factor” and default parameters.
Assembly: GRCh38/hg38
Supplementary files format and content: RNA-seq tab-delimited text files include FPKM values for each sample. Tab-delimited BED files containing peak positions for each ChIP-seq experiment.

source_name: Human blood monocytes derived

growth_protocol: Human peripheral blood was separated using Histopaque 1077 and centrifuged at 300xg for 30 min at 4˚C. The buffy coat was washed once, and red blood cells were lysed with molecular grade water. Monocytes were negatively selected from the buffy coat using the human pan monocyte isolation kit (Miltenyi Biotec) as described by the manufacturer. Cells were seeded at 1.5 x 106 cells/mL onto polystyrene plates and differentiated for 7 days in hDC media composed of RPMI 1640 Medium, GlutaMAX™ Supplement, 1% penicillin/streptomycin, 2.5% HEPES buffer, and freshly added cytokines including 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) and 100 ng/ml recombinant human interleukin 4 (rhIL-4). Cells were incubated at 37˚C, 5% CO2 and media was changed every 2-3 days.

extract_protocol:
For RNA-seq, after virus infection of hDCs for 24 hours, cells were collected and stained with Zombie Violet™ Fixable Viability stain (BioLegend) for 20 min at 4˚C. After washing, cells were fixed and permeabilized with 4% paraformadehyde (PFA), 0.1% saponin in the presence of RNasin Ribonuclease inhibitor (400 U/mL). After centrifugation, samples were resuspended in wash buffer (0.2% BSA, 0.1% saponin and 400 U/mL of RNasin Ribonuclease inhibitor). Sample were blocked with human Fc blocker diluted in staining buffer (1% Bovine serum albumin (BSA), 0.1% saponin, 1600 U/mL RNasin Ribonuclease inhibitor) for 5 min, 4˚C. Then, 4G2-AF647 antibody was added to samples and incubated for 30 min, 4˚C. Samples were centrifuged at 1000xg for 3 min, 4˚C. Cells were washed using wash buffer and centrifuged at 1000xg for 3 min, 4˚C. Samples were resuspended in sort buffer containing 0.5% BSA and 1600 U/mL of RNase inhibitor in 1XPBS and sorted into ZIKV+ or DENV+ and ZIKV− or DENV- cells on a FACS cell sorter. After sorting, cells were pelleted at 4˚C, supernatant discarded and total RNA isolated using Ambion’s RecoverAll Total Nucleic Acid Isolation Kit [AM1975], starting at the protease digestion step. All steps were performed per manufacturer recommendations with the following modification. Cells were incubated in digestion buffer for 3 hours at 50˚C supplemented with RNasin Plus RNase Inhibitor. RNA was treated with in column DNase per manufacturer instructions, eluted and RNA quality determined by BioAnalyzer using the Eukaryote Total RNA Pico Chip. Samples with RIN values greater than 8.0 were used for library preparation. For chromatin immunoprecipitation-sequencing (ChIP-seq) experiments, moDCs were cross-linked with 4 mM disuccinimidyl glutarate (DSG) in PBS for 30 minutes at RT followed by 1% formaldehyde for 15 minutes at RT and quenched with 0.125 M glycine. Preparation of moDCs for FACS was performed as described above for RNA-seq except that 1x cOmplete protease inhibitors (Roche) were included in all buffers instead of RNasin Plus RNase Inhibitor. After separation by FACS, cells were washed, separated into 500,000 cell aliquots, pelleted, snap-frozen and stored at -80°C.
For RNA-seq, RNA libraries were generated using the TruSeq stranded total RNA-seq [Illumina] kit per manufacturer instructions and sequenced on an Illumina Hi-Seq 2000, NextSeq 500, or NovaSeq per manufacturer instructions. For ChIP-seq, samples of 500,000 cells were resuspended on ice in 500 µl RIPA buffer (50 mM Tris-HCl, pH 7.4, 1% IGEPAL CA-630, 0.25% sodium deoxycholate, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.5 mM DTT, 1x protease inhibitor cocktail). All subsequent steps were performed at 4°C. Chromatin was sheared by sonication in epitubes using 14 cycles of 10 s at ~13 W output and 30 s pause with a Sonic Dismembrator 60 (Fisher Scientific, Hampton, NH). Samples were recovered and spun at 21,000g for 5 min and the pellet was discarded. An aliquot of 2% of the sample volume was reserved as DNA input control and stored at −20°C. To prepare antibody-coupled beads for ChIP, protein A Dynabeads (20 μl per sample; Invitrogen cat. #10002D) were washed twice with 1 ml 0.5% BSA in TET (10 mM Tris-HCl, pH 8, 1 mM EDTA, 0.1% Tween 20), and resuspended in the same buffer. Anti-NFκB p65 antibody (C-20, Santa Cruz Biotechnology cat. # sc-372) was added to the beads and the sample was rotated for 1 h at room temperature. The supernatant was then removed and the Dynabeads were collected using a magnet, washed once with 0.1% BSA/TET, and resuspended in 10 µl RIPA buffer. For ChIP, 10 μl of prepared antibody-conjugated Dynabeads was added to each sample and rotated overnight at 4°C. The beads were then washed three times with 20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), three times with 10 mM Tris-HCl, pH 7.4, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, 0.7% sodium deoxycholate, and twice with TET/0.2% (as above except 0.2% Tween 20). Dynabeads were resuspended in 25 μl TT (10 mM Tris-HCl, pH 8, 0.05% Tween 20). Input samples were resuspended in 25 μl TT and libraries were generated in parallel with ChIP samples. Library NEBNext End Prep and Adaptor Ligation were performed using NEBNext Ultra II DNA Library Prep kit (New England BioLabs, cat. #E7645L) according to the manufacturer’s instructions with barcoded adapters (NextFlex, Bio Scientific. Cat #514123). Libraries were incubated with proteinase K at 55°C for 1 h and then at 65°C overnight to reverse formaldehyde crosslinks. Libraries were PCR amplified for 14 cycles with NEBNext High Fidelity 2X PCR MasterMix (New England BioLabs, cat. #NEBM0541). Libraries were size selected for 200–400 bp fragments by gel extraction (10% TBE gels; Life Technologies) and were single-end sequenced on an Illumina NextSeq 500 (San Diego, CA).
Samples were sequenced using the Illumina NextSeq 500 platform using 51 cycles (ChIP-seq). RNA-seq samples were single-end sequenced for 51 cycles on an Illumina NovaSeq 6000 or Hi-Seq 4000 (Illumina, San Diego, CA)

treatment_protocol: After monocyte differentiation, on day 7 of culture, moDCs were infected with ZIKV PRVABC59 or DENV UIS353 at MOI 1. Briefly, moDCs were incubated 2 hours with the virus, washed with PBS, and incubated in fresh medium for the for 24h at 37˚C, 5% CO2. For KLA treatment experiments, moDCs were infected with ZIKV PRVABC59 MOI 0.8 for 1h with rocking and incubated for 23h. After 23h the moDCs were treated with or without KLA 0.1 microgram/ml for 1 additional hour. 24h post-infection moDCs +/- KLA were analyzed.

