title: Blood T cells DEN ALIOS Rep 2

description: JMR18190809_S06_R1_001_JM6_RCN21__2b_B_T


title: 20_5346-T42

status: Public on Mar 22 2023

type: genomic

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: DNA methylation was quantified using Illumina Infinium Human Methylation EPIC Bead Chip array (Illumina Inc., San Diego, CA) according to the manufacturer’s instructions at University of Minnesota Genomic Center. Briefly, 500ng of DNA from each sample was treated with sodium bisulfite, using the EZ-96 DNA Methylation-Gold kit (Zymo Research, CA, USA). The bisulfite-converted amplified DNA products were denatured into single strands and hybridized to the Illumina Infinium Human Methylation EPIC Bead Chip array (Illumina Inc., San Diego, CA). The hybridized BeadChips were stained, washed, and scanned for the intensities of the unmethylated and methylated bead types using Illumina’s iScan System.

data_processing:
The DNA methylation beta values were obtained and normalized from the raw IDAT files by using the ChAMP package in R.
normalized.csv: Normalized Beta values

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: EDTA blood

label_protocol: Standard Illumina protocol.

growth_protocol: All biosamples were collected in accordance with the guidelines of Institutional Review Boards of Icahn School of Medicine and the Naval Medical Research Center (protocol number NMRC.2020.0006) in compliance with all applicable U.S. federal regulations governing the protection of human subjects.

extract_protocol: Genomic DNA was extracted from cryopreserved PBMC or blood collected in EDTA tubes using Genfind V3 (Beckman Coulter) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter). All DNA samples were quantified using both absorbance (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA) and fluorescence-based methods (Qubit; Thermo Fisher Scientific, Waltham, MA) using standard dyes selective for double-stranded DNA, minimizing the effects of contaminants that affect the quantitation.

treatment_protocol: Blood collected in EDTA tubes and PBMCs were used for DNA extraction. All samples were frozen at -80 °C after collection prior to processing for methylation analysis.

tag: meth-plate

tag: enrollment batch

value: Longitudinal Study

tag: biocollection id

tag: participant id

tag: sample collection time point (days since t0)

tag: enrollment date t0

tag: gender

value: M

tag: age

tag: ethnicity

value: Non-Hispanic

tag: group

value: Mid

tag: tissue

value: blood


title: 12_r2_5

type: SRA

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description:
sample name: 1236
Embryonic blastomere transcriptome

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: WS230
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: embryo

extract_protocol:
Egg shells were removed from a C. elegans embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.

tag: developmental stage

tag: cell type

value: embryonic cells


title: 20_5342-T28

scan_protocol: The hybridized BeadChips were stained, washed, and scanned for the intensities of the unmethylated and methylated bead types using Illumina’s iScan System.

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: Blood T cells DEN ALIOS Rep 1

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.95 using HISAT2 version 2.1.0
Raw counts per gene were determined using Htseq-count version 0.11.2 with the following options: -s reverse --mode=intersection-nonempty --type=exon --idattr=gene_id
Assembly: GRCm38.95
Supplementary files format and content: Matrix of raw counts

molecule: total RNA

organism: Mus musculus

source_name: T cells

extract_protocol:
Ly6G+ neutrophils and CD3+ T cells were FACS-sorted from the peripheral blood and tumours of DEN/ALIOS mice. Purity of isolated populations was analysed by flow cytometry at ≥ 97%. RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA quality and quantity was checked on an Agilent Bioanalyser 2100 using RNA Pico 6000 chip.  Whole tumor and healthy tissue was snap frozen and stored at -80C. Tissue was homogenized using the Precellys Evolution homogenizer and bulk RNA was isolated using the Rneasy Kit (Qiagen) according to the manufacturer’s instructions, including the optional Dnase I step. RNA quality and quantity was analysed on a Nanodrop 2000 (Thermo Fisher Scientific) and an Agilent 2200 TapeStation (D1000 screentape). Only samples with a RIN value >7 were used for library preparation. Libraries were prepared using the TruSeq stranded mRNA Kit. Library quality and quantity were assessed using 2200 TapeStation (Agilent) and Qubit (ThermoFisher Scientific).
Libraries for cluster generation and DNA sequencing were prepared following the TaKaRa SMARTer Stranded Total RNA-Seq Kit- Pico Input Mammalian v2 protocol. Quality and quantity of the DNA libraries was assessed on an Agilent 2200 Tapestation (D1000 screentape) and Qubit (Thermo Fisher Scientific) respectively.
The libraries were run on the Illumina NextSeq 500 using the High Output v2.5, 75 cycles kit (2 x 36cycles, paired-end reads).

treatment_protocol: mice treated as described in each sample characteristics: treatment field

tag: source tissue

value: Blood

tag: Sex

value: Male

tag: genotype

value: WT (C57BL/6 from in-house colony)

value: T cells

tag: treatment

value: DEN ALIOS


title: 20_5326-T28

tag: meth-plate

value: F

value: Hispanic


title: 20_5316-T56

tag: enrollment batch

value: EarlyPost


title: 20_5340-T14

tag: biocollection id


title: 12_r1_5

description:
sample name: 1235
Embryonic blastomere transcriptome


title: 12_r11_4

description:
sample name: 1254
Embryonic blastomere transcriptome


title: 20_5316-T35

tag: participant id


title: 20_5316-T00

tag: sample collection time point (days since t0)

value: Control


title: 12_r10_4

description:
sample name: 1253
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS Rep 6

description: JMR18190810_S05_R1_001_JM13_RCN24_2d_B_N

source_name: Neutrophils

value: Neutrophils


title: 20_5316-T77

value: Longitudinal Study

tag: enrollment date t0

value: LatePost


title: Blood Neutrophils DEN ALIOS Rep 5


title: 12_r9_4

description:
sample name: 1252
Embryonic blastomere transcriptome


title: 20_5346-T35

tag: gender

value: M

value: Non-Hispanic

value: Mid


title: Blood Neutrophils DEN ALIOS Rep 4

description: JMR18190809_S11_R1_001_JM23_RCN25_3h_B_N

value: DEN ALIOS/Vehicle


title: 12_r8_4

description:
sample name: 1251
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_5303-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: age

value: SARS-CoV-2 Sero+

value: blood


title: 20_5288-T35

tag: ethnicity

value: First


title: 20_5293-T00

value: Arrival at quarantine vs Later (all uninfected)

tag: group

value: Arrival at quarantine


title: 12_r7_4

description:
sample name: 1250
Embryonic blastomere transcriptome


title: 20_5281-T56

value: F

tag: tissue


title: 20_5285-T28

value: SARS-CoV-2 Sero-


title: Blood Neutrophils DEN ALIOS Rep 2

description: JMR18190809_S05_R1_001_JM5_RCN21__2b_B_N

value: Blood

value: Male

value: WT (C57BL/6 from in-house colony)

value: DEN ALIOS


title: 12_r6_4

description:
sample name: 1249
Embryonic blastomere transcriptome

tag: developmental stage


title: Blood Neutrophils DEN ALIOS Rep 1

tag: cell type

value: Neutrophils


title: 20_5275-T91

value: Longitudinal Study

value: M

value: Hispanic

value: LatePost


title: 20_5281-T42

value: Non-Hispanic


title: Blood Neutrophils DEN ALIOS Rep 7

description: JMR18190810_S09_R1_001_JM17_RCJ22_3b_B_N

tag: source tissue


title: Blood T cells CXCR2i Rep 6

description: JMR18200318_S22_R1_001_JM22_RCA46_1d_B_T

tag: Sex

value: T cells


title: 20_5274-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+

value: blood


title: 20_5268-T00

value: Control


title: 20_5288-T49

value: EarlyPost


title: 20_5288-T39

value: Mid


title: Blood T cells CXCR2i Rep 5

description: JMR18200318_S18_R1_001_JM18_RCA46_1c_B_T

value: Blood

tag: genotype


title: Blood Neutrophils DEN ALIOS Rep 3

description: JMR18190809_S09_R1_001_JM21_RCN25_3e_B_N

value: Male

tag: treatment

value: DEN ALIOS/Vehicle


title: 20_5268-T46

tag: meth-plate

value: First


title: 20_5275-T77

tag: enrollment batch


title: 12_r5_4

description:
sample name: 1248
Embryonic blastomere transcriptome

value: embryonic cells


title: 12_r2_4

description:
sample name: 1245
Embryonic blastomere transcriptome


title: Blood T cells CXCR2i Rep 3

description: JMR18200318_S10_R1_001_JM10_RCA46_1a_B_T

value: WT (C57BL/6 from in-house colony)


title: Blood T cells CXCR2i Rep 4

description: JMR18200318_S14_R1_001_JM14_RCA46_1b_B_T


title: 20_5225-T39

value: Longitudinal Study

tag: biocollection id

value: M


title: 20_5225-T42

tag: participant id


title: 20_5225-T00

tag: sample collection time point (days since t0)


title: Blood T cells CXCR2i Rep 2


title: 12_r10_3

description:
sample name: 207
Embryonic blastomere transcriptome


title: 20_5189-T63

tag: enrollment date t0


title: 12_r4_4

description:
sample name: 1247
Embryonic blastomere transcriptome


title: 12_r9_3

description:
sample name: 206
Embryonic blastomere transcriptome


title: 20_5190-T28

tag: gender

value: Hispanic

value: SARS-CoV-2 Sero-


title: 20_5189-T35

tag: age


title: 12_2r3_4

description:
sample name: 1246
Embryonic blastomere transcriptome


title: Blood T cells CXCR2i Rep 1

value: T cells


title: 20_5246-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: ethnicity


title: 20_5189-T00

tag: group


title: E14 mES, Rif1-KO-3

city: Beijing

first: Wang

last: Li

address: 167 Beilishi Rd

department: State Key Laboratory of Cardiovascular Disease

country: China

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences

data_processing:
The reads were aligned to genome (mm9) with STAR (v020201) and annotated to Ref Seq genes using feature Counts (v1.6.2)
Genes with reads less than 50 in all samples were removed. The DEG analysis was conducted by edge R (v3.28.1) with cutoff of p-value 0.05 and FC > 1.5
Assembly: mm9
Supplementary files format and content: tab-delimited text. Gene names and their raw counts in each sample

growth_protocol: mESCs were cultured on 0.1% gelatin coated plates in the 2i medium and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cells using the GeneJet RNA purification kit (Thermo Scientific). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  the KAPA mRNA HyperPrep Kits (KK8580, KapaBiosystems).

treatment_protocol: the cells were treated with 4-OHT (0.1 μM) for 2 days and cultured for another day without treatment.

