title: GRID-Seq Naive cells_rep1

description:
Naive cells_rep1
GRID-seq
Nuclear RNA and genomic DNA

data_processing:
All the GRID-seq libraries were sequenced with single-end 100 bp reads on HiSeq400 (Illumina, 200 million reads/sample). Raw reads were firstly evaluated by FastQC and trimmed by Cutadapt to get high-quallity clean reads, and those clean reads  were then filtered out if the length were below 85 bp as suggested according to previous report (Li et al., 2017; Zhou et al., 2019).
The designed linker sequence of GRID-seq library were identified identified by matefq in GridTools (Zhou et al., 2019) and the paired reads consisting of transcribed RNA and genomic DNA were then seprated. Paired RNA and DNA reads were then mapped to the mouse genome (GRCm38/mm10) by BWA respectively. Read counts were generally summarized into 1kb genomic bins for downstream analyses.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data are in gzipped tsv (*.xbed.bgz) recording: RNA_Chrom, RNA_Start, RNA_End, DNA_Chrom, DNA_Start, DNA_End, RNA_Strand, DNA_Strand.

source_name: Naïve cells

growth_protocol: Mouse naive T cells were purified from spleens and lymph nodes of 8-12 weeks old mice using the Naive CD4+ T Cell Isolation Kit. Naïve CD4+ T cells  was p cultured under Th17  polarization condition with 0.1ng/m L TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).

extract_protocol:
Two independent biological replicates (5-10 x106) were crosslinked with disuccinimidyl glutarate (DSG) and formaldehyde. DNA in isolated nuclei were digested with AluI. A biotinylated bivalent linker was ligated to chromatin-associated RNA (with the ssRNA stretch on the linker) and nearby fragmented genomic DNA and captured by streptavidin microbeads for library construction.
To amplify each library, 20 μl of PCR amplification mix (9.4 μl of H2O, 5 μl of DNA sample, 4 μl of 5× Phusion HF Buffer, 40 pmol dNTP, 5 pmol Primer#1, 5 pmol Primer#2, 0.4 U Phusion High-Fidelity DNA Polymerase (Thermo Fisher)) was prepared. PCR primers consist of Primer#1 (5′-AATGATACGGCGACCACCGAGATCTACACBBBBBACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′ (BBBBB: 5 nt barcode for multiplexing libraries)) and Primer#2 (5′-CAAGCAGAAGACGGCATACGAGACGTGTGCTCTTCCGATCT-3′). PCR was performed initially for 30 seconds at 98°C, and then 16 cycles of 10 sec denaturation at 98°C, 30 sec annealing at 65°C, and 15 sec extension at 72°C. The PCR product was resolved by native 10% polyacrylamide gel and the band of 194 bp in size was recovered.Sequencing was performed on HiSeq400 (Illumina, 200 million reads/sample).
GRID-seq

treatment_protocol: Th17 [treated with 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems) for 72hrs].

value: Naive CD4+

value: untreated


title: 218 RNA

status: Public on Dec 31 2024

type: SRA

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

country: USA

institute: Moffitt Cancer Center

library_source: transcriptomic

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapping against human reference genome hs37d5 using STAR-2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region (Gencode29) associated with each gene.
To account for differences in library size between samples, Trimmed Mean of M values (TMM) normalization using calcNormFactors(), also from edgeR, was applied.
All data were then transformed using voom.
Assembly: hs37d5
Supplementary files format and content: tab-delimited text files include raw gene count for each sample

molecule: total RNA

organism: Homo sapiens

source_name: ovarian tumors

extract_protocol:
RNA was harvested using the Qiagen All-Prep RNA isolation kit
RNA libraries were prepared by using Illumina TruSeqTM RNA Exome Library Preparation Kit (Illumina Inc., San Diego, CA) , following the manufacturer’s protocol

tag: yob decade

tag: pre/post menopause

value: post


title: OVDMSO 2

city: Noida

first: Adhiraj

last: Roy

state: Uttar Pradesh

address: Sector 125

department: AIMMSCR

country: India

institute: Amity University

data_processing:
All 150 bp paired end raw reads from Illumina NovaSeq 6000 sequencer were quality checked for low quality bases and adapter sequences, i.e AGATCGGAAGA (Processing of raw reads). Quality check was done using in-house perl scripts.
All the processed reads were aligned to Human hg38 genome (https://asia.ensembl.org/Homo_sapiens/Info/Index) using Hisat2-2.2.1.
StringTie-2-2.1  a fast and highly efficient assembler was used for  alignments into potential transcripts.
The "R" package DESeq2 has been used for differential gene expression analysis based on the negative binomial distribution. DeSeq2 estimates variance-mean dependence in count data from high_x0002_throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Assembly: Human hg38 genome
Supplementary files format and content: gtf

source_name: Ovary

growth_protocol: Epithelial ovarian cancer (EOC) cell lines OVCAR8 & SKOV3 were grown in DMEM and McCoy's media supplemented with 10% fetal bovine serum (FBS), 1× penicillin/streptomycin and maintained in humidified incubator containing 5% CO2 at 37 ◦C

extract_protocol:
Total RNA was isolated using Trizol reagent (Life technologies, USA) and 250  ng of total RNA was used for the construction of sequencing libraries
Library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (Catalog: E7775S, New England Biolabs).
mRNAs were primed with NEBNext Random Primers and chemically fragmented in a magnesium-based buffer in order to get an inserts of ~200 nucleotides. The fragmented mRNAs were reverse transcribed to form cDNA and the first strand cDNA reactions were converted to ds DNA. The double stranded cDNA fragments obtained were cleaned up by using 1.8X of AMPure XP beads (Catalog: A63881, Beckman Coulter). The library concentration was determined in a Qubit.3 Fluorometer (Catalog: Q33216, Life technologies using The Qubit dsDNA HS (High Sensitivity) Assay Kit (Catalog: Q32854, ThermoFisher Scientific). The library quality assessment was done using Agilent D5000 ScreenTape System (Catalog: 5067-5588, Agilent) and Agilent D1000 ScreenTape System (Catalog: 5067- 5582, Agilent) in a 4150 TapeStation System (Catalog: G2992AA, Agilent).

treatment_protocol: EOC cell lines were treated with 1 μM of PKD inhibitors CRT0066101 and kb-NB142-70 for 16 Hrs.

tag: tissue

value: Ovary

tag: cell line

tag: cell type

value: Ovarian cancer

tag: genotype

value: Wild type

tag: treatment

value: Untreated


title: GRID-Seq Th17 cell_rep2

city: San Diego

first: Wendy

last: Huang

state: CA

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
Th17 cell_rep2
GRID-seq
Nuclear RNA and genomic DNA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Th17 72h cells

value: Th17 cells


title: OVDMSO


title: ChIP_H3K27me3_Malat1KO_rep2

data_processing:
All the ChIP-seq libraries were sequenced with single-end 100 bp reads on NovaSeq 6000. Raw reads were firstly evaluated by FastQC and trimmed by Cutadapt to get high-quallity clean reads.
Single-end raw reads of ChIP-seq data were mapped to the mouse genome (GENCODE assembly GRCm38/mm10) by bowtie2 in the local mapping mode with parameter “--local”, followed by PCR deduplication by SAMTools with the utility markedup (Li et al., 2009). Peaks were called from the uniquely mapped reads using MACS2 (Version 2.2.6) (Zhang et al., 2008) in the narrow peak-calling mode with default parameters.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed data are in BigWig format

source_name: Th17 cells

extract_protocol:
Cells were washed once with ice-cold PBS and pelleted at 1000 g for 5 min at 4°C. Crosslinked cells were resuspended in ice-cold hypotonic buffer, and centrifuged at 1000 g for 5 min at 4°C to obtain a nuclear fraction. Nuclear pellets were resuspended in  either LB3 buffer for H3K27me3 (Active motif, 39155) or PIPA-NR buffer for SUZ12 (Abcam, ab12073). Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles. Samples were centrifuged at 15000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation. LB3 lysate was diluted 1.1-fold with 10% Triton X-100, and 1% of the lysate was kept as ChIP input.
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions. DNA was purified and eluted following by amplification for 16 cycles PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. The amplified libraries were purified, eluted and size selected using PAGE/TBE gel for 225-325 bp fragments by gel extraction, and single-end sequenced on NovaSeq 6000 (Illumina). The eluted input DNA was prepared for libraries as described for ChIP samples.

tag: strain

tag: antibody

value: Malat1 KO


title: GRID-Seq Th17 cell_rep1

description:
Th17 cell_rep1
GRID-seq
Nuclear RNA and genomic DNA


title: 217 RNA

value: pre


title: ChIP_H3K27me3_Malat1KO_rep1


title: 216 RNA


title: PDGF.BB,HiC-seq

city: shanghai

first: Xian

last: Guo

address: changhai road 168

country: China

institute: Changhai hospital

data_processing:
Then HiCUP (v 0.6.1) was used including aligning the clean data to reference genome and filtering invalid di-tag.
The unique valid di-tags were processed using CHiCAGO to identify significant interaction. Interactions with CHiCAGO scores ≥5 were considered high-confidence interactions.
Assembly: hg19
Supplementary files format and content: 2.1.Vehicle_loop.bedpe:tab-delimited text files include  the start and end positions of the two anchors of each chromosomal interactions (loop anchors) and CHiCAGO score in Vehicle group
Supplementary files format and content: 2.1.PDGF_loop.bedpe:tab-delimited text files include  the start and end positions of the two anchors of each chromosomal interactions (loop anchors) and CHiCAGO score in PDGF-BB treated group.
Supplementary files format and content: 2.1.Vehicle_PDGF.diff_loop23.08.31.tsv:tab-delimited text files include  the start and end positions of the two anchors of each chromosomal interactions (loop anchors) and CHiCAGO score in Vehicle and PDGF-BB treated group.

source_name: human aortic smooth muscle cell

extract_protocol:
Ten million cells were cross-linked for 10 min with 1% formaldehyde and quenched with 0.2 M final concentration glycine for 5 min. Cross-linked DNA was digested by 100U HindIII (NEB), and marked with biotin-14-dCTP (Invitrogen) and then ligated by 50 U T4 DNA ligase (NEB).
Purified DNA was sheared to 300- to 600-bp fragments and were further blunt-end repaired, followed by purification through biotin-streptavidin–mediated pull-down and PCR amplification. Capture Hi-C of promoters was then carried out with SureSelect XT Library Prep Kit ILM, using the custom-designed biotinylated RNA bait library and custom paired-end blockers (Agilent Technologies).
After library enrichment, a post-capture PCR amplification step was carried out . Finally, promoter capture Hi-C libraries were purified with AMPure XP beads (Beckman Coulter), determined by Bioanalyzer profiles (Agilent Technologies), and sequenced on the Illumina Nova-seq 6000 platform.