value: monocyte-derived dendritic cell

tag: viral infection

value: ZIKV-infected

tag: viral strain

tag: chip antibody

value: NF-kB p65 antibody (C-20, Santa Cruz Biotechnology cat. # sc-372)

tag: time post infection viral infection


title: Lamin A/C knockout Hela cells, ATAC-seq, biol rep 2

description: Library name: ATAC_KO_2

value: Hela

value: Lamin A/C knockout


title: E15.5 cre-negative paired kidneys

description:
Library name: Sample 1
10x Genomics

value: Cre-negative


title: NEO_IFNAR_FLU_48h_N25_S21

description:
Library name: N25-IFNAR-48h_S21
5-days-old

value: Lung

value: Type II alveolar epithelial cell

value: FLU


title: NEO_C57_FLU_48h_N22_S17

description:
Library name: N22-C57-38h_S17
5-days-old


title: Lamin A/C knockout Hela cells, ATAC-seq, biol rep 1

description: Library name: ATAC_KO_1


title: NEO_IFNAR_FLU_48h_N67_S20

description:
Library name: N67-IFNAR-48h_S20
5-days-old


title: K562 cells, shMETTL14-1

description: Library name: sample 5


title: K562 cells, shMETTL3-2

description: Library name: sample 4


title: THP1, 2 hr nigericin, replicate 3

description:
Library name: Sample_6
NT_2H_Rep3

value: WT

value: 18 hr PMA differentiation, 2 hr nigericin


title: NEO_C57_FLU_48h_N62_S16

description:
Library name: N62-C57-48h_S16
5-days-old


title: E15.5 Six2creTGC paired kidneys_biol rep 1

description:
Library name: Sample 2
10x Genomics


title: Human9_p65ChIPseq_Mock_input

description: input

value: mock infected

value: input


title: THP1, 2 hr nigericin, replicate 1

description:
Library name: Sample_4
NT_2H_Rep1


title: NEO_C57_FLU_48h_N20_S19

description:
Library name: N20-C57-48h_S19
5-days-old


title: Human9_p65ChIPseq_ZIKVNeg

description: NF-kB p65 ChIP-seq

value: ZIKV-bystander


title: K562 cells, shCTR-1

description: Library name: sample 1

value: chronic myeloid leukemia cells in acute myeloid blast phase


title: THP1, 4 hr nigericin, replicate 2

description:
Library name: Sample_8
NT_4H_Rep2

value: monocyte

value: 18 hr PMA differentiation, 4 hr nigericin


title: THP1, 4 hr nigericin, replicate 1

description:
Library name: Sample_7
NT_4H_Rep1


title: Human9_p65ChIPseq_ZIKVPos_input

description: input

value: monocyte-derived dendritic cell


title: Human9_p65ChIPseq_ZIKVNeg_input

description: input


title: NEO_C57_FLU_48h_N64_S18

description:
Library name: N64-C57-48h_S18
5-days-old


title: NEO_C57_FLU_48h_N21_S15

description:
Library name: N21-C57-48h_S15
5-days-old


title: NEO_IFNAR_FLU_24h_N61_S13

description:
Library name: N61-IFNAR-24h_S13
4-days-old


title: Human4_RNAseq_DENVnegative_24h

description:
Ribosome-depleted RNA-seq
hDC4_DENVneg

value: DENV-bystander


title: Human4_RNAseq_DENVpositive_24h

description:
Ribosome-depleted RNA-seq
hDC4_DENVpos

value: DENV-infected


title: NEO_IFNAR_FLU_24h_N60_S12

description:
Library name: N60-IFNAR-24h_S12
4-days-old


title: Human9_p65ChIPseq_DENVNeg

description: NF-kB p65 ChIP-seq

value: NF-kB p65 antibody (C-20, Santa Cruz Biotechnology cat. # sc-372)


title: THP1, 2 hr nigericin, replicate 2

description:
Library name: Sample_5
NT_2H_Rep2


title: Human9_p65ChIPseq_DENVPos_input

description: input


title: Human9_p65ChIPseq_DENVNeg_input

description: input


title: Human9_p65ChIPseq_DENVPos

description: NF-kB p65 ChIP-seq


title: Human3_RNAseq_DENVpositive_24h

description:
Ribosome-depleted RNA-seq
hDC3_DENVPos


title: NEO_IFNAR_FLU_24h_N59_S14

description:
Library name: N59-IFNAR-24h_S14
4-days-old


title: Human9_p65ChIPseq_Mock

description: NF-kB p65 ChIP-seq


title: Human13_RNAseq_ZIKVpos_24h

description:
Ribosome-depleted RNA-seq
hDC13_ZIKVpos_RNAseq

value: ZIKV-infected


title: Human4_RNAseq_Mockinfected_24h

description:
Ribosome-depleted RNA-seq
hDC4_Mock


title: THP1, 0 hr nigericin, replicate 2

description:
Library name: Sample_2
NT_0H_Rep2

value: 18 hr PMA differentiation


title: THP1, 0 hr nigericin, replicate 3

description:
Library name: Sample_3
NT_0H_Rep3


title: Human3_RNAseq_Mockinfected_24h

description:
Ribosome-depleted RNA-seq
hDC3_Mock


title: Human13_RNAseq_ZIKVpos_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC13_ZIKVpos_KLA_RNAseq