tag: tissue

tag: cell line

value: mouse embryonic stem cells

value: Day 0


title: 12_r8_3

description:
sample name: 205
Embryonic blastomere transcriptome

tag: developmental stage

tag: cell type


title: 20_5228-T28

value: F

value: Non-Hispanic

value: SARS-CoV-2 Sero+

value: blood


title: 12_r7_3

description:
sample name: 204
Embryonic blastomere transcriptome


title: 20_5275-T49

value: Mid


title: 20_5162-T91

value: LatePost


title: E14 mES, Rif1-KO-2


title: 20_5139-T00

value: Arrival at quarantine vs Later (all uninfected)

value: Arrival at quarantine


title: 20_5162-T49


title: 20_5162-T56

value: EarlyPost


title: 20_5134-T28


title: 12_r1_4

description:
sample name: 1244
Embryonic blastomere transcriptome

value: embryonic cells


title: E14 mES, Rif1-KO-1


title: E14 mES, Control-3

value: WT


title: 20_5108-T70

value: Longitudinal Study

value: M


title: 20_5108-T63


title: E14 mES, Control-2


title: 12_r5_3

description:
sample name: 202
Embryonic blastomere transcriptome


title: 20_5089-T91


title: E14 mES, Control-1


title: 12_r6_3

description:
sample name: 203
Embryonic blastomere transcriptome


title: 20_5108-T74


title: 20_5108-T00

value: Control


title: 12_r2_3

description:
sample name: 199
Embryonic blastomere transcriptome


title: Mouse B-PolyTrauma 9, small RNA

city: Baltimore

first: Brittney

last: Williams

state: Maryland

address: 22 South Greene St, S11C00

department: Anesthesiology

institute: University of Maryland Baltimore

data_processing:
Raw reads and counts were determined for small RNA
Normalization was performed using cel-mir-39-spike in for human and mouse samples and counts were averaged across all human and mouse samples, respectively
A normilization factor for cel-mir-39-spike was calculated within each individual sample and then applied to the raw read count to generate the processed files
Supplementary files format and content: .txt files for small RNA species for each sample

source_name: Plasma

extract_protocol:
RNA was isolated using Trizol LS from 100 µl of cell-free plasma and was analyzed by an Agilent 2100 Bioanalyzer with the Small RNA kit
Libraries were sequenced on an Illumina HiSeq2500 using six microliters of each RNA solution and used for small RNA sequencing library preparation.
small RNAseq, Library creation using  Norgen Biotek Small RNA Library Prep Kit for miRNA and exceRpt small RNA-seq Pipeline (v4.6.2)

value: Plasma

value: Trauma


title: Mouse B-PolyTrauma 8, small RNA


title: 20_5054-T84


title: 20_5054-T17


title: 12_r1_3

description:
sample name: 198
Embryonic blastomere transcriptome


title: 12_r4_3

description:
sample name: 201
Embryonic blastomere transcriptome


title: 20_5039-T84


title: 12_r3_3

description:
sample name: 200
Embryonic blastomere transcriptome


title: 20_5048-T00


title: 20_5089-T42


title: Mouse B-PolyTrauma 7, small RNA


title: 12_2r8_2

description:
sample name: 174
Embryonic blastomere transcriptome


title: 20_5068-T56


title: 20_5054-T14


title: 20_5039-T42


title: 12_r7_2

description:
sample name: 173
Embryonic blastomere transcriptome


title: 20_5039-T00


title: Mouse B-PolyTrauma 4, small RNA


title: 12_r6_2

description:
sample name: 172
Embryonic blastomere transcriptome


title: 20_5002-T91


title: Mouse B-PolyTrauma 5, small RNA


title: 12_r5_2

description:
sample name: 171
Embryonic blastomere transcriptome


title: 20_5063-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: Hispanic


title: 20_5002-T56

value: Non-Hispanic


title: 20_5039-T56


title: 20_5062-T28

value: SARS-CoV-2 Sero+


title: 12_2r9_2

description:
sample name: 175
Embryonic blastomere transcriptome


title: Mouse B-PolyTrauma 6, small RNA


title: CPT0078510004_snATAC

city: St. Louis

first: Yige

last: Wu

state: MO

address: 4520 McPherson Ave

department: Department of Medicine

institute: Washington University in St. Louis

description: 10x Genomics

library_source: genomic

data_processing:
After single-nuclei prep and sequencing, Cell Ranger (v3.1.0) from 10X Genomics (with Count functionality) was used for aligning reads to the human genome reference (GRCh38) with the addition of pre-mRNA reference (v3.0.0). The reference file was downloaded from the 10X Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). The pre-mRNA reference was added using the following code: awk 'BEGIN{FS="\t"; OFS="\t"} $3 == "transcript"{ $3="exon"; print}' refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf > GRCh38-3.0.0.premrna.gtf; cellranger mkref --genome=GRCh38-3.0.0.premrna --fasta=refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa --genes=GRCh38-3.0.0.premrna.gtf --nthreads 50. The parameters used with Count functionality include --chemistry=threeprime --expect-cells=6000 --jobmode=local --localcores=20 --localmem=350. The resulting gene-by-cell UMI count matrix was used by the R package Seurat (v.3.1.0)122 for all subsequent processing.  Quality filters were applied to the data to remove barcodes that fell into any of the following categories: too few genes expressed (possible debris), too many associated UMIs (possibly more than one cell), and too high mitochondrial gene expression (possible dead cell). The cut-offs for these filters were based on recommendations by Seurat package documentation and manually adjusted to keep the number of cells after filtering under 6500 (detailed filtering parameters see Supplementary Data 2). Finally, doublets were filtered out using Scrublet (v.0.2.1). Scrublet was run on each sample separately with the following parameter settings: expected_doublet_rate=0.06, min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30. The doublet score threshold was adjusted manually, which can separate the two peaks of a bimodal simulated doublet score histogram.
The Cell Ranger ATAC tool (v.1.2.0, 10X Genomics) was used to process the raw snATAC-seq data (FASTQ). We utilized the cellranger-atac count pipeline to filter and map snATAC-reads and to identify transposase cut sites. The GRCh38 human reference was used for the reads mapping. Next, MACS2126 (v2.2.7.1) was used to perform peak calling. All peaks were resized to 501 bp centered at the peak summit defined by MACS2. After this, we combined all peaks and removed the ones overlapping with the peaks with greater signal, to get the set of non-overlapping peaks, as described in Schep et al127. The resulting set of sample peaks was used to calculate the peak-count matrix using FeatureMatrix function from the R package Signac (v.1.2.0; https://github.com/timoast/signac), which was also used for downstream analysis. QC-filtering of the snATAC-seq data was performed using functions from the Signac package. Filters that were applied for the cell calling include: 1,000 < number of fragments in peaks < 20,000, percentage of reads in peaks > 15, ENCODE blacklist regions percentage < 0.05 (https://www.encodeproject.org/annotations/ENCSR636HFF/), nucleosome banding pattern score < 10, and enrichment-score for Tn5-integration events at transcriptional start sites > 2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Kidney

extract_protocol:
15-25 mg of pulverized tissue was placed in a 5mL Eppendorf tube on ice. Using a wide-bore pipette tip (Rainin), a lysis buffer prepared from the Nuclei Isolation protocol (10X Genomics) and SuperRNase inhibitor (Invitrogen) was added to the tube. The tissue solution was gently pipetted until the lysis liquid turned a slightly cloudy color. (The number of pipetting iterations depended on the specific tissue.) The tissue homogenate was then filtered through a 40-micron strainer (pluriSelect) and washed with a BSA wash buffer (2% BSA + 1x PBS + RNase inhibitor). The filtrate was collected, centrifuged at 500 x g for 6 minutes at 4°C, and resuspended with a BSA wash buffer.  100 uL of cell lysis solution was set aside for unstained reference, while the rest was stained with DRAQ5 or 7AAD for RNA or ATAC sequencing, respectively. Namely, snRNA-seq nuclei were stained with 1 uL of DRAQ5 per 300 uL of the sample, and snATAC-seq nuclei were stained with 1 uL of 7AAD per 500 uL of the sample. Sorting gates were based on size, granularity, and dye staining signal.   Nuclei and barcoded beads were isolated in oil droplets via the 10x Genomics Chromium instrument. Single nuclei suspensions were counted and adjusted to a range of 500 to 1800 nuclei/µL using a hemocytometer. Reverse transcription was subsequently performed to incorporate cell and transcript-specific barcodes.
All snRNA-seq samples were run using the Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1 (10x Genomics). For snATAC-seq, Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1.1 prep (10x Genomics) were used for all samples. Barcoded libraries were then pooled and sequenced on the Illumina NovaSeq 6000 system with specific flow cell types (snRNA-seq: S4; snATAC-seq: S1).

value: tissue

value: Kidney


title: Mouse B-PolyTrauma 1, small RNA


title: Mouse B-PolyTrauma 2, small RNA


title: 12_r3_2

description:
sample name: 169
Embryonic blastomere transcriptome


title: CPT0012550012_snATAC

description: 10x Genomics


title: CPT0012280004_snATAC

description: 10x Genomics


title: 12_r2_2

description:
sample name: 168
Embryonic blastomere transcriptome


title: Mouse A-Sham 5, small RNA


title: 12_r1_2

description:
sample name: 167
Embryonic blastomere transcriptome


title: CPT0063630004_snATAC

description: 10x Genomics


title: CPT0086350004_snATAC

description: 10x Genomics


title: CPT0079410004_snATAC

description: 10x Genomics


title: CPT0086820004_snATAC

description: 10x Genomics


title: Mouse B-PolyTrauma 3, small RNA


title: Mouse A-Sham 4, small RNA


title: CPT0023690004_snATAC

description: 10x Genomics


title: Mouse A-Sham 6, small RNA


title: CPT0010160004_snATAC

description: 10x Genomics


title: CPT0019130004_snATAC

description: 10x Genomics


title: CPT0010100001_snATAC

description: 10x Genomics


title: CPT0001180011_snATAC

description: 10x Genomics


title: Mouse A-Sham 3, small RNA


title: 12_r10_1

description:
sample name: 165
Embryonic blastomere transcriptome


title: 12_r11_1

description:
sample name: 166
Embryonic blastomere transcriptome


title: CPT0000880001_snATAC

description: 10x Genomics


title: CPT0000890002_snATAC

description: 10x Genomics


title: 12_r4_2

description:
sample name: 170
Embryonic blastomere transcriptome


title: 12_r9_1

description:
sample name: 164
Embryonic blastomere transcriptome


title: CPT0001260013_snATAC

description: 10x Genomics


title: JY_09_GEM_TF_3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
The annotation file was parsed to exclude mitochondria and ribosomal protein genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 21,965 gene locations.
Assembly: mm10

source_name: IM GEM TX, replicate 3

growth_protocol: Ex vivo isolated lung intertiatial macrophages (IMs)

extract_protocol:
RNA was extracted using a QIAGEN RNAeasy Kit.
Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant (NuGEN Cat# 0520-24) and PolyA selection.

treatment_protocol: Tumro-free B6 WT mice were treated with Gemcitabine (GEM, 60 mg/kg, IP) 4 times in two weeks. Lung intertiatial macrophages were purified two days later after last treatment.

