title: LOVO-ASO-30nM-2

city: Beijing

first: wanru

last: ma

address: No.1 Dahua Road, Dongcheng District

institute: Beijing hospital

data_processing:
For knockdown of circrna in cells, FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis. For overexpression of circ86591, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited text file includes TPM or RPKM values for each sample

source_name: colorectal

extract_protocol:
For RNA extraction. total RNA was isolated according to the protocol of Trizol, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of  the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For knockdown of circrna in cells,  using the polyA structure at the 3'end of the messenger RNA and related molecular biology techniques, the four RNA samples in this project were subjected to mRNA isolation, fragmentation, double-stranded cDNA synthesis, cDNA fragmentation modification, magnetic bead purification and fragmentation sorting, library amplification and other processes. After testing and quality control, the sequencing libraries were finally obtained, which are suitable for Illumina platform. For overexpression of circrna, Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: colorectal

value: LOVO

value: colorectal cancer

value: circ86591 knockdown

value: cell transfected with ASO-circ86591


title: A549 cells, NS, 2h, rep2

status: Public on Oct 31 2025

type: SRA

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

description: Library name: Sample 22

library_source: transcriptomic

data_processing:
Good-quality reads were mapped to GRCh38/hg38 reference human transcriptome using kallisto with 100 bootstraps per sample.
Normalization and differential expression analysis was performed using the R package, sleuth. Genes with low abundance (<5 estimated counts in at least 90% of all samples) were filtered out before subsequent analysis. The Wald test was used to determine fold change (b value) and false-discovery rate (FDR) for each treatment when compared to NS control at each time point separately. Differentially expressed genes (DEGs) were taken as showing FDR ≤0.05 and log2(fold) ≥1 or ≤-1.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains TPM values for each sample
Supplementary files format and content: tab-delimited text file contains fold change and FDR values for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: The human pulmonary type II cell line, A549, was grown under standard culture condition using Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine. Cells were incubated at 37°C in 5% CO2 and were grown to confluence either in 100mm, or 6/12/24-well plates, as appropriate. Prior to experiments, cells were incubated overnight in basal media that was serum- and additive-free.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Extraction kit (MN-740955, Macherey-Nagel) and cDNA prepared from 0.5μg of RNA.
RNA sequencing libraries, from 4 independent experiments, were prepared using Illumina TruSeq Stranded mRNA Library Prep kits with the poly(A) mRNA magnetic isolation module as described by the manufacturer. Libraries were validated by D1000 Screen Tape assay on an Agilent 2200 TapeStation system and quantified using Kapa qPCR Library Quantification kits.

treatment_protocol: Budesonide was dissolved in DMSO as a 10mM stock. Unless specifically indicated, budesonide was used at 300nM on cells, representing a concentration that was maximally effective/near maximal on a 2×GRE reporter and gene expression in A549 cells. Final DMSO concentrations on cells were ≤ 0.1%. Recombinant human IL1B was dissolved in phosphate-buffered saline (PBS) containing 0.1% bovine serum albumin (BSA). IL1B was previously found to be maximally or near maximally effective on NF-κB reporters and gene expression at 1ng/ml and this concentration was used in all experiments unless specifically indicated. Following overnight incubation in serum free medium, cells were changed to fresh serum free medium and either not stimulated (NS) or treated with, IL1B, budesonide or IL1B plus budesonide for the indicated times prior to harvesting for RNA extraction. Data are from four independent experiments with the exception of the 12 h time point which was from three independent experiments.

tag: cell line

tag: cell type

value: lung carcinoma epithelial cells

tag: genotype

value: WT

tag: treatment

value: NS

tag: time


title: Hippo_AMI_50_11

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14.
Samples demultiplexing transforms the raw paired-end fastq files into a single-end fastq file for each sample.
All sixteen bases of the first read (from the read pairs) must have quality scores of at least 10 and the first six bases must correspond exactly to a designed well-specific barcode.
The second reads were aligned to the human reference transcriptome
Assembly: rn6
Supplementary files format and content: Expression file in dat format (tab-delimited). Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17483 genes detected.

organism: Rattus norvegicus

source_name: Hippo, AMI, 50mg/kg/d

growth_protocol: The dams, and their litters, were housed in semi-transparent polysulfone (PSU) cages of 15 x 27 x 43 cm (PSU) (Techniplast S.p.A, Buguggiate, Italy) in ventilated cabinets (ScanTainers, Scanbur, Karlslunde, Denmark) with ScanClime (Scanbur, Karlslunde, Denmark) controlled environment: 55 ± 5% humidity, 21 ± 1°C, air-change 50 times/hr, reversed light/dark cycles (light form 9 PM to 9 AM, dark form 9 AM to 9 PM). The animals had ad libitum access to water (acidified, in PSU bottles from Techniplast) and soy and alfalfa-free Altromin 1314 feed (Altromin GmbH, Lage, Germany). The diet contained 1.52 mg/kg iodine and 0.26 mg/kg selenium.

extract_protocol:
Hippocampi were extracted from one PD16 male pup per litter (n = 11-12), flash frozen in liquid nitrogen and stored at -80°C. The samples were homogenized using a TissueLyser II (Qiagen, Hilden, Germany) at 30 oscillations per sec for 2 minutes. The Qiagen RNeasy Mini Kit with on-column DNase I digestion was used to extract total RNA. RNA quality and quantity was assessed according to manufacturer’s instructions using Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer System (Agilent Technologies, Waldbroon, Germany). All samples had RNA integrity number (RIN) ≥9.
sample-specific barcoded oligo-dT and 4 µL total RNA at a concentration of 2.5 ng/µL were used for reverse transcription and template switching. The cDNA was purified and PCR used to make Double-strand (ds) cDNAs. 50 ng of cDNA was used to make sequencing libraries by tagmentation and using the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following manufacturer’s protocol.
3'Bulk RNA Barcoding and sequencing (BRB-seq)

treatment_protocol: Time-mated nulliparous Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River Europe and distributed by SCANBUR, Denmark) arrived on gestation day (GD) 3 and were exposed to test compounds from GD7 to pup day (PD) 22. The day of expected birth (GD23) was designated as PD1. The test compounds were methimazole, also known as thiamazole, (MMI) (CAS no: 60-56-0, Sigma-Aldrich 301507-5G, batch: WXBC9951 V, purity 99.0 %) and 3-Amino-1H-1,2,4-triazole (amitrole or Ami) (CAS no: 61-82-5, Sigma-Aldrich 8144950100, batch: S7075495 925, purity 99.7 %). Administration of test compounds took place once daily by oral gavage to animals pseudo-randomly divided into 5 groups (n = 11-12): control (vehicle, corn oil, Sigma-Aldrich), 8 mg/kg bodyweight/day (mg/kg/d) MMI, 16 mg/kg/d MMI, 25 mg/kg/d amitrole and 50 mg/kg/d amitrole. Exposure was performed at aconstant volume of 2 mL/kg/d.

tag: tissue

value: hippocampus

tag: developmental stage

tag: strain

tag: exposure

value: amitrole


title: A549 cells, NS, 1h, rep2

description: Library name: Sample 21


title: LOVO-ASO-30nM-1

country: China


title: A549 cells, IL1B+Bud, 24h, rep1

description: Library name: Sample 20

value: IL1B + Budesonide


title: LOVO-ASO-NC-2

value: ASO control

value: cell transfected with ASO-nc


title: RNA_5_Nephron progenitor cells wildtype

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

source_name: HiPSC from healthy donor differentiated into nephron progenitor cells

growth_protocol: CiPodocytes were cultured in RPMI medium containing 10% fetal calf serum, 1% Insulin-Transferrin-Selenium,1% penicillin-streptomycin at 33°C for proliferation and at 37°C for differentiation for 10 days. HiPSCs were cultured in mTeSR1 medium (Stem Cell Technologies) containing 1% penicillin-streptomycin. Nephron progenitor cells were generated by differentiation of hiPSCs for 2 days in DMEM/F12 containing 1x B27 supplement, 1% penicillin-streptomycin, 3 μM CHIR99021, 50 ng/mL activin A and 10 μM ROCK inhibitor Y27632 with additional culture for 14 days in DMEM/F12 containing 1x B27 supplement, 1% penicillin-streptomycin, 3 μM CHIR99021, 50 ng/mL activin A, and 50 ng/mL BMP7. HiPSC-derived podocytes were generated by further differentiation of nephron progenitor cells for additional 5 days in DMEM/F12 medium containing containing 1x B27 supplement, 1% penicillin-streptomycin, 3 μM CHIR99021, 50 ng/mL activin A, 50 ng/mL BMP7, 25 ng/μL VEGF, and 0.5 μM all-trans retinoic acid.

extract_protocol:
RNA was isolated using the ReliaPrep™ RNA Miniprep Systems (Promega, Walldorf, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on IlluminaNovaseq 6000  (Illumina).

value: Nephron progenitor cells

value: Wildtype

value: untreated


title: Hippo_AMI_50_9

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: RNA_4_HiPSC wildtype

source_name: HiPSC from healthy donor generated from dermal fibroblasts

value: HiPSC


title: LOVO-ASO-NC-1

value: colorectal

value: LOVO


title: A549 cells, IL1B+Bud, 12h, rep1

description: Library name: Sample 19


title: Hippo_AMI_50_8


title: RNA_3_HiPSC wildtype

value: HiPSC from healthy donor generated from dermal fibroblasts


title: A549 cells, IL1B+Bud, 6h, rep1

description: Library name: Sample 18


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K27ac, ABCAM

city: Shanghai

first: Xiuqi

last: Gui

address: 320 Yue Yang Rd

institute: Shanghai Institute of Nutrition and Health

description: H3K27ac share the same input control with H3K4me1(GEO accession GSE245611)

library_source: genomic

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 0.6.7,discarding reads left with < 20 bp
Each read was mapped against the C. reinhardtii reference sequence (CC-4532 v6) using Bowtie 2 version 2.4.2
Duplicate reads were removed by Picard MarkDuplicates.Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <0.01.
narrowPeak files were generated using MACS2 callpeak.
bigWig files were generated from aligned reads using deepTools bamCoverage v 3.5.1 with parameter 'normalizeUsing=RPKM'. Scale factors were calculated using reads mapped to non-peak regions across all samples. The RPKM score represents normalized DNA fragment coverage at specific genomic coordinates.
Assembly: C. reinhardtii reference sequence (CC-4532 Assembly-version = v6)
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Chlamydomonas reinhardtii

growth_protocol: Cells were grown photo mixotrophically in liquid Tris-acetate-phosphate (TAP) medium on a rotary shaker at 22–25°C or on agar-solidified TAP medium under continuous light (50–100 μE∙m-2∙s-1, cool-white fluorescent lamps).

extract_protocol:
Cells were fixed with 0.35% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Covaris S220.
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Cat. ND607, Vazyme). 1 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using VAHTS DNA Clean Beads (Cat. N411, Vazyme).