value: human aortic smooth muscle cell

value: PDGF-BB


title: 223 RNA


title: C57BL/6NTac, NASH Whole Liver 2

city: Indianapolis

first: Sarath

middle: Chandra

last: Janga

state: Indiana

address: 535 West Michigan Street

department: Informatics and Computing

institute: Indiana University-Purdue University Indianapolis

data_processing:
Reads were analyzed for base and read quality and trimmed using Trimgalore (v0.4.5) in conjunction with FastQC (v0.11.9) and Cutadapt (v1.18) (options -paired -phred33)
Trimmed sequences were aligned with GrCM38/mm10 using hisat2 (v2.1.0)
Aligned sequences were sorted by chromosome number using samtools (v1.9)
Assembly: mm10
Supplementary files format and content: counts

source_name: whole liver

extract_protocol:
Whole livers were perfused with 1X PBS and isolated from both groups of mice for trizol lysis and RNA extraction. Six mice per group were included in the study and the liver lysate was pooled together to split into two technical replicates for each group.
NA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the KAPA HyperPrep RNA kit (Roche).

value: whole liver

value: NASH

value: GAN


title: Vehicle,HiC-seq

value: vehicle


title: 214 RNA


title: Malat1KO_Th17 rep2

description:
RNA-seq
Ribosome depeted RNA

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM19 annotation
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
Those with confidence score less than 0.99 were filtered out
Known genomic variations were obtained from the Mouse Genomes Project (ftp://ftp-mouse.sanger.ac.uk/current_snps/mgp.v5.merged.snps_all.dbSNP142.vcf.gz). Variants were removed from the resulting candidate list if they overlapped with the known genomic variations
All remaining candidates were annotated based on GENCODE.vM19
Genome_build: mm10
Supplementary_files_format_and_content: differential analysis tab-delimited text files include raw counts, normalized counts values log2FoldChange and pvalue for each gene
Supplementary_files_format_and_content: sailor analysis tab-delimited text files include position and edit % of each edited sites

growth_protocol: Naïve CD4+ T cells was cultured under Th17 polarization condition with 0.1 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).

extract_protocol:
RNA were isoalted using Qiagen Rneasy mini kit (74106)
Ribosome-depleted RNAs were used to generate the cDNA libraries using the KAPA Hyper Prep Kit (KR0961) according to the instructions. Briefly, DNA was end-repaired and A-tailing to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-liagation clean was used to remove the extra adapters. Then the adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles, follwed with post-ampilcation clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: Naïve [untreated] or Th17 [treated with 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems) for 48 and 72hrs].

value: culture Th17

value: Malat2 knockout


title: SP064_030: APPPS1 snRNA-seq

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

department: BIMSB

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
fastqc to check quality of sequencing reads
bulit pre-mrna reference
cellranger (v3.1) mkfastq to demultiplex fastq files
cellranger (v3.1) count to align sequencing files to a reference transcriptome
cellranger (v3.1) aggr to aggregate multiple samples
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated UMI counts in matrix.mtx. List of genes in features.tsv List of cell barcodes in barcodes.tsv

source_name: Hippocampus

extract_protocol:
Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3â€²end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3Ê¹ GEM
According to manufacturer recommendation of  Chromium Next GEM Single Cell 3Ê¹ GEM, Library & Gel Bead Kit v3.1

value: Hippocampus

tag: age

value: 250 day

tag: mutation

value: APP KM670/671NL (Swedish), PSEN1 L166P


title: C57BL/6NTac, NASH Whole Liver 1


title: 213 RNA


title: SP064_029: APPPS1.p40KO snRNA-seq

value: APP KM670/671NL (Swedish), PSEN1 L166P, Il12b knock out exon 1-4


title: C57BL/6NTac, WT Whole Liver 2

value: WT

value: chow


title: hTERT, UVB-Exposed, AB5D-25x, R4

city: Singapore

first: Tze Hau

last: Lam

address: 70 Biopolis Street

country: Singapore

institute: Procter and Gamble

data_processing:
Raw reads underwent quality control with the following criteria: (1) trimming the 3’ end of the reads with a base Phred score below 30, (2) requiring an average base Phred score of 30 for each read and (3) maintaining a minimum read length of 120bp after trimming.
Assembly: hg38
Supplementary files format and content: tab-delimited text file incluide expected counts, TPM and FPKM for each sample.

source_name: hTERT

growth_protocol: Human Tert-immortalized (hTERT) keratinocytes were maintained, passaged, and expanded in a 5% CO2, 37°C incubator using EpiLife™ media with human keratinocyte growth supplement and Penicillin/Streptomycin.

extract_protocol:
hTERT keratinocytes were then lysed in RLT buffer and the total RNA (>1ug) was extracted using RNeasy Mini Kit for the construction of sequencing libraries.
RNA-seq libraries were prepared using the TruSeq stranded mRNA kit following manufacturer's protocols

value: hTERT

value: Keratinocytes

value: UVB-exposed, AB5D-25x


title: GRID-Seq Naive cells_rep2

description:
Naive cells_rep2
GRID-seq
Nuclear RNA and genomic DNA

value: Naive CD4+

value: untreated


title: SP064_028: WT snRNA-seq


title: hTERT, UVB-Exposed, AB5D-25x, R3


title: C57BL/6NTac, WT Whole Liver 1

value: whole liver


title: SP064_026: APPPS1.p40KO snRNA-seq

value: APP KM670/671NL (Swedish), PSEN1 L166P, Il12b knock out exon 1-3


title: hTERT, UVB-Exposed, AB5D-25x, R1


title: 211 RNA

value: post


title: 210 RNA

value: pre


title: SP064_027: APPPS1 snRNA-seq


title: Skin, rFGF4-treated wounds, d6, rep4

city: Wenzhou

first: Jian

last: Sun

address: chashan

institute: wenzhou medical university

data_processing:
Illumina novaseq 6000 software used for basecalling.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Skin

extract_protocol:
Total RNA was isolated from wounds of mice (2 mm around the wounds) using TRIzol reagent (Invitrogen) following the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: 6-8 weeks

value: wounds were treated with Rfgf4

tag: time

value: 6 days


title: Skin, rFGF4-treated wounds, d6, rep3


title: 209 RNA


title: Skin, rFGF4-treated wounds, d6, rep2


title: SP064_024: APPPS1 snRNA-seq

value: Hippocampus

value: 250 day

value: APP KM670/671NL (Swedish), PSEN1 L166P


title: 208 RNA


title: hTERT, UVB-Exposed, AB5D-5x, R4

value: UVB-exposed, AB5D-5x


title: hTERT, UVB-Exposed, AB5D-5x, R3

value: hTERT


title: SP064_025: WT snRNA-seq


title: hTERT, UVB-Exposed, AB5D-5x, R2

value: Keratinocytes


title: Skin, PBS-treated wounds, d6, rep4

value: wounds were treated with PBS


title: 207 RNA


title: SP064_023: APPPS1.p40KO snRNA-seq

value: APP KM670/671NL (Swedish), PSEN1 L166P, Il12b knock out exon 1-2


title: hTERT, UVB-Exposed, AB5D-5x, R1


title: SP064_022: WT snRNA-seq


title: 212 RNA


title: Skin, PBS-treated wounds, d6, rep3


title: DDX5∆T_rep2

description:
Ribosome depeted RNA
Th17_72hr_DDX5_KO2
processed data file:
sailor_Th17_72hr_WT_DDX5KO_0.99conf_edited_sites.txt

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM19 annotation
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
RNA editing sites were detected using SAILOR version 1.0.4 with paired-end mode
Those with confidence score less than 0.99 were filtered out
Known genomic variations were obtained from the Mouse Genomes Project (ftp://ftp-mouse.sanger.ac.uk/current_snps/mgp.v5.merged.snps_all.dbSNP142.vcf.gz). Variants were removed from the resulting candidate list if they overlapped with the known genomic variations
All remaining candidates were annotated based on GENCODE.vM19
Genome_build: mm10
Supplementary_files_format_and_content: differential analysis tab-delimited text files include raw counts, normalized counts values log2FoldChange and pvalue for each gene
Supplementary_files_format_and_content: sailor analysis tab-delimited text files include position and edit % of each edited sites

growth_protocol: Naïve CD4+ T cells  was cultured under Th17  polarization condition with 0.1-5.0 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).

tag: genotype/variation

value: (72hr) 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems)


title: 205 RNA


title: 206 RNA


title: hTERT, UVB-Exposed, AB5D-25x, R2

value: UVB-exposed, AB5D-25x


title: DDX5∆T_rep1

description:
Ribosome depeted RNA
Th17_72hr_DDX5_KO1
processed data file:
sailor_Th17_72hr_WT_DDX5KO_0.99conf_edited_sites.txt


title: hTERT, UVB-Exposed, AB5D-1x, R4

value: UVB-exposed, AB5D-1x


title: Skin, PBS-treated wounds, d6, rep2


title: hTERT, UVB-Exposed, AB5D-1x, R3


title: 204 RNA

value: post


title: Skin, PBS-treated wounds, d6, rep1


title: hTERT, UVB-Exposed, AB5D-1x, R2


title: 203 RNA


title: WT_rep1

description:
Ribosome depeted RNA
Th17_72hr_WT1
processed data file:
sailor_Th17_72hr_WT_DDX5KO_0.99conf_edited_sites.txt

source_name: WT

value: wild type


title: Skin, rFGF4-treated wounds, d6, rep1

value: Skin


title: hTERT, UVB-Exposed, AB5D-1x, R1


title: hTERT, UVB-Exposed, R4

value: UVB-exposed


title: 201 RNA


title: Colon_Ecsit cKO

city: Nanjing

first: Yuying

last: Jiang

state: Jiangsu

address: 101 Longmian Avenue

institute: Nanjing Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 40%;
 Cell Gene Number < Median Gene Number * 2;
 Cell Gene Number > 800.
PCA and tSNE analysis was used for the single cell to cell relation description.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Colon_Ecsit cKO

growth_protocol: Mice were housed in conventional cages in an animal room at constant temperature (19–23 °C) and humidity (55 ± 10%) under a 12-h light–dark cycle and were allowed access to standard diet and water ad libitum.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-8 week old Ecsit fl/fl and Ecsit cKO mice were injected tamoxifen (3mg) intraperitoneally for 5 consecutive days and  were euthanized 12 days after the last injection..

value: Ecsit cKO

value: Colon


title: Th17 cell_rep2

description:
Ribosome depeted RNA
4333_Th17_S8_L004
processed data file:
DESeq_naive_th17.txt
sailor_Naive_Th17_0.99_edited_sites.txt

source_name: Th17 cell


title: Colon_Ecsit fl/fl

source_name: Colon_Ecsit fl/fl

value: Ecsit fl/fl


title: 200 RNA

value: pre


title: hTERT, UVB-Exposed, R3


title: Small intestine_Ecsit cKO 2

source_name: Small intestine_Ecsit cKO

value: Small intestine


title: Naive cells_rep2

description:
Ribosome depeted RNA
4333_Naive_S18_L004
processed data file:
DESeq_naive_th17.txt
sailor_Naive_Th17_0.99_edited_sites.txt

source_name: Naive cells

growth_protocol: Naive CD4+ T cells  was cultured under Th17  polarization condition with 0.1-5.0 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).

treatment_protocol: Naive [untreated] or Th17 [treated with 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems) for 48 and 72hrs].