value: ZIKV-infected + KLA

value: 24h & 1h post-KLA


title: NEO_IFNAR_FLU_24h_N80_S9

description:
Library name: N80-IFNAR-24h_S9
4-days-old

value: Lung

value: Type II alveolar epithelial cell

value: FLU


title: Human8_p65ChIPseq_ZIKVPos

description: NF-kB p65 ChIP-seq


title: Human8_p65ChIPseq_ZIKVNeg

description: NF-kB p65 ChIP-seq


title: Human8_p65ChIPseq_ZIKVPos_input

description: input


title: Human3_RNAseq_DENVnegative_24h

description:
Ribosome-depleted RNA-seq
hDC3_DENVNeg


title: Human1_RNAseq_Mockinfected_24h

description:
Ribosome-depleted RNA-seq
hDC1_Mock

value: mock infected


title: Human13_RNAseq_Mock_24h

description:
Ribosome-depleted RNA-seq
hDC13_Mock_RNAseq


title: Human8_p65ChIPseq_ZIKVNeg_input

description: input

value: input


title: NEO_IFNAR_FLU_24h_N79_S8

description:
Library name: N79-IFNAR-24h_S8
4-days-old -- QC Fail


title: Human12_RNAseq_ZIKVpos_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC12_ZIKVpos_KLA_RNAseq


title: NEO_IFNAR_FLU_24h_N81_S11

description:
Library name: N81-IFNAR-24h_S11
4-days-old -- QC Fail


title: Human1_RNAseq_DENVpositive_24h

description:
Ribosome-depleted RNA-seq
hDC1_DENVPos


title: Human13_RNAseq_Mock_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC13_Mock_KLA_RNAseq

value: mock infected + KLA


title: NEO_C57_FLU_24h_N58_S7

description:
Library name: N58-C57-24h_S7
4-days-old


title: THP1, 0 hr nigericin, replicate 1

description:
Library name: Sample_1
NT_0H_Rep1

value: WT


title: Human8_p65ChIPseq_Mock

description: NF-kB p65 ChIP-seq


title: Human8_p65ChIPseq_Mock_input

description: input


title: NEO_IFNAR_FLU_24h_N82_S10

description:
Library name: N82-IFNAR-24h_S10
4-days-old


title: NEO_C57_FLU_24h_N73_S6

description:
Library name: N73-C57-24h_S6
4-days-old


title: NEO_C57_FLU_24h_N76_S5

description:
Library name: N76-C57-24h_S5
4-days-old


title: Human12_RNAseq_Mock_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC12_Mock_KLA_RNAseq


title: Human12_RNAseq_ZIKVpos_24h

description:
Ribosome-depleted RNA-seq
hDC12_ZIKVpos_RNAseq


title: NEO_C57_FLU_24h_N72_S3

description:
Library name: N72-C57-24h_S3
4-days-old


title: Human8_p65ChIPseq_DENVNeg

description: NF-kB p65 ChIP-seq


title: Human11_RNAseq_ZIKVpos_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC11_ZIKVpos_KLA_RNAseq


title: Human8_p65ChIPseq_DENVNeg_input

description: input


title: Human1_RNAseq_DENVnegative_24h

description:
Ribosome-depleted RNA-seq
hDC1_DENVNeg


title: Human8_p65ChIPseq_DENVPos

description: NF-kB p65 ChIP-seq


title: NEO_C57_FLU_24h_N75_S2

description:
Library name: N75-C57-24h_S2
4-days-old


title: Human12_RNAseq_Mock_24h

description:
Ribosome-depleted RNA-seq
hDC12_Mock_RNAseq


title: Human11_RNAseq_Mock_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC11_Mock_KLA_RNAseq


title: Human11_RNAseq_ZIKVpos_24h

description:
Ribosome-depleted RNA-seq
hDC11_ZIKVpos_RNAseq


title: Human8_p65ChIPseq_DENVPos_input

description: input


title: Sham4

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd

institute: The University of Texas at Dallas

description:
Library name: Sham4
Parse Technology.

data_processing:
The sequencing output was processed using the parse pipeline
https://support.parsebiosciences.com/hc/en-us/articles/27066395947412-How-Do-I-Analyze-my-Parse-Biosciences-Data
Assembly: mRatBN7.2
Supplementary files format and content: matrix file and cell metadata

organism: Rattus norvegicus

source_name: Dorsal Root Ganglion

extract_protocol:
Nuclei were isolated following the Parse Evercode V2 kit protocol and published methods. T13-L1 bilateral DRGs were minced (<1mm) using Bonn scissors and mechanically dissociated with a Dounce homogenizer (15 strokes). The isolation buffer contained sucrose, KCl, MgCl₂, Tris (pH 8.0), DTT, protease inhibitor, Triton X-100, and RNAsin. The tissue was filtered through a 70 µm strainer, centrifuged, and the nuclei pellet was washed with a BSA/RNase inhibitor/DPBS buffer. Nuclei were counted using Trypan Blue and a hemocytometer, then fixed and processed following the Evercode Nuclei Fixation v2 kit. Library preparation followed the manufacturer’s instructions.
https://support.parsebiosciences.com/hc/en-us/categories/18950704717076-User-Guides

value: Dorsal Root Ganglion

value: Female

tag: sample group

value: Sham


title: Injured1

description:
Library name: Injured1
Parse Technology.

value: Injured


title: NEO_C57_FLU_24h_N57_S1

description:
Library name: N57-C57-24h_S1
4-days-old -- QC Fail


title: NEO_C57_FLU_24h_N74_S4

description:
Library name: N74-C57-24h_S4
4-days-old


title: RNA-Seq_humanTcell_PILRA-hlg_replicate3

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR version 2.7.10.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Primary T cell

growth_protocol: For T-cell isolation and expansion, PBMCs were cultured and stimulated with anti-CD3 and anti-CD28 antibodies in X-VIVO medium supplemented with IL-2 and IL-15.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform.

treatment_protocol: We performed transcriptomic analysis on T cells incubated with control hIg protein or PILRα-hIg protein.

value: Primary T cell

value: PILRA-hlg treated


title: Sham3

description:
Library name: Sham3
Parse Technology.


title: Injured4

description:
Library name: Injured4
Parse Technology.


title: Human11_RNAseq_Mock_24h

description:
Ribosome-depleted RNA-seq
hDC11_Mock_RNAseq

value: monocyte-derived dendritic cell


title: Injured3

description:
Library name: Injured3
Parse Technology.


title: Injured2

description:
Library name: Injured2
Parse Technology.


title: RNA-Seq_humanTcell_PILRA-hlg_replicate2


title: RNA-Seq_humanTcell_PILRA-hlg_replicate1


title: Human10_RNAseq_ZIKVpos_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC10_ZIKVpos_KLA_RNAseq


title: Sham2

description:
Library name: Sham2
Parse Technology.