value: lung

value: Interstitial macrophage

value: Gemcitabine (GEM)


title: CPT0001500003_snATAC

description: 10x Genomics


title: CPT0001270002_snATAC

description: 10x Genomics


title: Mouse A-Sham 1, small RNA


title: 12_r8_1

description:
sample name: 163
Embryonic blastomere transcriptome


title: Mouse A-Sham 2, small RNA


title: CPT0001220012_snATAC

description: 10x Genomics


title: CPT0001540013_snATAC

description: 10x Genomics


title: JY_07_GEM_TF_1

source_name: IM GEM TX, replicate 1


title: 12_r5_1

description:
sample name: 160
Embryonic blastomere transcriptome


title: CPT0075170013_snATAC

description: 10x Genomics


title: 12_r7_1

description:
sample name: 162
Embryonic blastomere transcriptome


title: CPT0025880013_snATAC

description: 10x Genomics


title: JY_03_PBS_TF_3

source_name: IM Control PBS, replicate 3

value: PBS


title: CPT0075720013_snATAC

description: 10x Genomics


title: 12_r4_1

description:
sample name: 159
Embryonic blastomere transcriptome

value: embryonic cells


title: CPT0014450005_snATAC

description: 10x Genomics


title: CPT0075130004_snATAC

description: 10x Genomics


title: 12_r3_1

description:
sample name: 158
Embryonic blastomere transcriptome


title: CPT0065690004_snATAC

description: 10x Genomics


title: JY_02_PBS_TF_2

source_name: IM Control PBS, replicate 2


title: CPT0014470002_snATAC

description: 10x Genomics


title: JY_01_PBS_TF_1

source_name: IM Control PBS, replicate 1


title: CPT0000870003_snATAC

description: 10x Genomics


title: 12_r2_1

description:
sample name: 157
Embryonic blastomere transcriptome


title: CPT0075140002_snRNA

description: 10x Genomics

molecule: nuclear RNA


title: mESC, Sox15 KO, rep3

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
Data were processed using bcbio-nextgen v1.1.3.
Reads were quantified using Salmon v0.12.0 mapped against mm10 of the mouse reference.
Counts were imported into R using tximport (Soneson, Love, and Robinson 2016) and DESeq2 (Love, Huber, and Anders 2014).
Assembly: mm10
Supplementary files format and content: tab delimited text file containing combined  salmon counts for all samples

source_name: Mouse embryonic stem cells

growth_protocol: ESCs were cultured in serum/LIF medium conditions.

extract_protocol:
Total RNAs were purified from ESCs using Trizol reagent
Ribosomal RNAs depletion and libraries preparation were conducted using KAPA HyperPrep kit with Ribo-Erase (Roche) according to manufacturer instructions.

value: Mouse embryonic stem cells

value: Sox15 KO


title: JY_08_GEM_TF_2

source_name: IM GEM TX, replicate 2


title: 12_r1_1

description:
sample name: 156
Embryonic blastomere transcriptome


title: CPT0075120002_snRNA

description: 10x Genomics


title: 12_r6_1

description:
sample name: 161
Embryonic blastomere transcriptome


title: 10_r10_1

description:
sample name: 1649
Embryonic blastomere transcriptome


title: CPT0025110004_snATAC

description: 10x Genomics


title: CPT0025890002_snRNA

description: 10x Genomics


title: CPT0012550012_snRNA

description: 10x Genomics


title: mESC, Sox15 KO, rep2


title: 10_r8_1

description:
sample name: 1647
Embryonic blastomere transcriptome


title: CPT0015810004_snRNA

description: 10x Genomics


title: CPT0020120013_snRNA

description: 10x Genomics


title: mESC, WT, rep2

value: WT


title: 10_r9_1

description:
sample name: 1648
Embryonic blastomere transcriptome


title: CPT0012280004_snRNA

description: 10x Genomics


title: CPT0063630004_snRNA

description: 10x Genomics


title: 10_r7_1

description:
sample name: 1646
Embryonic blastomere transcriptome


title: mESC, WT, rep1


title: mESC, Sox15 KO, rep1


title: 10_r6_1

description:
sample name: 1645
Embryonic blastomere transcriptome


title: CPT0079410004_snRNA

description: 10x Genomics


title: CPT0023690004_snRNA

description: 10x Genomics


title: CPT0086820004_snRNA

description: 10x Genomics


title: 10_r5_1

description:
sample name: 1644
Embryonic blastomere transcriptome


title: CPT0086350004_snRNA

description: 10x Genomics


title: CPT0019130004_snRNA

description: 10x Genomics


title: 10_r4_1

description:
sample name: 1643
Embryonic blastomere transcriptome


title: mESC_Sox15 input rep3

data_processing:
Data were processed using bcbio-nextgen 1.2.0 that includes the following steps:
Atropos trimming, v1.1.29: atropos trim --overlap 8
bowtie2 alignment, v2,2.3.5:  -X 2000 after removing duplicates and multimapping reads
macs2 peak calling, v2.2.7.1: -g 2730871774 -q 0.01
bamCoverage bigwig file creation, v3.5.0: bamCoverage  --binSize 20 --effectiveGenomeSize 2730871774 --smoothLength 60 --extendReads 150 --centerReads --normalizeUsing CPM --ignoreForNormalization chrM
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: ESCs were cultured in 2i/LIF medium conditions.

extract_protocol:
Crosslinked chromatin was extracted in Shearing Buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris, pH 8.1) using a Covaris S2 sonicator.
DNA libraries were constructed using the KAPA HyperPlus DNA Library Prep Kit for Illumina (Roche) according to the manufacturer instructions.

treatment_protocol: ESCs were crosslinked with 1% formaldehyde for 5 min.

tag: chip antibody

tag: replicate


title: CPT0010100001_snRNA

description: 10x Genomics


title: mESC Sox15-HA chip rep2


title: CPT0010110013_snRNA

description: 10x Genomics


title: 10_r3_1

description:
sample name: 1642
Embryonic blastomere transcriptome


title: CPT0000870003_snRNA

description: 10x Genomics


title: CPT0000880001_snRNA

description: 10x Genomics


title: 10_r2_1

description:
sample name: 1641
Embryonic blastomere transcriptome


title: mESC Sox15-HA chip rep1


title: mESC Sox15-HA chip rep3


title: mESC Sox2-HA chip rep2


title: CPT0001270002_snRNA

description: 10x Genomics


title: CPT0001220012_snRNA

description: 10x Genomics


title: CPT0001500003_snRNA

description: 10x Genomics


title: 10_r1_1

description:
sample name: 1640
Embryonic blastomere transcriptome


title: CPT0000890002_snRNA

description: 10x Genomics


title: mESC Sox2-HA chip rep1


title: CPT0001540013_snRNA

description: 10x Genomics


title: 8_2r7_4

description:
sample name: 1631
Embryonic blastomere transcriptome


title: CPT0001180011_snRNA

description: 10x Genomics


title: mESC Sox15 input rep2


title: CPT0075720013_snRNA

description: 10x Genomics


title: CPT0010160004_snRNA

description: 10x Genomics


title: mESC Sox15 input rep1


title: CPT0075130004_snRNA

description: 10x Genomics


title: 8_r6_4

description:
sample name: 1630
Embryonic blastomere transcriptome


title: CPT0078510004_snRNA

description: 10x Genomics


title: mESC Sox2 input rep2


title: mESC, WT, rep

tag: genotype


title: CPT0001260013_snRNA

description: 10x Genomics


title: CPT0014450005_snRNA

description: 10x Genomics


title: mESC Sox2 input rep1


title: 8_r5_4

description:
sample name: 1629
Embryonic blastomere transcriptome


title: CPT0075170013_snRNA

description: 10x Genomics


title: CPT0065690004_snRNA

description: 10x Genomics


title: CPT0014470002_snRNA

description: 10x Genomics


title: 8_r3_4

description:
sample name: 1627
Embryonic blastomere transcriptome


title: IL221b_3

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

description: colonoid, IL-1b+IL-22, replicate-3

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Transcript Per Million mapped reads (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: .txt, raw counts matrix that contains all gene names and counts for each sample

source_name: colonoid, IL-1b+IL-22, replicate-3

growth_protocol: Mouse colons were dissected and and used to isolate crypts. Dispersed crypts were plated overnight in Matrigel with  growth media (Advanced DMEM/F12, 2 mM GlutaMax, 10 mM HEPES, 100 U/ml penicillin, 100 μg/ml streptomycin, 1× N2 supplement, 1× B27 supplement) containing EGF (50 ng/ml), 20% L-WRN conditioned media.

extract_protocol:
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.

treatment_protocol: The mouse spheroids were  stimulated with mouse recombinant IL-1b (100 ng/mL) and recombinant mouse IL-22 (1 ng/mL) for  12 hours.

value: colonoid

tag: strain

tag: treatment


title: IL221b_2

description: colonoid, IL-1b+IL-22, replicate-2

source_name: colonoid, IL-1b+IL-22, replicate-2


title: CPT0025110004_snRNA

description: 10x Genomics


title: IL221b_1

description: colonoid, IL-1b+IL-22, replicate-1

source_name: colonoid, IL-1b+IL-22, replicate-1


title: 8_r1_4

description:
sample name: 1625
Embryonic blastomere transcriptome


title: 8_r2_4

description:
sample name: 1626
Embryonic blastomere transcriptome


title: IL1b_3

description: colonoid, IL-1b, replicate-3

source_name: colonoid, IL-1b, replicate-3


title: BeeSTINGseq_GDO-B

first: John

middle: A

last: Morris

state: New York

address: 101 Avenue of the Americas, 4th Floor

institute: New York Genome Center

library_source: other

data_processing:
cDNA reads were mapped to the human genome (hg38, ensembl v96). cDNA, HTO, ADT, and GDO reads were quantified using 10x Cell Ranger v.6.0.0 to generate UMI count matrices.
Cells were demultiplexed based on their HTO counts into their singlets after normalization (centered log ratio transformation) using the HTOdemux function in Seurat v.4.0.1.
For STINGseq-v1 and STINGseq-v2, gRNAs per cell were identitied with the 10x Cell Ranger v.6.0.0 determined threshold (with a minimum UMI = 3 threshold applied). For BeeSTINGseq, we tested each gRNA at UMI thresholds from 1-5.
Assembly: hg38
Supplementary files format and content: Processed data provided in standard UMI count matrix format for cDNA, GDO, HTO, and ADT modalities. Each sample has three files separated into features, barcodes and a sparse matrix file. STINGseq-v1 and STINGseq-v2 GDO files have the UMI threshold files included.

molecule: other

source_name: Human erythroleukemic cell line, K562, expressing FNLS-BE3-SpRY

extract_protocol:
For STINGseq-v1, we ran one lane of a 10x Genomics 5’ kit (Chromium Single Cell Immune Profiling Solution v1.0, 1000014, 1000020, 1000151) with cell hashing performed using four hashtag-derived oligonucleotides (HTOs). For STINGseq-v2, we ran four lanes of a 10x Genomics 5' kit (Chromium Next GEM Single Cell 5' Kit v2 1000265) with cell hashing performed using eight HTOs. For BeeSTINGseq, we ran three lanes of a 10x Genomics 5’ v2 kit (Chromium Next GEM Single Cell 5' Kit v2 1000265) with cell hashing performed using nine HTOs.
Gene expression (cDNA), hashtags (HTOs), guide RNA (Guide-derived oligos, GDOs) libraries, and oligo-tagged antibodies (ADTs) were constructed by following 10x Genomics and ECCITE-seq protocols. We sequenced all cDNA, HTO, GDO, and ADT libraries with  a NextSeq 500 or NovaSeq 6000 (Illumina).
ECCITE-seq sequencing strategy, with the following read recipe: R1 = 26; i7 = 8; R2 = 57


