title: RpoN_ChIP-exo WT mid-log phase rep 1

description: Salmonella enterica serovar Typhimurium LT2 RpoN ChIP-exo mid-log phase replicate 1

data_processing:
The sequencing was performed on HiSeq 2500 (Illumina).
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the reference genome (NC_003197) using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, peaks with signal-to-noise (S/N) ratio less than 1.5 were removed
The noise level was set to the top 5% of signals at genomic positions because top 5% makes a background level in plateau and top 5% intensities from each ChIP-exo replicates across conditions correlate well with the total number of reads.The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: Salmonella enterica serovar Typhimurium LT2 genome (NC_003197)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: glycerol stocks of Salmonellaonella enterica serovar Typhimurium strain LT2 were inoculated into M9 minimal media with 0.2% (w/v) glucose. M9 minimal media was also supplemented with 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates from sonicated ceratin sigma factors-DNA complexes were isolated with specific antibodies.
ChIP-exo experiment was performed following the procedures: to identify each sigma factor binding maps in vivo, we isolated the DNA bound to each sigma factor from formaldehyde cross-linked Salmonellaonella enterica serovar Typhimurium LT2 cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognize subunits of RNA polymerase (cat# WP002, neoclone), sigma factor 70 (cat# WP004, neoclone), sigma factor 54 (cat# W0005,neoclone), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.


title: ChIP_3WT_RH1_Zfp281_Rep1

status: Public on Dec 14 2023

type: SRA

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

country: USA

institute: Columbia University Irving Medical Center

library_source: genomic

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.5) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v1.10)
ChIP-seq peaks were determined by the MACS program (v.2.2.7), using input as the control data, and all other parameters followed the default settings.
bigWig files were generated using the bamCoverage program.
Assembly: mm9
Supplementary files format and content: bigWig, bed

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin-coated plates and in ES medium: DMEM medium supplemented with 15% fetal bovine serum (FBS), leukemia inhibitory factor (LIF, lab prepared), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock), and 50 U/mL Penicillin/Streptomycin (P/S). Mouse EpiSCs were cultured on fibronectin-coated (10 μg/mL/cm2) plates and in serum-free N2B27 medium supplemented with 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM NEAA, 50 U/mL P/S, and supplemented with fresh Fgf2 (12 ng/mL) and Activin A (20 ng/mL) (FA medium). For ESC-EpiLC-EpiSC differentiation, ESCs were seeded on fibronectin-coated (10 μg/mL/cm2) plates, in ES medium overnight, and switched to FA medium next day. The adapted cells in FA medium for 2 days (FA-D2) and 4 days (FA-D4) were collected. After more than two weeks of FA culture, adapted cells were considered stable converted EpiSCs (cEpiSCs).

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006).
ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol.

treatment_protocol: For Enaseh1 overexpression, piggyBac-Rnaseh1-Hygro and empty piggyBac-Hygro vectors were cotransfected with helper PBase (encodes the transposase) vector in ESCs with Lipofectamine 3000 (Invitrogen). Transfected ESCs were selected with 100 µg/ml Hygromycin for one week with at least two passages.

tag: cell line

tag: cell type

value: Embryonic stem cells (ESCs)

tag: genotype

value: WT

tag: antibody

value: Abcam, ab101318

tag: treatment

value: Rnaseh1 overexpression (RH1)


title: FA_D2_Zfp281degron_UT_rep2

library_source: transcriptomic

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
A tab-delimited matrix file containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
Assembly: mm9
Supplementary files format and content: tab-delimited text file

molecule: total RNA

extract_protocol:
Total RNA was extracted using the GeneJet RNA Purification Kit (Thermo Scientific, K0732) according to the manufacturer’s instructions
RNA-seq library construction was performed at Novogene with a standard polyA-enrichment protocol.

treatment_protocol: Zfp281degron ESCs and cEpiSCs were treated with dTAG13 (500 nM in DMSO, Tocris, 6605) for degradation of ZFP281 protein

value: ESCs adapted in FA culture


title: 3543_OF1B_1-2-B11-P4

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

organism: Homo sapiens

source_name: OF1B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: 3543_OF1B_1-2-B11-P3


title: RpoD_ChIP-exo WT mid-log phase rep 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

description: Salmonella enterica serovar Typhimurium LT2 RpoD ChIP-exo mid-log phase replicate 2

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Bacteria

tag: strain

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

value: wild type


title: Female, Young, Early Induction, Input, S49

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description:
1441HCInput_S49(raw)
Kellogg2023_FullDataGEO.txt

data_processing:
Following sequencing, reads were trimmed and aligned before differential expression statistics and correlation analyses in Strand NGS software package (v4.0; Strand Life Sciences).
Alignment and filtering criteria included the following: adapter trimming, fixed 2-bp trim from 5′ and 2 bp from 3′ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum 5% gap, and trimming of 3′ ends with Q < 30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. All duplicate reads were then removed.
Normalization was performed with the DESeq2 algorithm. Transcripts with an average read count value >5 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
For statistical analysis of differential expression with aging a One-Way ANOVA with Benjamini–Hochberg multiple testing correction (BHMTC) was performed with SNK pairwise post-hoc testing. For those transcripts meeting this statistical criterion, a fold change >|1.25| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable because of their very small magnitude of change.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw gene expression values