tag: mate type

value: mt–

tag: Stage

value: vegetative stage

value: DNMT1 knockout

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: Hippo_AMI_50_7

value: hippocampus


title: RNA_2_CiPodocytes

source_name: Conditionally immortalized human podocytes cell line (M. Saleem)

value: Podocyte


title: A549 cells, IL1B+Bud, 2h, rep1

description: Library name: Sample 17

value: lung carcinoma epithelial cells

value: WT

value: IL1B + Budesonide


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K27ac, ABCAM

value: mt+


title: RNA_1_CiPodocytes

value: Conditionally immortalized human podocytes cell line (M. Saleem)

value: Wildtype


title: Hippo_AMI_50_6

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River

value: amitrole


title: Hippo_AMI_50_5


title: CC-5325 strains, WT, mt–, vegetative stage, H3K27ac, ABCAM


title: A549 cells, IL1B+Bud, 1h, rep1

description: Library name: Sample 16


title: A549 cells, Bud, 24h, rep1

description: Library name: Sample 15

value: Budesonide


title: RNA_6_Nephron progenitor cells wildtype

value: HiPSC from healthy donor differentiated into nephron progenitor cells

value: Nephron progenitor cells

value: untreated


title: CC-5155 strains, WT, mt+, vegetative stage, H3K27ac, ABCAM

value: vegetative stage


title: Hippo_AMI_50_10


title: genomic DNA from IDH-mutant oligodendroglioma component

type: genomic

city: Hidaka

first: Mitsuaki

middle: Shirahata

last: Shirahata

state: Saitama

department: Neurosurgery/Neuro-oncology

country: Japan

institute: Saitama Medical University International Medical Center

hyb_protocol: Bisulphite converted DNA was hybridized to human Infinium Methylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.
Processed data value: Average Beta

label: Cy3 and Cy5

source_name: Genomic DNA from IDH-mutant oligodendroglioma component

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from surgical resected tissue using Maxwell® RSC Tissue DNA Kit (Promega) according to standard instructions

value: astrocytoma

value: IDH-mutant


title: A549 cells, Bud, 12h, rep1

description: Library name: Sample 14


title: Hippo_AMI_50_3

value: hippocampus


title: Neurons_HuC_72hpf

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
Raw reads were mapped with vast-tools align v2.5.1
Assembly: danRer10
Supplementary files format and content: Files with raw read counts to each mouse gene in Ensembl v80 and cRPKMs.

organism: Danio rerio

source_name: FACS sorted HuC:GFP+ neurons at 72 hpf

growth_protocol: Zebrafish were grown at 28°C 14 h light/10 h dark cycle.

extract_protocol:
Multiple zebrafish 5 dpf larvae of the same genotype were pulled for RNA extraction using RNA RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols
polyA-selected stranded RNA-seq

value: FACS sorted HuC:GFP+ neurons at 72 hpf


title: RNA_7_HiPSC-derived Podocytes wildtype

source_name: HiPSC from healthy donor terminally differentiated into podocytes

value: Podocyte


title: A549 cells, Bud, 6h, rep1

description: Library name: Sample 13

value: lung carcinoma epithelial cells

value: WT


title: genomic DNA from IDH-wildtype astrocytoma component

source_name: Genomic DNA from IDH-wildtype astrocytoma component

value: IDH-wildtype


title: Embr_5dpf_srrm3_KO_17A_b

source_name: Larva 5 days post-fertilization

value: Larva 5 days post-fertilization


title: A549 cells, Bud, 2h, rep1

description: Library name: Sample 12


title: seedling_Col_R_1

city: Chicago

first: Shun

last: Liu

state: IL

address: 929 E. 57th. Street

department: Chemistry

country: USA

institute: University of Chicago

data_processing:
Base mutations of each A site from each sample were called by pileup2var. Mutation counts from two replicates were merged and sites with coverage less than 5 were discarded. m6A site detection and quantification was calculated according to the spike-in data. Firstly, the overall mutation rate background (MRB) of each genotype group was determined by merging 0% A-modified spike-in data from all treated replicates of the corresponding group. Then MRB normalization factor for each group was defined as MRB of that group divided by median MRB. MRB of each motif (NNANN) was calculated from 0% A-modified spike-in data from all merged treated samples and was scaled by the MRB normalization factor of each group to represent the final MRB of each motif in the corresponding group. Secondly, each group’s overall conversion efficiency (CR) of mutation rates into m6A fractions was determined by merging 100% A-modified spike-in data from all treated replicates of the corresponding group. Then CR normalization factor for each group was defined as CR of that group divided by median CR. CR of each motif (NNANN) was defined as the coefficient of a linear function (if r2 > 0.9) or mutation rate of 100% A-modified spike-in of that motif (if r2 ≤ 0.9) and was scaled by the CR normalization factor of each group to represent the final CR of each motif in the corresponding group. Finally, high confidence m6A sites were identified according to the following criteria: (1) mutation rates of input samples < 5% or the number of mutations < 2; (2) mutation rates of treated samples > mutation rates of input samples x 3; (3) mutation rates of treated samples > 2% and the number of mutations ≥ 2; (4) m6A fractions converted from mutation rates using the final CR of individual motif ≥ 10%; (5) p-values of fisher’s exact test between treated and input samples < 0.1; (6) adjusted p-values of binomial test in the treated samples using the final MRB of individual motif < 0.05.
Assembly: TAIR10
Supplementary files format and content: m6A sites with fractions in BED format
Library strategy: m6A-Sac-seq

organism: Arabidopsis thaliana

growth_protocol: WT and mutant seedlings grown in the dark, far-red light (5 μmol m−2 s−1) or red light (25 μmol  m−2 s−1) for 6 days were used.

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Kits (Zymo, Cat. # R2052). Polyadenylated RNA was purified from total RNA with two rounds of polyA-tail purification using the Dynabeads® mRNA DIRECT™ kit (Thermo Scientific, Cat. # 61012).
All the libraries were constructed by the m6A-Sac-seq protocol{Ge, 2023 #34}. The resulting library was purified by AMPure XP beads (Beckman Coulter) following the manufacturer’s directions and subjected to next-generation sequencing.

value: seedling

value: MjDim1 + red light

value: wild type


title: Hippo_AMI_50_1

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River

value: amitrole


title: A549 cells, Bud, 1h, rep1

description: Library name: Sample 11

value: Budesonide


title: A549 cells, IL1B, 24h, rep1

description: Library name: Sample 10


title: Embr_5dpf_srrm34_WT_b


title: A549 cells, IL1B, 12h, rep1

description: Library name: Sample 9


title: Embr_5dpf_srrm34_DKO_b


title: Hippo_AMI_50_2


title: Hippo_AMI_25_10

source_name: Hippo, AMI, 25mg/kg/d


title: A549 cells, IL1B, 6h, rep1

description: Library name: Sample 8


title: Hippo_AMI_50_4


title: UHL6

city: Wuhan

first: Zhao

middle: Ke

last: Wei

state: Hubei

address: 109 Machang Road, Jianghan District

department: Tongji Medical College

institute: Huazhong University of Science and Technology

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw gene expression matrix was generated for each sample using Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) provided by 10x Genomics. The R package Seurat (https://satijalab.org/seurat/) was used to perform quality control. Gene counts per cell, unique molecular identifier (UMI) counts per cell, and percentages of mitochondrial and ribosomal transcripts were calculated using the functions of the Seurat package. The genes expressed in less than three cells were removed. Cells that had less than 200 expressed genes or more than 7,000 expressed genes were removed. Cells in which the fraction of mitochondrial genes exceeded 10% also were removed. After removing low-quality cells, we analyzed scRNA-seq profiles of 9044 cells with an average sequencing depth of approximately 1667 genes per cell.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: diffuse large B-cell lymphoma

growth_protocol: A multi-drug resistant R/R DLBCL patient was enrolled in this study. Written informed consent was obtained from the patient.

extract_protocol:
The qualified cells are washed and resuspended to prepare the appropriate cell concentration of 700-1200 cells/ul for on-board operation of the 10x Genomics Chromium™ system.
The following steps, such as generating single cell gel bead emulsions (GEMs), synthesizing complementary DNA, building second generation sequencing libraries were carried out according to the manufacturer’s instructions. The resulted libraries were sequenced on the llumina Novaseq 6000 platform with paired end 150 bp sequencing. Each sample was sequenced to depth of ∼120 G of raw reads.

treatment_protocol: The preparation of single-cell suspension is performed by puncture tissue from the patient's lesion mass. The survival rate of cells is generally required to be above 80%.

value: diffuse large B-cell lymphoma


title: Embr_5dpf_Vti1a_1_WT_c


title: Embr_5dpf_srrm3_WT_17A_a


title: Hippo_AMI_25_9


title: Hippo_AMI_25_11


title: A549 cells, IL1B, 2h, rep1

description: Library name: Sample 7


title: Hippo_AMI_25_8


title: Embr_5dpf_Vti1a_1_DEL_c


title: 544079-6

type: RNA

city: Edmonton

first: Truong An

last: Bui

address: 8440 112 Street NW

department: Psychiatry

institute: University of Alberta

hyb_protocol: Hybridization performed by GeneChip® WT PLUS Reagent Kit by Affymetrix

scan_protocol: Scanned by GeneTitan Instrument by appliedbiosystems

data_processing: The limma package, which allows for variance stabilization, was used to normalize reads and identify differentially expressed genes (DEGs) across sex and age from raw data CEL files (|log2FC| ≥1.5, p-vale ≤ 0.05)

label: biotin

organism: Mus musculus

source_name: Blood

label_protocol: Labelled using GeneTitan™ Reagent Trays for Expression Array Plates

extract_protocol: All mice were anesthetized with an intraperitoneal injection of 20% urethane. Blood samples were obtained immediately with retro-orbital sampling, collected in 500µL RNAprotect animal blood tubes (Qiagen, Germany), and stored at -20°C until RNA purification.