title: BeeSTINGseq_GDO-C

value: Human erythroleukemic cell line, K562, expressing FNLS-BE3-SpRY


title: BeeSTINGseq_HTO-A


title: BeeSTINGseq_HTO-B


title: IL1b_2

description: colonoid, IL-1b, replicate-2

source_name: colonoid, IL-1b, replicate-2


title: BeeSTINGseq_cDNA-B


title: BeeSTINGseq_cDNA-C


title: CPT0025880013_snRNA

description: 10x Genomics


title: 8_r7_3

description:
sample name: 245
Embryonic blastomere transcriptome

source_name: embryo


title: BeeSTINGseq_GDO-A


title: 8_r6_3

description:
sample name: 244
Embryonic blastomere transcriptome


title: IL1b_1

description: colonoid, IL-1b, replicate-1

source_name: colonoid, IL-1b, replicate-1


title: 8_r4_4

description:
sample name: 1628
Embryonic blastomere transcriptome


title: 8_2r5_3

description:
sample name: 243
Embryonic blastomere transcriptome


title: STINGseq-v2_ADT-C

source_name: Human erythroleukemic cell line, K562, expressing KRAB-dCas9-MeCP2


title: BeeSTINGseq_HTO-C


title: BeeSTINGseq_cDNA-A


title: 8_2r8_4

description:
sample name: 1632
Embryonic blastomere transcriptome


title: STINGseq-v2_ADT-D

value: Human erythroleukemic cell line, K562, expressing KRAB-dCas9-MeCP2


title: lL22_3

description: colonoid, IL-22, replicate-3

source_name: colonoid, IL-22, replicate-3


title: 8_2r4_3

description:
sample name: 242
Embryonic blastomere transcriptome


title: lL22_2

description: colonoid, IL-22, replicate-2

source_name: colonoid, IL-22, replicate-2


title: lL22_1

description: colonoid, IL-22, replicate-1

source_name: colonoid, IL-22, replicate-1


title: STINGseq-v2_ADT-B


title: STINGseq-v2_ADT-A


title: STINGseq-v2_HTO-C


title: STINGseq-v2_HTO-B


title: 8_r2_3

description:
sample name: 240
Embryonic blastomere transcriptome


title: UNS_3

description: colonoid, unstimulated, replicate-3

source_name: colonoid, unstimulated, replicate-3


title: STINGseq-v2_GDO-D


title: STINGseq-v2_GDO-C


title: 8_r7_2

description:
sample name: 83
Embryonic blastomere transcriptome


title: 8_r6_2

description:
sample name: 82
Embryonic blastomere transcriptome


title: STINGseq-v2_GDO-B


title: UNS_1

description: colonoid, unstimulated, replicate-1

source_name: colonoid, unstimulated, replicate-1


title: STINGseq-v2_GDO-A


title: STINGseq-v2_cDNA-C


title: 8_r5_2

description:
sample name: 81
Embryonic blastomere transcriptome


title: STINGseq-v2_cDNA-D


title: TR5

city: Hefei

first: weibin

last: wu

address: Changjiang Western Road 130

institute: Anhui Agricultural University

description: Hu sheep

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Fragment per kilobase of exon model per million mapped reads (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Ovis aries

source_name: Cecum

growth_protocol: Ewes at 115 days of gestation.

extract_protocol:
RNA was harvested using  Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Restricted feeding.

value: Cecum

value: Not available

value: Restricted feeding


title: TR4

description: Hu sheep


title: 8_2r3_3

description:
sample name: 241
Embryonic blastomere transcriptome


title: STINGseq-v2_cDNA-A


title: STINGseq-v2_HTO-D


title: 8_r4_2

description:
sample name: 80
Embryonic blastomere transcriptome


title: TR3

description: Hu sheep


title: 8_r2_2

description:
sample name: 78
Embryonic blastomere transcriptome


title: 8_r3_2

description:
sample name: 79
Embryonic blastomere transcriptome


title: TR2

description: Hu sheep


title: 8_r1_3

description:
sample name: 239
Embryonic blastomere transcriptome


title: sora_769_3_FRAS210017241-1r

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

institute: Department of nutrition

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2software to obtain mapped read
FeatureCounts was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Assembly: GRCH38

source_name: HCT 15

growth_protocol: HCT-15 cells were cultured in RPMI1640 medium (Gibco). All media were supplemented with 10% fetal bovine serum. All cells were maintained in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from CRC cells using TRIzol Reagent (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA), and mRNA was extracted.
mRNA was extracted and sheared into 200-base fragments. The fragmented mRNA was reverse-transcribed into complementary DNA (cDNA), which was amplified by PCR to generate the cDNA library. The cDNA library was sequenced using the Illumina NovaSeq 6000 platform.

treatment_protocol: CRC cell lines HCT-15  were treated with an initial concentration of 0.5 μM oxaliplatin for 7 days. After passage, the cells were incrementally treated with higher oxaliplatin concentrations (1μM, 2μM, and 4μM) from day 10 to day 30. After 30 days, the cells were maintained in 4μM oxaliplatin. Similarly, HCT-15 cells were treated with sorafenib to generate the sorafenib-resistant cell lines.

value: HCT 15

value: Human colorectal adenocarcinoma cells

value: sorafenib


title: osha_769_2_FRAS210017238-1r

value: oxaliplatin


title: sora_769_2_FRAS210017241-1r


title: STINGseq-v2_HTO-A


title: osha_769_1_FRAS210017238-1r


title: con_769_3_FRAS210017232-1r


title: UNS_2

description: colonoid, unstimulated, replicate-2

source_name: colonoid, unstimulated, replicate-2


title: osha_769_3_FRAS210017238-1r


title: con_769_2_FRAS210017232-1r


title: sora_769_1_FRAS210017241-1r


title: CON5

description: Hu sheep

value: Normal feeding


title: TR1

description: Hu sheep


title: con_769_1_FRAS210017232-1r


title: 8_r7_1

description:
sample name: 76
Embryonic blastomere transcriptome


title: CON4

description: Hu sheep


title: 8_r6_1

description:
sample name: 75
Embryonic blastomere transcriptome


title: 8_2r5_1

description:
sample name: 74
Embryonic blastomere transcriptome


title: CON3

description: Hu sheep


title: CON2

description: Hu sheep


title: HCT15_CoCL2_3

treatment_protocol: CoCl2, brefeldin A, or low glucose-resistant HCT-15 cells were generated by growing cells in increasing concentrations of the agents until the cells became tolerant.  The resulting cell lines were HCT-15-CoCl2, HCT-15-Bre, and HCT-15-Lowg, respectively


title: HCT15_CoCL2_2


title: HCT15_CoCL2_1


title: HCT15_Lowg_2

value: low glucose


title: HCT15_Lowg_3


title: 8_r4_1

description:
sample name: 73
Embryonic blastomere transcriptome


title: CON1

description: Hu sheep


title: HCT15_con_3


title: HCT15_con_2


title: 8_r3_1

description:
sample name: 72
Embryonic blastomere transcriptome


title: 8_r1_2

description:
sample name: 77
Embryonic blastomere transcriptome


title: 8_r2_1

description:
sample name: 71
Embryonic blastomere transcriptome


title: RNA-seq C23S (-Dox) rep1

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of RNA-seq libraries, raw data were trimmed using Trimmomatic software. And the PSI values were calculated by the rMATS software using the clean reads fastq files.
Assembly: hg19
Supplementary files format and content: Genome-wide RNA-seq signal in bigwig format

source_name: HeLa

growth_protocol: HeLa cells were grown in a DMEM medium containing 10% Tet-free fetal bovine serum and 100 U/ml penicillin/streptomycin at 37 °C in 5% CO2 incubator.

extract_protocol:
Total RNAs of PTBP1-C23S (-Dox), and PTBP1-C23S (+Dox) were extracted with TRIzol Reagent. The polyA+ RNA was isolated using VAHTS mRNA Capture Beads (Vazyme, N401-01) according to the manufacturer’s instructions.
PolyA+ RNA was fragmented and purified for library preparation.Then, synthesized double-stranded DNA library was sequenced by Illumina paired-end sequencing.

treatment_protocol: Hela cells were treated with doxycycline.

value: HeLa

value: Cervical cancer cells

value: treated with the solvent of doxycycline

tag: time


title: HepG2 cells, Isoginkgetin-H3K27ac

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

institute: wuhan university

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to human reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.

source_name: Human hepatoblastoma

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604).

value: Isoginkgetin


title: RNA-seq C23S (+Dox) rep2

value: PTBP1 (C23S)

value: treated with doxycycline


title: HepG2 cells, Isoginkgetin-input


title: RNA-seq C23S (-Dox) rep2

value: WT


title: 8_r1_1

description:
sample name: 70
Embryonic blastomere transcriptome

value: embryonic cells


title: HCT15_con_1


title: RNA-seq C23S (+Dox) rep1


title: 7_r7_1

description:
sample name: 1639
Embryonic blastomere transcriptome


title: HepG2 cells, DMSO-H3K27ac

value: DMSO


title: HepG2 cells, DMSO-Input


title: HCT15_Lowg_1


title: 7_r6_1

description:
sample name: 1638
Embryonic blastomere transcriptome


title: RIC-seq hnRNPA1 KD rep2

data_processing:
library strategy: RNA in situ conformation sequencing (RIC-seq)
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of RIC-seq libraries, raw data were trimmed and aligned to human genome using the RICpipe program as previously described (Liang Liang, 2022). Alignments from STAR and bwa were combined and sent to RICpipe to extract chimeric reads.
Assembly: hg19
Supplementary files format and content: Genome-wide RIC-seq signal in bigwig format

growth_protocol: HeLa cells were grown in a DMEM medium containing 10% fetal bovine serum and 100 U/ml penicillin/streptomycin at 37 °C in 5% CO2 incubator.

extract_protocol:
After cell permeabilization, MNase digestion, pCp labeling, and proximity ligation, the mixture of 200 μl of proteinase K buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 50 μl of proteinase K were applied to cell pellets and sequentially incubated at 37 °C for 60 min and 56 °C for 15 min. The RNA was extracted with 750 μl of TRIzol LS and 220 μl of chloroform following the manufacturer’s instruction.
To remove the potential joining of DNA to RNA mediated by T4 RNA ligase, 20 μg of total RNA was treated with 10 μl of 10 × RQ1 DNase I buffer, 3 μl of RNase Inhibitor and 5 μl of DNase I at 37 °C for 20 min. RNA was then purified by acid Phenol: chloroform extraction and ethanol precipitation. Next, the rRNA can be optionally removed using the Ribo-Zero rRNA Removal Kit (Illumina, MRZH11124) or one can directly proceed to the next step (to probe the rRNA structure and interactions). To fragment RNA, 16 μl of total RNA was added with 4 μl of 5 × first-strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl, 15 mM MgCl2), incubated at 94 °C for 5 min and immediately put on ice. To enrich pCp-biotin-labeled chimeric RNAs, 20 μl of MyOne Streptavidin C1 beads (Thermo Fisher, 65002) were first washed twice with solution A (0.1M NaOH, 0.05M NaCl) and once with solution B (0.1M NaCl) and then blocked with yeast RNA (Roche, 10109223001). The blocked C1 beads, 30 μl of nuclease-free water, and 50 μl of 2 × TWB buffer were applied to the fragmented RNA. The mixture was incubated by rotating at RT for 30 min, after which the beads were washed four times with 1 × TWB buffer. To elute RNA from C1 beads, the beads were resuspended in 100 μl of PK buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS) and incubated in Thermomixer at 95 °C for 10 min at 1000 rpm. Then the sample was placed on a DynaMag-2 magnet stand (Invitrogen, 12321D) for 1 min, and the aqueous phase was transferred to a new Eppendorf tube. Repeat the elution process once, and rinse the beads with 100 μl PK buffer. Finally, RNA was extracted from the 300 μl eluted sample with phenol chloroform 5:1 solution and precipitated overnight at a final concentration of 300 mM NaCl, with 3 volumes of ethanol and 1 μl of glycoblue at -20 °C. RNA was pelleted at 13,000 rpm, washed twice with 75% ethanol and dissolved in 10 μl of nuclease-free water. Strand-specific library construction for paired-end high throughput sequencing was performed as previously described (Cai et al., 2020). Briefly, first-strand cDNA was synthesized with random hexamer primer, and second-strand cDNA was synthesized by introducing dUTP in the dATP, dTTP, dCTP, and dGTP mix to achieve strand-specificity. Then the cDNA was performed end-repair, dA-tailing, and adaptor ligation, followed by PCR amplification.