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
For Cx3cr1-TRAP: Hippocampal tissue was isolated from Cx3cr1-NuTRAP mice of both sexes at 6 and 22 mo (n=5-7/sex/age). The hippocampi from both hemispheres were minced into small pieces and homogenized in 100 µL ice-cold TRAP homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1 mM DTT; 100 μg/ml cycloheximide [#C4859-1ML, Millipore Sigma]; 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor [#10777019; Thermo Fisher Scientific]; 1× complete EDTA-free Protease Inhibitor Cocktail [#11836170001; Millipore Sigma] with a Kimble pellet pestle mixer [#749540-0000; DWK Life Sciences), as previously described (7, 8). Volume was brought up to 1.5 mL with TRAP homogenization buffer. Homogenates were centrifuged at 12,000 × g for 10 min at 4°C. After centrifugation, 100 μL of the cleared supernatant was saved as TRAP Input. The remaining supernatant was incubated with 5 μg/μL of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for 1 hour. A volume of 50 µL per sample of Protein G Dynabeads (#10003D; Thermo Fisher Scientific) was washed three times in 1-mL ice-cold low-salt wash buffer (50 mM Tris, pH 7.5; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 100 μg/ml cycloheximide; 1 mM DTT) and then resuspended in the original volume of low salt wash buffer. 50 µL of washed beads were added to each cleared homogenate and incubated at 4°C with end-over-end rotation overnight. Following overnight incubation, the beads and GFP-bound polysomes were washed three times with 0.5 mL of high-salt wash buffer (50 mM Tris, pH 7.5; 12 mM MgCl2; 300 mM KCl; 1% NP-40; 100 μg/mL cycloheximide; 2 mM DTT) using a magnetic stand for separation. After the last wash, 350 μL of Buffer RLT (Qiagen) was supplemented with 3.5 μl of 2-β mercaptoethanol (#444203, Millipore Sigma) and added to the washed beads. Samples were incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated, and the supernatant (Positive Fraction) was transferred to a new tube. RNA was isolated using the RNeasy Mini kit (#74104, QIAGEN) according to the manufacturer’s instructions. RNA was quantified with a Nanodrop Onec spectrophotometer (#ND-ONEC-W, Thermo Fisher Scientific), and its quality was assessed by HSRNA ScreenTape (#5067-5579, Agilent Technologies) with a 4150 Tapestation analyzer (#G2992AA, Agilent Technologies).
RNA was isolated using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions.
Directional RNA-Seq libraries were made according to the manufacturer’s protocol from 5-100 ng RNA. Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (#NEBE7490L, New England Biolabs) and then processed using NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L, New England Biolabs) for the creation of cDNA libraries. Library sizing was performed with HSD1000 ScreenTape (#5067-5584, Agilent Technologies) and quantified by Qubit dsDNA HS Assay Kit (#Q32851, ThermoFisher Scientific) on a Qubit 4 Fluorometer (#Q33226, ThermoFisher Scientific). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system (SP PE50bp, S4 PE150).

tag: tissue

value: hippocampus

value: whole tissue

value: Young

value: Early Induction


title: Female, Young, Early Induction, Input, S47

description:
1440HCInput_S47(raw)
Kellogg2023_FullDataGEO.txt


title: ChIP_3WT_RH1_input


title: ChIP_3WT_EV_Zfp281_Rep1

value: Empty vector (EV)


title: RpoD_ChIP-exo WT mid-log phase rep 1

description: Salmonella enterica serovar Typhimurium LT2 RpoD ChIP-exo mid-log phase replicate 1


title: ChIP_3WT_EV_input


title: ChIP_OEC2_Zfp281

value: Epiblast stem cells (EpiSCs)


title: 3543_OF1B_1-2-B11-O4


title: Male, Young, Early Induction, Input, S43

description:
1438HCInput_S43(raw)
Kellogg2023_FullDataGEO.txt

value: Male


title: 3543_OF1B_1-2-B11-P15


title: Male, Young, Early Induction, Input, S45

description:
1439HCInput_S45(raw)
Kellogg2023_FullDataGEO.txt


title: ChIP_OEC2_Tet1

value: WT

value: GeneTex, GTX125888


title: RpoB_ChIP-exo WT mid-log phase rep 2

description: Salmonella enterica serovar Typhimurium LT2 RpoB ChIP-exo mid-log phase replicate 2


title: Male, Young, Early Induction, Input, S41

description:
1437HCInput_S41(raw)
Kellogg2023_FullDataGEO.txt


title: RpoB_ChIP-exo WT mid-log phase rep 1

description: Salmonella enterica serovar Typhimurium LT2 RpoB ChIP-exo mid-log phase replicate 1


title: ChIP_OEC2_Dnmt3b


title: Male, Young, Early Induction, Input, S39

description:
1436HCInput_S39(raw)
Kellogg2023_FullDataGEO.txt


title: ChIP_OEC2_Dnmt3a

value: Cell Signaling, 3598


title: 3543_OF1B_1-2-B11-O16


title: Dnmt3a cKO CD45+, snRNA-seq [d4]

city: Boston

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

description:
10x Genomics
MouseRetina_DNMTsKO_vs_WT_all_cluster2.rds
cellchat_total_KO.rds
cellchat_RGC_KO.rds

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Software used for preprocessing includes bcl2fastq v2.20, fastqc 0.11.9, multiqc 1.12.0.
Assembly: mm10_re93_premRNA_all-4.0.0
Supplementary files format and content: .rds files with Seurat and CellChat objects

source_name: Retina

extract_protocol:
Frozen retinas were homogenized in a Dounce homogenizer in 1ml Tris based lysis buffer with 0.1% NP-40. Six retinas were pooled for each group. Nuclei were stained for NEUN and CD45 and counterstained with DAPI. NEUN+ and CD45+ single nuelci were collected seprately using a flow cytometer. The sorted nuclei were pelleted, resuspended in PBS solution, and adjusted to a concentration of 1000 nuclei/µL before loading into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation and 5’ adaptor and sample index attachment to yield the final libraries.