treatment_protocol: Total RNA was isolated using the Rneasy Kits, which was automated by the QIAcube (Qiagen, Germany). RNA was cleaned, and contaminants were removed using the Rneasy MinElute CleanUp Kit (Qiagen, Germany). NanoDrop 2000 (Thermo Fisher Scientific, U.S.) and Agilent Bioanalyzer 2100 (Agilent Technologies, U.S.) were used to measure RNA yield and detect integrity before microarray analysis. Samples with an RNA integrity number (RIN) of less than 7, A260/A280 ratio of less than 1.8, and samples of less than 35uL each at 50ng/uL were excluded from the dataset (Thermo Fisher Scientific, U.S.). mRNA was measured by Affymetrix Clariom S microarray

tag: gender

value: Female

tag: development stage

value: Young

value: SHAM


title: 534634-25

value: Male


title: 548325-5


title: Hippo_AMI_25_7

value: hippocampus


title: Embr_5dpf_Vdac3_5_WT_b


title: Embr_5dpf_srrm3_KO_17A_a


title: 526047-56

value: MCAO


title: Embr_5dpf_Vdac3_5_DEL_b


title: A549 cells, IL1B, 1h, rep1

description: Library name: Sample 6

value: lung carcinoma epithelial cells


title: A549 cells, NS, 24h, rep1

description: Library name: Sample 5

value: WT

value: NS


title: Hippo_AMI_25_6


title: Hippo_AMI_25_4


title: Embr_5dpf_Vav2_2_WT_d

value: Larva 5 days post-fertilization


title: 526047-54


title: A549 cells, NS, 6h, rep1

description: Library name: Sample 3


title: 529725-4


title: Embr_5dpf_Vav2_2_DEL_d


title: Hippo_AMI_25_3


title: Embr_5dpf_Vav2_1_WT_d


title: 526047-46


title: A549 cells, NS, 2h, rep1

description: Library name: Sample 2


title: Hippo_AMI_25_2


title: 526047-55

value: MCAO+Recan


title: Hippo_AMI_25_1


title: Embr_5dpf_Src_1_WT_d


title: Hippo_MMI_16_11

source_name: Hippo, MMI, 16mg/kg/d

value: methimazole


title: Embr_5dpf_Src_1_DEL_d


title: Hippo_AMI_25_5


title: 524245-36


title: Hippo_MMI_16_10


title: 524245-1


title: HD03

city: Singapore

first: Zhiyong

last: Poon

address: Outram Road

country: Singapore

institute: SGH

data_processing:
After sequencing, the reads were analyzed on Partek Flow software (Partek Inc.). The reads were mapped to the hg38 reference genome using STAR aligner and the aligned reads were quantified and annotated based on RefSeq transcripts (version 99).
Assembly: mm10
Supplementary files format and content: tab delimited files include raw data for each sample

source_name: Bone marrow

growth_protocol: Bulk sequencing: Cells were cultured in 10%FBS for 1 passage following derivation from bone marrow aspirate.

extract_protocol:
Bulk sequencing: Total RNA was extracted from MSCs using the RNeasy Mini Kit (Qiagen), which was then quantified via nanodrop and its quality and integrity assessed by capillary electrophoresis (Agilent 2100).
Bulk sequencing: cDNA libraries were then prepared from mRNA and next sequenced with Illumina NextSeq 500 to generate on average 100 million reads per sample.

value: Bone marrow

tag: disease state

value: Healthy Donor

value: Mesenchymal stromal cells


title: A549 cells, NS, 12h, rep1

description: Library name: Sample 4


title: Embr_5dpf_Shank3b_2_WT_d


title: 520837-22


title: HD02


title: A549 cells, NS, 1h, rep1

description: Library name: Sample 1


title: Embr_5dpf_Shank3b_2_DEL_d


title: Hippo_MMI_16_9

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: Embr_5dpf_Vav2_1_DEL_d


title: Hippo_MMI_16_8


title: HD01


title: Embr_5dpf_Shank3b_1_WT_d


title: 526047-44


title: 519669-47


title: 520837-21


title: Embr_5dpf_Shank3b_1_DEL_d


title: HD04


title: BM2598

value: MDSslow


title: Hippo_MMI_16_6


title: Hippo_MMI_16_7


title: Embr_5dpf_Shank3a_2_DEL_c


title: BM2589


title: BM2565


title: 519059-21


title: Hippo_MMI_16_4


title: 518828-32


title: 519059-20


title: BM1254


title: BM2651


title: 519669-35

value: Female


title: 518828-26

value: Young


title: Embr_5dpf_Reln_2_DEL_c


title: BM797


title: Hippo_MMI_16_3


title: 514766-85

value: Aged

value: SHAM


title: Embr_5dpf_Shank3a_2_WT_c


title: Hippo_MMI_16_2

value: hippocampus


title: Embr_5dpf_Mef2ca_1_WT_b


title: BM659


title: Embr_5dpf_Mef2ca_1_DEL_b


title: BM625


title: Hippo_MMI_8_12

source_name: Hippo, MMI, 8mg/kg/d


title: 514766-50

value: Male


title: Embr_5dpf_Reln_2_WT_c


title: Hippo_MMI_16_5


title: 510546-15

value: MCAO


title: BM613

value: WT


title: Embr_5dpf_Madd_1_DEL_c


title: BM455


title: Hippo_MMI_8_10


title: Embr_5dpf_Kif1b_1_WT_a


title: BM630


title: Hippo_MMI_16_1


title: 510268-56


title: 510268-55


title: Hippo_MMI_8_9


title: Embr_5dpf_Kif1b_1_DEL_a


title: 510546-20


title: BM305


title: Embr_5dpf_Madd_1_WT_c


title: Embr_5dpf_Itsn1_3_WT_d


title: Hippo_MMI_8_8


title: BM290


title: Embr_5dpf_Itsn1_3_DEL_d


title: 504036-62


title: Hippo_MMI_8_7


title: Hippo_MMI_8_11


title: BM819

value: MDSfast


title: Hippo_MMI_8_6


title: BM808


title: BM775


title: Embr_5dpf_Itsn1_1_DEL_a

value: Larva 5 days post-fertilization


title: 504036-61

value: MCAO+Recan


title: Embr_5dpf_Itsn1_1_WT_a


title: BM768


title: Embr_5dpf_Gli3_9_WT_d


title: Hippo_MMI_8_3

value: methimazole


title: 501373-36


title: 504036-63


title: Embr_5dpf_Gli3_9_DEL_d


title: KP4_E5_Folfirinox_96h

city: Montréal

first: Paloma

last: Kalegari

state: Quebéc

address: 900 Saint Denis St

department: Biochemestry

institute: CRCHUM

data_processing:
Trimmomatic version 0.3570
Sequences were aligned to thereference human genome version GRCh38 (gene annotation from Gencode version 26, based on Ensembl 88) using STAR version 2.5.1b.
Assembly: human genome version GRCh38
Supplementary files format and content: normalized_readcounts
Supplementary files format and content: FPKM.stranded.annotated

growth_protocol: KP4 cells were maintained in DMEM supplemented with 10% FBS, incubted at 37C and 5% CO2

extract_protocol:
RNA extraction was performed using the RNeasy® Mini Kit (#74104, QIAGEN), according to the manufacturer’s instructions.
KAPA mRNAseq Hyperprep kit following manufactures instructions

treatment_protocol: Cells were treated either wit DMSO or FOLFIRINOX ( 25 nM Sn-38,10 µM 5-F, 5µM Oxaliplatin)

value: PDAC cell line


title: 501373-41


title: Hippo_MMI_8_2


title: Hippo_MMI_8_1


title: Embr_5dpf_Gli3_7_DEL_a


title: Hippo_Ctrl_12

source_name: Hippo, Ctrl

value: control


title: KP4_E5_Vehicle_96h


title: 500559-24


title: KP4_Ctrl_Folfirinox_96h


title: Hippo_MMI_8_5


title: Embr_5dpf_Gli2b_1_DEL_b


title: KP4_Ctrl_Vehicle_96h


title: Hippo_MMI_8_4


title: Embr_5dpf_Gli2b_1_WT_b


title: Embr_5dpf_Gli3_7_WT_a


title: Hippo_Ctrl_11


title: 500664-2


title: BM378

value: Bone marrow

value: Mesenchymal stromal cells


title: Hippo_Ctrl_10

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: 499422-52

value: Female


title: Embr_5dpf_Evi5b_6_WT_b


title: 499422-55


title: 499422-7


title: ChIP-Seq of MYC, overexpreesing EPIC1, IP

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

data_processing:
Reads were aligned using bowtie2 and duplicates were removed using sambamba.
MACS2 was used to do peak calling.
bedgraph files were generated by bedtools and the difference between IP and Input were calculated using an ad-hoc script. Then they were converted to bw files.
Assembly: hg38
Supplementary files format and content: bw files showing the difference between IP and Input contains the read distribution across the genome.

source_name: Mammary gland/Breast

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: MCF-7 cells were transiently transfected for 48 h with siRNA targeting EPIC1. MCF-7 cells stably expressing EPIC1.

value: Mammary gland/Breast

tag: disease

value: Adenocarcinoma

value: Human epithelial cell

value: EPIC1 overexpression

value: EPIC1 overexpression vector


title: Hippo_Ctrl_9

value: hippocampus


title: 498422-1

value: Aged

value: SHAM


title: 499422-46


title: 499422-50


title: Hippo_Ctrl_8


title: Hippo_Ctrl_7


title: Embr_5dpf_Evi5b_3_DEL_b

value: Larva 5 days post-fertilization


title: ChIP-Seq of MYC, overexperssing control, Input

value: WT

value: empty vector


title: Embr_5dpf_Evi5b_3_WT_b


title: 498198-62

value: MCAO


title: ChIP-Seq of MYC, overexpreesing EPIC1, Input

value: EPIC1 overexpressing vector


title: Hippo_Ctrl_6

value: control


title: ChIP-Seq of MYC, siEPIC1-B, IP

value: EPIC1 knockdown


title: Hippo_Ctrl_5

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: Embr_5dpf_Evi5b_6_DEL_b


title: Embr_5dpf_Cdon_1_WT_c


title: ChIP-Seq of MYC, overexperssing control, IP


title: ChIP-Seq of MYC, siEPIC1-A, IP


title: Hippo_Ctrl_4


title: Embr_5dpf_Asap1b_7_WT_b


title: ChIP-Seq of MYC, siControl, IP

value: siControl


title: Embr_5dpf_Asap1b_7_DEL_b


title: 497727-36

value: Female


title: 498198-12

value: MCAO+Recan


title: ChIP-Seq of MYC, siEPIC1-B, Input

value: Mammary gland/Breast

value: Adenocarcinoma

value: Human epithelial cell


title: Pol II ChIP-seq, yeast, Thiolutin 8mins, Input, rep3

city: Boston

first: Chenxi

last: Qiu

state: MA

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Paired-end raw fastq files were first trimmed for TruSeq3-PE-2 adaptors using Trimmomatic 0.38 to remove adaptor readthrough. FastQC was used for quality control analysis. Adapter-trimmed fastq were then aligned to a hybrid genome combining S. cerevisiae and S. pombe genomes using bowtie2/2.4.5 (38), allowing 1 mismatch and disallowing insert size > 1000 (‘bowtie2 -q -N 1 -X 1000 –x'). The hybrid genome was generated by combining S. cerevisiae genome version R64-3-1 with S. pombe genome 2018-9-4, after appending a suffix of “pom_” to S. pombe chromosomes to allow reads mapping to S. pombe to be filtered later.
Sam files generated from bowtie2 alignment were then converted to bam, which were then sorted and indexed using bamtools. Duplicates were then removed by picard 2.8.12, followed by indexing of newly generated bam files. Subsequent to duplicate removal, reads aligned to hybrid genome were segregated into separate species-specific (S. cerevisiae or S. pombe) input or IP bam files (‘samtools idxstats <non_duplicated-hybrid.bam> | cut -f 1 | grep -v “pom_” | xargs samtools view -b <non_duplicated-hybrid.bam>   > <output_S.ce.bam>’; ‘samtools idxstats <non_duplicated-hybrid.bam> | cut -f 1 | grep “pom_” | xargs samtools view -b <non_duplicated-hybrid.bam>   > <output_pombe.bam>’). Bams were then indexed using samtools/1.14. This segregation of species-specific reads allows counting species specific reads in both input and IP bam files for normalization factor quantification.
Total number of unique reads (samtools flag -F 260) per bam file of S. cerevisiae and S. pombe were counted for both input and IP data for calculating normalization factor combining input and spike-in reads, using an R script.
These factors were then used to scale the S.cerevisiae IP bams to generate scaled or normalized bigwigs using bamCoverage function of deeptools/3.3.0. Wiggletools/1.2.11 was then used to generate mean bedgraphs of three replicates which were then converted to mean bigwigs using bedGraphtoBigWig of kentutils/v.370.
Differential bigwigs were generated by log2 operation function of bigwigCompare under the deeptools/3.3.0 package which were then used for generating heatmaps.
Assembly: R64-3-1 for S.cerevisiae and genome version 2018-9-4 for S. pombe
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Yeast were grown in SC media to mid-log (1X107 cells/mL)