title: hep3B, fiin2, rep 1

city: Changsha

first: Maoyu

last: Li

state: Hunan

address: 87 xiangya road

institute: Xiangya Hospital

description: Library name: Sample4

data_processing:
The DNBSEQ platform was used for sequencing, and the results produced 150 bp (PE150) paired-end reads. The raw sequencing data were preprocessed, and low-quality and short reads (≤20 bp) were removed. For quality control, the clean reads were aligned to the reference genome via HISAT. The DESeq2 package was used to perform differential gene expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text includes raw counts for each Sample
Supplementary files format and content: tab-delimited text includes FPKM values for each Sample

source_name: epithelial

growth_protocol: Hep3B cells were obtained from the Cell Bank of the Chinese Academy of Sciences and were cultured in Minimum Essential Medium (MEM) and Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS. All the cells were grown in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol:
The cells were harvested and stored in TRIzol reagent for RNA sequencing.
Library construction and sequencing were performed on a BGISEQ-500 by Beijing Genomic Institution

treatment_protocol: The cells were treated with DMSO (as a control) or 1 μM FIIN-2 for 6 hours.

value: epithelial

value: Hep 3B

value: Hepatocellular carcinoma cell

value: wt


title: hep3B, fiin2, rep 3

description: Library name: Sample6


title: hep3B, fiin2, rep 2

description: Library name: Sample5


title: Sham1

description:
Library name: Sham1
Parse Technology.


title: hep3B, dmso, rep 3

description: Library name: Sample3

value: dmso


title: RNA-Seq_humanTcell_hlg_replicate3

value: hIg protein treated


title: Control8

description:
Library name: Control 8
Parse Technology.

value: Male

value: Control


title: Human10_RNAseq_Mock_KLA_24h

description:
Ribosome-depleted RNA-seq
hDC10_Mock_KLA_RNAseq

value: mock infected + KLA

value: 24h & 1h post-KLA


title: hep3B, dmso, rep 2

description: Library name: Sample2


title: RNA-Seq_humanTcell_hlg_replicate2

value: WT


title: Human10_RNAseq_Mock_24h

description:
Ribosome-depleted RNA-seq
hDC10_Mock_RNAseq

value: mock infected


title: Control7

description:
Library name: Control 7
Parse Technology.

value: Dorsal Root Ganglion

value: Female


title: RNA-Seq_humanTcell_hlg_replicate1

value: Primary T cell


title: hep3B, dmso, rep 1

description: Library name: Sample1


title: HUVEC_RBP4_rep2

city: Guangzhou

first: Lei

last: Su

address: Zhongshan Second Road

institute: Sun Yat-sen University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

source_name: HUVEC

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

value: Umbilical Vein

value: treated with RBP4 for 24 h


title: DC LECs Replicate 3

type: RNA

city: Shang Hai

first: Xiaoyan

last: Han

address: 83 Fenyang Road, Shanghai 200031, People’s Republic of China.

institute: Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University

description: Biological replicate 3 of 3. diabetic cataract LECs

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10 Blocking Agent and 1 μL of 25 Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2 Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

scan_protocol: Scanned on an Agilent  scanner.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: Diabetic cataract LECs Replicate 3 -IP

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: Anterior lens capsule tissues were collected from DC patients who had diabetes for more than 10 years. Lens opacity grading were diagnosed according to the Lens Opacities Classification III (LOCS III) classification . In addition, anterior lens capsules collected from age-matched transparent crystals of cadaveric eyes were used as normal control (NC).

extract_protocol: 1-3 μg total RNA and m6A spike-in control mixture were added to 300 μL 1IP buffer (50mM Tris-HCl, pH7.4, 150mM NaCl, 0.1% NP40, 40U/μL RNase Inhibitor) containing 2 μg anti-m6A rabbit polyclonal antibody (Synaptic Systems). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. 20 L Dynabeads™ M-280 Sheep Anti-Rabbit IgG suspension per sample was blocked with freshly prepared 0.5% BSA at 4°C for 2 hours, washed three times with 300 μL 1IP buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m6A-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed three times with 500 μL 1IP buffer and twice with 500 μL Wash buffer (50 mM Tris-HCl, pH7.4, 50 mM NaCl, 0.1% NP40, 40 U/μL RNase Inhibitor). The enriched RNA was eluted with 200 μL Elution buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.05% SDS, 40U Proteinase K) at 50°C for 1 hour. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

tag: tissues

value: lens epithelial cells

source_name: Diabetic cataract LECs Replicate 3 -SUP


title: Control5

description:
Library name: Control 5
Parse Technology.

tag: tissue


title: DC LECs Replicate 1

description: Biological replicate 1 of 3. diabetic cataract LECs

source_name: Diabetic cataract LECs Replicate 1 -IP

source_name: Diabetic cataract LECs Replicate 1 -SUP


title: EMS03

city: China

first: Yuan

last: Zhu

address: Hankou Road 22, Nanjing 210008

institute: Nanjing University medical school

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human endometrium of endometriosis patients

extract_protocol:
1.1 Tissue Sample Fragmentation and Lysis 1.1.1 Grinding Machine 1.1.1.1 Transfer appropriate sample to corresponding grinding tube, 1.1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min 1.1.2 Liquid Nitrogen Grinding and Crushing 1.1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. 1.1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer. Stand flat for 5 min for the fully lysis of tissue cells. 1.2 Sample Purification 1.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 1.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 1.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 1.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 1.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 1.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 1.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 1.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
1.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 1.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 1.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 1.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 1.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 1.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 1.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 1.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 1.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).


title: EMS01

value: human endometrium of endometriosis patients


title: Human10_RNAseq_ZIKVpos_24h

description:
Ribosome-depleted RNA-seq
hDC10_ZIKVpos_RNAseq

tag: cell type

value: monocyte-derived dendritic cell

value: ZIKV-infected


title: NC LECs Replicate 3

description: Biological replicate 3 of 3. Normal Control LECs

source_name: Transparent LECs Replicate 3 -IP

source_name: Transparent LECs Replicate 3 -SUP


title: HUVEC_control_rep3

value: treated with control medium for 24 h


title: DC LECs Replicate 2

description: Biological replicate 2 of 3. diabetic cataract LECs

source_name: Diabetic cataract LECs Replicate 2 -IP

source_name: Diabetic cataract LECs Replicate 2 -SUP


title: HUVEC_RBP4_rep1


title: Control4

description:
Library name: Control 4
Parse Technology.

tag: genotype


title: CTL03

source_name: human endometrium of control women

value: human endometrium of control women


title: CTL02


title: HUVEC_control_rep2

tag: treatment


title: NC LECs Replicate 2

description: Biological replicate 2 of 3. Normal Control LECs

source_name: Transparent LECs Replicate 2 -IP

value: Male

source_name: Transparent LECs Replicate 2 -SUP


title: Control1

description:
Library name: Control 1
Parse Technology.