treatment_protocol: Cells were crosslinked with PBS containing 1% formaldehyde, and then the crosslinking was quenched with 0.125M  glycine. After washing with PBS three times, cells were scraped and collected by centrifugation. Then the cell pellet was permeablized. MNase digestion, pCp-biotin labeling, and proximity ligation were performed in situ and under native conditions.

value: hnRNPA1 knockdown

value: treated with hnRNPA1 shRNA


title: RIC-seq PTBP1 KD rep1

value: PTBP1 knockdown

value: treated with PTBP1 shRNA


title: RIC-seq hnRNPA1 KD rep1


title: RIC-seq PTBP1 KD rep2


title: HepG2 cells, Isoginkgetin rep2

data_processing:
Illumina RTA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.7.0 with default parameters
The gene expression level was calculated by featureCounts with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).


title: 7_r5_1

description:
sample name: 1637
Embryonic blastomere transcriptome


title: 7_r4_1

description:
sample name: 1636
Embryonic blastomere transcriptome


title: CRIC-seq WT (-Dox) rep2

data_processing:
library strategy: capture RNA in situ conformation sequencing (CRIC-seq)
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of CRIC-seq libraries, raw data were trimmed and aligned to human genome using the RICpipe program as previously described (Liang Liang, 2022). Alignments from STAR and bwa were combined and sent to RICpipe to extract chimeric reads.
After the collection of chimeric reads, high confidence chimeric reads bound by a specific RBP were obtained by removing the non-specific background using homemade scripts. Briefly, reads from IgG IP (+pCp) and RBP IP (-pCp) CRIC-seq libraries were combined as background. Then if the number of chimeric reads from RBP IP (+pCp) libraries showed 5-fold more than the background in pairs of 10-nt genomic windows, and the chimeric reads from RBP IP (+pCp) libraries owning junction sites within the same 10-nt windows, these chimeric reads were assembled into a cluster. The chimeras in the clusters supported by at least 2 reads were finally defined as high confidence reads mediated by specific RBP.
Assembly: hg19
Supplementary files format and content: Genome-wide CRIC-seq signal in bigwig format
Supplementary files format and content: Genome-wide CRIC-seq clusters of SRSF1 IP (+pCp) in txt format

extract_protocol:
Cells were lysed and sonicated. RNA bound by the target protein was pulled down by a specific antibody. The RNA-protein complex was treated with protease K, and the RNA was extracted with TRIzol LS.
To remove the potential joining of DNA to RNA mediated by T4 RNA ligase, 15 μl of RNA was treated with 10 μl of 10 × RQ1 DNase I buffer, 3 μl of RNase Inhibitor and 5 μl of DNase I at 37 °C for 20 min. RNA was purified with ZYMO RESEARCH RNA Clean and Concentrator-5. To fragment RNA, 16 μl of total RNA was added with 4 μl of 5 × first-strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl, 15 mM MgCl2), incubated at 94 °C for 5 min and immediately put on ice. To enrich pCp-biotin-labeled chimeric RNAs, 20 μl of MyOne Streptavidin C1 beads (Thermo Fisher, 65002) were first washed twice with solution A (0.1M NaOH, 0.05M NaCl) and once with solution B (0.1M NaCl) and then blocked with yeast RNA (Roche, 10109223001). The blocked C1 beads, 30 μl of nuclease-free water, and 50 μl of 2 × TWB buffer were applied to the fragmented RNA. The mixture was incubated by rotating at RT for 30 min, after which the beads were washed four times with 1 × TWB buffer. To elute RNA from C1 beads, the beads were resuspended in 100 μl of PK buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS) and incubated in Thermomixer at 95 °C for 10 min at 1000 rpm. Then the sample was placed on a DynaMag-2 magnet stand (Invitrogen, 12321D) for 1 min, and the aqueous phase was transferred to a new Eppendorf tube. Repeat the elution process once, and rinse the beads with 100 μl PK buffer. Finally, RNA was extracted from the 300 μl eluted sample with phenol chloroform 5:1 solution and precipitated overnight at a final concentration of 300 mM NaCl, with 3 volumes of ethanol and 1 μl of glycoblue at -20 °C. RNA was pelleted at 13,000 rpm, washed twice with 75% ethanol and dissolved in 10 μl of nuclease-free water. Strand-specific library construction for paired-end high throughput sequencing was performed as previously described (Cai et al., 2020). Briefly, first-strand cDNA was synthesized with random hexamer primer, and second-strand cDNA was synthesized by introducing dUTP in the dATP, dTTP, dCTP, and dGTP mix to achieve strand-specificity. Then the cDNA was performed end-repair, dA-tailing, and adaptor ligation, followed by PCR amplification.

tag: antibody

value: anti-PTBP1 (BB7)


title: HepG2 cells, Isoginkgetin rep1


title: CRIC-seq WT (+Dox) rep2


title: CRIC-seq WT (+Dox) rep1


title: HepG2 cells, DMSO rep2


title: 7_r3_1

description:
sample name: 1635
Embryonic blastomere transcriptome

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: WS230
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

extract_protocol:
Egg shells were removed from a C. elegans embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.


title: 7_r2_1

description:
sample name: 1634
Embryonic blastomere transcriptome


title: CRIC-seq C23S (-Dox) rep2


title: 7_r1_1

description:
sample name: 1633
Embryonic blastomere transcriptome


title: CRIC-seq C23S (+Dox) rep1


title: CRIC-seq C23S (+Dox) rep2


title: CRIC-seq PTBP1 KD rep2


title: 6_r26_2

description:
sample name: 1234
Embryonic blastomere transcriptome


title: CRIC-seq hnRNPA1 KD rep1

value: anti-hnRNPA1 (Santa Cruz, sc-32301)


title: CRIC-seq PTBP1 KD rep1


title: PDO716 + IL13

city: Philadelphia

first: Amanda

last: Muir

state: PA

address: 3401 Civic Center Boulevard

institute: Children's Hospital of Philadelphia

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Seurat
Assembly: GRCh38
Supplementary files format and content: .txt files of cell x gene matrices

source_name: PDO 716

extract_protocol:
single cell suspension was obtained by digesting the day 11 organoids in 0.05% Trypsin-EDTA, followed by depletion of dead cells using the Dead Cell Removal kit (Miltenyi Biotec)
https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/technical-note-chromium-single-cell-3-v3-reagent-workflow-and-software-updates

treatment_protocol: IL13 or PBS treatment was initiated on day 7 of organoid culture and maintained till harvest on day 11

value: esophageal organoids


title: PDO696 + IL13

source_name: PDO 696


title: 6_2r5_2

description:
sample name: 1233
Embryonic blastomere transcriptome


title: CRIC-seq SRSF1 IP (-pCp) rep1

value: anti-SRSF1 (Santa Cruz, sc-33652)


title: CRIC-seq WT (-Dox) rep1

value: HeLa


title: CRIC-seq SRSF1 IP (-pCp) rep2

value: Cervical cancer cells


title: PDO694 + IL13

source_name: PDO 694


title: CRIC-seq SRSF1 IP (+pCp) rep1

description: replicates were merged for processing


title: 6_2r3_2

description:
sample name: 1231
Embryonic blastomere transcriptome


title: PDO694 + PBS

value: PBS


title: CRIC-seq C23S (-Dox) rep1

value: treated with the solvent of doxycycline


title: PDO717 + PBS

source_name: PDO 717


title: HepG2 cells, DMSO rep1


title: Huh7 cell sh-ALYREF, rep3, Immunoprecipitation

city: Hangzhou

first: Xue

last: Chen

state: Zhejiang

address: No.79, Qingchun Road, Shangcheng Distric

department: The First Affiliated Hospital

institute: Zhejiang University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4) and STAR software
The circRNAs were identified by DCC software using the STAR alignment results
Methylated sites on RNAs (peaks) were identified by MACS software
Assembly: HG38
Supplementary files format and content: XLS sheet "Gene Expression Profiling.xlsx" illustrated the raw counts(column B to column M) and normalized score(column N to column Y, calculated by edgeR) of each mRNA transcripts from the input samples. Additional gene annotation information was also provided in column Z to column AL.
Supplementary files format and content: XLS sheet "LncRNA Expression Profiling.xlsx" illustrated the raw counts(column B to column M) and normalized score(column N to column Y, calculated by edgeR) of each lncRNA transcripts from the input samples. Additional gene annotation information was also provided in column Z to column AL.
Supplementary files format and content: XLS sheet "CircRNA Expression Profiling.xlsx" illustrated the raw counts(column B to column M) and normalized score(column N to column Y, calculated by edgeR) of each circRNA from the input samples. Additional gene annotation information was also provided in column Z to column AJ.
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.mRNA.xlsx" illustrated the m5C methylation sites information in mRNA,  including m5C peak start site, peak stop site, peak ID, m5C peak score, peak length, generated by MACS software. Additional statistical enrichment information and gene annotation information was also provided
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.LncRNA.xlsx" illustrated the m5C methylation sites information in lncRNAs,  including m5C peak start site, peak stop site, peak ID, m5C peak score, peak length, generated by MACS software. Additional statistical enrichment information and gene annotation information was also provided
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.circRNA.xlsx" illustrated the m5C methylation sites information in circRNAs,  including m5C peak start site, peak stop site, peak ID, m5C peak score, peak length, generated by MACS software. Additional statistical enrichment information and gene annotation information was also provided

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® m5C-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m5C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).
RNA-seq(MeRIP-seq)

value: human liver cancer cell line

value: sh-ALYREF


title: Huh7 cell sh-ALYREF, rep2, Immunoprecipitation


title: 6_r2_2

description:
sample name: 1230
Embryonic blastomere transcriptome

source_name: embryo


title: Huh7 cell sh-NC, rep3, Immunoprecipitation

value: WT


title: PDO716 + PBS


title: 6_r1_2

description:
sample name: 1229
Embryonic blastomere transcriptome

value: embryonic cells


title: Huh7 cell sh-NC, rep1, Immunoprecipitation


title: PDO696 + PBS


title: Huh7 cell sh-NC, rep2, Immunoprecipitation


title: CRIC-seq hnRNPA1 KD rep2


title: PDO717 + IL13


title: HepG2 cell sh-ALYREF, rep3, Immunoprecipitation


title: HepG2 cell sh-ALYREF, rep2, Immunoprecipitation


title: 4_r4_5

description:
sample name: 1228
Embryonic blastomere transcriptome


title: ISO-H4K8ac

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to human reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Assembly: hg38
Supplementary files format and content: bigWig files were generated from bam files; Scores represent the RPM value