extract_protocol:
Yeast cells were cross-linked with 1% formaldehyde solution (1% formaldehyde, 10mM NaCl, 100µM EDTA and 5mM HEPES-KOH, pH 7.5) for 20 minutes and quenched by 3M glycine (final concentration 360mM) for 5 minutes. In brief, cross-linked cells were disrupted by bead beating and cell lysate was centrifuged at 1500 rpm for 1 min at 4˚◦C to remove cell-debris, followed by centrifugation of chromatin pellets, subsequent washing of pellets (twice) with 1 ml FA buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.1% Triton X-100, 0.01% sodium deoxycholate, 0.1% SDS and 1 mM PMSF) at 14000 rpm for 20 min at 4˚C. Chromatin for ChIP-seq was washed one additional time in special FA buffer lacking SDS and sodium deoxycholate. Chromatin pellets were sonicated using a Diagenode Bioruptor (ChIP-qPCR, 45 cycles – 3 × 15 cycles; 30 s ON/45 s OFF) or a Diagenode Bioruptor Pico (ChIP-seq, 20 cycles; 30 s ON/30-50 s OFF) and used for IP with anti-FLAG antibody (FLAG M2 magnetic beads, Sigma-Aldrich). For ChIP-seq, 1100 µg of chromatin material as determined by BCA assay (Thermo Fisher) was used for each IP with addition of 110 µg S. pombe spike-in chromatin from CKP025 (h- ura4-D18 rpb3+::6gly-3Flag-ura4+). Concentration of SDS in IP for ChIP-seq after addition of S. pombe chromatin was 0.1% and concentration of sodium deoxycholate was 0.01%. SDS and sodium deoxycholate were omitted from all washes for ChIP-seq IPs as they reduce efficiency of FLAG M2 antibody (MilliporeSigma). 10% of the total IP material was used as input. Input or immunoprecipitated DNA was purified by standard phenol–chloroform extraction and ethanol precipitated with pellet paint (MilliporeSigma) or glycoblue (ThermoFisher). Immunoprecipitated DNA and 10% of corresponding input DNA (1:10 diluted) were used for qPCR with SsoAdvanced Universal SYBR Green supermix (Bio-Rad) using CFX 96 (Bio-Rad).
Libraries for ChIP-seq were prepared with NEBNext Ultra II DNA Library kit (NEB) according to the manufacturer’s instructions with the following modifications. Starting DNA for ChIP or input samples was 10 ng. Index primers were from NEBNext Multiplex Oligos for Illumina Dual Index Primer Set 1 and were diluted 1/2.5 before use. Library amplification during indexing amplification was between 6-8 cycles Samples were sequenced (paired-end) on an Illumina NextSeq 2000 P2 flow cell.

treatment_protocol: Yeast were then treated with 10 µg/mL thiolutin for 2, 4, 8 or 10 mins (ChIP-qPCR) or for 1, 2, 4, or 8 mins (ChIP-seq).

value: yeast cell

value: Thiolutin 8min


title: Embr_5dpf_Apbb1_1_WT_c


title: Hippo_Ctrl_2

value: hippocampus


title: Pol II ChIP-seq, yeast, Thiolutin 8mins, IP, rep3

value: FLAG M2 antibody (Sigma)


title: 497727-35

value: Aged


title: Pol II ChIP-seq, yeast, Thiolutin 8mins, Input, rep2


title: 498198-11


title: Hippo_Ctrl_1


title: Embr_5dpf_Apbb1_1_DEL_c

value: Larva 5 days post-fertilization


title: ChIP-Seq of MYC, siControl, Input

value: WT


title: ChIP-Seq of MYC, siEPIC1-A, Input


title: Embr_5dpf_Ap1g1_1_WT_c


title: Pol II ChIP-seq, yeast, Thiolutin 8mins, IP, rep2


title: 3P-phod2

city: Zhe jiang

first: Shenghong

last: Ge

address: No. 2318, Yuhangtang Road, Hangzhou, Zhejiang, China

institute: Hangzhou Normal University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples

source_name: seedlings

extract_protocol:
Using a RNeasy Plant Mini Kit to eetracted total RNA (Qiagen, R415102).
Total RNAs were extracted from 8-day-old seedlings under HP or LP conditions using a RNeasy Plant Mini Kit (Qiagen, R415102) according to the instruction manual. 1.3μg of total RNA was used for the construction of sequencing libraries

value: seedlings


title: Embr_5dpf_Cdon_1_DEL_c


title: Pol II ChIP-seq, yeast, Thiolutin 8mins, Input, rep1


title: Hippo_Ctrl_3

value: control


title: 497727-3


title: HCC827ER cells

city: Shenzhen

first: Shuwei

last: Zhang

state: State...

address: Shenzhen,Guangdong province,China

institute: Tsinghua university

data_processing:
The cDNA library was prepared using the library preparation kits (TruSeq Stranded RNA LT Ribo-Zero H/M/R Kit) according to the manufacturer’s protocols.
After quality control, the clean reads were mapped to the homo sapiens genome (GRCh38.p13) using HISAT2 (v2.0.4). Differentially expressed transcripts were defined with Cuffdiff tools.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: raw counts for each sample

source_name: HCC827ER cell line

growth_protocol: All the cell lines were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin, in a humidified incubator at 37°C with 5% CO2

extract_protocol:
0.2ug of total RNA was used for the construction of sequencing libraries
The libraries was prepared by using TruSeq Stranded RNA LT Ribo-Zero H/M/R Kit according to the manufacturer’s protocols

value: HCC827ER cell line

value: lung adenocarcinoma cell line


title: HCC827 cells

source_name: HCC827 cell line

value: HCC827 cell line


title: HCC82GR cells

source_name: HCC82GR cell line

value: HCC82GR cell line


title: Embr_5dpf_Ap1g1_1_DEL_c


title: Pol II ChIP-seq, yeast, Thiolutin 4mins, Input, rep3

value: Thiolutin 4min


title: Pol II ChIP-seq, yeast, Thiolutin 8mins, IP, rep1


title: 2P-phod2


title: Zebrafish_PBS_injected_ctrl_exp2

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

data_processing:
Sequencing data were assessed for quality using fastqc 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The RNAseq reads  were mapped against the zebrafish Danio rerio GRCz11 genome (accesion numbers NC_007112.7-NC_007136.7) using botwie2. Samtools was used to convert and sort the output and featureCounts summarized the aligned reads. Data normalization and determination of significance of differential expression was performed in R (R-project.org) using the GLM method in the EdgeR package.
Assembly: GRCz11 genome (NC_007112.7-NC_007136.7)

source_name: larvae

extract_protocol:
Bacteria and mock injected larvae hold in a petri dish with fresh embryo medium and incubated at 28 °C until development of typical signs of disease such as axis curvature and necrosis which was observed at approx. 36 h dpi. 60 randomly chosen zebrafish larvae from each group (infected, mock-infected) were euthanized by a prolonged immersion in an overdose of 50 mg/L Tricaine solution, followed by decapitation with a sharp blade, their heads collected and transferred into 1.5ml Eppendorf tubes Excess E3 medium was removed and   replaced by RNAlater (Ambion) and stored at 4°C until further processing. For the extraction of total RNA, RNAlater was replaced by 600 ul of Qiazol, and the tissue was homogenized using a pestle motor followed by drawing of sample with a needle until the tissue was completely homogenized. As a control, RNA was isolated from z3032 cultures grown in LB to stationary phase (18 - 24 h). For both the zebrafish and bacterial culture, RNA extractions were performed using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocols. An additional DNase treatment was performed with a TURBO DNA-free kit (Ambion) according to the manufacturer's protocols. The concentration of the extracted RNA was measured using a NanoDrop Spectrophotometer.
RNA Sequencing on a HiSeq2500 (Illumina) were performed at the Functional Genomic Center at University Zurich (FGCZ), Zurich, Switzerland, accoring to the Illumina protocl

value: larvae

value: casper mutant

value: PBS


title: 1P-phod2


title: Pol II ChIP-seq, yeast, Thiolutin 4mins, IP, rep3

value: yeast cell


title: PC-9ER cells

source_name: PC-9ER cell line

value: PC-9ER cell line


title: Zebrafish_PBS_injected_ctrl_exp1


title: 3P+phod2


title: PC-9GR cells

source_name: PC-9GR cell line

value: PC-9GR cell line


title: Zebrafish_Cronobacter_infected_EXP2

value: infection


title: 1k, postsort, sc

city: San Francisco

first: Sixuan

last: Pan

state: California

address: 1450 3rd Street

department: Bioengineering

institute: UCSF

description:
PIP-seq
1k_dilution_sc

data_processing:
Library demultiplexing, read alignment, identification of empty droplets, and UMI quantification were performed with PIPseeker 1.0.0 (Fluent Biosciences) with default parameters.
Assembly: GRCh38, GRCm39
Supplementary files format and content: barcodes.tsv.gz contains the barcode sequences, features.tsv.gz contains the gene names, and the matrix.mtx.gz contains the gene expression matrix table. All files are after filtering.

organism:
Homo sapiens
Mus musculus

growth_protocol: Human HEK 293T and mouse NIH 3T3 cells (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher, 11995073) supplemented with 10% fetal bovine serum (FBS; Gibco, 10082147) and 1× Antibiotic-Antimycotic (Gibco, 15240062) at 37°C and 5% CO2.