value: Control


title: HUVEC_control_rep1


title: CTL01


title: HUVEC_RBP4_rep3


title: Control6

description:
Library name: Control 6
Parse Technology.


title: ZGA

status: Public on Feb 21 2025

city: Nanchang

first: Zhengjie

last: XIANG

address: 1 Minde Road, Donghu District, Nanchang City, Jiangxi Province, China

institute: The Second Affiliated Hospital of Nanchang University

description: Library name: Sample12

data_processing:
This includes bioinformatics analysis steps, such as read trimming, alignment, differential expression analysis, and validation methods.
Assembly: The reference genome used for mapping, or details of any genome assembly if applicable.
Supplementary files format and content: The format of the output data files from sequencing, such as FASTQ, BAM, or FPKM values, and what each file contains .

source_name: Prostate tissue

extract_protocol:
The method for extracting RNA or miRNA from the tissue samples.
The specific procedures for constructing the RNA sequencing libraries, such as kits used and protocols for reverse transcription and library preparation.

value: Prostate tissue

value: Prostate cancer cells


title: XW

description: Library name: Sample11


title: WWC1

description: Library name: Sample9


title: WXH

description: Library name: Sample10


title: WJQ

description: Library name: Sample8


title: QCL

description: Library name: Sample7


title: EMS02


title: HQ

description: Library name: Sample4


title: PWJ

description: Library name: Sample6


title: LCY

description: Library name: Sample5


title: CYC

description: Library name: Sample2


title: Control3

description:
Library name: Control 3
Parse Technology.

source_name: Dorsal Root Ganglion


title: NC LECs Replicate 1

description: Biological replicate 1 of 3. Normal Control LECs

source_name: Transparent LECs Replicate 1 -IP

source_name: Transparent LECs Replicate 1 -SUP


title: HLZ

description: Library name: Sample3


title: OVCAR4 cells, chemo-resistant, H3K27ac ChIP, rep1

city: Chicago

first: Harun

last: Ozturk

state: Illinois

address: 303. E. Superior, Lurie cancer center

institute: Northwestern University

description: Library name: Sample3

data_processing:
Data were quality checked using FASTQC.
Reads were aligned to T2T genome assembly using Bowtie2 software (settings: --local --very-sensitive).
PCR duplicates and blacklisted regions were removed using Picard and Bedtools, respectively.
Peak calling was performed using MACS2 (settings: -f BAMPE --call-summits --keep-dup all).
BigWig files were generated using deeptools (settings: --binSize 1 --normalizeUsing CPM).
Assembly: T2T
Supplementary files format and content: BigWig files

source_name: ovarian

growth_protocol: OVCAR4 cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum and 1% Pen-Strep.The cells were maintained in a humidified incubator at 37 °C.

extract_protocol:
Phenol-choloroform extraction was used to isolate PRMT5 and H3K27ac bound regions.
Libraries were constructed using the the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® protocol.

value: ovarian

tag: cell line

value: high-grade sereous ovarian cancer cell line

value: WT

value: H3K27ac (ab4729, Abcam)


title: Control2

description:
Library name: Control 2
Parse Technology.

value: Dorsal Root Ganglion

value: Female


title: OVCAR4 cells, chemo-resistant, H3K27ac ChIP, rep2

description: Library name: Sample4


title: OVCAR4 cells, chemo-resistant, prmt5i treated, rep3

description:
Library name: Sample9
ov4_res_epz_rep3_S24

data_processing:
Data were quality checked using FASTQC.
Reads were aligned to T2T genome assembly using STAR (settings: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard)
The DESeq2 package was used with default settings to determine differentially expressed genes.
Assembly: T2T
Supplementary files format and content: The CSV file contains raw count numbers for each sample.

extract_protocol:
Quick-RNA Miniprep Kit (Zymo) were used for RNA isolation.
1 µg RNA was used for library preparation. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® protocol.

treatment_protocol: Chemoresistant OVCAR4 were treated with 5 µM EPZ015666 for 5 days.


title: CAG

description: Library name: Sample1


title: OVCAR4 cells, chemo-resistant, rep2

description:
Library name: Sample5
ov4_res_rep2_S20

value: DMSO


title: OVCAR4 cells, chemo-resistant, rep1

description:
Library name: Sample4
ov4_res_rep1_S19


title: OVCAR4 cells, chemo-naïve, rep3

description:
Library name: Sample3
ov4_wt_rep3_S18


title: OVCAR4 cells, chemo-naïve, rep2

description:
Library name: Sample2
ov4_wt_rep2_S17


title: OVCAR4 cells, chemo-naïve, rep1

description:
Library name: Sample1
ov4_wt_rep1_S16


title: IRF6-sg8-B

city: Stanford

first: Vanessa

last: Lopez-Pajares

state: CA

address: 269 Campus Dr., CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR aligner (version 2.5.4b) with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
TPM were obtained from the mapped by using RSEM (version 1.3.0) with the following settings (--paired-end --seed-length 21 --no-bam-output --calc-pme --calc-ci –alignments).
Differential analysis was performed using DESeq2 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include TPM values for each sample

source_name: RNA from organoid with IRF6 targeting sgRNA 8

growth_protocol: Epidermal organoids were maintained in keratinocyte growth media

extract_protocol:
Primary keratinocytes were isolated from foreskin and transduced with Cas9 and non-targeting or IRF6 targeting sgRNA;  0.5e6 cells were seeded onto devitalized human dermis to generate skin organoids grown in keratinocyte growth media and harvested at d7 post-seeding.
Organoids were harvested at d7 of differentiation. Total RNA was isolated using a Qiagen RNeasy Plus kit (Qiagen) using the manufacturer’s protocol. Samples were then QCed using bioanalyzer and subjected to paired end sequencing (Illumina platform).
The Lexogen Quant-seq 3’ mRNA-seq Library Prep Kit FWD for Illumina was used to generate PAS-seq libraries (cat# 015.96). Double-stranded cDNA was synthesized and i7 adapters for Illumina sequencing were added during PCR amplification. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 instrument at a depth of 30 million reads per sample.
3' mRNA-seq

treatment_protocol: Where noted, keratinocyte growth media was supplemented with 4.5g/L glucose (normal) or 0.5g/L glucose (low); for IRF6 KO, cells were first transduced with Cas9 then with targeting or non-targeting sgRNA.