value: Naive CD4+

value: untreated


title: hTERT, UVB-Exposed, R2

value: hTERT

value: Keratinocytes


title: 199 RNA


title: hTERT, UVB-Exposed, R1


title: Small intestine_Ecsit fl/fl 2

source_name: Small intestine_Ecsit fl/fl


title: Th17 cells - input_DNA_rep2

description:
1914_Input_S22_L008
Input

data_processing:
the single-end raw reads of two repeats of each example were mapped to the mouse genome (GENCODE assembly GRCm38) by bowtie2 (Version 2.3.4.1) in the local mapping mode with parameter “--local”, followed by PCR deduplication by SAMTools (Version 1.9) with the utility markedup
these mapped reads from each sample repeats were further merged into single BAM file by SAMTools followed by peak-calling procedure using MACS2 (Version 2.2.6) in narrow peak-calling mode with default parameters
these peak regions with peak-score above 30 were considered as reliable peaks
bigwig files were generated using bamCoverage function in deepTools with parameters with '--binSize 1 --normalizeUsing CPM'
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage function in deepTools
Supplementary_files_format_and_content: peak text files

source_name: Th17 cells - input_DNA

extract_protocol:
Protein-DNA were crosslinked with formaldehyde. Cells were then lysed and crude extracts were sonicated to shear the DNA. The cross-linked protein-DNA was immunoprecipitated. The immunoprecipitates were then reverse cross-linked and the DNA fragments are purified .
Libraries were prepared using KAPA Hyper Prep Kit (KR0961) according to the instructions. Briefly, DNA was end-repaired and A-tailing to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-liagation clean was used to remove the extra adapters. Then the adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles, follwed with post-ampilcation clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: (72hr) 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems)

value: culture Th17


title: 198 RNA

source_name: ovarian tumors


title: hTERT, No UVB, R4

tag: treatment:


title: Small intestine_Ecsit fl/fl 1


title: WT_rep2

description:
Ribosome depeted RNA
Th17_72hr_WT2
processed data file:
sailor_Th17_72hr_WT_DDX5KO_0.99conf_edited_sites.txt

value: (72hr) 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems)


title: 197 RNA


title: Th17 cells - H3K27ac_rep2

description:
1914_H3K27ac_S14_L008
Immunoprecipitation

source_name: Th17 cells - H3K27ac

tag: chip antibody

value: H3K27ac (ActiveMotif, 39133)


title: 202 RNA


title: hTERT, No UVB, R3


title: 195 RNA


title: hTERT, No UVB, R2


title: anti-LIF

city: Beijing

first: Rong

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: 3 samples were combined for analysis

data_processing:
used Seurat（4.0.3）to filter low quality cells，cells with number of detected genes <200 or >5000 and cells with >300 of the UMI counts belonging to mitochondrial genes were also omitted.
the clustering and visualization was finished by Seurat (V4.0.3)
applied the Monocle (version 2.3.6) to determine the potential lineage differentiation with default parameters between cell populations.
Gene Ontology (GO) enrichment analysis of marker genes was implemented by the ClusterProfiler R package.
ClusterProfiler R package to test the statistical enrichment of markergenes in KEGG pathways.
GSEA (http://software.broadinstitute.org/gsea/msigdb/annotate.jsp) software was used to perform biological process enrichment analysis on the differentially expressed genes in each cluster or subset.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

source_name: pancreatic cancer

growth_protocol: C57BL/6 mice, 6-7 weeks, female,  were subcutaneously injected at the right flank with 5×106 Pan02 cells diluted in 100 μL solution (PBS and Matrigel, 1:1 ratio). When the tumor size reached approximately 50 mm3, mice with analogous types of tumors were divided randomly into four groups.

extract_protocol:
After harvested, tissues were washed in ice-cold RPMI1640 and dissociated using multi-tissue dissociation kit 2 (Miltenyi) from Miltenyi Biotec according to manufacturer’s instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then depending on the sample conditions debris and dead cells removal was also optional (Miltenyi 130-109-398/130-090-101). Finally, fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3’ library preparation kit (SeekGene). The indexed sequencing libraries were cleaned up with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE100 read length.

treatment_protocol: Mice were injected intraperitoneally with 200 μg of anti-PD-1 antibody (BioXcell, Clone RMP1-14, USA) together with 25 mg/kg IgG or anti-LIF monoclonal antibody three times weekly until the study endpoint.

value: pancreatic cancer cell PAN02

value: anti-LIF


title: Th17 cell_rep1

description:
Ribosome depeted RNA
4330_Th17_S5_L004
processed data file:
DESeq_naive_th17.txt
sailor_Naive_Th17_0.99_edited_sites.txt


title: 194 RNA


title: hTERT, No UVB, R1


title: Th17 cells - H3K27ac_rep1

description:
1765_H3K27ac_S15_L008
Immunoprecipitation


title: 193 RNA

value: post


title: Th17 cells - input_DNA_rep1

description:
1765_Input_S23_L008
Input


title: anti-PD-1

description: 3 samples were combined for analysis


title: Small intestine_Ecsit cKO 1


title: Th17 72h cells_rep2 [ATAC-seq]

data_processing:
the single-end raw reads of two repeats of each example were mapped to the mouse genome (GENCODE assembly GRCm38) by bowtie2 (Version 2.3.4.1) in the local mapping mode with parameter “--local”, followed by PCR deduplication by SAMTools (Version 1.9) with the utility markedup
these mapped reads from each sample repeats were further merged into single BAM file by SAMTools followed by peak-calling procedure using MACS2 (Version 2.2.6) in narrow peak-calling mode with specific parameters of “callpeak --nomodel --extsize 100”
these peak regions with peak-score above 30 were considered as reliable peaks
bigwig files were generated using bamCoverage function in deepTools with parameters with '--binSize 1 --normalizeUsing CPM'
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage function in deepTools
Supplementary_files_format_and_content: peak text files

source_name: Th17 72h cells

growth_protocol: Th17 cells were grown from isolated naïve CD4+ T cells  in the preence of 0.1ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).

extract_protocol:
10000 cells were lysed and Tagmented with Tn5, followed with purification with Qiagen MinElute PCR purification Kit
Libraries were generated with KAPA Real-Time Library amplification kit (cat#KK2701). Library fragments of 150-350 product were purifed with KAPA Pure Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.


title: control

description: 3 samples were combined for analysis

value: IgG


title: 192 RNA


title: TMDP + Fluvastatin mevalonate biol rep 2 [CK20]

city: Baltimore

first: Peter

middle: J

last: Espenshade

address: 725 N Wolfe St

institute: Johns Hopkins University

description:
raw_counts.csv
TPM_values.csv
CK20

data_processing:
Sequences were trimmed using Trimmomatic v.0.36.
Trimmed reads were mapped to GRCh38 reference genome using STAR aligner v.2.5.2b.
Unique gene hits were identified using featureCounts from Subread package v.1.5.2.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample
Supplementary files format and content: comma-delimited text file includes TPM values for each sample

source_name: pancreas

growth_protocol: Pa03c cells were maintained in DMEM supplemented with 10% FBS and 1% penicilin-streptomycin at 37˚C and 5% CO2.

extract_protocol:
RNA was collected using NEB Monarch Total RNA Miniprep Kit (#T2010S); 2 µg total RNA was used for library prep.
mRNA was enriched by polyA selection, reverse transcribed to cDNA, then end repaired, adenylated, and ligated to adaptors.

treatment_protocol: 2.5 µM TMDP and/or 5 µM Fluvastatin in DMEM supplemented with 10% lipoprotein deficient serum and 1% penicilin-streptomycin with/without 1 mM mevalonate for 16 hours.

value: pancreas

value: pancreatic cancer liver metastasis

value: KRAS G12D; TP53 L344P

value: TMDP + Fluvastatin mevalonate

value: 16 hours


title: P3-PBS2

city: Paris

first: Adrien

last: Dufour

address: 48, boulevard serurier

country: France

institute: INSERM

data_processing:
UMI Barcode read:  Read1
UMI barcode offset:  38 or 41bp (depending on barcode1 size) => cf D73
UMI barcode size:  6
Cell barcode read:  Read1
Cell barcode offset:  0
Cell barcode size:  38 to 41bp (barcode1 = [8 to 11bp], spacer w1=22bp, barcode2=8bp) => cf D73
cDNA read:  Read2
cDNA read offset:  0
cDNA read size:  50
Sample barcode read:  index2
Sample barcode offset:  0
Sample barcode size:  6
Data analysis protocol:  https://github.com/Goultard59/indrops
Genome_build: GRCm38.85 Mus musculus
Supplementary_files_format_and_content:  gene count matrix

source_name: brain

extract_protocol:
Tissue dissociation:  NTDK miltenyi
Cell enrichment:  MACS
Enrichment markers:  CD11B microbeads (Miltenyi 130-049-601)
Single cell isolation:  droplet-based cell isolation
Single cell entity:  whole cell
Single cell quality metric:  Cell encapsulation follows Poisson distribution (lambda 0.1) => flow rate control with syringe pump and Droplet size and bead loading control with droplet dye and laser detection + high speed camera (Phantom)
Single cell identifier:  bc*_1
Single cell isolation protocol:  droplet-based cell isolation
Nucleic acid library construction protocol:  inDrops like, adapted from Zilionis et al (Nature Protocols 2017), https://doi.org/10.1038/nprot.2016.154
Nucleic acid sequencing protocol:  Illumina PE sequencing
Library construction:  inDrops like, adapted from Zilionis et al (Nature Protocols 2017), https://doi.org/10.1038/nprot.2016.154
Input molecule:  polyadenylated RNA
Primer:  oligodT
Amplification method:  IVT (In vitro Transcription)
Amplification cycles:  12 to 17 cycles (Finale PCR to incorporate Illimuna index)
End bias:  3'
Library strand:  both (PE sequencing)
Spike in:  NO

treatment_protocol: In brief, a 5µL volume of phosphate-buffered saline (PBS) containing 10µg/kg injection of recombinant mouse IL1B or of PBS alone (control) was injected intraperitoneally twice a day (morning and evening) on days postnatal P1 to P4 and once in the morning on day P5.

tag: disease state

value: neonatal neuroinflammation mice model

tag: developmental stage

value: post natal day 3

value: brain

value: CD11b positive

tag: Sex

value: male

tag: biological replicate

tag: technical replicate

value: PBS

tag: expected cell number


title: Naive cells_rep1

description:
Ribosome depeted RNA
3381_Naive_S20_L004
processed data file:
DESeq_naive_th17.txt
sailor_Naive_Th17_0.99_edited_sites.txt

tag: cell type

value: Naive CD4+

value: untreated


title: Th17 72h cells_rep1 [ATAC-seq]

value: (72hr) 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems)


title: TMDP + Fluvastatin mevalonate biol rep 1 [CK19]

description:
raw_counts.csv
TPM_values.csv
CK19

tag: tissue

tag: cell line

tag: genotype


title: 191 RNA

tag: yob decade

tag: pre/post menopause

value: pre


title: combo

description: 3 samples were combined for analysis

value: pancreatic cancer cell PAN02

tag: strain

tag: treatment


title: Th17 48h cells_rep2 [ATAC-seq]

source_name: Th17 48h cells

value: (48hr) 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems)


title: P3-PBS1


title: Fluvastatin mevalonate biol rep 2 [CK18]

description:
raw_counts.csv
TPM_values.csv
CK18

value: pancreas

value: Fluvastatin mevalonate

tag: time


title: 190 RNA

value: post


title: Th17 48h cells_rep1 [ATAC-seq]


title: P3-IL1-2


title: Fluvastatin mevalonate biol rep 1 [CK17]

description:
raw_counts.csv
TPM_values.csv
CK17

value: pancreatic cancer liver metastasis

value: KRAS G12D; TP53 L344P


title: 189 RNA


title: P3-IL1-1

value: neonatal neuroinflammation mice model


title: 188 RNA


title: Naive cells_rep1 [ATAC-seq]

growth_protocol: Th17 cells were grown from isolated Naive CD4+ T cells  in the preence of 0.1ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).