value: Retinal ganglion cells, Muller glia, Rod, RPE, Amacrine cells, Astrocyte, Bipolar cells, Cone, Horizontal cells, Immune cells

value: Retina

value: 2-4 months old


title: Control CD45+, snRNA-seq [d3]

description:
10x Genomics
MouseRetina_DNMTsKO_vs_WT_all_cluster2.rds
cellchat_total_WT.rds
cellchat_RGC_WT.rds


title: Female, Old, Late Induction, Pos, S38

description:
1360HCPOS_S38(raw)
Kellogg2023_FullDataGEO.txt

value: Female

value: microglia

value: Old

value: Late Induction


title: 3543_OF1B_1-2-B11-P16

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: nuclear RNA + genomic DNA


title: ChIP_Zfp281degron_HA_FAD4

value: ESCs adapted in FA culture

value: Abcam, ab9110


title: 3543_OF1B_1-2-B11-N4


title: Dnmt3a cKO NeuN+  snRNA-seq [d2]


title: 3543_OF1B_1-2-B11-O15


title: Female, Old, Late Induction, Input, S37

description:
1360HCInput_S37(raw)
Kellogg2023_FullDataGEO.txt

value: hippocampus

value: whole tissue


title: RpoN_ChIP-exo WT mid-log phase rep 2

description: Salmonella enterica serovar Typhimurium LT2 RpoN ChIP-exo mid-log phase replicate 2

value: glucose M9 minimal

value: mid-log phase

value: wild type


title: Control NeuN+ , snRNA-seq [d1]


title: ChIP_OEC2_Input

value: Epiblast stem cells (EpiSCs)

value: WT


title: VLC1.F.N984

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Liver tissue from Female mice fed 1%-VLCPUFA diet, replicate no N984

data_processing:
Post quality check, reads were mapped to the reference transcriptome using kallisto. Alignments were imported into R and processed with tximport and the Mus musculus Ensembl annotation (GRCm39 v104) to summarize gene counts.
Lowly expressing genes were filtered out by only retaining genes that had greater than 3 CPM expression in two or more samples.
Differential expression analysis was performed with the edgeR and limma-voom pipeline, and thresholds of 0.1 FDR and 1.5-fold change (abs(log2FC) > 0.58) were used to determine significantly differential genes.
Assembly: GRCm39 v104
Supplementary files format and content: Tab-delimited text files containing transcript level counts, gene level counts, or normalized gene level counts-per-million, and differential expression results.

source_name: mouse liver

growth_protocol: In a dietary supplementation feeding experiment, 9-month-old male and female C57BL/6J mice were fed a chow diet AIN-93G (Envigo, Frederick, MD) supplemented with 1% or 5% (w/w) VLCPUFA concentrate oil, or none (control) for 8 weeks.

extract_protocol:
RNA was isolated from liver samples using a RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.  RNA purity and concentration were assessed using a NanoDropTM spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).  A 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA) was used with RNA screentapes to generate RNA integrity numbers (RIN) for RNA samples. All RNA samples selected for RNA-seq library preparation had a RIN greater than 7.
RNA-seq libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA)

treatment_protocol: After 8 weeks of diet consumption, the 5 hr-fasted mice were euthanized via intraperitoneal injection of tribromoethanol, and liver tissue was harvested for gene expression analysis.

tag: diet

value: Liver

tag: replicate


title: 3543_OF1B_1-2-B11-O3


title: 3543_OF1B_1-2-B11-N3


title: 3543_OF1B_1-2-B11-N16


title: ChIP_Zfp281degron_HA_ESC

value: Embryonic stem cells (ESCs)


title: ChIP_Zfp281degron_HA_FAD2


title: 3543_OF1B_1-2-B11-N15

value: Female


title: ChIP_3WT_Zfp281_FAD4

value: Abcam, ab101318


title: mEC RNAiSvb rep2

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative de Toulouse

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Sequenced reads were mapped on Drosophila genome (r6.13 Flybase) with STAR (v 2.5.2b default parameters)
Reads were counted with HTseq-count (v 0.6.0, parameter -t gene -r pos - i gene_symbol)
Statistical analysis were performed with edgeR using the negative binomial generalized log-linear model to the read counts ( gmLRT), the TMM normalization and decideTest were used to determine the differentially expressed genes.
Clustering analysis was performed on the matrix of the reads count average centrered and reduced for each condition previously filtered for the gene expression (difference of read > 50 between condition.
Two steps of clustering were done. The hierarchical ascendant clustering was performed with R function hclust() with the Spearman distance and the Ward.D2 option.
The k-means clustering was done with R function kmeans() with default options and k = 5. The kmeans clustering was repeated 15 times ( 5 times with predefined centroid and 10 with random centroids). The predefined centroids are genes of differents cluster defined by the hierarchical clustering.
Different k-means clusters obtained by each repetition were compared with cluster_similarity (Clusteval v 0.1). Clustering is similar if the score eaqual 1.
Assembly: dm6
Supplementary files format and content: bigwig smooth
Supplementary files format and content: Matrix table with normalized counts, logFC, Pvalue, LogCPM, status for expressed genes

organism: Drosophila melanogaster

source_name: mEC RNAiSvb

growth_protocol: MyoIA-Gal4, UAS-GFP; tubGal80TS/SM66B flies were crossed to the following strains: Canton-S (BL#64349), UAS-SvbRNAi (VDRC# 41584), UAS-SvbACT::GFP (al Hayek et al., 2021), UAS-Svb3Kmut::GFP (al Hayek et al., 2021). Adult progeny (only virgin females) was aged 3 days at room temperature, then transferred at 29°C for 6 days prior to midgut dissection.