value: IRF6 targeting sgRNA 8

tag: time

value: d7 of differentiation

value: primary keratinocyte


title: IRF6-sg8-A


title: IRF6-sg2-B

source_name: RNA from organoid with IRF6 targeting sgRNA 2

value: IRF6 targeting sgRNA 2


title: IRF6-sg1-B

source_name: RNA from organoid with IRF6 targeting sgRNA 1

value: IRF6 targeting sgRNA 1


title: IRF6-sg2-A


title: IRF6-NT1-B

source_name: RNA from organoid with non-targeting sgRNA

value: non-targeting sgRNA


title: IRF6-NT1-A


title: RNA from organoid grown in low glucose

source_name: primary keratinocyte

extract_protocol:
Primary keratinocytes were isolated from foreskin and 0.5e6 cells were seeded onto devitalized human dermis to generate skin organoids and grown in keratinocyte growth media supplemented with 0.5g/L glucose and harvested at d7 post-seeding.
Organoids were harvested at d7 of differentiation. Total RNA was isolated using a Qiagen RNeasy Plus kit (Qiagen) using the manufacturer’s protocol. Samples were then QCed using bioanalyzer and subjected to paired end sequencing (Illumina platform).
The Lexogen Quant-seq 3’ mRNA-seq Library Prep Kit FWD for Illumina was used to generate PAS-seq libraries (cat# 015.96). Double-stranded cDNA was synthesized and i7 adapters for Illumina sequencing were added during PCR amplification. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 instrument at a depth of 30 million reads per sample.
3' mRNA-seq


title: OVCAR4 cells, chemo-resistant, PRMT5 ChIP, rep2

description: Library name: Sample2

value: PRMT5 (07-405, Millipore)


title: OVCAR4 cells, chemo-resistant, PRMT5 ChIP, rep1

description: Library name: Sample1


title: G000304_2_HTO

city: Parkville

first: Joanna

last: Groom

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

description: Library name: Sample 2_HTO

data_processing:
Reads from each capture were processed using 10X Genomics Cell Ranger software (v7.0.0). Firstly, ‘cellranger mkfastq’ and bcl2fastq (v2.19.1) were used to convert and demultiplex the Illumina sequencer’s BCL files into FASTQ files for each of the gene expression (GEX), antibody derived tag (ADT), and hashtag oligo (HTO) libraries. Secondly, ‘cellranger multi’ was used with default settings to generate count matrices. The GEX data were mapped and quantified against the 10X Genomics pre-built mm10 (GENCODE vM23/Ensembl 98) reference groups and transcriptome (2020-A (July 7, 2020) version) and the feature barcoding (ADT and HTO) data were quantified against a ‘feature.csv’ file containing the barcode sequences provided by BioLegend. Finally, the DropletUtils R/Bioconductor package (v1.18.1) was then used to load the Cell Ranger output files into R (v4.2.1) and to identify non-empty droplets using ‘emptyDrops’ method with default settings (Lun et al., 2019). For demultiplexing, the ‘demuxmix’ method from the demuxmix (v1.0.0) R/Bioconductor package was applied to the HTO data, with the ‘naive’ model and default parameters, to multiplex non-empty droplets to their sample of origin. This was performed separately for each capture. A droplet was assigned to a sample if the best demuxmix assignment matched the corresponding HTO combination of a sample or was otherwise assigned as a ‘multiplet,’ ‘negative,’ or ‘uncertain’ sample.
Assembly: 10X Genomics pre-built mm10 (GENCODE vM23/Ensembl 98) reference groups and transcriptome (2020-A (July 7, 2020) version)
Supplementary files format and content: features.tsv.gz is a compressed text file storing the information about the genes (features) measured in the experiment, typically including their gene names and corresponding identifiers (e.g. Ensembl IDs).
Supplementary files format and content: matrix.mtx.gz is a compressed tab-separated value file containing the gene expression count matrix, where each row represents a gene and each column represents a single cell.
Supplementary files format and content: barcodes.tsv.gz is a compressed text file containing the unique cell barcodes associated with each column in the gene expression matrix,  identifying each individual cell analyzed in the single-cell RNA seq experiment

source_name: Lymph node

extract_protocol:
Lymph nodes were harvested and processed to form a single cell suspension. Samples were stained for surface antigen expression using indicated antibodies and TotalSeq HashTags (BioLegend) for 30 minutes at 4°C, followed by viability dye staining for 10 minutes at 4°C. Sample suspensions were sorted using BD FACSAria Fusion Flow Cytometer (BD Biosciences) to isolate antigen specific P14 CD8+ T cells.
The library prep was done according to the 10X Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index) CG000315. Sequencing was done on the NextSeq2000 on a P3 flowcell.

treatment_protocol: Day 8 acute LCMV Armstrong, day 8 chronic LCMV Docile, or days 0-1 IFNAR blocked acute LCMV Armstrong at either day 8 or 14

value: Lymph node

value: CD8+ T cells

value: Wild type


title: IRF6-sg1-A


title: RNA from organoid grown in normal glucose

extract_protocol:
Primary keratinocytes were isolated from foreskin and 0.5e6 cells were seeded onto devitalized human dermis to generate skin organoids and grown in keratinocyte growth media supplemented with 4.5g/L glucose and harvested at d7 post-seeding.
Organoids were harvested at d7 of differentiation. Total RNA was isolated using a Qiagen RNeasy Plus kit (Qiagen) using the manufacturer’s protocol. Samples were then QCed using bioanalyzer and subjected to paired end sequencing (Illumina platform).
The Lexogen Quant-seq 3’ mRNA-seq Library Prep Kit FWD for Illumina was used to generate PAS-seq libraries (cat# 015.96). Double-stranded cDNA was synthesized and i7 adapters for Illumina sequencing were added during PCR amplification. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 instrument at a depth of 30 million reads per sample.
3' mRNA-seq


title: OVCAR4 cells, chemo-resistant, prmt5i treated, rep2

description:
Library name: Sample8
ov4_res_epz_rep2_S23

value: ovarian


title: G000304_2_ADT

description: Library name: Sample 2_ADT

value: Day 8 acute LCMV Armstrong, day 8 chronic LCMV Docile, or days 0-1 IFNAR blocked acute LCMV Armstrong at either day 8 or 14