value: Human hepatoblastoma

value: ISO


title: HepG2 cell sh-ALYREF, rep1, Immunoprecipitation


title: CRIC-seq SRSF1 IP (+pCp) rep2

description: replicates were merged for processing


title: 4_r3_5

description:
sample name: 1227
Embryonic blastomere transcriptome


title: 6_2r4_2

description:
sample name: 1232
Embryonic blastomere transcriptome


title: 4_r2_5

description:
sample name: 1226
Embryonic blastomere transcriptome


title: DMSO-H4K8ac

value: DMSO


title: HepG2 cell sh-NC, rep2, Immunoprecipitation


title: HepG2 cell sh-NC, rep3, Immunoprecipitation


title: Huh7 cell sh-ALYREF, rep1, Immunoprecipitation


title: HepG2 cell sh-NC, rep1, Immunoprecipitation


title: DMSO-H3K27me3


title: Huh7 cell sh-ALYREF, rep1, Input


title: Huh7 cell sh-NC, rep3, Input


title: 4_r1_5

description:
sample name: 1225
Embryonic blastomere transcriptome


title: 4_r4_3

description:
sample name: 69
Embryonic blastomere transcriptome


title: ISO-H3K9ac


title: Huh7 cell sh-NC, rep2, Input


title: HepG2 cell sh-ALYREF, rep3, Input


title: HepG2 cell sh-ALYREF, rep2, Input


title: 4_r2_3

description:
sample name: 67
Embryonic blastomere transcriptome


title: DMSO-H3K9ac


title: ISO-H3K4me1


title: HepG2 cell sh-NC, rep3, Input


title: 4_r4_2

description:
sample name: 65
Embryonic blastomere transcriptome


title: 4_r3_2

description:
sample name: 64
Embryonic blastomere transcriptome


title: HepG2 cell sh-NC, rep1, Input


title: DMSO-Input

value: none (input)


title: DMSO-H3K4me1


title: Huh7 cell sh-ALYREF, rep2, Input


title: ISO-H3K27me3


title: NTRK1_3

city: Wuhan

first: Bo

last: Jiao

state: Hubei Province

address: 1095 Jiefang Avenue

institute: Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Raw reads containing more than 2-N bases were first discarded.
Adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Ver. 0.0.13). The short reads ˂ 16-nt were also dropped.
Clean reads were aligned to the GRCh38 genome by HISAT2 allowing 4 mismatches.
Uniquely mapped reads were used for counting the number of reads mapped to each gene and calculation of fragments per kilobase of transcript per million fragments mapped (FPKM).
Assembly: GRCh38 genome
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: SHSY5Y cells

growth_protocol: The SH-SY5Y cell lines were cultured at 37 °C with 5% CO2 in a minimum essential medium (MEM)/F12 supplemented with 10% fetal bovine serum, 100 μg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNAs were extracted from SH-SY5Y cells using TRIzol reagent. DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with the NanodropTM One Cspectrophotometer system
For high-throughput sequencing, the libraries were applied to llumina Novaseq 6000 system for paired-end sequencing.

treatment_protocol: Infected cells were harvested for 48 h for quantitative reverse transcription-polymerase chain reaction (RT-qPCR), Western blot, and Cell Counting Kit-8 (CCK-8) assays.

value: SHSY5Y cells

value: NTRK1 overexpression in SHSY5Y cells


title: NTRK1_2


title: NTRK1_1


title: HepG2 cell sh-NC, rep2, Input


title: 4_r3_3

description:
sample name: 68
Embryonic blastomere transcriptome


title: 4_r2_2

description:
sample name: 63
Embryonic blastomere transcriptome


title: Huh7 cell sh-NC, rep1, Input


title: NC_2

value: SHSY5Y cells(empty lentiviral vector)


title: NC_3


title: dcSSc_MT2103 [MT2.103]

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Quality filtering according to the BGI pipeline
Reads were aligned to the GrCh38 reference human genome and the homo sapiens transcriptome (Ensembl, version 79), using the STAR aligner
Summed exon read counts per gene were calculated using the Python package HTSeq, using annotations from the GrCh38 built from the human genome
Between lane normalization using the upper quartile normalization method was performed using the Bioconductor/R package EDAseq
To account for batch effects arising from the inclusion of samples from different geographic locations (The Netherlands and Italy), we applied the generalized linear model from the Bioconductor/R package RUVseq using the RUVr function for k = 2 factors of unwanted variation
Differential expression analysis was performed using the negative binomial distribution-based method implemented in DESeq2 on the normalized summed exon read counts per gene
Normalized gene expression levels were converted variance stabilised data (VSD), calculated according to DESeq2 instructions
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab delimited .txt files include counts and normalized expression values (VSD) for each sample.

source_name: CD1c+ cDCs

extract_protocol:
Human CD1c+ dendritic cells were purified from heparinised whole blood of SSc patients and matched healthy donors after centrifugation over Ficoll-Paque gradient. Briefly,  CD1c+ dendritic cells were purified from PBMCs using the anti-BDCA1 microbeads (Miltenyi Biotec), on the autoMACs Pro Separator (Miltenyi Biotec) according to manufacturer’s protocol. Cells were lysed in RLTplus buffer (Qiagen) containing 1% (v/v) beta-mercaptoethanol (Sigma). Total RNA was purified with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. DNAse treatment (RNAse Free DNase I set, Qiagen) on column was performed.
RNA-Seq libraries were prepared using the TruSeq Stranded kit (Illumina, San Diego, CA, USA) after poly (A) capture, according to the manufacturer’s instructions. Libraries were sequenced on the HiSeq 2000 system (Illumina), using 100bp paired-end reads.

value: CD1c+ cDCs

value: Peripheral blood

tag: disease state

value: diffuse systemic sclerosis

tag: location

value: Milan

tag: seks

value: Male


title: 4_r1_2

first: Alison

last: Cole

address: Djerassiplatz 1

institute: University of Vienna

description:
sample name: 62
Embryonic blastomere transcriptome


title: Huh7 cell sh-ALYREF, rep3, Input


title: dcSSc_MT2102 [MT2.102]

value: Female


title: 4_r1_3

description:
sample name: 66
Embryonic blastomere transcriptome


title: 4_r4_1

description:
sample name: 61
Embryonic blastomere transcriptome


title: NC_1


title: 22RV1-STEAP1-KO+Addback #4

city: Seattle

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: AddBackvsCGW_DESEq2_results.csv; AddbackvsKO_DESEq2_padj_results.csv; KOvsCGW_DESEq2_results.csv

data_processing:
UCSC TOIL processing pipeline was used to align the reads to the reference genome and generating count matrix files. DESeq2 was used for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: comma-separated values files include RSEM values for each Sample and DESeq output files are provided

extract_protocol:
RNA was harvested using Purelink™ RNA Mini Kit (Thermo Scientific). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer's protocols.

value: Human prostate epithelial cells

value: STEAP1 knockout + rescue of STEAP1


title: dcSSc_MT2042 [MT2.042]


title: HepG2 cell sh-ALYREF, rep1, Input

value: human liver cancer cell line

value: sh-ALYREF


title: ISO-Input

value: Human hepatoblastoma

value: WT


title: 22RV1-STEAP1-KO+Addback #2


title: 4_r3_1

description:
sample name: 60
Embryonic blastomere transcriptome

value: embryonic cells


title: 22RV1-STEAP1-KO #4

value: STEAP1 knockout


title: 4_r2_1

description:
sample name: 59
Embryonic blastomere transcriptome


title: dcSSc_MT2013 [MT2.013]


title: 22RV1-STEAP1-KO+Addback #1


title: 22RV1-STEAP1-KO #3


title: 22RV1-STEAP1-KO #1


title: 22RV1-STEAP1-KO #2


title: 4_r1_1

description:
sample name: 58
Embryonic blastomere transcriptome


title: dcSSc_MT2011 [MT2.011]


title: 22RV1-WT #4

value: Wildtype


title: dcSSc_4 [X4]

value: Utrecht


title: 22RV1-WT #2


title: dcSSc_37 [X37]

value: Rotterdam


title: 2_r2_5

description:
sample name: 55
Embryonic blastomere transcriptome


title: 2_r1_5

description:
sample name: 54
Embryonic blastomere transcriptome


title: UT-2-1_MLN

description: STEAP1_vs_UT_DESEq2_Tumor.csv; 22RV1_STEAP1Tumors_rsem_genes.hugo.csv

source_name: 22Rv1 cells, metastaised to lymph node

value: 22Rv1 cells, metastaised to lymph node

value: Untransduced T cells treated


title: 22RV1-WT #3


title: 22RV1-STEAP1-KO+Addback #3


title: 22RV1-WT #1


title: dcSSc_35 [X35]

value: CD1c+ cDCs

value: Peripheral blood

value: diffuse systemic sclerosis


title: UT-2-1_Liver

source_name: 22Rv1 cells, metastaised to liver

value: 22Rv1 cells, metastaised to liver


title: 2_r2_4

description:
sample name: 53
Embryonic blastomere transcriptome


title: UT-2-1_IALN

value: Human prostate epithelial cells


title: 2_r1_4

description:
sample name: 52
Embryonic blastomere transcriptome


title: S1-T-2-4_Liver

value: STEAP1 CAR T cells treated


title: S1-T-2-2_Liver


title: 2_r2_3

description:
sample name: 57
Embryonic blastomere transcriptome


title: S1-T-1-B_RPLN


title: dcSSc_34 [X34]

value: Male


title: dcSSc_32 [X32]

value: Female


title: 2_r1_2

description:
sample name: 56
Embryonic blastomere transcriptome


title: Day3, 5m, 40%surfacePAR, inc5days, biolrep3

city: OLD BRIDGE

first: Benjamin

last: Diaz

state: New Jersey

address: K12B Pine Tree Boulevard

department: Department of Biochemistry and Microbiology

institute: Rutgers University

description: Marine phytoplankton community <0.8 µm diameter

data_processing:
Supplementary files format and content: Only data from in situ samples were analyzed with differential expression, however our intial plan was to use incubation samples as well, so the asssembly was done with the incubated samples as well.
The set of transcripts belonging to the most abundant autotrophic phyotplankton genera present (Minutocellus, Chaetoceros, Thalassiosira, Extubocellulus, Fragilariopsis, Bathycoccus, Micromonas, Ostreococcocus) was subset before performing differential expression analysis.
Supplementary files format and content: DeSeq2 output of each genera analyzed with the comparisons made in the paper is presented in "Deseqoutputbygenera.xlsx" (using the column 'Sample number correspong to Fig. 1': "1V2", "1V3", "2V3", "4V6","2V5","3V6","4V6","5V6","4V5" as well as the comparisons used for Fig. 8a, "Shallow vs. Deep" , which is 1, 2, 3 vs. 4)
The raw reads from all samples were searched for sequencing adapters and low-quality nucleotides which were trimmed using CLC Genomic Workbench.
Protein coding regions within the metatranscriptome assembly were predicted with TransDecoder
To reduce redundancy in the metatranscriptome, the predicted coding regions were clustered at 95% identity using CD-HIT(37) which resulted in 2 053 751 sequences
Trimmed reads from each sample were then mapped to the assembly with CLC Workbench, and only uniquely mapped reads were counted.
Contigs with less than 50 total mapped reads across all samples were filtered out resulting in 673 142 contigs that were used for downstream analysis
Functional annotations were identified using EggNOG
Translated protein sequences were assigned phylogeny by using DIAMOND (v. 2.0.11, ultra-sensitive mode) against a custom database of MetaEuk, MaTOU, MMETSP, and Uniref100 (May 2020).  The highest bitscore matching to an organism was used, with a lower bitscore cutoff of 50.
The trimmed reads were assembled using Trinity yielding 11 046 104 contigs
Assembly: (no reference genomes used)
Supplementary files format and content: Count matrix of read counts for all samples are presented in "CountMatrixsamples.xlsx"
Supplementary files format and content: TPM of samples from the count matrix are presented in "TPMallsamples.xlsx"
Supplementary files format and content: Translated protein sequences are presented in "Aaseqs.fasta"

organism: phytoplankton metagenome

source_name: Marine phytoplankton community <0.8 um diameter

extract_protocol:
RNA was extracted with Trizol kit from frozen 0.8 µm filters, without modifications.
PolyA-enriched messenger RNA was reverse transcribed using Invitrogen SuperScript II Reverse Transcriptase at the Rutgers Genome Cooperative. Libraries were prepared from this cDNA (TruSeq RNA Library Prep Kit v2.)