extract_protocol:
Mice were humanely euthanized using CO2. BM cells from their limb bones were isolated and resuspended in FACS buffer (PBS + 2% FBS) by centrifugation at 8,000 × g for 1 minute. After removing red blood cells (RBC) with a commercial lysis buffer (BioLegend, 420302), diluted to 1X with distilled water, single-cell suspensions were depleted of hematopoietic cells committed to a specific lineage using a Lineage Cell Depletion Kit (EasySep, StemCell Technologies, Inc., 19856A). To label LT-HSC cells, the following fluorophore-conjugated antibodies were used at the indicated dilutions: CD117 (c-Kit) BV785 (clone 2B8, BioLegend; 1:200 dilution), Ly-6A/E (Sca-1) PE/Cy7 (clone D7, BioLegend; 1:1000 dilution), CD48 PerCP/Cy5.5 (clone HM48-1, BioLegend; 1:100 dilution) and CD150 (SLAM) APC (clone TC15-12F12.2, BioLegend; 1:50 dilution). After adding the rat serum and isolation cocktail of the Lineage Cell Depletion Kit, the LT-HSC-labeling antibodies were also added for a 30-minute-long incubation in the dark at 4°C. Following the removal of lineage-positive cells, samples were spun down in FACS buffer and subsequently resuspended in 200-300 μL of FACS buffer containing DAPI at a final concentration of 1 μg/mL. Cells from 2/3 age-matched mice were combined to generate each pool sample, with a total of 2 replicates for the young condition and 3 replicates for the middle-aged and old conditions, respectively (total n=10 mice).
Single cells were processed for scRNA-seq using the PIP-seq T2 3’ Single Cell RNA kit (v3.0) according to the manufacturer's protocol (Fluent Biosciences, FB0001026).

treatment_protocol: HEK or 3T3 cells were treated with 0.05% Trypsin-EDTA with Phenol red (Gibco, 25200114) for 3 min, quenched with growth medium, and centrifuged for 3 min at 300g. The supernatant was removed, and the cells were resuspended in 1X DPBS without calcium or magnesium. Fresh-frozen human peripheral blood mononuclear cells (PBMCs) were obtained from STEMCELL Technologies. DMEM with 10% FBS was warmed up to 37°C, and the frozen PBMCs were thawed by adding 1 mL of warm media on top of the frozen cells and immediately transferring the media to a 15-mL conical. This process was repeated until all PBMCs were thawed and transferred. Cells were centrifuged for 3 min at 300g and resuspended in 1X DPBS. For the 10-3, 10-4, and 10-5 target cell fraction samples, human HEK 293T cells were the target population mixed with mouse NIH 3T3 cells background population. For the 10-6 target cell fraction sample, mouse NIH 3T3 cells were the target population mixed with the human PBMCs background population. The target population was treated with 1 μg/mL Calcein Red-Orange (Invitrogen, C34851), and the background population was treated with 1 μg/mL Calcein Green (Invitrogen, C34852) for 15 min at 37°C, followed by washing and dilution to the final concentration in 1× DPBS with 0.1% BSA. The viability and cell concentration were evaluated by an automated cell counter (Bio-Rad, TC20) after adding Trypan Blue (Gibco, 15250061). The mixed cell suspension was filtered through a 40 µm cell strainer (Flowmi, BAH136800040) and processed through the PURE-seq workflow described above to enrich for Calcein Red-Orange labeled cells.

value: mixed


title: Pol II ChIP-seq, yeast, Thiolutin 4mins, Input, rep2


title: 3P-KC

value: P-KC


title: PC-9 cells

source_name: PC-9 cell line

value: PC-9 cell line


title: SKG_synovium_rAAV-sIL-1Ra_rep2

city: Worcester

first: Yen

address: 366 Plantation st, NERB / N9-3004D

department: Genetic and Cellular Medicine

institute: Umass Chan Medical school

description: Library name: T2

data_processing:
Adapter sequences and low-quality bases were removed.Reads were aligned to the Mus Musculus reference genome(GRCm39).
Assembly: GRCm38 (mm10) (Mus musculus, older but still widely used)
Supplementary files format and content: a tab-delimited text file (.txt) containing gene-level expression values.

source_name: ankle synovium Area

extract_protocol:
Total RNA was extacted from dissected tissues using Trilzol and purelink RNA mini kit
RNA-seq libraries were generated from 1 µg total RNA per sample/platform to produce 150 bp paired-end reads.

value: ankle synovium Area

value: SKG


title: Zebrafish_Cronobacter_infected_EXP1


title: Pol II ChIP-seq, yeast, Thiolutin 4mins, IP, rep2

value: FLAG M2 antibody (Sigma)


title: 2P-KC

value: seedlings


title: Pol II ChIP-seq, yeast, Thiolutin 4mins, IP, rep1


title: SKG_synovium_rAAV-sIL-1Ra_rep3

description: Library name: T3


title: 1k, presort

description:
PIP-seq
1k_dilution_presort


title: 2P+phod2


title: 1P-KC


title: 1k, postsort, yield

description:
PIP-seq
1k_dilution_yield


title: SKG_synovium_rAAV-sIL-1Ra_rep1

description: Library name: T1


title: 1M, postsort

description:
PIP-seq
1M_dilution


title: 1P+phod2


title: Pol II ChIP-seq, yeast, Thiolutin 2mins, Input, rep3

value: Thiolutin 2min


title: SKG_synovium_rAAV-control_rep3

description: Library name: C3


title: 3P+KC

value: P+KC


title: Pol II ChIP-seq, yeast, Thiolutin 2mins, IP, rep3


title: SKG_synovium_rAAV-control_rep2

description: Library name: C2


title: Pol II ChIP-seq, yeast, Thiolutin 4mins, Input, rep1

value: Thiolutin 4min


title: 100k, postsort

description:
PIP-seq
100k_dilutiion


title: 1P+KC


title: 2P+KC


title: Pol II ChIP-seq, yeast, Thiolutin 2mins, Input, rep2


title: SKG_synovium_rAAV-control_rep1

description: Library name: C1


title: Pol II ChIP-seq, yeast, Thiolutin 2mins, IP, rep2


title: 10k, postsort

description:
PIP-seq
10k_dilution


title: 1k, postsort

description:
PIP-seq
1k_dilution


title: Pol II ChIP-seq, yeast, Thiolutin 2mins, Input, rep1


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 48 hour, replicate 3

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

description:
30C48H3
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 48 hour, replicate 3

data_processing:
The RNAseq raw sequences were processed as follows. Initially, sequences of adapter and primers were removed from bacterial RNA sequences by FASTP. Quality of the sequence was assessed and reported by FASTQC and MultiQC, respectively. Next, the processed RNA sequences were mapped with the reference genome sequences by HISAT2, resulting in mapped reads in Binary Alignment Map (BAM) format.
Assembly: Burkholderia stagnalis TBRC 18363
Supplementary files format and content: Comma-separated values (CSV) for read_count.csv
Supplementary files format and content: tab-delimited text file for individual read count sample file

organism: Burkholderia stagnalis

source_name: bacterial cell

growth_protocol: Burkholderia stagnalis TBRC 18363 was cultivated in LB, LS2, and BMPM media for cell refreshment, RNAseq analysis, and icosalide production, respectively.

extract_protocol:
RNA of B. stagnalis TBRC 18363 was extracted using RiboPure™ RNA Purification Kit, bacteria (Invitrogen, U.S.A.). Cells were harvested from 250–600 microliter cultures in LS2 medium by centrifugation and resuspended with 300 microliter RNAwiz solution. Then, RNA extraction was performed following the kit protocol. RNA eluted from the kit columns were treated with DNaseI. Concentration and quality of RNA was measured by using nanodrop and 0.8% agarose gel electrophoresis, respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B. stagnalis TBRC 18363

value: bacterial cell

value: 30 degree celcius, 48 hour, replicate 3


title: Epithelial cells, HiPt2

city: Birmingham

first: Runhua

state: AL

address: 1720 2nd Avenue South

institute: University of Alabama at Birmingham

description:
Library name: Sample 8
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt

data_processing:
The final sequenced data will be processed by 10xGenomics Cell Ranger pipeline and then visualized by Loupe browser or Partek software, or by “R” Seurat package. RNA-seq data was analyzed with Partek software.
Assembly: Mus_musculus (mm10)

source_name: Prostate

extract_protocol:
For RNA-seq, epithelial cells were stained with EPCAM, viability dye, and 7-AAD, and viable cells were sorted from the digested prostate and further extracted with QIAGEN Rneasy RNA Micro Kit. 150 ng RNA was used for the construction of a sequencing library. For scRNA-seq, the whole prostate was digested by collagenase/hyaluronidase (Cat# 07912) StemCell) for 1-2 h. Viable cells were sorted from whole digested prostate, 10,000 cells were collected for further sequencing library.
Sorted viable single cells will loaded into 10xcontroller and individual cells will be captured into oil droplets to form Gel Bead-In-EMulsions (GEMs). The single cell cDNA libraries will be constructed by following 10xGenomics Chromium GEM-X Single Cell 3' v4 Gene Expression User Guide, and then sequenced by illumina Nextseq500 or Novaseq 6000 machine, with targeting minimum 20,000 reads/cell.

value: Prostate

value: Epithelial cells

value: Hi-Myc/Ptenf/f


title: Pol II ChIP-seq, yeast, Thiolutin 2mins, IP, rep1

value: yeast cell


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 48 hour, replicate 1

description:
30C48H1
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 48 hour, replicate 1

value: 30 degree celcius, 48 hour, replicate 1


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 48 hour, replicate 2

description:
30C48H2
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 48 hour, replicate 2

value: 30 degree celcius, 48 hour, replicate 2


title: BCG+ Celecoxib- Rv- [R12665]

city: New Delhi

first: DHIRAJ

last: KUMAR

state: Delhi

address: ARUNA  ASAF ALI MARG

department: Cellular Immunology

country: India

institute: ICGEB, New Delhi

description: 2 X 151bp

data_processing:
Reads mapped using Salmon against Gencode mouse genome GRCm39 primary assembly
Used tximeta, fishpond and SummarizedExperiment to obtain genes expression based on GENCODE  annotation v.M30
Normalisation done using approach as described in fishpond library for swish methodology
Assembly: GRCm39
Supplementary files format and content: merged comma-separated text files include expression values for each Sample

source_name: BCG+ Celecoxib- Rv-

extract_protocol:
Total RNA was extracted from flow-sorted lung neutrophils from Mtb-infected WT mice, treated or not with BCG and/or Celecoxib, following a double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany).
cDNA libraries were prepared using 0.5 ng of total RNA using the Smart-seq2 protocol with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA).
The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq X system (28 samples/lane).

value: Polymorphonuclear Neutrophil

tag: bcg

value: positive

tag: celecoxib

value: negative

tag: infected


title: Epithelial cells, HiPt1

description:
Library name: Sample 7
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt

tag: cell type

tag: genotype


title: Epithelial cells, Pten KO 2

description:
Library name: Sample 6
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt

value: Ptenf/f


title: Pol II ChIP-seq, yeast, Thiolutin 1min, Input, rep3

tag: treatment

value: Thiolutin 1min


title: BCG+ Celecoxib- Rv- [R12664]

description: 2 X 151bp


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 30 hour, replicate 3

description:
30C30H3
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 30 hour, replicate 3

value: 30 degree celcius, 30 hour, replicate 3


title: BCG+ Celecoxib- Rv- [R12663]

description: 2 X 151bp


title: Epithelial cells, Pten KO1

description:
Library name: Sample 5
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt

tag: tissue


title: Pol II ChIP-seq, yeast, Thiolutin 1min, IP, rep3

value: FLAG M2 antibody (Sigma)