title: Low glucose replicate 1 Input

data_processing:
Sequencing reads were uniquely aligned to hg19 with Bowtie2 (Langmead and Salzberg, 2012)
Reads that were unmapped, duplicate, or had less than 10 mapping quality were filtered out. ChIP signals were normalized to 10 million mapped reads with peaks called using MACS2 (p-value<10-5, FDR<0.3, fold-enrichment>5) (Zhang et al., 2008) on the filtered bam files, controlling ChIP samples to input samples, using the default parameters plus -f BAMPE --bdg.
Peak regions across all samples were merged using bedtools (Quinlan and Hall, 2010). Reads in peak regions were determined using bedtools multicov, passing the bam files and the merged peak file as parameters. Further analysis was performed using the ChIPpeakAnno (Zhu et al., 2010) R package , DESeq2 (Love et al., 2014)  and the annotation dataset TxDb.Hsapiens.UCSC.hg19.knownGene.
Genome_build: hg19
Supplementary_files_format_and_content: called peaks for each treatment condition in bed file format

source_name: Human keratinocytes

extract_protocol:
ChIP samples were crosslinked with 1% formaldehyde, lysed in nuclear lysis buffer and sheared using a Diagenode Bioruptor at high power 30sec on/off for 4 hours to achieve ~250bp. Lysates were then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C. We used 8 ug of IRF6 antibody per 60ug chromatin and captured the chromatin-antibody complex with 80 uL Protein G beads (Thermo Fisher). ChIP DNA was then quantified by Qubit.
Libraries were constructed using the NEBNext Ultra II DNA library prep kit using 10ng of input material. ChIP libraries were size selected by PAGE purification (300-700 bp) for effective paired-end tag mapping and where therefore removed of all primer contamination. All libraries were sequenced on the Illumina HiSeq 4000 instrument to an average read depth of 300 million total reads.

treatment_protocol: Differentiated keratinocytes were grown in normal (4.5g/L) glucose media or low (0.5g/L) glucose media and harvested at d3 of differentiation.

value: keratinocyte

value: neonatal

value: Low glucose


title: G000304_1_HTO

description: Library name: Sample 1_HTO


title: OVCAR4 cells, chemo-resistant, prmt5i treated, rep1

description:
Library name: Sample7
ov4_res_epz_rep1_S22

value: high-grade sereous ovarian cancer cell line

value: WT


title: G000304_1_ADT

description: Library name: Sample 1_ADT


title: G000304_2_GEX

description: Library name: Sample 2_GEX


title: Low glucose replicate 2 Input


title: OVCAR4 cells, chemo-resistant, rep3

description:
Library name: Sample6
ov4_res_rep3_S21

value: DMSO


title: Low glucose replicate 2 IRF6 ChIP


title: Low glucose replicate 1 IRF6 ChIP


title: G000304_1_GEX

description: Library name: Sample 1_GEX


title: Norm glucose replicate 1 Input

value: Normal glucose


title: Wildtype TSCs 6-2 RNA rep 2

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

institute: UNC Chapel Hill

description:
Library name: cb_tsc_6_2_no_flavo_rep2_rna_b6
wiggle is pooled replicates and downsampled and merged
TSC_rna_+_if_reverse_stranded_f16.wig.gz
TSC_rna_-_if_reverse_stranded_F16.wig.gz

data_processing:
Sequencing reads (fastq files) were mapped both to the GENCODE vM25 mouse genome (“basic CHR” from https://www.gencodegenes.org/mouse/release_M25.html) [for B6] and to a version of the same genome modified to incorporate CAST single-nucleotide polymorphisms (SNPs) [for CAST]. Mapping was performed with STAR (v2.7.9a), using two-pass mapping and the option “--outFilterMultimapNmax 1” to consider only uniquely mapping reads.
Using a custom Perl script (intersect_reads_snps16.pl) and a file containing a list of CAST SNPs (sangercast07_30_20), aligned reads in the B6 and CAST SAM files were parsed to identify reads clearly originating from either the B6 or CAST allele (i.e. reads that overlap at least 1 B6 or CAST SNP).
For genome browser viewing, strand-specific mm10-aligned reads were separated using samtools: samtools view -Sq 30 (negative) -F 0x10 or (positive) -f 0x10
Assembly: mm10
Supplementary files format and content: Wiggle density files were created using github.com/CalabreseLab/seekr2.0_update_manuscript/blob/main/wiggles/

source_name: TSC 6-2

growth_protocol: B6/CAST F1-hybrid Rosa26-RMCE ESCs were grown on gelatin-coated plastic dishes in a humidified Thermo Fisher Forma Series II water-jacketed incubator at 37°C and under 5% CO2. Cells were grown in DMEM high glucose plus sodium pyruvate (Gibco 11995-065), 15% ESC-qualified fetal bovine serum (Gibco 26140-079), 0.1mM non-essential amino acids (Gibco 11140-050), 100U/mL penicillin-streptomycin (Gibco 15140-122), 2mM L-glutamine (Gibco 25030-081), 0.1mM β-mercaptoethanol, and 1:500 LIF conditioned media produced from Lif-1Cα (COS) cells (kind gift of N. Hathaway). TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco 11875093], 20% qualified FBS [Gibco 26140079], 0.1mM penicillin-streptomycin [Gibco 15140122], 1mM sodium pyruvate [Gibco 11360070], 2mM L-glutamine [Gibco 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich 63689]) supplemented with 25ng/mL FGF4 (Gibco PHG0154) and 1ug/mL Heparin (Sigma-Aldrich H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
RMCE ESCs or MEF feeder-free TSCs were washed twice with ice-cold PBS and harvested with 1 mL TRIzol (Thermo Fisher 15596026). Total RNA was prepared via standard TRIzol-chlorofom extraction, per manufacturer’s instructions, except for the addition of 4μL 5μg/μL linear acrylamide (Thermo Fisher AM9520) to promote precipitation in isopropanol. RNA pellets were fully resuspended in RNase-free water, RNA concentrations were measured via Qubit 2.0 fluorometer (RNA high sensitivity kit, Thermo Fisher Q32852), and integrity of RNA was confirmed by visualizing rRNA bands on an agarose gel. Working stocks of 100ng/μL total RNA were prepared, and all RNA samples were stored at -80°C.
Libraries for RNA sequencing were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche 08098140702) and KAPA Unique Dual-Indexed Adapters (Roche 08861919702) or TruSeq adapters, with each library’s input consisting of 9μL 100ng/μL total RNA (900 ng) mixed with 1μL of a 1:250 dilution of ERCC RNA spike-in controls (Thermo Fisher 4456740). RNA fragmentation was performed at 94°C for 6min. Libraries were pooled and sequenced on an Illumina NextSeq500 platform with a 75-cycle NextSeq 500/550 High Output Kit v2.5 (Illumina 20024906) or  on an Illumina NextSeq1000 platform with a 100-cycle NextSeq 1000/2000 P2 Reagents v3 kit (Illumina 20046811).