extract_protocol:
RNA were purified from each cell sample using MasterPure RNA purification kit (Epicentre), following manufacturer’s recommendation. Sorted cells were incubated at 65°C with rocking for 15 minutes. Samples were put on ice then total nucleic acid were precipitated. Contaminating DNA was removed using DNase, then nucleic acids were precipitated again. RNAs were finally resuspended in 10uL TE and 1uL RiboGuard (RNases inhibitor) and stored at -20°C.
Construction of RNA banks and sequencing was made at the Montpellier GenomiX Platform (MGX). RNA banks were obtained using the Ovation SoLo RNAseq System kit (Nugen). Bank validation was done with the quantification of the complementary DNA with the Standard Sensitivity NGS kit on Fragment Analyzer and with qPCR (ROCHE Light Cycler 480). 100nt single-reads sequencing was performed on NovaSeq 6000 (Illumina) with NovaSeq Reagent Kits (100cycles).

treatment_protocol:
Batches of >20 virgin females are CO2-anaethesized and put on ice. From then, all solutions are used cold and samples kept on ice whenever possible. Their midgut are dissected in 1XPBS and transferred to a clean PBS dish. Malpighian tubules and hindgut are removed and only the posterior part of the midgut is kept (R3, R4, R5). PBS was replaced by PBS1X-EDTA 1mM. Posterior midguts were transferred on a glass slide in a droplet of PBS, and shrinked into pieces using a razorblade. Samples were transferred into a fresh tube and spun 3- 5minutes at 1000rpm 4°C to pellet the tissue and remove all supernatant except 50μL. 200uL TrypLE 10X (8X final with 0.2mM EDTA) was added for enzymatic digestion. Then the guts were incubated at 37°C and rocked vigorously for 10 minutes. Digestions were stopped with 750μL SSM (Serum Supplemented Medium = S2 Cell culture medium). Trituration was made by pipetting up and down using low binding, flame-rounded narrow tips (only 5 times with narrow tip, no use of the very narrow tip).
Transfer tissue onto a PBT-coated 70μM nylon cell strainer in SSM. Transfer the strainer into clean SSM, then transfer into PBS-EGTA. The aim is to have dissociated individual cells (comprising progenitors) flow through the strainer while patches of multiple ECs stay on the strainer. After an additional PBS-EGTA wash, turn the strainer bottom up on a petri dish and rinse abundantly with PBS-EDTA (5mL) then 2mL SSM to detach the EC patches. Make sure your EC samples look healthy under fluorescent microscope. Transfer samples into tubes, spin (700 rcf at 4°C for >10minutes) to pellet the cells in 150uL, add 150uL Tissue and Cell Lysis solution + 1ug Proteinase K [50ug/uL], vortex and proceed with RNA extraction.

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in ISCs for 6 days before midgut dissection

value: Posterior midgut (R3 to R5)

value: 9 days (6 days of induction)

value: female

value: Enterocytes (mature)

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: mEC RNAiSvb rep1


title: ChIP_3WT_Zfp281_FAD2

value: ESCs adapted in FA culture


title: Female, Old, Late Induction, Input, S33

description:
1357HCInput_S33(raw)
Kellogg2023_FullDataGEO.txt

value: hippocampus

value: whole tissue

value: Old

value: Late Induction


title: Female, Old, Late Induction, Pos, S34

description:
1357HCPOS_S34(raw)
Kellogg2023_FullDataGEO.txt

value: microglia


title: Female, Old, Late Induction, Pos, S36

description:
1359HCPOS_S36(raw)
Kellogg2023_FullDataGEO.txt


title: 3543_OF1B_1-2-B11-M4

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: nuclear RNA + genomic DNA


title: 3543_OF1B_1-2-B11-M3


title: mEC SvbAct rep 2

source_name: mEC SvbAct


title: Female, Old, Late Induction, Pos, S32

description:
1356HCPOS_S32(raw)
Kellogg2023_FullDataGEO.txt


title: ChIP_3WT_Zfp281_ESC

value: Embryonic stem cells (ESCs)

value: WT


title: mEC SvbAct rep 1


title: 3543_OF1B_1-2-B11-M16

value: Female


title: ChIP_3WT_Tet1_FAD4

value: GeneTex, GTX125888


title: mEC RNAiSvb rep3

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in ISCs for 6 days before midgut dissection

value: Posterior midgut (R3 to R5)


title: mEC Ctrl rep 2

source_name: mEC Ctrl

value: 9 days (6 days of induction)

value: female

value: MyoIA-Gal4, UAS-GFP/+; tubGal80TS/+


title: 3543_OF1B_1-2-B11-M15


title: ChIP_3WT_Tet1_FAD2

value: ESCs adapted in FA culture


title: Female, Old, Late Induction, Pos, S30

description:
1355HCPOS_S30(raw)
Kellogg2023_FullDataGEO.txt

value: hippocampus


title: Female, Old, Late Induction, Input, S29

description:
1355HCInput_S29(raw)
Kellogg2023_FullDataGEO.txt

value: whole tissue


title: Female, Old, Late Induction, Input, S35

description:
1359HCInput_S35(raw)
Kellogg2023_FullDataGEO.txt

value: Old


title: 3543_OF1B_1-2-B11-L4


title: mEC Ctrl rep 1

value: Enterocytes (mature)