title: P1-PBS2

value: post natal day 1


title: 186 RNA


title: TMDP mevalonate biol rep 1 [CK15]

description:
raw_counts.csv
TPM_values.csv
CK15

value: TMDP mevalonate

value: 16 hours


title: 187 RNA


title: Vehicle mevalonate biol rep 1 [CK13]

description:
raw_counts.csv
TPM_values.csv
CK13

value: Vehicle mevalonate


title: P1-PBS1

value: brain

value: CD11b positive

value: male

value: PBS


title: P1-IL1-2


title: ALFA-Pho4

city: Boston

first: Shubham

last: Khetan

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description: Library name: ALFA-Pho4

library_source: other

data_processing:
Defining PADIT-seq activity and calling active k-mers: Barcodes from sequencing libraries were mapped to the associated TFBS based on previously obtained TFBS-BC pairings. Barcode counts per TFBS were obtained for each library and merged into a single data frame. Quality control was performed by generating Pearson correlation heatmaps and principal component analysis (PCA) plots to assess reproducibility between replicates and overall structure of the data. For differential activity analysis, read counts for the DBD of interest and a ‘no DBD’ control, across 3-5 replicates each, were analyzed using DESeq2. TFBS significantly bound by the DBD of interest (active k-mers) were identified by applying a false discovery rate (FDR) threshold of 5%.
Assembly: Custom: TFBS_BC_Combinations_all_10-mers_library.csv and TFBS_BC_Combinations_Output_UNIQUE.txt
Supplementary files format and content: ReadCounts_perTFBS_all10mers_4TFs-NKX2.5-TBX5-Pho4-Cbf1.txt.gz: Tab separated read count matrix
Supplementary files format and content: dds_results_NKX2.5_df.txt.gz: DESeq2 output comparing read counts from ALFA-NKX2.5 to the No-DBD control.
Supplementary files format and content: dds_results_TBX5_df.txt.gz: DESeq2 output comparing read counts from TBX5-ALFA to the No-DBD control.
Supplementary files format and content: dds_results_PHO4_df.txt.gz: DESeq2 output comparing read counts from ALFA-Pho4 to the No-DBD control.
Supplementary files format and content: dds_results_CBF1_df.txt.gz: DESeq2 output comparing read counts from ALFA-Cbf1 to the No-DBD control.

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
PADIT-seq experiments: To remove any supercoiling, PADIT-seq reporter libraries were first linearized with DrdI (NEB), which cuts a 12-bp DNA sequence (GACNNNN/NNGTC) only once in the pGL4.23 vector. For every DBD tested, the following 30 μl PURExpress IVTT reactions (NEB) were assembled: 10 μl Solution A, 7.5 μl Solution B, 1 μl murine Rnase inhibitor (NEB), 3 μl 100 mM rNTPs, 0.45 μl 1000 mM magnesium acetate, 3 μl previously purified nbALFA-T7-RNA-Polymerase, ~300 ng linearized PADIT-seq reporter plasmid library, and ‘pT7 -DBD-T7Term’. The linearized PADIT-seq reporter plasmid library was mixed with ‘pT7 -DBD-T7Term’ amplicons in a 2:1 molar ratio. For PADIT-seq experiments with HOXD13 and EGR1, the 30 μl PURExpress IVTT reactions were split into three wells, and all subsequent steps were performed separately (3 biological replicates). For PADIT-seq experiments with NKX2.5, TBX5, Pho4 and Cbf1, the PURExpress IVTT reactions were scaled to 50 μl, split into five wells, and all subsequent steps were performed separately (5 biological replicates). We performed a total of 7 control ‘no DBD’ reactions (10 μl each), 3 for the first experiment with HOXD13 and EGR1, and 4 for the second experiment with NKX2.5, TBX5, Pho4 and Cbf1.  cDNA synthesis of PADIT-seq reporter RNAs: After 4 hours at 37°C, the 10 μl reactions were purified with RNAClean XP (Beckman Coulter) according to manufacturer’s instructions, eluting in 35 μl nuclease-free water. 2 μl barcoded cDNA synthesis primers (each at 0.1 uM final concentration) were added to 18 μl purified RNA, incubated at 75°C for 3 mins, then placed on ice. cDNA was synthesized by adding 10 2X Multiscribe reaction mix (Thermo Fisher Scientific), and incubating at 25°C for 20 minutes, followed by 37°C for 120 minutes. Minus reverse transcriptase controls were performed in parallel. Excess primers were removed from the cDNA:RNA duplexes by adding exonuclease I (NEB) and incubating at 37°C for 60 mins, followed by heat inactivation at 80°C for 20 mins. Quantitative PCR was performed to verify degradation of all excess primers and to determine the threshold cycle of sample cDNAs.   PADIT-seq library preparation for Illumina sequencing: For PADIT-seq experiments with HOXD13 and EGR1 using the small-scale PADIT-seq library, barcoded cDNAs synthesized from reporter RNAs were pooled prior to PCR amplification. The pooled cDNA was amplified in a single PCR reaction using KAPA HiFi polymerase with primers 'MPRA_AmpliconEZ_FWD' and 'MPRA_AmpEZ_REV2.0'. This generated a PCR-1 product that was then used as template for a second PCR with primers '#34_MPRA' and ‘169_TruSeq_Multiplex_220_2’ to attach Illumina adapters and sample barcodes. For PADIT-seq experiment with HOXD13 and EGR1 using the all-10-mers library, barcoded cDNAs were kept separate and amplified in individual PCR reactions rather than pooled. For PADIT-seq experiments with NKX2.5, TBX5, Pho4 and Cbf1 using the all-10-mers library, barcoded cDNAs from replicates were pooled for each TF. The cDNA from PADIT-seq reporter RNAs was amplified using KAPA HiFi HotStart Polymerase (Roche) with primers 'MPRA_AmpliconEZ_FWD' and 'MPRA_AmpEZ_REV2.0'. This generated PCR-1 products that was then used as template for a second PCR with primers '#34_MPRA' and indexed TruSeq primers to attach Illumina adapters and sample barcodes. This was followed by Illumina sequencing, aiming for >50X coverage for each replicate (sample sequencing statistics in Table S4).
Construction of the all-10mers PADIT-seq reporter library: We designed and ordered two IDT Ultramers - one containing all possible 10-bp DNA sequences as candidate TFBS (‘All10mersTFBS_Top’), and another containing all possible 25-bp DNA sequences to serve as barcodes (‘25bpsBC_Bottom’). The two Ultramers were mixed in an equimolar ratio and double stranded in a single PCR cycle using KAPA HiFi polymerase. The pGL4.23 plasmid vector backbone was again PCR amplified in 2 steps with Q5 High-Fidelity 2X Master Mix. First, the backbone was amplified with primers ‘pGL4.23_FWD’ and ‘pGL4.23_REV’ to exclude the luciferase open reading frame. The resulting amplicon (2359-bps) was then further amplified with primers 'T7Term_pGL4.23_F_2.0' and 'pGL4.23_REV' to add a 56-bps DNA sequence as an overlapping region for Gibson Assembly, which was performed with the resulting amplicon (2415-bps) and the double-stranded oligo-pool mixed in equimolar ratios. Following desalting with a mixed cellulose esters (MCE) hydrophilic membrane (0.025 um), the assembled reporter library plasmid was electroporated into E. cloni 10G Supreme cells (n = 13 transformations). Based on plating experiments, the total number of transformants obtained was estimated to be 110 million, providing an average of ~100 barcodes per TFBS. The transformed cells were recovered, grown for 6.5 hrs, and maxi-prepped to obtain the complete all-10mers PADIT-seq reporter plasmid library containing over 100 million clones. Correct library assembly was validated by diagnostic PCR and Sanger sequencing of 10 colonies.  Obtaining TFBS-BC pairing in the all-10mers PADIT-seq reporter library: To obtain TFBS-BC pairings, the all-10mers PADIT-seq reporter library was PCR amplified using KAPA HiFi polymerase. Four forward primers were designed with partial Illumina adapters, 6N randomized bases, and 2-bps staggers (‘All_10mers_LibSeq_F1-4’). These were used individually with a single reverse primer (‘All_10mers_LibSeq_R’) to generate 4 PCR-1 products of expected sizes 213-219-bps (9 cycles). The 4 PCR-1 products were then used as template in PCR-2 (5 cycles) with TruSeq indexed primers to attach Illumina sample indexes. This generated 4 PCR-2 products of expected size 272-278-bps. After PCR amplification, the 4 products were SPRI cleaned and analyzed on Tapestation to confirm expected sizes. The 4 indexed libraries were sequenced separately on a NovaSeq6000 (2x150 bp reads). The sequencing data from each of the 4 indexed libraries (F1-F4) was combined and processed using custom scripts to extract unique TFBS-BC combinations along with their counts by matching the constant flanking regions. Barcodes unambiguously associated with only 1 TFBS across all 4 libraries were classified as ‘single TFBS barcodes’ and retained. The all-10mers PADIT-seq reporter plasmid library was amplified in 4 separate PCR reactions (F1-F4) with different TruSeq indexes to identify potential PCR-mediated recombination artifacts in the following way: for barcodes associated with multiple TFBS, an initial filter retained only TFBS observed independently in at least 2 of the 4 libraries. The rationale being that TFBS-BC occurrence in multiple independent libraries indicates likely true pairings versus artifacts of PCR-mediated recombination. After this first multi-library filtering step, any barcodes still associated with multiple TFBS were removed entirely to eliminate ambiguities. As an additional filter, barcodes where the top TFBS had fewer reads than the sum of discarded TFBS were removed. The ‘single TFBS barcodes’ and  vetted multiple TFBS barcodes were combined to obtain high-confidence 1:1 TFBS-BC pairs for downstream analysis. This multi-step filtering process leveraged the independently prepared sequencing libraries to remove incorrect and ambiguous TFBS-BC pairings arising from PCR-mediated recombination. It enabled retaining high-confidence barcode-TFBS pairs reproducibly identified across multiple libraries while discarding likely PCR artifacts and errors.

value: synthetic construct


title: ALFA-Cbf1

description: Library name: ALFA-Cbf1


title: P1-IL1-1


title: PF + Fluvastatin biol rep 2 [CK12]

description:
raw_counts.csv
TPM_values.csv
CK12

value: PF + Fluvastatin


title: ALFA-NKX2.5

description: Library name: ALFA-NKX2.5


title: PF + Fluvastatin biol rep 1 [CK11]

description:
raw_counts.csv
TPM_values.csv
CK11


title: P5-PBS-4

value: post natal day 5


title: 183 RNA

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapping against human reference genome hs37d5 using STAR-2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region (Gencode29) associated with each gene.
To account for differences in library size between samples, Trimmed Mean of M values (TMM) normalization using calcNormFactors(), also from edgeR, was applied.
All data were then transformed using voom.
Assembly: hs37d5
Supplementary files format and content: tab-delimited text files include raw gene count for each sample

value: pre


title: 184 RNA


title: P5-IL1B-4


title: NoDBD_Batch2

description: Library name: NoDBD_Batch2


title: 182 RNA


title: TBX5-ALFA

description: Library name: TBX5-ALFA


title: P5-PBS-3


title: Naive cells_rep2 [ATAC-seq]

value: Naive CD4+

value: untreated


title: TMDP + Fluvastatin biol rep 1 [CK9]

description:
raw_counts.csv
TPM_values.csv
CK9

value: pancreas

value: pancreatic cancer liver metastasis

value: TMDP + Fluvastatin


title: Vehicle mevalonate biol rep 2 [CK14]

description:
raw_counts.csv
TPM_values.csv
CK14

value: KRAS G12D; TP53 L344P


title: 181 RNA


title: yeast extract 1.0%, starch 5% medium, day4, replicate 3

city: Tobuki-machi, Hachioji-shi

first: Kentaro

last: Mine

state: Tokyo

country: Japan

institute: Nissin Foods Holdings Co., Ltd.