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 30 hour, replicate 2

description:
30C30H2
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 30 hour, replicate 2

value: 30 degree celcius, 30 hour, replicate 2


title: Epithelial cells, HiMyc2

description:
Library name: Sample 4
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt

value: Hi-Myc


title: Pol II ChIP-seq, yeast, Thiolutin 1min, Input, rep2


title: Epithelial cells, HiMyc1

description:
Library name: Sample 3
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt


title: BCG+ Celecoxib- Rv- [R12662]

description: 2 X 151bp


title: BCG+ Celecoxib- Rv- [R12652]

description: 2 X 151bp


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 24 hour, replicate 3

description:
30C24H3
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 24 hour, replicate 3

value: B. stagnalis TBRC 18363

value: bacterial cell

value: 30 degree celcius, 24 hour, replicate 3


title: BCG+ Celecoxib+ Rv+ [R12661]

description: 2 X 151bp

source_name: BCG+ Celecoxib+ Rv+


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 30 hour, replicate 1

description:
30C30H1
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 30 hour, replicate 1

value: 30 degree celcius, 30 hour, replicate 1


title: Pol II ChIP-seq, yeast, Thiolutin 1min, Input, rep1


title: Epithelial cells, Scr2

description:
Library name: Sample 2
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt

value: Prostate

value: Epithelial cells

value: WT


title: Pol II ChIP-seq, yeast, Thiolutin 1min, IP, rep2

value: yeast cell


title: BCG+ Celecoxib+ Rv+ [R12660]

description: 2 X 151bp

value: Polymorphonuclear Neutrophil


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 24 hour, replicate 2

description:
30C24H2
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 24 hour, replicate 2

value: 30 degree celcius, 24 hour, replicate 2


title: Pol II ChIP-seq, yeast, Thiolutin 1min, IP, rep1


title: Pol II ChIP-seq, yeast, DMSO, Input, rep3

value: DMSO


title: Epithelial cells, Scr1

description:
Library name: Sample 1
Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt


title: RNA from bacterial cell, LS2 medium, 30 degree celcius, 24 hour, replicate 1

description:
30C24H1
RNA-Seq from bacterial cell, LS2 medium, 30 degree celcius, 24 hour, replicate 1

value: 30 degree celcius, 24 hour, replicate 1


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 48 hour, replicate 3

description:
25C48H3
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 48 hour, replicate 3

value: 25 degree celcius, 48 hour, replicate 3


title: BCG+ Celecoxib- Rv+ [R12657]

description: 2 X 151bp

source_name: BCG+ Celecoxib- Rv+

value: positive

value: negative


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 48 hour, replicate 2

description:
25C48H2
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 48 hour, replicate 2

value: 25 degree celcius, 48 hour, replicate 2


title: Pol II ChIP-seq, yeast, DMSO, IP, rep3

value: FLAG M2 antibody (Sigma)


title: Pol II ChIP-seq, yeast, DMSO, Input, rep2


title: BCG+ Celecoxib- Rv+ [R12656]

description: 2 X 151bp


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 48 hour, replicate 1

description:
25C48H1
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 48 hour, replicate 1

value: B. stagnalis TBRC 18363

value: 25 degree celcius, 48 hour, replicate 1


title: BCG+ Celecoxib- Rv+ [R12649]

description: 2 X 151bp


title: Pol II ChIP-seq, yeast, DMSO, IP, rep2


title: BCG+ Celecoxib+ Rv+ [R12651]

description: 2 X 151bp


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 30 hour, replicate 2

description:
25C30H2
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 30 hour, replicate 2

value: bacterial cell

value: 25 degree celcius, 30 hour, replicate 2


title: Pol II ChIP-seq, yeast, DMSO, Input, rep1


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 30 hour, replicate 3

description:
25C30H3
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 30 hour, replicate 3

value: 25 degree celcius, 30 hour, replicate 3


title: hskm_136_subject3

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 3ug of biotin labeld final target was hybidized  to Human Gene 2.0 ST Arrays in Affymetrix GeneChip Hybridization Oven 645

scan_protocol: The arrays were scanned in Affymetrix Gene Chip Scanner 3000

data_processing: RMA processing in Affymetrix Comand Console

source_name: primary human skeletal muscle cell (Subject 3), miR-136-3p transfected

label_protocol: 150ng total RNA was used to prepare final targets using Affymetrix User manual for GeneChip  WT Plus Kit.

extract_protocol: Extraction of total RNA was performed with miRNeasy kit (QIAGEN) according to the manufacturer's instructions.

tag: subject id

value: Subject 3

value: primary human skeletal muscle cells

value: miR-136-3p transfected


title: BCG- Celecoxib- Rv- [R12666]

description: 2 X 151bp

source_name: BCG- Celecoxib- Rv-

value: Polymorphonuclear Neutrophil


title: Pol II ChIP-seq, yeast, DMSO, IP, rep1

source_name: yeast cell

value: yeast cell


title: BCG- Celecoxib- Rv- [R12668]

description: 2 X 151bp


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 24 hour, replicate 3

description:
25C24H3
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 24 hour, replicate 3

tag: strain

value: 25 degree celcius, 24 hour, replicate 3


title: Pol II ChIP-seq, yeast, untreated, Input, rep3

value: Ut


title: BCG- Celecoxib- Rv- [R12667]

description: 2 X 151bp


title: Pol II ChIP-seq, yeast, untreated, IP, rep3


title: BCG- Celecoxib- Rv- [R12653]

description: 2 X 151bp


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 30 hour, replicate 1

description:
25C30H1
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 30 hour, replicate 1

value: 25 degree celcius, 30 hour, replicate 1


title: RIP-seq-HEK293T-Ctrlrep3

city: Shanghai, P.R. China

first: weiying

last: meng

address: 1239 Siping Road, Shanghai, P.R. China

institute: Tongji University

description: Library name: RIP-seq-HEK293T-Ctrl3

data_processing:
Raw sequencing reads were trimmed using Cutadapt (v4.2) to remove adapters and low-quality bases.
Trimmed reads were aligned to the GRCh38 reference genome using STAR (v2.7.10b).
Enriched binding regions (peaks) were identified using MACS2 (v2.2.9.1) with the parameters ‘--nomodel --extsize 150’.
Assembly: hg38
Supplementary files format and content: narrowPeak file containing RIP-seq peaks for each sample.
Supplementary files format and content: narrowPeak file containing RIP-seq peaks for each sample.

source_name: cell line

extract_protocol:
Total RNA was extracted from HEK293T or other cell lines using TRIzol™ reagent (Thermo Scientific, 15596018) following the manufacturer’s instructions.
Total RNA was extracted from HEK293T and HuCCT1 cells using TRIzol™ reagent according to the manufacturer’s instructions. RNA-seq library preparation was conducted using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, following the manufacturer’s protocol. This process included ribosomal RNA depletion to enrich the library for mRNA and pre-mRNAs. After rRNA depletion, the RNA was fragmented and denatured to generate appropriate RNA fragments for cDNA synthesis. First-strand cDNA was synthesized, and an A-tail was subsequently added to the 3’ end of the cDNA to facilitate adapter ligation. Illumina sequencing adapters were then ligated to the cDNA fragments, and the adapter-ligated library was amplified via PCR to enrich for the desired fragments. The final RNA-seq library was quantified and normalized to ensure uniform sequencing depth across samples. High-throughput sequencing was performed on the Illumina HiSeq2500 platform.

value: cell line

tag: cell line

value: Ctrl


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 24 hour, replicate 2

description:
25C24H2
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 24 hour, replicate 2

value: 25 degree celcius, 24 hour, replicate 2


title: BCG- Celecoxib+ Rv+ [R12659]

description: 2 X 151bp

source_name: BCG- Celecoxib+ Rv+

value: negative

value: positive


title: hskm_136_subject4

source_name: primary human skeletal muscle cell (Subject 4), miR-136-3p transfected

value: Subject 4


title: RNA from bacterial cell, LS2 medium, 25 degree celcius, 24 hour, replicate 1

description:
25C24H1
RNA-Seq from bacterial cell, LS2 medium, 25 degree celcius, 24 hour, replicate 1

value: B. stagnalis TBRC 18363

value: bacterial cell

value: 25 degree celcius, 24 hour, replicate 1


title: BCG- Celecoxib+ Rv+ [R12658]

description: 2 X 151bp


title: hskm_136_subject2

source_name: primary human skeletal muscle cell (Subject 2), miR-136-3p transfected

value: Subject 2


title: Pol II ChIP-seq, yeast, untreated, IP, rep2

value: FLAG M2 antibody (Sigma)


title: RIP-seq-HEK293T-Ctrlrep2

description: Library name: RIP-seq-HEK293T-Ctrl2


title: BCG- Celecoxib+ Rv+ [R12650]

description: 2 X 151bp


title: hskm_nc_subject1

source_name: primary human skeletal muscle cell (Subject 1), miRNA-negative control transfected

value: Subject 1

value: primary human skeletal muscle cells

value: miRNA-negative control transfected


title: hskm_136_subject1

source_name: primary human skeletal muscle cell (Subject 1), miR-136-3p transfected

value: miR-136-3p transfected


title: hskm_nc_subject4

source_name: primary human skeletal muscle cell (Subject 4), miRNA-negative control transfected


title: hskm_nc_subject2

source_name: primary human skeletal muscle cell (Subject 2), miRNA-negative control transfected


title: hskm_nc_subject3

source_name: primary human skeletal muscle cell (Subject 3), miRNA-negative control transfected

value: Subject 3


title: Pol II ChIP-seq, yeast, untreated, Input, rep1

value: yeast cell

value: Ut


title: A.bruennichi,warm, replicate 3

city: Greifswald

first: Carolina

last: Ortiz Movliav

state: Mecklenburg-Vorpommern

address: Loitzer Straße 26

department: Zoological Institute and Museum

institute: University of Greifswald

description:
Library name: Sample 11
Column name in CountTable_Star.csv Warm_S11

data_processing:
Sequencing was done on a NextSeq® 500/550 System using a High Output Kit v2.5 flow cell (150 cycles) and 2 x 75 bp paired-end sequencing.
The sequencing lanes were merged for each paired end.
We mapped the reads to the genome of the species (accession No. GCA_947563725.1) using the program STAR 2.7.11a in two-pass mode with default parameters.
We used the resultant BAM files to generate a count table on Subread 2.0.6, using the feautureCounts function. The count data was normalized with the R package DESq2 1.38.3.
Assembly: GCA_947563725.1
Supplementary files format and content: CountTable_Star.csv

organism: Argiope bruennichi

source_name: 15 spiderlings

growth_protocol: Collected mated  A. Bruennichi females, were kept in plastic containers (1000 mL) under shared conditions (20°C, 70% relative humidity) until oviposition, where they laid eggs into a silk-woven egg sac. The females were misted with water daily and fed regularly with house flies (Calliphora sp.). Egg sacs containing first instar spiderlings were kept in climate cabinets for three months and spayed with water every day in the evening.