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: mEC SvbAct rep 3


title: Male, Old, Late Induction, Pos, S28

description:
1353HCPOS_S28(raw)
Kellogg2023_FullDataGEO.txt

value: Male

value: microglia

value: Late Induction


title: eEC RNAiSvb rep3

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Sequenced reads were mapped on Drosophila genome (r6.13 Flybase) with STAR (v 2.5.2b default parameters)
Reads were counted with HTseq-count (v 0.6.0, parameter -t gene -r pos - i gene_symbol)
Statistical analysis were performed with edgeR using the negative binomial generalized log-linear model to the read counts ( gmLRT), the TMM normalization and decideTest were used to determine the differentially expressed genes.
Clustering analysis was performed on the matrix of the reads count average centrered and reduced for each condition previously filtered for the gene expression (difference of read > 50 between condition.
Two steps of clustering were done. The hierarchical ascendant clustering was performed with R function hclust() with the Spearman distance and the Ward.D2 option.
The k-means clustering was done with R function kmeans() with default options and k = 5. The kmeans clustering was repeated 15 times ( 5 times with predefined centroid and 10 with random centroids). The predefined centroids are genes of differents cluster defined by the hierarchical clustering.
Different k-means clusters obtained by each repetition were compared with cluster_similarity (Clusteval v 0.1). Clustering is similar if the score eaqual 1.
Assembly: dm6
Supplementary files format and content: bigwig file of each condition Smooth (bin:200) for representation
Supplementary files format and content: Matrix table with normalized counts, logFC, Pvalue, LogCPM, status for expressed genes

source_name: eEC RNAiSvb

growth_protocol: myoIA-Gal4, UAS-GFP; tubGal80TS/SM66B flies were crossed to the following strains: Canton-S (BL#64349), UAS-SvbRNAi (VDRC# 41584), UAS-SvbACT::GFP (al Hayek et al., 2021), UAS-Svb3Kmut::GFP (al Hayek et al., 2021). Adult progeny (only virgin females) was aged 3 days at room temperature, then transferred at 29°C for 6 days prior to midgut dissection.

treatment_protocol:
Batches of >20 virgin females are CO2-anaethesized and put on ice. From then, all solutions are used cold and samples kept on ice whenever possible. Their midgut are dissected in 1XPBS and transferred to a clean PBS dish. Malpighian tubules and hindgut are removed and only the posterior part of the midgut is kept (R3, R4, R5). PBS was replaced by PBS1X-EDTA 1mM. Posterior midguts were transferred on a glass slide in a droplet of PBS, and shrinked into pieces using a razorblade. Samples were transferred into a fresh tube and spun 3- 5minutes at 1000rpm 4°C to pellet the tissue and remove all supernatant except 50μL. 200uL TrypLE 10X (8X final with 0.2mM EDTA) was added for enzymatic digestion. Then the guts were incubated at 37°C and rocked vigorously for 15 minutes. Digestions were stopped with 750μL SSM (Serum Supplemented Medium = S2 Cell culture medium). Trituration was made by pipetting up and down using low binding, flame-rounded narrow tips (5 times with narrow tip; 2-3 times with very narrow tip).
Strain the cell solution (70μM nylon cell strainer, pre-wet with SSM) into a falcon tube. The tube and the strain were rinsed thrice with 1mL PBS-EDTA. The quality of the dissociation and the health of the cells in solution can be checked under a fluorescent macroscope. Samples were spun at 700rcf, 4°c, for >10 minutes and supernatant carefully removed except 100/200μL. 200μL PBS + 3μL clean NGS were added to obtain final samples for FACS. For each cell sample a tube was prepared with 300μL Tissue and Cell Lysis solution + 1μg Proteinase K [50μg/μL]. Cells are sorted in this buffer, vortexed and placed on ice just after sorting. RNA extraction was started less than 1 hour after sorting

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in ECs for 6 days before midgut dissection

value: Enterocytes (early)


title: Male, Old, Late Induction, Input, S27

description:
1353HCInput_S27(raw)
Kellogg2023_FullDataGEO.txt


title: eEC RNAiSvb rep2


title: ChIP_3WT_Tet1_ESC

value: Embryonic stem cells (ESCs)

value: WT

value: GeneTex, GTX125888


title: ChIP_3WT_Input_FAD4


title: Male, Old, Late Induction, Pos, S26

description:
1351HCPOS_S26(raw)
Kellogg2023_FullDataGEO.txt


title: 3543_OF1B_1-2-B11-L3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: ChIP_3WT_Input_ESC


title: Male, Old, Late Induction, Input, S25

description:
1351HCInput_S25(raw)
Kellogg2023_FullDataGEO.txt


title: eEC SvbRep rep3

source_name: eEC SvbRep

value: Posterior midgut (R3 to R5)

value: 9 days (6 days of induction)

value: female


title: Female, Old, Late Induction, Input, S31

description:
1356HCInput_S31(raw)
Kellogg2023_FullDataGEO.txt

value: hippocampus

value: whole tissue

value: Old


title: ChIP_3WT_Input_FAD2

value: ESCs adapted in FA culture


title: eEC RNAiSvb rep1

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: 3543_OF1B_1-2-B11-K4


title: 3543_OF1B_1-2-B11-K3


title: muscle, LNP+mRNA, scRNA

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description:
10X 3' chemistry
MS_spike_40hr

data_processing:
Sequence data were processed with CellRanger (v.6.0.2) to generate count matrices
Assembly: mm10
Supplementary files format and content: CellRanger filtered cellxgene count matrices in h5 format

source_name: muscle

extract_protocol:
To make single cell suspension, freshly collected anterior thigh muscles were chopped with scissors and enzymatically dissociated with collagenase, inguinal lymph nodes were physically dissociated with mesh strainer, and blood cells were RBC-lysed with RBC lysis buffer.
Library was constucted according to the manufacturer's instructions (10X 3' v3)