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: Lipst1 1: https://mycocosm.jgi.doe.gov/Lipst1_1/Lipst1_1.home.html
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

organism: Lipomyces starkeyi NRRL Y-11557

source_name: yeast cells

growth_protocol: Yeast cells were cultivated in "Y1D5 (1% yeast extract, 5% glucose) and Y1S5 medium (1% yeast extract, 5% starch)" or "Y0.5D5 (0.5% yeast extract, 5% glucose) and Y0.5S5 medium (0.5% yeast extract, 5% starch)" at 30℃ for 4 days.

extract_protocol:
The total RNA was isolated from cells using ISOGEN II Reagent (Nippongene) and purified using Nucleospin RNA (Takara) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

value: yeast cells

tag: medium

value: starch medium


title: P5-PBS-2

value: neonatal neuroinflammation mice model


title: yeast extract 1.0%, starch 5% medium, day4, replicate 2


title: TMDP mevalonate biol rep 2 [CK16]

description:
raw_counts.csv
TPM_values.csv
CK16

value: TMDP mevalonate

value: 16 hours


title: PF biol rep 2 [CK8]

description:
raw_counts.csv
TPM_values.csv
CK8

value: PF


title: 185 RNA

extract_protocol:
RNA was harvested using the Qiagen All-Prep RNA isolation kit
RNA libraries were prepared by using Illumina TruSeqTM RNA Exome Library Preparation Kit (Illumina Inc., San Diego, CA) , following the manufacturer’s protocol

value: post


title: yeast extract 1.0%, starch 5% medium, day4, replicate 1


title: P5-IL1B-3

value: brain

value: CD11b positive

value: male


title: PF biol rep 1 [CK7]

description:
raw_counts.csv
TPM_values.csv
CK7


title: Fluvastatin biol rep 2 [CK6]

description:
raw_counts.csv
TPM_values.csv
CK6

value: Fluvastatin


title: TMDP + Fluvastatin biol rep 2 [CK10]

description:
raw_counts.csv
TPM_values.csv
CK10


title: yeast extract 0.5%, starch 5% medium, day4, replicate 3


title: 179 RNA

value: pre


title: 178 RNA


title: yeast extract 0.5%, starch 5% medium, day4, replicate 2


title: P5-PBS-1

value: post natal day 5

value: PBS


title: Fluvastatin biol rep 1 [CK5]

description:
raw_counts.csv
TPM_values.csv
CK5

value: pancreas

value: pancreatic cancer liver metastasis


title: yeast extract 0.5%, starch 5% medium, day4, replicate 1


title: 175 RNA


title: TMDP biol rep 1 [CK3]

description:
raw_counts.csv
TPM_values.csv
CK3

value: KRAS G12D; TP53 L344P

value: TMDP


title: yeast extract 1.0%, glucose 5% medium, day4, replicate 3

value: yeast cells

value: glucose medium


title: 177 RNA


title: bm0677 mutant rep 3

city: Shenzhen

first: Shanshan

last: Xu

address: Xueyuan Avenue, No. 1066

institute: Shenzhen University

data_processing:
Illumina Casava1.8 software used for base-calling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 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.
Assembly: acession number: CP009679
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Bacillus velezensis

source_name: biofilm and planktonic bacteria

extract_protocol:
The growth status of samples in MSgg medium were analyzed and 36 hours was selected. The cells at the selected time point were collected and total RNA was extracted using the Total RNA Kit (OMEGA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 174 RNA


title: yeast extract 1.0%, glucose 5% medium, day4, replicate 2


title: Vehicle biol rep 2 [CK2]

description:
raw_counts.csv
TPM_values.csv
CK2

value: Vehicle


title: bm0677 mutant rep 2


title: bm0677 mutant rep 1


title: yeast extract 1.0%, glucose 5% medium, day4, replicate 1


title: 180 RNA


title: Vehicle biol rep 1 [CK1]

description:
raw_counts.csv
TPM_values.csv
CK1

value: 16 hours


title: P5-IL1B-2

value: neonatal neuroinflammation mice model


title: 172 RNA


title: yeast extract 0.5%, glucose 5% medium, day4, replicate 3


title: MS-13_TCR

city: Munich

first: Klaus

last: Dornmair

address: Grosshaderner Strasse 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital LMU Munich

description: 10x Genomics

data_processing:
Raw data obtained from sequencing was pre-processed and aligned to the human reference genome GRCh38-2020-A using Cell Ranger (10 Genomics, v6.0.2).
Pre-processed data were then further processed and analysed in JupyterLab (v3.2.1) using an R kernel (R v4.1.3and the R package Seurat (v4.1.1). In summary, data from GEX and CSP (=ADT) libraries were combined for each sample and quality-filtered to remove low-quality cells, doublets, and dead cells. Cells were kept if the contained >500 and <20,000 RNA molecules, >200 and <2,500 genes, and ≤7.5% mitochondrial RNA. Read counts from GEX and CSP assays were normalized by sample using the NormalizeData-function with normalization-method set to “LogNormalize” and “CLR”, respectively. .
CD8+ and CD4+ T-cell subsets were identified based on normalized CSP (=ADT) barcode read count data. Cells that were at ≥1.5-fold enriched in CD8A compared to CD4 were assigned the cell type CD8+ T cells. Conversely, cells that were at least 1.5-fold depleted in CD8A compared to CD4 were assigned the cell type CD4+ T cells. The remaining cells were assigned to CD8+ T cells if their normalized CD8A RNA count in the RNA assay was ≥0.8 and CD4 expression was <0.2, and to CD4+ T cells if the opposite was the case. Cells that could not be assigned to CD4+ T cells or CD8+ T cells and cells that expressed no TCR chain were categorized as ambiguous
Assembly: GRCh38-2020-A
Supplementary files format and content: Cellranger output files: mRNA+ADT_matrix.mtx.gz,  mRNA+ADT_barcodes.tsv.gz,  mRNA+ADT_features.tsv.gz
Supplementary files format and content: Cellranger output files: TCR_filtered_contig_annotations.csv, TCR_clonotypes.csv

source_name: cerebrospinal fluid cells

extract_protocol:
Single cells from CSF were labelled with barcoded antibodies targeting CD4 or CD8A (cell surface protein (CSP) staining with antibody-derived tags (ADT)) using the TotalSeq-C with 10x Feature Barcoding Technology (Biolegend) as described in 10x Genomics protocol CG000149 (Rev B).
Single-cell gene expression (GEX), T-cell receptor (TCR), and cell surface protein (CSP = antibody-derived tags (ADT)) libraries were prepared using the 10x Genomics platform according to protocol CG000208 (Rev F). All antibody-labelled CSF cells from each sample were used as input. Nuclease-free water was added to the barcode antibody-labelled cells to a final volume of 37.8 µL and the protocol was carried out with minor alterations: TE buffer (Affymetrix #J75793) was used instead of elution buffer EB. ThermoScientific 2x Phusion MasterMix with HF (#F-531) was used instead of the Amplification Master Mix at step 4.1 and 4.3.
OTHER: scRNAseq, CITE-seq, TCRseq

value: cerebrospinal fluid cells

value: primary cells

value: untreated

tag: library type

value: TCR


title: wild-type rep 2

value: wild-type


title: 171 RNA

value: pre


title: yeast extract 0.5%, glucose 5% medium, day4, replicate 2


title: MS-12_TCR

description: 10x Genomics


title: 170 RNA


title: TMDP biol rep 2 [CK4]

description:
raw_counts.csv
TPM_values.csv
CK4


title: P5-IL1B-1

tag: disease state

value: post natal day 5

value: brain

value: CD11b positive

value: male


title: wild-type rep 1


title: MS-5_TCR

description: 10x Genomics


title: yeast extract 0.5%, glucose 5% medium, day4, replicate 1


title: RIS-3_TCR

description: 10x Genomics


title: yeast extract 1.0%, starch 5% medium, day3, replicate 3

value: starch medium


title: 168 RNA


title: WT-1-2

city: Kunming

first: Juan

last: Li

state: Yunnan

address: North Cuihu Road #@

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Assembly: HiSat2 and StringTie
Supplementary files format and content: xls file includes tpm value for each sample

organism: Orbilia oligospora

growth_protocol: The wild-type and  mutant strains were cultured on Water Agar(WA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

value: Fungal hyphae cells

value: wild type

value: Trap induction with nematode extract


title: 173 RNA

city: Tampa

first: Chia-Ho

institute: Moffitt Cancer Center


title: yeast extract 1.0%, starch 5% medium, day3, replicate 1

value: yeast cells


title: IIH-5_TCR

description: 10x Genomics


title: RIS-2_TCR

description: 10x Genomics


title: wild-type rep 3


title: WT-0-3

value: no treatment


title: 167 RNA


title: 166 RNA


title: WT-1-1


title: yeast extract 0.5%, starch 5% medium, day3, replicate 3


title: WT-1-3


title: WT-0-2


title: 165 RNA


title: yeast extract 0.5%, starch 5% medium, day3, replicate 2


title: IIH-3_TCR

description: 10x Genomics


title: yeast extract 0.5%, starch 5% medium, day3, replicate 1


title: 164 RNA


title: 169 RNA


title: IIH-4_TCR

description: 10x Genomics


title: WT-0-1


title: IIH-2_TCR

description: 10x Genomics


title: yeast extract 1.0%, starch 5% medium, day3, replicate 2


title: 163 RNA


title: IIH-1_TCR

description: 10x Genomics


title: 162 RNA


title: yeast extract 1.0%, glucose 5% medium, day3, replicate 2

value: glucose medium


title: Ao129-1-3

value: delta-AobZip129 mutant strain


title: Ao129-1-2


title: MS-13_GEX

description: 10x Genomics

molecule: polyA RNA

value: cerebrospinal fluid cells

value: primary cells

value: mRNA, ADT

tag: adt

value: TotalSeq-C0072 anti-human CD4 Antibody, TotalSeq-C0046 anti-human CD8 Antibody