extract_protocol:
A pool of 15 spiderlings per sample were mechanically homogenized using non-sticky pellet pestles in the presence of 500 μL RNA-Solv Reagent (Omega Bio-tek), following the manufacturer’s recommendations.
2 μg total RNA from each sample was subject to ribosomal depletion (rRNA) using a custom designed Argiope bruennichi riboPOOL depletion kit dp-K096-000074 (siTOOLs Biotech).100 ng of ribosomal depleted RNA for library construction using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

treatment_protocol: Egg sacs containing the first instar spiderlings were kept in climate cabinets simulating three different winter conditions for three months. Cold (5°C day, -15°C night), moderate (5°C day, -5°C night), and warm (15°C day, -5°C night)

value: 15 spiderlings

value: warm


title: RIP-seq-HEK293T-Ctrlrep1

description: Library name: RIP-seq-HEK293T-Ctrl1

value: cell line

value: Ctrl


title: BCG- Celecoxib- Rv+ [R12655]

description: 2 X 151bp

source_name: BCG- Celecoxib- Rv+

value: Polymorphonuclear Neutrophil

value: negative

value: positive


title: A.bruennichi,warm, replicate 2

description:
Library name: Sample 10
Column name in CountTable_Star.csv Warm_S10


title: RIP-seq-HEK293T-SNRPD2OErep3

description: Library name: RIP-seq-HEK293T-SNRPD2OE3


title: Pol II ChIP-seq, yeast, untreated, IP, rep1


title: RIP-seq-HEK293T-SNRPD2OErep2

description: Library name: RIP-seq-HEK293T-SNRPD2OE2


title: BCG- Celecoxib- Rv+ [R12654]

description: 2 X 151bp


title: A.bruennichi,warm, replicate 1

description:
Library name: Sample 9
Column name in CountTable_Star.csv Warm_S9


title: CR030T, CR031T

city: Daejeon

first: Inkyung

last: Jung

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description:
Library name: CRTU10
10X Genomics

library_source: genomic single cell

data_processing:
The feature-barcode matrix was generated using cellranger-atac count (10x Genomics, v1.1.0), with sequenced reads aligned to the human reference genome (hg38). To demultiplex pooled libraries, barcodes were clustered based on germline variants using souporcell (PMID: 32366989) with previously described parameters (--min_alt 8 --min_ref 8 --no_umi True --skip_remap True --ignore True) (PMID: 34675424). Germline variants for each donor were identified using WGS data generated from the same donor as part of the Center for Integrative Omics and Precision Medicine (CoPM) consortium, using freebayes (-iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 20 --pooled-continuous). The number of demultiplexed barcodes from each library, along with the full list of assigned barcodes and their corresponding donors, is provided in the Supplementary Data of the cited reference.
Assembly: GRCh38
Supplementary files format and content: Fragment and cell-to-peak count matrix files

source_name: Colorectal tumor and nonmaligant adjacent tissue

extract_protocol:
Cryopreserved cells were thawed, and 100k cells were transferred to a microtube, and centrifuged at 1,000 g for 5 min at 4 °C. The pellet was washed twice with 200 µL of 0.04% BSA in PBS and resuspended in 50 µL of the same buffer. A 5 µL aliquot was used for cell counting on a Cellometer Auto 2000 (Nexcelom Biosicence) with AO/PI staining. Equal numbers of cells from 2-4 individual donors were pooled to prepare a total of 200k cells, filtered through a 40 µm Flowmi strainer (SP Bel-Art, 136800040), and centrifuged again. The pellet was resuspended in 90 µL of cold 0.1× Lysis Buffer, containing 10mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% Nonidet P40 Substitute (Sigma-Aldrich, 74385), 0.001% digitonin (Thermo Fisher Scientific, BN2006), and 1% BSA, with gentle pipetting and incubated on ice for 5 min. Following incubation, 100 µL of Wash Buffer with 10mM Tris-HCL (pH7.4), 10mM NaCl, 3mM MgCl2, 1% BSA, and 0.1% Tween-20, was added, the sample was centrifuged, and the supernatant was removed. The pellet was then washed twice with gentle pipetting and resuspended in 100 µL of 1× Nuclei Buffer (10x Genomics). After centrifugation, 80uL of supernatant was removed, leaving 20 uL to minimize loss, and 5 uL was used for cell counting. A total of 25k nuclei ware prepared for tagmentation.
Libraries were prepared with 10X Genomics Chromium Single Cell ATAC Library & Gel Bead Kit v1 following manufacturer’s instructions.


title: BCG- Celecoxib- Rv+ [R12648]

description: 2 X 151bp


title: RIP-seq-HEK293T-SNRPD2OErep1

description: Library name: RIP-seq-HEK293T-SNRPD2OE1


title: A.bruennichi, moderate, replicate 4

description:
Library name: Sample 8
Column name in CountTable_Star.csv Moderate_S8

value: moderate


title: CR035T, CR049T

description:
Library name: CRTU9
10X Genomics

value: Colorectal tumor and nonmaligant adjacent tissue


title: Pol II ChIP-seq, yeast, untreated, Input, rep2


title: WGC097529

city: suzhou

first: xiangtong

last: xie

address: wansheng street

institute: Suzhou Kowloon Hospital,Shanghai Jiao Tong University School of Medicine,Suzhou 215028

data_processing:
All the sequencing data with STAR software (https://github.com/alexdobin/STAR) compared to the mouse genome (the Ensemble R78)
With RSEM software (1.2.26) (http://deweylab.github.io/RSEM/) and the default parameters for gene expression analysis.
DESeq2 (Love et al., 2014) was used to analyze the differences in gene expression between different times and tissues. The final differentially expressed genes were defined as the Fold change absolute value greater than 2 and the p-value smaller than 0.05.
Assembly: Ensemble R78
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Normal mouse bone marrow mesenchymal stem cells

growth_protocol: iTAMD cells(C12, ihCTC, ihDCTC, ihSTC_BM)and its precursor cells(MDSC and MSC) cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent.
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Sample Pre Kit following manufacturer's protocols.

treatment_protocol:
The malignant immune cells, MDSC and MSC were subcultured and cultured.
The malignant cells, MDSC and MSC were cultured by monoclonal culture and transcriptomic analysis.

value: Nude Mouse

value: MSC


title: RNA-seq-HuCCT1-Ctrlrep3

description:
Library name: HuCCT1-C t r l3
Column name in CHOL_exp.raw_counts All_Samples.txt: S3

data_processing:
Raw sequencing reads were trimmed using Cutadapt (v4.2) to remove adapters and low-quality bases.
Clean reads were aligned to the human reference genome (hg38) using HISAT2 (v2.2.1) with the ‘—dta’ parameter.
Gene-level expression values were quantified using RSEM.
Gene-level expression values were quantified using RSEM.
Gene-level expression values were quantified using RSEM.
Assembly: hg38
Supplementary files format and content: txt file containing raw counts s for each sample.
Supplementary files format and content: txt file containing raw counts s for each sample.

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, C11995500CP) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S; BasalMedia, S110JV)，HuCCT1 cells were maintained in RPMI-1640 medium (ThermoFisher, C11875500BT) supplemented with 10% FBS and 1% P/S. All cell lines were incubated at 37°C in a humidified atmosphere with 5% CO2. Cells were passaged every 2-3 days when they reached approximately 90% confluency.

extract_protocol:
Total RNA was extracted from HEK293T or other cell lines using TRIzol™ reagent (Thermo Scientific, 15596018) following the manufacturer’s instructions.
Total RNA was extracted from HEK293T and HuCCT1 cells using TRIzol™ reagent according to the manufacturer’s instructions. RNA-seq library preparation was conducted using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, following the manufacturer’s protocol. This process included ribosomal RNA depletion to enrich the library for mRNA and pre-mRNAs. After rRNA depletion, the RNA was fragmented and denatured to generate appropriate RNA fragments for cDNA synthesis. First-strand cDNA was synthesized, and an A-tail was subsequently added to the 3’ end of the cDNA to facilitate adapter ligation. Illumina sequencing adapters were then ligated to the cDNA fragments, and the adapter-ligated library was amplified via PCR to enrich for the desired fragments. The final RNA-seq library was quantified and normalized to ensure uniform sequencing depth across samples. High-throughput sequencing was performed on the Illumina HiSeq2000 platform.


title: CR027T, CR028T, CR029T

description:
Library name: CRTU8
10X Genomics


title: A.bruennichi,warm, replicate 4

description:
Library name: Sample 12
Column name in CountTable_Star.csv Warm_S12


title: CR008T, CR012T, CR026T

description:
Library name: CRTU7
10X Genomics


title: CR034T, CR057T, CR061T

description:
Library name: CRTU6
10X Genomics


title: A.bruennichi, moderate, replicate 1

description:
Library name: Sample 5
Column name in CountTable_Star.csv Moderate_S5


title: A.bruennichi, moderate, replicate 2

description:
Library name: Sample 6
Column name in CountTable_Star.csv Moderate_S6


title: RNA-seq-HuCCT1-SNRPD2KOrep3

description:
Library name: HuCCT1-SNRPD2KO3
Column name in CHOL_exp.raw_counts All_Samples.txt: C3

treatment_protocol: Total RNA was extracted from HEK293T or other cell lines using TRIzol™ reagent (Thermo Scientific, 15596018) following the manufacturer’s instructions.


title: WGC097528


title: WGC097526

source_name: Myeloid-derived immunosuppressive cells

value: MDSC


title: WGC097524


title: WGC097525


title: CR028T, CR029T, CR030T, CR031T

description:
Library name: CRTU5
10X Genomics


title: A.bruennichi, cold, replicate 4

description:
Library name: Sample 4
Column name in CountTable_Star.csv Cold_S4

value: cold


title: CR016T, CR025T, CR026T, CR027T

description:
Library name: CRTU4
10X Genomics


title: WGC097520

source_name: SU3 bone marrow damaged and reconstructed mouse transplanted tumor tissue and cultured malignant transformed mesenchymal stem cells


title: RNA-seq-HuCCT1-SNRPD2KOrep1

description:
Library name: HuCCT1-SNRPD2KO1
Column name in CHOL_exp.raw_counts All_Samples.txt: C1


title: A.bruennichi, cold, replicate 2

description:
Library name: Sample 2
Column name in CountTable_Star.csv Cold_S2


title: RNA-seq-HEK293T-Ctrlrep3

description:
Library name: HEK293T-C t r l3
Column name in HEK293T_exp.raw_counts All_Samples.txt: S3


title: A.bruennichi, cold, replicate 1

description:
Library name: Sample 1
Column name in CountTable_Star.csv Cold_S1


title: WGC097519


title: CR014T, CR015T, CR020T

description:
Library name: CRTU2
10X Genomics


title: RNA-seq-HEK293T-Ctrlrep2

description:
Library name: HEK293T-C t r l2
Column name in HEK293T_exp.raw_counts All_Samples.txt: S2


title: A.bruennichi, moderate, replicate 3

description:
Library name: Sample 7
Column name in CountTable_Star.csv Moderate_S7


title: RNA-seq-HuCCT1-Ctrlrep2

description:
Library name: HuCCT1-C t r l2
Column name in CHOL_exp.raw_counts All_Samples.txt: S2


title: CR008T, CR009T, CR011T, CR012T

description:
Library name: CRTU1
10X Genomics


title: RNA-seq-HuCCT1-Ctrlrep1

description:
Library name: HuCCT1-C t r l1
Column name in CHOL_exp.raw_counts All_Samples.txt: S1


title: WGC097523

source_name: Malignant transformed oligodendrocytes obtained by reculture of SU3 brain transplanted tumor tissue


title: WGC097518


title: RNA-seq-HuCCT1-SNRPD2KOrep2

description:
Library name: HuCCT1-SNRPD2KO2
Column name in CHOL_exp.raw_counts All_Samples.txt: C2


title: RNA-seq-HEK293T-Ctrlrep1

description:
Library name: HEK293T-C t r l1
Column name in HEK293T_exp.raw_counts All_Samples.txt: S1


title: HIB4_2

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

description: Influenza + Bacterial infection

data_processing: Data were processed using the NanoString nSolver software v4.0 comparing HIB vs. HB (including initial QC, negative control count thresholding using geometric mean , positive control normalization using geometric mean with default settings but excluding housekeeping genes that were found to vary in expression in our assays, and calculation of expression ratios of HIB vs HB).