treatment_protocol: Prior to harvesting, RMCE cell lines (with rtTA) were treated with 0-1000ng/ml doxycycline (1000ng/ml if not otherwise specified) for 72 hours (or longer, 7 days).

value: TSC 6-2

value: wildtype


title: Wildtype TSCs 6-2 RNA rep 1

description:
Library name: cb_tsc_6_2_no_flavo_rep1_rna_b6
wiggle is pooled replicates and downsampled and merged
TSC_rna_+_if_reverse_stranded_f16.wig.gz
TSC_rna_-_if_reverse_stranded_F16.wig.gz


title: Norm glucose replicate 1 IRF6 ChIP


title: Normal glucose replicate 2 IRF6 ChIP


title: 3-day 1000ng/mL dox-treated X872-Airn-RMCE clone 2 Suz12

description: Library name: XA2_Suz12

data_processing:
ChIP-Seq reads were aligned using bowtie2 with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools 28, and allele-specific read retention (i.e., reads that overlap at least one B6 or CAST SNP) was performed as in 30,31 using a custom Perl script (intersect_reads_snps16.pl).
Assembly: mm10
Supplementary files format and content: WIG files were created using a custom perl script. Total, non-allelic read counts are divided by total aligned reads to mm10 of the dataset in million (i.e. RPM).

source_name: RMCE Embryonic Stem Cells

growth_protocol: B6/CAST F1-hybrid Rosa26-RMCE ESCs from 12 were grown on gelatin-coated plastic dishes in a humidified Thermo Fisher Forma Series II water-jacketed incubator at 37°C and under 5% CO2. Cells were grown in DMEM high glucose plus sodium pyruvate (Gibco 11995-065), 15% ESC-qualified fetal bovine serum (Gibco 26140-079), 0.1mM non-essential amino acids (Gibco 11140-050), 100U/mL penicillin-streptomycin (Gibco 15140-122), 2mM L-glutamine (Gibco 25030-081), 0.1mM β-mercaptoethanol (Sigma-Aldrich 63689), and 1:500 LIF conditioned media produced from Lif-1Cα (COS) cells (kind gift of N. Hathaway).

extract_protocol:
ChIP beads were resuspended in Elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and placed on a 65°C heat block for 17 minutes with frequent vortexing. ChIP DNA was then reverse crosslinked in 0.5% SDS and 100mM NaCl overnight at 65°C, followed by a 1-h RNaseA (3L; Thermo Scientific EN0531) treatment at 37°C and a 2.5-h Proteinase K (10L; Invitrogen 25530015) treatment at 56°C. DNA was then extracted with 1 volume of phenol:chloroform:isoamyl alcohol (Sigma-Aldrich P3803) and precipitated with 2 volumes 100% ethanol, 1/10 volume 3M sodium-acetate pH 5.4, and 1/1000 volume linear acrylamide (Invitrogen AM9520) overnight at -20°C. Precipitated DNA was then extracted with a 30-minute max speed spin at 4°C, washed once with ice-cold 80% ethanol, and resuspended in TE.
ChIP-Seq libraries were prepared with NEBNext End Repair Module (NEB, cat #: E6050S), A-tailing by Klenow Fragment (3’--5’ exo-; NEB, cat #: M0212S), and TruSeq 6-bp index adaptor ligation by Quick ligase (NEB, cat #: M2200S), and NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat #: M0541S). All DNA clean-up steps were performed with AMPure XP beads (Beckman Coulter, cat #: A63880). Single-end, 100-bp sequencing was performed using an Illumina NextSeq 500/550 High Output v2.5 kit (Illumina, cat #: 20024906) on a NextSeq 500 System on an Illumina NextSeq1000 platform with a 100-cycle NextSeq 1000/2000 P2 Reagents v3 kit (Illumina 20046811)

treatment_protocol: Prior to crosslinking, RMCE cell lines (with rtTA) were treated with 0-1000ng/mL doxycycline (1000ng/mL if not otherwise specified) for 72 hours (or longer, 7 days). Adhered cells were crosslinked with 0.6% formaldehyde (Fisher Scientific BP531-500) in DMEM media with 5% FBS for 10min at room temperature, then quenched with 125mM glycine for 5min at room temperature. Crosslinked cells were then washed twice with ice-cold PBS and scraped with ice-cold PBS with 0.05% Tween (Fisher Scientific EW-88065-31) and PIC (Sigma Aldrich P8340). The cells were then spun at 1,200 x g at 4°C to remove PBS, followed by resuspension in ice-cold PBS with PIC and divided into 10-million cell aliquots.

value: RMCE Embryonic Stem Cells

value: 3 days with 1000ng/mL doxycycline

value: Suz12 (D39F6) (Cell Signaling, cat #:3737)


title: 3-day 1000ng/mL dox-treated Xist-RMCE clone 1 Suz12

description: Library name: X1_1000ng_Suz12

value: Xist-RMCEs


title: d3 IRF6 sg8 ATAC

description: d3 IRF6 sg8 ATAC

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
ATAC-seq read alignment, quality filtering, duplicate removal, transposase shifting, peak calling, and signal generation were all performed through the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapter sequences were trimmed, sequences were mapped to the hg19 reference genome using Bowtie2 (-X2000), poor quality reads were removed, PCR duplicates were removed (Picard Tools MarkDuplicates), chrM reads were removed, and read ends were shifted +4 on the positive strand or -5 on the negative strand to produce a set of filtered high-quality reads. These reads were put through MACS2 to get peak calls and signal files. Finally, IDR analysis was run on the two replicate peak files to produce an IDR peak file that is the reproducible set of peaks across both replicates. The full pipeline can be found on the ENCODE portal.
Differential analysis was performed using DESeq2 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: peak files of significantly called peak

source_name: keratinocyte

extract_protocol:
keratinocytes transduced with Cas9 then non-targeting or IRF6 targeting sgRNA, differentiated for 3d
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

treatment_protocol: Keratinocytes were grown in 50/50 growth media to maintain progenitor state or in differentiation media supplemented with normal (4.5g/L) glucose or low (0.5g/L) glucose. For IRF6 KO, keratinocytes were first transduced with Cas9 and subsequently with non-targeting or IRF6 targeting sgRNA.

value: IRF6 sg8

value: day 3


title: d3 IRF6 sg2 ATAC

description: d3 IRF6 sg2 ATAC

value: IRF6 sg2