value: muscle

value: LNP+mRNA


title: eEC SvbRep rep2

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in ECs for 6 days before midgut dissection

value: Enterocytes (early)


title: eEC SvbRep rep1


title: muscle, LNP+sub, scRNA

description:
10X 3' chemistry
MS_Sub_lnp

value: LNP+sub


title: 3543_OF1B_1-2-B11-K16


title: 3543_OF1B_1-2-B11-K15


title: SW480 cells, oxaliplatin-treated, replicate 3

city: Rotterdam

first: Hannes

last: Lans

address: Wytemaweg 80

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.5a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.0.
Assembly: UCSC hg38 based on GRCh38
Supplementary files format and content: rnaseq_deseq_global_counts_raw.tsv.gz: Per gene and sample raw (integer) counts in tab-separated value (TSV) format
Supplementary files format and content: rnaseq_deseq_global_fpkms.tsv.gz: Per gene and sample DESeq2-calculated FPKMs in tab-separated value (TSV) format

growth_protocol: All cells were maintained at 37°C, in 20% O2 and 5% CO2, in a 1:1 mixture of Roswell Park Memorial Institute-1640 medium (RPMI, Sigma-Aldrich) and Ham's F-10 nutrient mix (Lonza), supplemented with 10% fetal bovine serum (FBS; Gibco), and 1% penicillin/streptomycin (PS; Sigma-Aldrich).

extract_protocol:
Total RNA isolation was performed using the RNeasy kit (Qiagen) in biological triplicates. The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad)
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 4000 instrument using 50 bp single-read chemistry.

treatment_protocol: Manuscript reports RNA seq data from untreated cells. Treated cells data are not part of this manuscript.

value: colon cancer

value: wt

tag: phenotype

value: XPCoxa-active

value: 6h oxaliplatin


title: SW480 cells, oxaliplatin-treated, replicate 2


title: SW480 cells, oxaliplatin-treated, replicate 1


title: eEC SvbAct rep 3

source_name: eEC SvbAct

value: Posterior midgut (R3 to R5)


title: SW480 cells, untreated, replicate 1

value: untreated


title: muscle, LNP+mRNA 16hr, scRNA

description:
10X 3' chemistry
MS_spike_late

value: LNP+mRNA 16hr


title: eEC SvbAct rep 2

value: 9 days (6 days of induction)

value: female


title: SW480 cells, untreated, replicate 3


title: muscle, LNP+mRNA 2hr, scRNA

description:
10X 3' chemistry
MS_spike_early

value: LNP+mRNA 2hr


title: 3543_OF1B_1-2-B11-J4

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1B_1-2-B11-L15


title: muscle, PBS, scRNA

description:
10X 3' chemistry
MS_M_PBS

value: muscle

value: PBS


title: SW480 cells, untreated, replicate 2


title: muscle, LNP+sub+IFNB, scRNA

description:
10X 3' chemistry
MS_Sub_lnp_IFNB

value: LNP+sub+IFNB


title: eEC SvbAct rep 1

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in ECs for 6 days before midgut dissection

value: Enterocytes (early)

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: Lovo cells, oxaliplatin-treated, replicate 1

source_name: LOVO

value: LOVO

value: colon cancer

value: wt

value: XPCoxa-inactive


title: 3543_OF1B_1-2-B11-J16


title: eEC Ctrl rep 3

source_name: eEC Ctrl

value: Posterior midgut (R3 to R5)

value: MyoIA-Gal4, UAS-GFP/+; tubGal80TS/+


title: eEC Ctrl rep 2

value: 9 days (6 days of induction)

value: female


title: 3543_OF1B_1-2-B11-J15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Lovo cells, oxaliplatin-treated, replicate 3

value: 6h oxaliplatin


title: muscle, LNP 16hr, scRNA

description:
10X 3' chemistry
MS_M_LNP

value: LNP 16hr


title: eEC Ctrl rep 1


title: muscle, LNP+mRNA 2hr 2nd, scRNA

description:
10X 3' chemistry
MS_M-SE

value: muscle

value: LNP+mRNA 2hr 2nd


title: muscle, LNP+mRNA  16hr 2nd, scRNA

description:
10X 3' chemistry
MS_M-SL

value: LNP+mRNA  16hr 2nd


title: 3543_OF1B_1-2-B11-I4

value: Female

value: nuclear RNA + genomic DNA


title: Lovo cells, oxaliplatin-treated, replicate 2


title: EB RNAiSvb rep3

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Sequenced reads were mapped on Drosophila genome (r6.13 Flybase) with STAR (v 2.5.2b default parameters)
Reads were counted with HTseq-count (v 0.6.0, parameter -t gene -r pos - i gene_symbol)
Statistical analysis were performed with edgeR using the negative binomial generalized log-linear model to the read counts ( gmLRT), the TMM normalization and decideTest were used to determine the differentially expressed genes.
Clustering analysis was performed on the matrix of the reads count average centrered and reduced for each condition previously filtered for the gene expression (difference of read > 50 between condition.
Two steps of clustering were done. The hierarchical ascendant clustering was performed with R function hclust() with the Spearman distance and the Ward.D2 option.
The k-means clustering was done with R function kmeans() with default options and k = 5. The kmeans clustering was repeated 15 times ( 5 times with predefined centroid and 10 with random centroids). The predefined centroids are genes of differents cluster defined by the hierarchical clustering.
Different k-means clusters obtained by each repetition were compared with cluster_similarity (Clusteval v 0.1). Clustering is similar if the score eaqual 1.
Assembly: dm6
Supplementary files format and content: Matrix table with normalized counts, logFC, Pvalue, LogCPM, status for expressed genes
Supplementary files format and content: bigwig file of each condition Smooth (bin:200) for representation

source_name: EB RNAiSvb

growth_protocol: esg-Gal4, UAS-GFP; tubGal80TS/SM66B flies were crossed to the following strains: Canton-S (BL#64349), UAS-SvbRNAi (VDRC# 41584), UAS-SvbACT::GFP (al Hayek et al., 2021), UAS-Svb3Kmut::GFP (al Hayek et al., 2021). Adult progeny (only virgin females) was aged 3 days at room temperature, then transferred at 29°C for 6 days prior to midgut dissection.