organism:
Streptococcus pneumoniae
Homo sapiens
Influenza A virus

source_name: Human Lung

growth_protocol: Primary human bronchial epithelial cells were obtained from human lung tissue through the tissue donation program by the International Institute for the Advancement of Medicine . Cells were harvested from the human tracheobronchial tissues and plated onto collagen-coated 100-mm plates (Biocoat; Becton Dickinson), in BEGM medium to ~80% confluency, followed by passaging onto 6.5-mm Transwell inserts (0.4-μm pore size) with FNC coating (0407, AthenaES) and differentiated at an Air-Liquid Interface (ALI) using Lonza tissue culture reagents. Differentiation was further enhanced by adding 10 nM recombinant human neuregulin-1α/epidermal growth factor-like domain of heregulin-α (296-HR-050, R&D Systems) to the basolateral ALI media . Cells were incubated for approximately two weeks until appearance of ciliated cells and mucus production was seen.

extract_protocol: On the day of RNA isolation, transwell samples were thawed and the membranes cut out using a scalpel. RNAprotect and isolated membranes were centrifuged at 10,000 rpm, to pellet the membrane and any dislodged cells, and the supernatant discarded. Pellets were then incubated in 100 μL of lysis buffer (10 μL of mutanolysin, 20 μL of proteinase K, 30 μL of lysozyme, 40 μL of TE buffer) for 10 minutes. Followed by mechanical disruption in 600 μL RLT buffer (RNeasy Mini Kit, Qiagen) containing 1% ß-mercaptoethanol, using a motorized pestle for 30 seconds. RNA was then captured on the RNeasy Mini Kit columns with DNase treatment on column (Qiagen protocol).  Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following culture of differentiated human bronchial epithelial cells on transwells, cells were infected with pH1N1 or mock infected (no pH1N1 controls) for 72 h (~50% of cells infected with IAV). pH1N1 infected cells were then exposed to 1000 CFUs of Streptococcus pneumoniae strain EF3030 for 6 h. For pneumococcal EF3030 control samples, ~50,000 CFUs of EF3030 were cultured in ALI media for 6 hours. 1ml of RNA protect was then added to all transwells and then stored in 5ml of RNAprotect Bacteria Reagent in 50 ml falcon tubes at -80C.

value: Infected human broncial epithelium

tag: replicate


title: A.bruennichi, cold, replicate 3

description:
Library name: Sample 3
Column name in CountTable_Star.csv Cold_S3


title: WGC097522


title: CR049N, CR065T

description:
Library name: CRNOTU1
10X Genomics


title: CR021T, CR022T, CR024T

description:
Library name: CRTU3
10X Genomics


title: RNA-seq-HEK293T-PUS7rep2

description:
Library name: HEK293T-PUS7KO2
Column name in HEK293T_exp.raw_counts All_Samples.txt: P2


title: HIB4_1

description: Influenza + Bacterial infection


title: CR007N, CR008N, CR011N

description:
Library name: CRNO3
10X Genomics


title: HIB3_2

description: Influenza + Bacterial infection


title: RNA-seq-HEK293T-PUS7rep1

description:
Library name: HEK293T-PUS7KO1
Column name in HEK293T_exp.raw_counts All_Samples.txt: P1


title: WGC097516

source_name: malignant transformed DC cells co-cultured with SU3+ bone marrow dendritic cells in vitro


title: HIB1_2

description: Influenza + Bacterial infection


title: CR007N, CR008N, CR011N, CR012N

description:
Library name: CRNO1
10X Genomics


title: RNA-seq-HEK293T-SNRPD2KOrep3

description:
Library name: HEK293T-SNRPD2KO3
Column name in HEK293T_exp.raw_counts All_Samples.txt: C3


title: NK-Pox-3 (biol rep 3)

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

description: Cultured with complete medium

data_processing:
HISAT2 software (ver. 2.2.0) was used to index the reference genome and map sequencing reads of samples.
Samtools (ver. 1.15.1) was used to convert BAM files
FeatureCounts (ver. 2.0.1) software was used to calculate the generated BAM files
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes CPM values for each Sample

growth_protocol: The culture method of NK-92 was consistent with the culture method recommended by ATCC

extract_protocol:
Total RNA was isolated by TRIzol Reagent
RNA libraries for RNA-seq were prepared using TruSeq Standarded Total RNA Library Prep Gold Kit following manufacturer's protocols.

treatment_protocol: Bulk RNA-seq of experiment: ctrl-NK-92, Poxin-NK-92. Samples were derived from total RNA extracted from 24 hours cultured NK-92 cells.

value: human natural killer cell line

tag: genetic modification

value: Poxin

value: Poxin transgene


title: WGC097515


title: WGC097514

source_name: peritoneal xenograft malignant transformed macrophage


title: RNA-seq-HEK293T-SNRPD2KOrep2

description:
Library name: HEK293T-SNRPD2KO2
Column name in HEK293T_exp.raw_counts All_Samples.txt: C2


title: RNA-seq-HEK293T-SNRPD2KOrep1

description:
Library name: HEK293T-SNRPD2KO1
Column name in HEK293T_exp.raw_counts All_Samples.txt: C1


title: HB4_2

description: Bacterial infection

organism:
Streptococcus pneumoniae
Homo sapiens


title: WGC097531


title: WGC097513


title: CR034N, CR074T

description:
Library name: CRNOTU2
10X Genomics


title: HIB1_1

description: Influenza + Bacterial infection


title: RNA-seq-HEK293T-PUS7rep3

description:
Library name: HEK293T-PUS7KO3
Column name in HEK293T_exp.raw_counts All_Samples.txt: P3


title: NK-Pox-2 (biol rep 2)

description: Cultured with complete medium


title: HCT116-ADV-circ86591-2

city: Beijing

first: wanru

last: ma

address: No.1 Dahua Road, Dongcheng District

institute: Beijing hospital

data_processing:
For knockdown of circrna in cells, FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis. For overexpression of circ86591, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited text file includes TPM or RPKM values for each sample

source_name: colorectal

extract_protocol:
For RNA extraction. total RNA was isolated according to the protocol of Trizol, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of  the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For knockdown of circrna in cells,  using the polyA structure at the 3'end of the messenger RNA and related molecular biology techniques, the four RNA samples in this project were subjected to mRNA isolation, fragmentation, double-stranded cDNA synthesis, cDNA fragmentation modification, magnetic bead purification and fragmentation sorting, library amplification and other processes. After testing and quality control, the sequencing libraries were finally obtained, which are suitable for Illumina platform. For overexpression of circrna, Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: colorectal

value: colorectal cancer

value: circ86591 overexpression

value: cell infected with ADV circ86591


title: NK-Pox-1 (biol rep 1)

description: Cultured with complete medium


title: HCT116-ADV-circ86591-1


title: CR014N, CR015N, CR016N

description:
Library name: CRNO2
10X Genomics


title: NK-Ctrl-3 (biol rep 3)

description: Cultured with complete medium

value: WT

value: Control group


title: HB4_1

description: Bacterial infection


title: HIB3_1

description: Influenza + Bacterial infection


title: WGC097517


title: WGC097511

source_name: SU3+ peritoneal washing cells, malignant transformed macrophages under in vitro co-culture conditions


title: WGC097512


title: HB3_2

description: Bacterial infection


title: WGC097510


title: HB1_2

description: Bacterial infection


title: HB3_1

description: Bacterial infection


title: HCT116-ADV-ctrl-1

value: ADV control

value: cell infected with ADV ctrl


title: WGC097509


title: HB1_1

description: Bacterial infection


title: HCT116-ADV-ctrl-2


title: NK-Ctrl-2 (biol rep 2)

description: Cultured with complete medium


title: NK-Ctrl-1 (biol rep 1)

description: Cultured with complete medium


title: Opa1 KO Treg_rep2

status: Public on Oct 30 2025

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦C while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.4.1.46

source_name: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from Foxp3CreOpa1fl/fl mixed BM chimera mice

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Mixed BM chimera mice were generated at a 1:1 ratio with BM from CD45.1+ and Foxp3Cre (called WT) or Foxp3CreOpa1fl/fl (called Opa1 KO) mice.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy micro kit (74004, Qiagen) according to manufacturer’s instructions.

treatment_protocol: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera and Foxp3CreOpa1fl/fl mixed BM chimera mice (n = 4 biological replicates per group).

tag: strain background


title: Cd4CreFlcnfl/flTfebfl/fl iTreg rep1

source_name: Flcnfl/flTfebfl/fl iTreg

growth_protocol: iTreg cells were generated in vitro by culturing naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1) (n = 2 biological replicates per group).

treatment_protocol: iTreg cells were harvested and enriched for live cells using LymphoSep (MP Biomedicals).

value: Cd4CreFlcnfl/flTfebfl/fl iTreg cells were generated in vitro by culturing Cd4CreFlcnfl/flTfebfl/fl naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: Opa1 KO Treg_rep4

value: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from Foxp3CreOpa1fl/fl mixed BM chimera mice


title: WT Treg_rep4

source_name: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera


title: WT Treg_rep1

value: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera


title: WT Treg_rep3


title: Cd4CreTfebfl/fl iTreg rep1

source_name: Tfebfl/fl iTreg

value: Cd4CreTfebfl/fl iTreg cells were generated in vitro by culturing Cd4CreTfebfl/fl naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: Opa1 KO Treg_rep1


title: Cd4CreFlcnfl/flTfebfl/flTfe3–/– iTreg rep1

source_name: Flcnfl/flTfebfl/flTfe3–/– iTreg

value: Cd4CreFlcnfl/flTfebfl/flTfe3–/– iTreg cells were generated in vitro by culturing Cd4CreFlcnfl/flTfebfl/flTfe3–/– naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: Opa1 KO Treg_rep3


title: Cd4CreFlcnfl/flTfebfl/flTfe3–/– iTreg rep2


title: WT iTreg rep2

source_name: WT iTreg

value: WT iTreg cells were generated in vitro by culturing WT naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).