treatment_protocol: For incubated samples, seawater from the same depths as in situ samples was also emptied directly into acid-washed, 9 L bottles and placed in on-deck incubators, which were continuously circulated with surface water to maintain ambient temperatures and covered with neutral density screening to simulate 40, 20, and 1% surface irradiance.

tag: depth (m)

tag: time (days)

tag: mixed layer_depth_at_sampling_(m)

value: Incubated 5 days

tag: sample number_corresponding_to_fig._1

value: Sample 4 Incubation


title: dcSSc_22 [X22]

tag: tissue


title: S1-T-1-4_Liver

tag: cell line


title: 2_r2_1

city: Vienna

description:
sample name: 51
Embryonic blastomere transcriptome

tag: developmental stage

tag: cell type

value: embryonic cells


title: lcSSc_MT2089 [MT2.089]

value: limited systemic sclerosis

value: Milan


title: Day3, 5m, 40%surfacePAR, inc5days, biolrep1

value: Marine phytoplankton community <0.8 um diameter


title: Day3, 5m, 40%surfacePAR, inc5days, biolrep2


title: 2_r1_1

description:
sample name: 50
Embryonic blastomere transcriptome


title: lcSSc_MT2064 [MT2.064]


title: Day1, 51m, 1%surfacePAR, inc3days, biolrep3

value: Incubated 3 days

value: Sample 3 Incubation


title: 1_P0_4

description:
sample name: 49
Embryonic blastomere transcriptome


title: dcSSc_36 [X36]

value: Utrecht


title: lcSSc_MT2029 [MT2.029]

value: CD1c+ cDCs


title: lcSSc_MT2027 [MT2.027]

value: Peripheral blood


title: CRIC-seq hnRNPA1 IP (-pCp) rep1

description: replicates were merged for processing

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of CRIC-seq libraries, raw data were trimmed and aligned to human genome using the RICpipe program as previously described (Liang Liang, 2022). Alignments from STAR and bwa were combined and sent to RICpipe to extract chimeric reads.
After the collection of chimeric reads, high confidence chimeric reads bound by a specific RBP were obtained by removing the non-specific background using homemade scripts. Briefly, reads from IgG IP (+pCp) and RBP IP (-pCp) CRIC-seq libraries were combined as background. Then if the number of chimeric reads from RBP IP (+pCp) libraries showed 5-fold more than the background in pairs of 10-nt genomic windows, and the chimeric reads from RBP IP (+pCp) libraries owning junction sites within the same 10-nt windows, these chimeric reads were assembled into a cluster. The chimeras in the clusters supported by at least 2 reads were finally defined as high confidence reads mediated by specific RBP.
Assembly: hg19
Supplementary files format and content: Genome-wide CRIC-seq signal in bigwig format
Supplementary files format and content: Genome-wide CRIC-seq clusters of PTBP1 and hnRNPA1 IP (+pCp) in txt format
Library strategy: RIC-seq

extract_protocol:
Cells were lysed and sonicated. RNA bound by the target protein was pulled down by a specific antibody. The RNA-protein complex was treated with protease K, and the RNA was extracted with TRIzol LS.
To remove the potential joining of DNA to RNA mediated by T4 RNA ligase, 15 μl of RNA was treated with 10 μl of 10 × RQ1 DNase I buffer, 3 μl of RNase Inhibitor and 5 μl of DNase I at 37 °C for 20 min. RNA was purified with ZYMO RESEARCH RNA Clean and Concentrator-5.To fragment RNA, 16 μl of total RNA was added with 4 μl of 5 × first-strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl, 15 mM MgCl2), incubated at 94 °C for 5 min and immediately put on ice. To enrich pCp-biotin-labeled chimeric RNAs, 20 μl of MyOne Streptavidin C1 beads (Thermo Fisher, 65002) were first washed twice with solution A (0.1M NaOH, 0.05M NaCl) and once with solution B (0.1M NaCl) and then blocked with yeast RNA (Roche, 10109223001). The blocked C1 beads, 30 μl of nuclease-free water, and 50 μl of 2 × TWB buffer were applied to the fragmented RNA. The mixture was incubated by rotating at RT for 30 min, after which the beads were washed four times with 1 × TWB buffer. To elute RNA from C1 beads, the beads were resuspended in 100 μl of PK buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS) and incubated in Thermomixer at 95 °C for 10 min at 1000 rpm. Then the sample was placed on a DynaMag-2 magnet stand (Invitrogen, 12321D) for 1 min, and the aqueous phase was transferred to a new Eppendorf tube. Repeat the elution process once, and rinse the beads with 100 μl PK buffer. Finally, RNA was extracted from the 300 μl eluted sample with phenol chloroform 5:1 solution and precipitated overnight at a final concentration of 300 mM NaCl, with 3 volumes of ethanol and 1 μl of glycoblue at -20 °C. RNA was pelleted at 13,000 rpm, washed twice with 75% ethanol and dissolved in 10 μl of nuclease-free water.Strand-specific library construction for paired-end high throughput sequencing was performed as previously described (Cai et al., 2020). Briefly, first-strand cDNA was synthesized with random hexamer primer, and second-strand cDNA was synthesized by introducing dUTP in the dATP, dTTP, dCTP, and dGTP mix to achieve strand-specificity. Then the cDNA was performed end-repair, dA-tailing, and adaptor ligation, followed by PCR amplification.

value: HeLa

value: Cervical cancer cells

value: anti-hnRNPA1 (Santa Cruz, sc-32301)


title: CRIC-seq PTBP1 IP (-pCp) rep2

description: replicates were merged for processing

value: anti-PTBP1 (BB7)


title: Day1, 51m, 1%surfacePAR, inc3days, biolrep2


title: 1_P0_3

description:
sample name: 48
Embryonic blastomere transcriptome


title: CRIC-seq hnRNPA1 IP (-pCp) rep2

description: replicates were merged for processing


title: Day1, 51m, 1%surfacePAR, inc3days, biolrep1


title: Day1, 18m, 20%surfacePAR, inc3days, biolrep3

value: Sample 2 Incubatbin


title: lcSSc_MT2003 [MT2.003]

value: Female


title: CRIC-seq IgG IP (+pCp) rep2

description: replicates were merged for processing

value: anti-IgG (Santa Cruz, sc-2025)


title: CRIC-seq PTBP1 IP (-pCp) rep1

description: replicates were merged for processing


title: Mouse cancer cells : Human stellate cells  [Sample_10_R3]

city: London

first: Ed

last: Carter

address: John Vane Science Centre

institute: Barts Cancer Institute

data_processing:
Partek Flow Genomic Analysis Software
Data aligned to genome (Homo Sapiens Hg38, Mus Musculus mm10) - Star version STAR 2.7.3A
Read count extraction and normalization were performed using Partek software
Assembly: Hg38 , mm10
Supplementary files format and content: Excel file_Raw counts for each species

organism:
Homo sapiens
Mus musculus

source_name: Pancreas

growth_protocol: Cancer and Stellate cells were formed into spheres, embedded in collagen : matrigel hydrogels and cultured for 72 hours in DMEM:F12 supplemented with 10% FBS.

extract_protocol:
RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB), following manufacturers instructions.
RNA libraries for RNAseq was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Pancreas

value: Cancer Cell, Stellate Cell

value: WT


title: Day1, 18m, 20%surfacePAR, inc3days, biolrep2


title: Mouse cancer cells : Human stellate cells  [Sample_9_R2]


title: lcSSc_MT2026 [MT2.026]

value: limited systemic sclerosis

value: Milan


title: S1-T-1-B_Liver

value: 22Rv1 cells, metastaised to liver

value: Human prostate epithelial cells

value: STEAP1 CAR T cells treated


title: Day1, 18m, 20%surfacePAR, inc3days, biolrep1

value: Marine phytoplankton community <0.8 um diameter

value: Incubated 3 days


title: Mouse cancer cells : Human stellate cells  [Sample_8_R1]


title: lcSSc_44 [X44]

value: CD1c+ cDCs

value: Peripheral blood

value: Utrecht


title: Day1, 5m, 40%surfacePAR, inc3days, biolrep4

value: Sample 1 incubation


title: Human cancer cells : Mouse stellate cells  [Sample_7_P3]

value: Panc1, mPSC


title: Day1, 5m, 40%surfacePAR, inc3days, biolrep3


title: CRIC-seq hnRNPA1 IP (+pCp) rep1

city: Beijing

description:
replicates were merged for processing
CRIC-seq_hnRNPA1_IP_pCp_plus_clusters.txt.gz

value: HeLa

value: Cervical cancer cells

value: anti-hnRNPA1 (Santa Cruz, sc-32301)


title: 1_P0_2

description:
sample name: 47
Embryonic blastomere transcriptome

value: embryonic cells


title: CRIC-seq hnRNPA1 IP (+pCp) rep2


title: lcSSc_3 [X3]

value: Female


title: Human cancer cells : Mouse stellate cells  [Sample_6_P2]

value: Pancreas

value: Cancer Cell, Stellate Cell

value: WT


title: Day1, 5m, 40%surfacePAR, inc3days, biolrep2


title: CRIC-seq PTBP1 IP (+pCp) rep2

description:
replicates were merged for processing
CRIC-seq_PTBP1_IP_pCp_plus_clusters.txt.gz

value: anti-PTBP1 (BB7)


title: lcSSc_27 [X27]

value: limited systemic sclerosis


title: CRIC-seq PTBP1 IP (+pCp) rep1


title: Day1, 5m, 40%surfacePAR, inc3days, biolrep1

value: Marine phytoplankton community <0.8 um diameter


title: lcSSc_25 [X25]


title: Human cancer cells : Mouse stellate cells  [Sample_5_M3]

value: Miapaca2, mPSC


title: Human cancer cells : Mouse stellate cells  [Sample_4_M2]


title: sicircWDR37 rep3

city: guangzhou

first: Yingqin

last: Li

state: guangdong

address: Guangzhou, 510060, P.R. China

institute: Sun Yat-sen University Cancer Center

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome (hg38) 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 was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: hg38
Supplementary files format and content: count, FPKM

growth_protocol: S18 cells were maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
TRIzol reagent was used to extract total RNA from S18 cell line.
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

treatment_protocol: S18 cells were treated with circWDR37 siRNA or control siRNA using Lipofectamine 3000 reagent. The cells were harvested after transfection at 48h for assays.