title: 161 RNA

value: pre


title: Ao129-1-1


title: yeast extract 1.0%, glucose 5% medium, day3, replicate 1


title: MS-12_GEX

description: 10x Genomics

value: untreated


title: Ao129-0-3


title: yeast extract 0.5%, glucose 5% medium, day3, replicate 3


title: 160 RNA


title: 159 RNA


title: MS-5_GEX

description: 10x Genomics


title: yeast extract 0.5%, glucose 5% medium, day3, replicate 2


title: Ao129-0-2


title: RIS-3_GEX

description: 10x Genomics


title: 158 RNA


title: Ao129-0-1


title: yeast extract 0.5%, glucose 5% medium, day3, replicate 1


title: yeast extract 1.0%, starch 5% medium, day2, replicate 3


title: 157 RNA


title: yeast extract 1.0%, glucose 5% medium, day3, replicate 3


title: IIH-5_GEX

description: 10x Genomics


title: 156 RNA

value: post


title: 93_D_0_rep3

city: Regensburg

first: Bernd

last: Daller

address: Franz-Josef-Strauß-Allee 11

institute: University Regensburg

data_processing:
Adapter were removed using cutadapt 4.4.
Further analysis was based on nextflow nf-core pipeline nfcore/rnaseq version 3.14. with salmon as quantifier
Assembly: The wildtye strain of each organism was used as reference PRJNA1158744
Supplementary files format and content: Tab-delimited text file containing tpm values of genes for each sample

organism: Streptococcus mitis

extract_protocol:
RNA was extracted using the Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research, Freiburg, Germany) according to the manufacturer's protocol. Genomic DNA contamination was eliminated using the TURBO DNase Kit (Thermo Fisher Scientific, Waltham, MA, USA). The RNA was further purified and concentrated using the RNAClean XP Reagent (Beckman Coulter, Brea, CA, USA). RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
High-quality RNA samples were reverse transcribed into cDNA using the Ion Torrent™ NGS Reverse Transcription Kit (Thermo Fisher Scientific). cDNA libraries were constructed with the Ion Torrent™ Ion Total RNA-Seq Kit v2, incorporating adapters from the Ion Torrent™ Ion Xpress™ Barcode Adapters 1-96 Kit for multiplexing. Library amplification and template preparation were performed using the Ion 550™ Kit on an IonChef system. Libraries were loaded onto four Ion 550 chips for sequencing on an Ion GeneStudio™ S5 Plus system (Thermo Fisher Scientific).

value: D

value: BHI broth

tag: treatment time

value: 5 min

tag: pool


title: yeast extract 1.0%, starch 5% medium, day2, replicate 2

value: starch medium


title: IIH-4_GEX

description: 10x Genomics


title: 93_D_0_rep2


title: yeast extract 1.0%, starch 5% medium, day2, replicate 1


title: 155 RNA

last: Cheng

address: 12902 USF Magnolia Drive


title: 154 RNA


title: IIH-3_GEX

description: 10x Genomics


title: 93_D_0_rep1


title: IIH-2_GEX

description: 10x Genomics


title: yeast extract 0.5%, starch 5% medium, day2, replicate 3


title: 153 RNA


title: 93_D_125_rep3

value: 125 µg/mL Chlorhexidine in BHI broth


title: IIH-1_GEX

description: 10x Genomics


title: 152 RNA


title: yeast extract 0.5%, starch 5% medium, day2, replicate 1


title: 93_D_125_rep2


title: 93_D_125_rep1


title: 151 RNA


title: RIS-2_GEX

description: 10x Genomics


title: yeast extract 0.5%, starch 5% medium, day2, replicate 2


title: D90, CMZ, snRNA

first: Chenghao

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

library_source: transcriptomic single cell

data_processing:
Raw 10x Genomics data were processed with the standard Cell Ranger pipeline (v3.0.2), apping to the GRCh38 human genome.
Assembly: hg38
Supplementary files format and content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)

molecule: nuclear RNA

source_name: retina

extract_protocol:
Wash the samples twice with PBS, add 0.5 ml of digestion solution (containing 0.25% Trypsin-EDTA, 50 μg/ml DNase I, 20 μg/ml Y-27632), and digest at 37°C for 10 minutes. Add 1 ml of culture medium to neutralize the digestion, filter through a mesh filter, centrifuge at 1000 rpm for 5 minutes, remove the supernatant, and resuspend in an appropriate volume of suspension solution (containing PBS, 50 μg/ml DNase I, 20 μg/ml Y-27632). Count and calculate the proportion of viable cells (≥90%), adjust the cell concentration to 1000 cells/μL, and keep on ice for further testing
Using the single-cell sequencing platform (10x Chromium Single Cell Platform), perform on-board processing of the cell samples (combining cells/enzymes with Gel beads to form GEMs, cell lysis, cDNA amplification, library construction, etc.)

value: retina

value: organoids derived from hPSCs


title: 20: KO, hypoxia, experiment 3

first: Yan

last: Zeng

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human.GRCh38 whole genome using hisat2-2.0.1.
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi et al., 2008.
Assembly: human.GRCh38
Supplementary files format and content: .txt files contain FPKM values

growth_protocol: Cells wre grown in DMEM supplemented with 10% FBS and 2 mM L-glutamine at 37oC and 5% CO2 in an incubator.

extract_protocol:
Total RNA was harvested using Trizol reagent.
1 μg total RNA was used for library preparation. Poly(A) mRNA was isolated using oligo(dT) beads.  mRNA was fragmented with divalent cations and high temperature. Random Primers were used to prime cDNA synthesis, and first strand cDNA and the second-strand cDNA synthesized. Double-stranded cDNA was treated to repair both ends and add a dA-tail, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. .Each sample was amplified by PCR using adapter sequence primers at both ends.  Libraries were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

treatment_protocol: Cells were treated with DMSO (control) or 0.5 mM DMOG for 48 hours.

value: miR-210 KO

value: DMOG


title: yeast extract 1.0%, glucose 5% medium, day2, replicate 3

value: yeast cells

value: glucose medium


title: 93_WT_0_rep3

value: WT


title: 150 RNA


title: 93_WT_0_rep2


title: 19: KO, experiment 3

value: Control


title: yeast extract 1.0%, glucose 5% medium, day2, replicate 2


title: 149 RNA


title: yeast extract 1.0%, glucose 5% medium, day2, replicate 1


title: 18: KO, hypoxia, experiment 3


title: 93_WT_0_rep1


title: 148 RNA


title: 93_WT_125_rep3


title: 17: KO, experiment 3


title: 145 RNA


title: yeast extract 0.5%, glucose 5% medium, day2, replicate 2


title: 16: KO, hypoxia, experiment 3


title: 93_WT_125_rep2


title: yeast extract 0.5%, glucose 5% medium, day2, replicate 1


title: 93_WT_125_rep1


title: 78_E_0_rep3

organism: Streptococcus vestibularis

value: E


title: 15: KO, experiment 3


title: 143 RNA

value: pre


title: 14: WT, hypoxia, experiment 3


title: 78_E_0_rep2


title: 142 RNA


title: 141 RNA


title: 13: WT, experiment 3


title: 12: KO, hypoxia, experiment 2


title: 140 RNA


title: yeast extract 0.5%, glucose 5% medium, day2, replicate 3


title: 139 RNA


title: 78_E_125_rep3


title: 78_E_125_rep2


title: 11: KO, experiment 2


title: Aeromonas hydrophila,brackish water (20 g/L NaCl), 18 h,rep2

city: guangdong

first: yuan

last: sun

state: shenzhen

address: Zhiyuan Building, Canghai Campus, 3688 Nanhai Avenue, Nanshan District, Shenzhen City

institute: shenzhen universuty

description: Library name: Ah20-2

data_processing:
Gene annotation was conducted using the NR, SwissProt, PFAM, GO, KEGG, and STRING databases. The FPKM values of the differentially expressed genes (DEGs) were normalized through log2 transformation and median-centered. Genes with an adjusted p-value < 0.001 and log2|fold-change| ≥ 1 were considered statistically significant
Assembly: Aeromonas hydrophila (ASM1602687v1)
Supplementary files format and content: Excel files include raw date for each sample

organism: Aeromonas hydrophila

source_name: Aeromonas hydrophila (Ah201416)

extract_protocol:
Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit (Promega, USA) following the manufacturer’s instructions. 2 μg of RNA samples were used to construct an RNA-Seq library using a TruseqTM RNA sample prep Kit for Illumina (NEB, USA).
The indexed libraries were subsequently pooled and subjected to sequencing on the HiSeq™ 2500 platform (Illumina, USA), which generated 2*150-bp paired-end reads. The reference genome used was A. hydrophila (ASM1602687v1).

value: Aeromonas hydrophila (Ah201416)

value: brackish water (20 g/L NaCl)


title: Aeromonas hydrophila,brackish water (20 g/L NaCl), 18 h,rep1

description: Library name: Ah20-1


title: 144 RNA

value: post


title: Aeromonas hydrophila,brackish water (10 g/L NaCl), 18 h,rep3

description: Library name: Ah10-3

value: brackish water (10 g/L NaCl)


title: Aeromonas hydrophila,brackish water (10 g/L NaCl), 18 h,rep2

description: Library name: Ah10-2


title: 10: KO, hypoxia, experiment 2


title: Aeromonas hydrophila,brackish water (20 g/L NaCl), 18 h,rep3

description: Library name: Ah20-3


title: 138 RNA


title: 78_E_125_rep1

value: 5 min


title: Aeromonas hydrophila,brackish water (10 g/L NaCl), 18 h,rep1

description: Library name: Ah10-1


title: 9: KO, experiment 2


title: 137 RNA


title: 78_WT_0_rep3

value: BHI broth


title: Aeromonas hydrophila,freshwater (salt-free, 0 g/L NaCl), 18 h,rep3

description: Library name: Ah0-3

value: freshwater (salt-free, 0 g/L NaCl)


title: 78_WT_0_rep2


title: 136 RNA


title: 78_E_0_rep1


title: 8: WT, hypoxia, experiment 2


title: 7: WT, experiment 2


title: 78_WT_0_rep1


title: 135 RNA


title: Aeromonas hydrophila,freshwater (salt-free, 0 g/L NaCl), 18 h,rep1

description: Library name: Ah0-1


title: 6: KO, hypoxia, experiment 1


title: 78_WT_125_rep3

value: 125 µg/mL Chlorhexidine in BHI broth


title: 133 RNA


title: 5: KO, experiment 1


title: 78_WT_125_rep1


title: 132 RNA


title: FO_OEFoabaA_STAGE4_R1

city: East Lansing

first: Frances

last: Trail

state: MI

address: 612 Wilson Road, Room 342

department: Plant Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. The low-quality reads were removed using the read filtering tool, Trimmomatic, Version 0.39. The 3’ ends of NovaSeq6000 single-end 100 bp reads were trimmed to 50 bp reads (keeping the first 50 bp) using Trimmomatic Version 0.39.
The trimmed reads were mapped to the indexed reference sequences using HISAT 2.2.1.
The HISAT alignments in SAM format were then sorted and converted to BAM format using SAM tools.
Count files were then generated using HTSeq Version 0.11.1.
The DESeq2 package Version 1.30.1 in R was used to normalize the read counts and to perform differential expression analysis.
Assembly: The reference sequence used for the alignment are A. fumigatus AF293 (GCA_000002655.1), A. nidulans A4 (GCA_000149205.2), and F. oxysporum NRRL 32931 (GCA_000271745.2)
Supplementary files format and content: Tab-demilited text file includes raw counts for each sample

organism: Fusarium oxysporum

source_name: Germinated conidia

growth_protocol: For total RNA extraction of each germination stage on standard medium (Bird agar medium), a 200 µL aliquot of the conidial suspension (1 x 106 conidia/mL) of each species was inoculated onto a sterile cellophane sheet overlaid on Bird medium in a Petri dish (60 x 15 mm). Petri dishes containing inoculated sheets were then incubated at RT till the conidia reached respective germination stages.