treatment_protocol:
Batches of >20 virgin females are CO2-anaethesized and put on ice. From then, all solutions are used cold and samples kept on ice whenever possible. Their midgut are dissected in 1XPBS and transferred to a clean PBS dish. Malpighian tubules and hindgut are removed and only the posterior part of the midgut is kept (R3, R4, R5). PBS was replaced by PBS1X-EDTA 1mM. Posterior midguts were transferred on a glass slide in a droplet of PBS, and shrinked into pieces using a razorblade. Samples were transferred into a fresh tube and spun 3- 5minutes at 1000rpm 4°C to pellet the tissue and remove all supernatant except 50μL. 200uL TrypLE 10X (8X final with 0.2mM EDTA) was added for enzymatic digestion. Then the guts were incubated at 37°C and rocked vigorously for 10 minutes. Digestions were stopped with 750μL SSM (Serum Supplemented Medium = S2 Cell culture medium). Trituration was made by pipetting up and down using low binding, flame-rounded narrow tips (5 times with narrow tip; 2-3 times with very narrow tip).
Strain the cell solution (70μM nylon cell strainer, pre-wet with SSM) into a falcon tube. The tube and the strain were rinsed thrice with 1mL PBS-EDTA. The quality of the dissociation and the health of the cells in solution can be checked under a fluorescent macroscope. Samples were spun at 700rcf, 4°c, for >10 minutes and supernatant carefully removed except 100/200μL. 200μL PBS + 3μL clean NGS were added to obtain final samples for FACS. EB cells are sorted based on high GFP exppression (esg>>GFP) and large size (estimated by forward scatter). For each cell sample a tube was prepared with 300μL Tissue and Cell Lysis solution + 1μg Proteinase K [50μg/μL]. Cells are sorted in this buffer, vortexed and placed on ice just after sorting. RNA extraction was started less than 1 hour after sorting

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in EBs for 6 days before midgut dissection

value: Enteroblasts

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: 3543_OF1B_1-2-B11-I16


title: 3543_OF1B_1-2-B11-I3


title: Lovo cells, untreated, replicate 2

value: LOVO

value: colon cancer

value: wt

value: untreated


title: muscle, LNP 16hr 2nd, scRNA

description:
10X 3' chemistry
MS_M-LNP

value: LNP 16hr 2nd


title: Lovo cells, untreated, replicate 3

value: XPCoxa-inactive


title: muscle, LNP 2hr rep, scRNA

description:
10X 3' chemistry
MS_LNP2

value: LNP 2hr rep


title: 3543_OF1B_1-2-B11-J3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: EB RNAiSvb rep2

value: Posterior midgut (R3 to R5)

value: 9 days (6 days of induction)

value: female


title: 3543_OF1B_1-2-B11-I15


title: muscle, LNP 2hr, scRNA

description:
10X 3' chemistry
MS_LNP1

value: muscle

value: LNP 2hr


title: 3543_OF1B_1-2-B11-L16

value: Female

value: nuclear RNA + genomic DNA


title: lymph, LNP 2nd, scRNA

description:
10X 3' chemistry
LN_4

source_name: lymph node

value: lymph node

value: LNP 2nd


title: HCT116 cells, oxaliplatin-treated, replicate 1

value: XPCoxa-active

value: 6h oxaliplatin


title: EB SvbRep rep2

source_name: EB SvbRep

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in EBs for 6 days before midgut dissection

value: Enteroblasts

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: Lovo cells, untreated, replicate 1

value: LOVO

value: colon cancer

value: wt

value: XPCoxa-inactive

value: untreated


title: lymph, LNP+mRNA 2nd, scRNA

description:
10X 3' chemistry
LN_3

value: LNP+mRNA 2nd


title: 3543_OF1B_1-2-B11-H3

source_name: OF1B human BA46

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1B_1-2-B11-H16


title: 3543_OF1B_1-2-B11-H4


title: EB SvbRep rep1

value: Posterior midgut (R3 to R5)

value: 9 days (6 days of induction)

value: female


title: EB SvbAct rep 3

source_name: EB SvbAct


title: lymph, LNP, scRNA

description:
10X 3' chemistry
LN_2

value: lymph node

value: LNP


title: HCT116 cells, oxaliplatin-treated, replicate 2

value: XPCoxa-active


title: HCT116 cells, untreated, replicate 3


title: HCT116 cells, untreated, replicate 2


title: blood, LNP and LNP+mRNA, scRNA

description:
10X 3' chemistry
BL_BL-GEX

source_name: blood

value: blood

value: LNP and LNP+mRNA


title: 3543_OF1B_1-2-B11-G4

value: Female

value: nuclear RNA + genomic DNA


title: HCT116 cells, untreated, replicate 1


title: EB SvbAct rep 1

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in EBs for 6 days before midgut dissection