value: nasopharyngeal carcinoma cell

value: transfection with circWDR37 siRNA


title: Day3, 40m, 1%surfacePAR, insitu, biolrep3

value: In situ

value: Sample 6


title: lcSSc_21 [X21]

value: CD1c+ cDCs

value: Peripheral blood

value: Utrecht


title: Human cancer cells : Mouse stellate cells  [Sample_3_M1]


title: ncSSc_MT2093 [MT2.093]

value: non-cutaneous systemic sclerosis

value: Milan


title: lcSSc_6 [X6]

value: Female


title: Mouse cancer cells : Human stellate cells  [Sample_2_DT3]

value: Pancreas


title: sicircWDR37 rep1


title: Day3, 40m, 1%surfacePAR, insitu, biolrep2


title: Day3, 40m, 1%surfacePAR, insitu, biolrep1


title: ncSSc_MT2083 [MT2.083]


title: ncSSc_MT2077 [MT2.077]


title: Mouse cancer cells : Human stellate cells  [Sample_1_DT1]

value: Cancer Cell, Stellate Cell


title: Day3, 15m, 20%surfacePAR, insitu, biolrep3

value: Sample 5


title: ncSSc_MT2070 [MT2.070]


title: Day3, 15m, 20%surfacePAR, insitu, biolrep2


title: CRIC-seq IgG IP (+pCp) rep1

description: replicates were merged for processing

value: HeLa

value: Cervical cancer cells

value: anti-IgG (Santa Cruz, sc-2025)


title: siSCR rep2

value: transfection with control siRNA


title: siSCR rep1

value: nasopharyngeal carcinoma cell


title: hTSC, H3K27ac, ChIPseq, rep2

city: Austin

first: Bum-Kyu

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description: Chromatin IP against H3K27ac

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to human hg38 genome using Bowtie 2.4.5
Peaks were called using MACS3 peak caller with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: Placenta

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in human TSCs. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E7370L ) following by manufacturer’s instructions.

value: Placenta

value: Human trophoblast stem cells


title: Day3, 15m, 20%surfacePAR, insitu, biolrep1

value: Marine phytoplankton community <0.8 um diameter

value: In situ


title: 6_NR4A3

description: H3HCVDRXY_104400-001-024_GTACCACA-TGTTGTGG

data_processing:
Quality check of the raw sequencing reads was performed using the FastQC tool.
Sequencing reads were mapped against the reference genome GRCh38.p13 built from the human genome (NCBI) using bowtie2
Peaks were called using MACS2, by comparing the IP samples to their matched input samples in paired end mode (BAMPE).
After calling, peaks from ENCODE blacklist regions and X- and Y-chromosome peaks were filtered out to reduce noise and exclude sex-specific peaks.
Peaks were annotated to the nearest genes using the ChIPseeker Bioconductor/R package. Peaks were considered to be associated to a gene when they were annotated within a 10kb range (up- or downstream) to the gene transcription start site (TSS).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: peak text files and bed files

source_name: CD1c+ DCs

growth_protocol: CD1c+ cDCs were isolated from PBMCs obtained from healthy donor buffy coats using the MACS human CD1c dendritic cell isolation kit. 1.5×106 freshly isolated cDCs were cultured overnight in RPMI 1640 medium with GlutaMAX™ (Life Technologies), supplemented with 10% heat inactived fetal bovine serum (Biowest) and 1% penicillin streptomycin (Life Technologies).

extract_protocol:
After culture, cDCs were washed with PBS and crosslinked using the truChIP® Ultra-Low Chromatin Shearing Kit (Covaris), according to the manufacturer’s instructions. Chromatin shearing was performed using AFA Fiber Pre-Slit Snap-Cap microTUBEs (Covaris) by sonication (peak incident power: 105, duty factor: 2%, cycles per burst: 200, treatment time: 12 minutes) on the Covaris S220 focused ultrasonicator (Woburn, MA, USA). After shearing, the chromatin was transferred into pre-chilled microcentrifuge tubes and centrifuged at 10.000 x g, 4˚C for 5 minutes to pellet insoluble material, and the chromatin was stored at -20˚C for downstream processing. Chromatin immunoprecipitation was performed with 3µg anti-NR4A1 (NB100-56745, Novusbio), anti-NR4A2 (NB110-40415, Novusbio) or anti-NR4A3 (NLS2341, Novusbio) antibodies, using the low cell ChIP-seq kit (Active Motif), according to the manufacturer’s instructions. For all conditions, 10% of the input chromatin was removed prior to addition of the antibodies and used to normalize the amount of immunoprecipitated DNA (input control). Following immunoprecipitation, ChIP DNA was de-crosslinked in the presence of NaCl and Proteinase K (Active Motif) in a thermocycler at 65°C overnight, and DNA was extracted by penol:chloroform:isoamylalcohol precipitation and dissolved in Low-EDTA TE buffer (Active Motif).
ChIP-seq libraries were generated by GenomeScan (Leiden, the Netherlands) with the NEBNext® Ultra II DNA Library Prep kit (Illumina), and were sequenced using Illumina NovaSeq 6000 generating ~20 million 150bp paired ended reads for each sample.

treatment_protocol: Cells were either left untreated or treated with TLR7/8 agonist R848 (Resiquimod, 100ng/mL, Invivogen) overnight.

value: CD1c+ dendritic cell

value: Periperal blood

tag: replicate

tag: treatement

value: R848 stimulated

tag: chip antibody

value: anti-NR4A3 (NLS2341, Novusbio)


title: ncSSc_MT2048 [MT2.048]

value: CD1c+ cDCs

value: Peripheral blood

value: non-cutaneous systemic sclerosis

value: Milan

value: Female


title: lytic_LCL_IP2

first: Erle

middle: S

last: Robertson

address: 3610 Hamilton Walk

institute: Otorhinolaryngology-Head and Neck Surgery Perelman School of Medicine

data_processing:
Quality control using fastqc version 0.11.5
Mapped to GRCh38 whole genome using STAR2.7.6a with parameters --runThreadN 4
Peaks calling using MACS3
Count the number of reads mapped to each gene using htseq-count version 0.12.4
Assembly: GRCh38
Supplementary files format and content: Narrow peaks for each group of sample
Supplementary files format and content: Table with raw gene counts for every gene in every sample

growth_protocol: LCL and AKATA cells were maitained in RPMI supplemented with 10% BGS and 1% antibiotics and maintained at 37 degree Celcius and maintained at a optimal concentration of 0.4 million/ml

extract_protocol:
EBV positive cells were induced to lytic reactivation by using TPA (20 ng/ml) and Butyric acid (3 mM) for 30 h induction.
RNAs were isolated and immune precipitated with m6A specific antibodies or with control IgG and the library was prepared using TrueSeq standard LT  RNA preparation kit

treatment_protocol: LCL and AKATA cells were induced with TPA and BA for 30 h for lytic reactivation

value: Lymphoid tissue

value: LCL

value: B cells

tag: genotype

value: Wild type

tag: treatment

value: Treated with TPA and Butyric acidand  IP with m6A specific antibody


title: hTSC, H3K27ac, ChIPseq, rep1

description: Chromatin IP against H3K27ac

value: Placenta

value: Human trophoblast stem cells

tag: antibody


title: ncSSc_MT2063 [MT2.063]

tag: disease state


title: Day3, 5m, 40%surfacePAR, insitu, biolrep3

value: Marine phytoplankton community <0.8 um diameter

value: In situ

value: Sample 4


title: sicircWDR37 rep2

value: nasopharyngeal carcinoma cell

value: transfection with circWDR37 siRNA


title: 6_NR4A2

description: H3HCVDRXY_104400-001-023_CAACACAG-TGGCTATC

value: CD1c+ dendritic cell

value: Periperal blood

value: R848 stimulated

value: anti-NR4A2 (NB110-40415, Novusbio)


title: lytic_LCL_input2

value: Treated with TPA and Butyric acidand  IP with IgG antibody


title: ncSSc_MT2045 [MT2.045]

value: CD1c+ cDCs

value: Peripheral blood

value: non-cutaneous systemic sclerosis

tag: location

value: Milan

value: Female


title: ncSSc_MT2016 [MT2.016]

tag: seks


title: lytic_AKV_input2

value: Lymphoid tissue

value: AKATA

value: B cells

value: Wild type


title: Day3, 5m, 40%surfacePAR, insitu, biolrep1

tag: depth (m)

value: Marine phytoplankton community <0.8 um diameter

value: In situ

value: Sample 4


title: 6_NR4A1

description: H3HCVDRXY_104400-001-022_AGACGCTA-TGTACACC

value: CD1c+ dendritic cell

value: anti-NR4A1 (NB100-56745, Novusbio)


title: siSCR rep3

value: nasopharyngeal carcinoma cell

value: transfection with control siRNA


title: Day3, 5m, 40%surfacePAR, insitu, biolrep2

tag: time (days)


title: ncSSc_46 [X46]

value: Utrecht


title: LCL_input2

value: LCL

value: Untreated IP with Control IgG specific antibody


title: 5_NR4A3

description: H3HCVDRXY_104400-001-020_CTTACAGC-CTTCACCA

value: Periperal blood

value: unstimulated

value: anti-NR4A3 (NLS2341, Novusbio)


title: ncSSc_41 [X41]

value: CD1c+ cDCs

value: Peripheral blood

value: non-cutaneous systemic sclerosis

value: Rotterdam

value: Female


title: AKV_IP2

value: Lymphoid tissue

value: AKATA

value: B cells

value: Wild type

value: Untreated IP with M6A specific antibody


title: Day1, 51m, 1%surfacePAR, insitu, biolrep2

value: Marine phytoplankton community <0.8 um diameter

tag: mixed layer_depth_at_sampling_(m)

value: In situ

value: Sample 3


title: 5_NR4A2

description: H2GNHDSX2_104400-001-019_AGGAACAC-GACATTCC

value: CD1c+ dendritic cell

value: anti-NR4A2 (NB110-40415, Novusbio)


title: ncSSc_17 [X17]

value: Utrecht


title: Day1, 51m, 1%surfacePAR, insitu, biolrep3

tag: sample number_corresponding_to_fig._1


title: AKV_input2

tag: tissue

value: Untreated IP with Control IgG specific antibody


title: 5_NR4A1

description: HYNLFDSXY_104400-001-018_CCTTCCAT-ATTGCGTG

value: Periperal blood

value: unstimulated

value: anti-NR4A1 (NB100-56745, Novusbio)


title: Day1, 51m, 1%surfacePAR, insitu, biolrep1


title: eaSSc_MT2106 [MT2.106]

value: CD1c+ cDCs

value: Peripheral blood

value: early systemic sclerosis

value: Milan


title: LCL_IP2

value: Lymphoid tissue

tag: cell line

value: LCL

value: B cells


title: lytic_AKV_IP2

value: AKATA

value: Wild type

value: Treated with TPA and Butyric acidand  IP with m6A specific antibody


title: ncSSc_16 [X16]

value: non-cutaneous systemic sclerosis

value: Female


title: Day1, 18m, 20%surfacePAR, insitu, biolrep2

value: Marine phytoplankton community <0.8 um diameter

value: In situ

value: Sample 2


title: eaSSc_MT2098 [MT2.098]


title: 5_Input

description: HYNLFDSXY_104400-001-017_GTCAGTCA-TAATGCCG

value: CD1c+ dendritic cell

value: Periperal blood

value: unstimulated

value: Input control


title: lytic_LCL_IP1


title: 4_NR4A3

description: H3HCVDRXY_104400-001-016_AACCAGAG-AACCGAAG

value: R848 stimulated

value: anti-NR4A3 (NLS2341, Novusbio)


title: Day1, 18m, 20%surfacePAR, insitu, biolrep1


title: eaSSc_MT2079 [MT2.079]

value: CD1c+ cDCs

value: Peripheral blood

value: early systemic sclerosis

value: Milan


title: Day1, 5m, 40%surfacePAR, insitu, biolrep3

value: Sample 1


title: lytic_AKV_IP1

value: Lymphoid tissue

value: AKATA

value: B cells

value: Wild type

value: Treated with TPA and Butyric acidand  IP with m6A specific antibody