extract_protocol:
Total RNA  from cellophane membranes was isolated using Trizol reagent. RNA was treated with RNase-Free DNase (Qiagen), purified further using RNA Clean and ConcentratorTM - 5 (ZymoResearch)
Libraries were prepared using the Illumina Stranded mRNA Prep - Ligation kit with IDT for Illumina RNA UD Indexes.

value: Germinated conidia

tag: Stage

value: Bird medium


title: FO_OEFoabaA_STAGE4_R3


title: FO_OEFoabaA_STAGE4_R2


title: 78_WT_125_rep2


title: 130 RNA


title: 73_A_0_rep3

organism: Streptococcus salivarius

value: A


title: 3: KO, experiment 1

value: miR-210 KO


title: FO_OEAfabaA_STAGE4_R2


title: Aeromonas hydrophila,freshwater (salt-free, 0 g/L NaCl), 18 h,rep2

description: Library name: Ah0-2


title: 2: WT, hypoxia, experiment 1

value: DMOG


title: 4: KO, hypoxia, experiment 1


title: 129 RNA


title: 73_A_0_rep1


title: 131 RNA


title: 1: WT, experiment 1

value: WT


title: FO_OEAfabaA_STAGE4_R1


title: FO_OEAfabaA_STAGE4_R3


title: D60, 40, CMZ, scRNA

value: retina

value: organoids derived from hPSCs


title: 134 RNA

value: pre


title: 73_A_125_rep3


title: 128 RNA


title: 127 RNA


title: FO_WT_STAGE4_R3


title: FO_WT_STAGE4_R2


title: 73_A_125_rep2


title: D60, 10, CMZ, scRNA


title: 73_A_125_rep1


title: 126 RNA


title: 73_A_0_rep2


title: 125 RNA


title: 73_WT_0_rep3


title: D60, 05, CMZ, scRNA


title: FO_WT_STAGE4_R1


title: FO_STAGE4_R3


title: D60, 0, CMZ, scRNA


title: 73_WT_0_rep2


title: FO_STAGE4_R2


title: 123 RNA


title: D60, 0, NR, snRNA


title: 122 RNA


title: FO_STAGE4_R1


title: 73_WT_0_rep1


title: 73_WT_125_rep3


title: NF3

city: shanghai

first: Zhenhao

last: Lin

address: shanghaixuhui

institute: Fudan University

data_processing:
3’ adaptor-trimming and low quality reads were removed by cutadapt software (v1.9.1)
TheBurrows-Wheeler Aligner (BWA) software (v0.7.17) was used to alignhigh-quality clean readsto the reference genome (UCSC hg19).
Circle-map software (v1.1.4) was used to detecteccDNAs within all samples, and samtoolssoftware(v1.7)was used to get raw soft-clipped read counts of the break point.
EdgeR (v3.32.1) software was used to perform normalization and differentially expressed eccDNA filter by p-value and fold change.
Bedtools (v2.30.0) software was used to annotate the eccDNAs.
Assembly: hg19
Supplementary files format and content: excel file includes raw counts and normalized values for each sample
Library strategy: Circle-Seq

source_name: Heart

extract_protocol:
samples of tissue were suspended in L1 solution (Plasmid Mini AX; A&A Biotechnology) and supplemented with Proteinase K (ThermoFisher) before incubation overnight at 50 °C with agitation. After Lysis, samples were alkaline treated,followed by precipitation of proteins and separation of chromosomal DNA from circular DNA through an ion exchange membrane column (Plasmid Mini AX; A&A Biotechnology). Column-purified DNA was treated with FastDigest MssI (Thermo Scientifific) to remove mitochondrial circular DNA and incubated at 37 °C for 16 h. Remaining linear DNA was removed by exonuclease (Plasmid-Safe ATP-dependent DNase, Epicentre) at 37 °C in a heating block and enzyme reaction was carried out continuously for 1 week, adding additional ATP and DNase every 24 h (30 units per day) according to the manufacturer’s protocol (Plasmid-Safe ATP-dependent DNase, Epicentre).
eccDNA-enriched samples were used as template for phi29 polymerase amplification reactions (REPLI-g Midi Kit) amplifying eccDNA at 30 °C for 2 days (46–48 h).Phi29-amplifified DNA was sheared by sonication (Bioruptor), and the fragmented DNA was subjected to library preparation with NEBNext® Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

value: Heart

tag: Sex

value: male

value: healthy


title: NF2


title: D60, 20, CMZ, scRNA

tag: cell type


title: 121 RNA


title: FO_STAGE3_R3

tag: tissue


title: 73_WT_125_rep2


title: FO_STAGE3_R2


title: 120 RNA


title: 73_WT_125_rep1


title: 124 RNA


title: FO_STAGE3_R1


title: F3

value: dilated cardiomyopathy


title: FO_STAGE2_R3


title: 119 RNA


title: F2


title: MCR3

city: Higashi-Hiroshima

first: Hirotsuna

last: Yamada

state: Hiroshima

address: 7-1 1-chome Kagamiyama

department: Graduate school of integrated science for life

institute: Hiroshima University

description: HiSeqX as an instrument model

data_processing:
Libraries were sequenced as 150 bp paired-end reads (HiSeqX; Macrogen Japan Corp., Tokyo, Japan) after being qualified and quantified by NEBNext Library Quant Kit for Illumina (MultiNA; Shimazu Corp., Kyoto, Japan).
Raw data were cleaned up by removing the adapter sequences and low-quality sequences in Trimmomatic (version 0.39; http://www.usadellab.org/cms/?page=trimmomatic).
After the assembly, the expression levels of contigs were quantified using Salmon (version 1.9.0; https://github.com/COMBINE-lab/salmon) and expressed as counts per million (CPM).
Contigs with low signal (CPM < 0.4) were removed. The expression data were normalized across these samples, and a 0.01 CPM was added to all normalized data to calculate the fold-change of gene expression between tips of cluster-bearing lateral roots (TCR) and mature cluster roots (MCR) using edgeR (version 4.0.14; https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Putative open reading frames and peptide sequences encoded by the assembled transcripts were predicted using TransDecoder (version　5.7.1; https://hpc.nih.gov/apps/TransDecoder.html). They were annotated using BLAST (blastp; version 2.12.0; https://blast.ncbi.nlm.nih.gov/Blast.cgi) with the proteome data of A. thaliana downloaded from the TAIR website (https://www.arabidopsis.org/download_files/Proteins/TAIR10_protein_lists/TAIR10_pep_20110103_representative_gene_model).
Annotated genes were detected through pairwise comparison analysis using edgeR, with a q-value < 0.05 and |log2 fold-change| ≧ 1, and they were considered differentially expressed genes (DEGs).
Assembly: The cleaned RNA-Seq reads were assembled using Trinity (version 2.15.1; https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/Trinity-v2.15.1) to obtain a reference de novo transcriptome of H. laurina.
Supplementary files format and content: raw counts.csv includes raw counts each sample
Supplementary files format and content: DEGs.csv file includes contig ID, annotation, counts per millions (CPM), log2|fold-change|,  p value, and q value of differentially expressed genes (q-value < 0.05 and |log2 fold-change| ≧ 1)

organism: Hakea laurina

source_name: tips of cluster-bearing lateral roots

growth_protocol: After germinating the Hakea laurina seedlings, six seedlings were transferred to a 4 L hydroponic solution with low P, specifically in a basic 0 µM P hydroponic setup supplemented with 6.4 µM NaH2PO4 every two to three months, and cultivated in the glasshouse at Hiroshima University.

extract_protocol:
The total RNA from frozen roots was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) with modifications for woody plant tissues. Briefly, 50 mg of frozen sample was homogenized with 1 mL of extraction buffer containing 4 M guanidine isothiocyanate, 0.2 M sodium acetate at pH 5.0, 25 mM EDTA, 2.5% (w/v) PVP-25 and 1% β-mercaptoethanol. The homogenates, to which 100 µL of 20% (w/v) sarkosyl was added, were incubated at 70˚C for 10 min with occasional vortexing. All lysates were transferred onto a QIAshredder Spin Column, followed by the standard protocol.
The cDNA libraries for RNA-Seq were prepared using an NEBNext Ultra ll Directional RNA Library Prep Kit for Illumina, NEBNext Multiplex Oligos for Illumina, and NEBNext Poly(A) mRNA  Magnetic Isolation Module (New England Biolabs Japan, Inc., Tokyo, Japan) following manufacturer's protocols.

value: tips of cluster-bearing lateral roots

value: low P hydroponics


title: 118 RNA

value: post


title: MCR2

description: HiSeqX as an instrument model


title: 117 RNA


title: MCR1

description: HiSeqX as an instrument model


title: FO_STAGE2_R2


title: 116 RNA


title: RA5 shFTO ip

city: Guangzhou

first: Yu

last: Kuang

address: No.58 Zhongshan Er Road Guangzhou

institute: The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China)

data_processing:
For meRIP-seq data procesing, Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Differential m6A peak were identified using exomePeak R package under parameters:
“PEAK_CUTOFF_PVALUE=NA,PEAK_CUTOFF_FDR=0.05,FRAGMENT_LENGTH=200” . GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0). m6A-RNA-related genomic features were visualized using Guitar R package (v1.16.0).
Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: Ensemble genome GRCh38
Supplementary files format and content: shFTOCONTROL_diff_peak_processed data file.txt

source_name: synovial tissues

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).
10μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Methylated RNA immunoprecipitation was performed using EpiTM m6A immunoprecipitation kit (Epibiotek, R1804). Briefly, the fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018). The library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.
meRIP-seq

value: rheumatoid arthritis

value: synovial tissues

tag: cell line

value: primary cell

value: rheumatoid arthritis fibroblast synoviocytes

value: FTO knockdown

value: shFTO-lentivirus infection

tag: rip antibody


title: TCR3

description: HiSeqX as an instrument model

source_name: mature cluster roots

value: mature cluster roots


title: FO_STAGE1_R3

source_name: Conidia

value: Conidia

tag: genotype

value: WT

value: Bird medium


title: 115 RNA

source_name: ovarian tumors

tag: yob decade

tag: pre/post menopause


title: TCR2

description: HiSeqX as an instrument model

tag: treatment


title: RA5 shCONTROL ip

description: shFTOCONTROL_diff_peak_processed data file.txt

value: control lentivirus infection

value: anti-m6A monoclonal antibody (abcam,ab208577)


title: 114 RNA


title: TCR1

description: HiSeqX as an instrument model


title: NF1

value: Heart

value: male

value: healthy


title: FO_STAGE1_R1


title: 113 RNA


title: Irradiated Sample 2

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

address: 515 LSA

department: Molecular and Cell Biology

institute: University of California Berkeley

description:
Library name: Irradiated Sample 2
PE150

data_processing:
Sequences were aligned to Drosophila transcriptome v6.55 using kallisto-bustools v0.28.2 (kallisto v0.50.1, bustools v0.43.2) with default settings.
Assembly: Drosophila transcriptome v6.55
Supplementary files format and content: Files from kallisto-bustools output were cells_x_genes.barcodes.txt (cell barcode identities), cells_x_genes.genes (genes captured), and cells_x_genes.mtx (transcript counts for each gene in each cell). These files can be turned into a sparse matrix using read_count_output() in R using the ‘BUSpaRse’ package.

organism: Drosophila melanogaster

source_name: Drosophila Wing Discs, Late Wandering Third Instar Larvae, Iirradiated, Sample 2

growth_protocol: Drosophila were reared at 25°C on Bloomington style food with dry yeast supplement.

extract_protocol:
Larvae were dissected 4 hours after the end x-ray exposure (or non-exposure in the case of control samples) and wing discs from many larvae pooled together. Wing discs were dissociated using a trypsin enzymatic digest.
Single-cell suspensions were FACS sorted to remove dead cells and cell debris and libraries were constructed using 10x v3.1 next gem chips.

treatment_protocol: Irradiated larvae were exposed to 4000 rad over ~35-45 minutes

tag: developmental stage

value: Late Wandering Third Instar Larvae

value: Wing imaginal disc

value: Epithelial, Myoblast

value: Oregon R (Wildtype)

value: 4000 rad X-ray exposure


title: Batch 5 EuI1  Selenite

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

data_processing:
bcl2fastq2 for conversion from the bcl files
Sequenced reads were trimmed for adaptor sequence, and mapped to Frankia whole genome using CLC genome 21.0 workstation
Genome_build: Frankia inefficax EuI1c
Supplementary_files_format_and_content: abundance measurements

organism: Pseudofrankia inefficax

source_name: culture

growth_protocol: 4 days growth at 30 C in MP growth medium with glucose as carbon source with or without 0.1 mM NaSelenite

extract_protocol:
Rneasy kit
Stable bacterial RNA removal via the Microbexppress kit.   RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Exposue to 0,1 mM NaSelenite or not

tag: strain

value: 0.1 mM Selenite

tag: temperature

tag: time

value: 4 days


title: F1

tag: disease state

value: dilated cardiomyopathy


title: 112 RNA

value: post


title: Irradiated Sample 1

description:
Library name: Irradiated Sample 1
PE150

source_name: Drosophila Wing Discs, Late Wandering Third Instar Larvae, Irradiated, Sample 1


title: 111 RNA


title: FO_STAGE2_R1

value: Germinated conidia


title: Unirradiated Sample 2

description:
Library name: Unirradiated Sample 2
PE150

source_name: Drosophila Wing Discs, Late Wandering Third Instar Larvae, Unirradiated, Sample 2


title: Batch 4 EuI1  Selenite


title: RA3 shFTO ip

value: rheumatoid arthritis

value: synovial tissues

value: primary cell

value: rheumatoid arthritis fibroblast synoviocytes

value: FTO knockdown

value: shFTO-lentivirus infection


title: RA3 shFTO input


title: RA5 shFTO input


title: FO_STAGE1_R2

value: Conidia

value: WT

value: Bird medium


title: MP_3C

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, version 20101214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Chlorine gas was used for surface-sterilization. After this, seeds were stratified for 2 d at 4°C. Seedlings were grown vertically on plates containing 1% (w/v) agar (Duchefa) with ½ Murashige and Skoog (MS, Duchefa, 0,5g/l MES, 1 % (w/v) sucrose, pH 5.8 adjusted with 1M KOH). Plants grown in growth chamber with following conditions: 60 % humidity, 22°C by day (16 h), 18°C by night (8 h), light intensity of 120 μmol photons m-2 s-1.

extract_protocol:
protocol from Plant Total RNA Mini Kit, Favorgen
KAPA HyperPrep kit

treatment_protocol: To treat the plants, 5d old plants were transferred to treatment-containing medium. Estradiol (Sigma, 20mM stock in DMSO, 2.5 μM working concentration) diluted in DMSO was used for treatments.

value: root

tag: biological replicates

value: MP

value: DMSO

tag: treatment time


title: Batch 2 EuI1  Selenite

value: 0.1 mM Selenite


title: RA3 shCONTROL input

value: control lentivirus infection


title: 109 RNA


title: MP_3B


title: RA5 shCONTROL input


title: Batch 1 EuI1  Selenite

value: 4 days


title: 110 RNA

value: post


title: 108 RNA

value: pre


title: MP_3A


title: RA1 shFTO input

value: rheumatoid arthritis


title: Batch 5 EuI1  Control

value: Control


title: RA1 shFTO ip

value: synovial tissues

value: primary cell

value: anti-m6A monoclonal antibody (abcam,ab208577)


title: 107 RNA


title: MP_2C

value: EST


title: Batch 4 EuI1  Control


title: Batch 3 EuI1  Selenite


title: 106 RNA


title: RA1 shCONTROL ip

value: rheumatoid arthritis fibroblast synoviocytes


title: RA3 shCONTROL ip

value: WT


title: MP_2B


title: RA1 shCONTROL input


title: 105 RNA


title: MP_2A


title: Batch 3 EuI1  Control


title: RA5 shFTO

description:
R5F-10L
lncRNA-shFTOVSCONTROL.log2FC1.Pvalue0.05.fpkm.anno
mRNA-shFTOVSCONTROL.All.fpkm.anno

data_processing:
Reads were aligned to the human Ensemble genome GRCh38 using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”.
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Differential gene expression analysis was performed using the DESeq2 R-package.
Assembly: human Ensemble genome GRCh38
Supplementary files format and content: shFTOVSCONTROL.processed data file.txt, All.HTSeq.counts.txt

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). Then, RNA samples undergo the following process. (1) DNase I digestion: Add DNase I to the RNA sample, digest at 37 ℃ for 30 minutes to remove residual DNA from the sample, and purify and recover RNA using magnetic beads. (2) Remove ribosomal RNA and RNA fragmentation: Add 5XRT Buffer and ribosomal RNA probe to the sample RNA, perform temperature gradient reaction on RNA sample fragmentation and remove rRNA. (3) Synthesis of first strand cDNA: Add EpiScriptTM IV, RNase inhibitor, DTT, TSO, random primers to the RNA sample in step 2. Mix gently with the tube wall and centrifuge rapidly. React in a PCR machine according to the following procedure: 37 ° C, 90 minutes; 70 ° C for 15 minutes. (4) First round of PCR amplification: Add 2XpfuMax HiFi PCR ProMix and sequencing primers to the first strand cDNA sample, mix well, and perform amplification reaction in the PCR instrument. (5) Purify the PCR amplification product using EpiTM DNA Clean Beads at a ratio of 1X, and recover 300-400bp of DNA fragments using magnetic beads at a ratio of 0.65X/0.2X for the purified product. (6) Perform a second round of PCR amplification on the purified product, enriching 300-400bp of DNA fragments. (7) Quality inspection: Use Biotic Qsep100 Analyzer to inspect the library and check if the distribution of library size meets the theoretical size.
EpiTM mini longRNA-seq kit (Epibiotek, E1802) was used for library preparation according to the instructions.

value: FTO knockdown

value: shFTO-lentivirus infection


title: 104 RNA

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapping against human reference genome hs37d5 using STAR-2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region (Gencode29) associated with each gene.
To account for differences in library size between samples, Trimmed Mean of M values (TMM) normalization using calcNormFactors(), also from edgeR, was applied.
All data were then transformed using voom.
Assembly: hs37d5
Supplementary files format and content: tab-delimited text files include raw gene count for each sample


title: MP_1C

value: root

value: MP


title: Batch 2 EuI1  Control


title: RA5 shCONTROL

description:
R5CTRL
lncRNA-shFTOVSCONTROL.log2FC1.Pvalue0.05.fpkm.anno
mRNA-shFTOVSCONTROL.All.fpkm.anno


title: Batch 1 EuI1  Control


title: MP_1B


title: △dinB_CIP_replicate_3

city: Hangzhou

first: min

last: yue

address: No.1, Sub-Lane Xiangshan, Xihu District, Hangzhou, China

institute: Hangzhou Institute for Advanced Study, University of Chinese Academy of Science

data_processing:
Raw data were processed by Trimmomatic (v.0.36).[Bolger, et al. Bioinformatics, 2014, PMID: 24695404]
Clean reads were mapped to NCBI Rfam databases, to remove the rRNA sequences by Bowtie2 (v2.33).[Langmead, et al. Nat Methods, 2012, PMID: 22388286]
The remaining mRNA sequences were mapped to the SL1344 genome (NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1) by Hisat2 (2.1.0).[Kim, et al. Nature Biotechnology, 2019, PMID]
The read numbers mapped to each gene were calculated using HTSeq-count (v0.9.1).[Anders, et al. Bioinformatics, 2015, PMID: 25260700]
For gene expression analysis, the read count number was calculated and then normalized to FPKM (fragments per kilobase per million mapped reads) value using RSEM software (v1.3.1).[Li, et al. BMC Bioinformatics, 2011, PMID: 21816040]
Assembly: SL1344 genome (NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1)
Supplementary files format and content: Comma-separated values file includes raw counts for each Sample
Supplementary files format and content: Comma-separated values files include FPKM values for each Sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: strain

growth_protocol: Single colonies were seeded into LB medium and cultured to ~0.1 of OD600.

extract_protocol:
Total mRNA was extracted with the HiPure RNA Kit (R4130-02, Magen, China)
cDNA libraries were generated using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420; New England Biolabs; Ipswich, USA) following the manufacturer’s recommendation

treatment_protocol: The bacterial solution containing 0.03125μg/ml CIP was subsequently incubated without shaking at room temperature for 10 min, and a liquid nitrogen flash freezer was used to stop the reaction.

value: strain

value: LB medium containing 0.03125μg/ml CIP, without shaking at room temperature for 10 min, and a liquid nitrogen flash freezer was used to stop the reaction.


title: 101 RNA

extract_protocol:
RNA was harvested using the Qiagen All-Prep RNA isolation kit
RNA libraries were prepared by using Illumina TruSeqTM RNA Exome Library Preparation Kit (Illumina Inc., San Diego, CA) , following the manufacturer’s protocol


title: △dinB_CIP_replicate_2


title: RA3 shCONTROL

description:
R3CTRL
lncRNA-shFTOVSCONTROL.log2FC1.Pvalue0.05.fpkm.anno
mRNA-shFTOVSCONTROL.All.fpkm.anno

value: control lentivirus infection


title: MP_1A


title: 100 RNA


title: Col_3C

value: DMSO


title: RA1 shFTO

description:
R1F-10L
lncRNA-shFTOVSCONTROL.log2FC1.Pvalue0.05.fpkm.anno
mRNA-shFTOVSCONTROL.All.fpkm.anno


title: Col_3B


title: Col_3A


title: dinBT_CIP_replicate_2

value: frameshift dinB (GeneID:1251832)