value: Enteroblasts

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: lymph, PBS and LNP+mRNA, scRNA

description:
10X 3' chemistry
LN_1

value: PBS and LNP+mRNA


title: 3543_OF1B_1-2-B11-G16


title: EB RNAiSvb rep1


title: EB SvbAct rep 2


title: EB SvbRep rep3


title: DLD-1 cells, oxaliplatin-treated, replicate 3

value: colon cancer

value: wt

value: XPCoxa-inactive

value: 6h oxaliplatin


title: HCT116 cells, oxaliplatin-treated, replicate 3


title: EB Ctrl rep 3

source_name: EB Ctrl

value: Posterior midgut (R3 to R5)

value: 9 days (6 days of induction)

value: esg-Gal4, UAS-GFP/+; tubGal80TS/+


title: EB Ctrl rep 2

value: female


title: d6_4_PGCLC_10X

city: Los Angeles

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

description: 10X Genomics

data_processing:
Raw GEX libraries were mapped to the mouse reference genome (refdata-gex-mm10-2020A) using cellranger count (version 6.1.2) from 10x genomics. The aligned data was filtered using SoupX default parameters and the output were analyzed using the R package Seurat(version 4.0). Cells with more than 10% mitochondrial expression and more than 7800, 12300, 7500, 6000 unique features were removed for aggregates 1,2,3 and 4, respectively. UMI counts were log normalized using NormalizeData default parameters, FindVariableFeatures to select the 2000 highest variable genes, ScaleData, and PCA at 30 components.
Supplementary files format and content: Raw H5 matrix from CellRanger version 6.1.2 using refdata-gex-mm10-2020A.

source_name: BVSC

growth_protocol: PGCLC-containing spheres are induced from BVSC reporter PSCs via EpiLC induction (Activin A, FGFbasic-TS) for 48 hours followed by aggregation and induction by addition of BMP-4, BMP-8a, Recombinant Mouse EGF Protein, Stem cell factor (SCF) mouse LIF for 6 days. For these experiments, the entire sphere was dissociated and processed via 10X geneomics.

extract_protocol:
PGCLC-containing spheres were dissociated using Trypsin, washed and immdiately proceeded to GEM encapsulation.
Libraries for 10X genomics were produced according to manufacturer's instructions.

value: BVSC

value: 129X1/svj x C57BL/6J

tag: time

value: differentiated spheres at day 6 of differentiation


title: DLD-1 cells, oxaliplatin-treated, replicate 1

tag: cell line


title: 3543_OF1B_1-2-B11-G3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3543_OF1B_1-2-B11-G15

value: nuclear RNA + genomic DNA


title: d6_3_PGCLC_10X

description: 10X Genomics


title: d6_2_PGCLC_10X

description: 10X Genomics


title: 3543_OF1B_1-2-B11-H15


title: d6_1_PGCLC_10X

description: 10X Genomics


title: DLD-1 cells, untreated, replicate 3

tag: cell type

value: untreated


title: 3543_OF1B_1-2-B11-F4


title: EB Ctrl rep 1

value: GAL4/GAL80TS system allows spatial and temporal control of UAS induction. UASs were activated in EBs for 6 days before midgut dissection

tag: genotype

value: Enteroblasts

value: 3 days old female flies were transferred to 29°C for 6 days, to induce UASs expression.


title: Npat siRNA Day3 TGF repeat1

city: Shreveport

first: Ana-Maria

last: Dragoi

state: Louisiana

address: 1501 Kings Hwy, Molecular and Cellular Physiology Room 4-208

institute: LSU-Health Shreveport

data_processing:
Reads were alligned to human genome (GRCh38.p10) using STAR_2.4.2a
Reads were counted using RSEM 1.2.31
Differentially expressed genes were identified with Ebseq 1.12
Assembly: GRCh38.p10

source_name: pancreas

growth_protocol: PANC-1 cells were maintained in DMEM with 10%FBS in an incubator at 37C and 5% CO2.

extract_protocol:
Total RNA was extracted with Rneasy kit from Qiagen and integrity was assessed on Agilent TapeStation 2200.
Libraries were prepared using Illumina TruSeq Stranded mRNA kit per manufacturer's protocol.

treatment_protocol: For TGFbeta treatments, cells were treated for 48h with 100ng/ml TGFbeta.

value: pancreas

value: epithelial cancer

value: Npat KD

value: TGFbeta


title: DLD-1 cells, untreated, replicate 2

value: colon cancer

value: wt

value: XPCoxa-inactive


title: Npat siRNA Day3 TGF repeat2


title: 3543_OF1B_1-2-B11-F16


title: 3543_OF1B_1-2-B11-F15


title: E12point5-FOLC-Lot-30

first: Fei-Man

last: Hsu

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
Valid cells and UMIs were determined by UMI-tools (Smith et al., 2017)  to generate the whitelist. Reads corresponding to valid barcodes were aligned to GRCm38 with STAR 2.7(Dobin et al., 2013), and only uniquely mapped reads were kept for downstream analyses.  Count matrices were generated by featureCounts v2.0.1 from the Subread R package (Liao et al., 2013),  with UMIs info further appended to the alignment .bam file.  The cell-by-gene count matrix was generated with umi_tools count function and served as input data for Seurat (Stuart et al., 2019).  We only kept the cells expressing at lease 200 genes and genes with expression in at least 3 cells.  The cells were also filtered by the maximum of 9,000 expressed genes and of 10% mitochondrial genes.  The UMI counts were then normalized for each cell by the total expression, multiplied by 10,000, and log-transformed.  We used Seurat’s default method to identify highly variable genes and scale data for regressing out variations. The scaled data with variable genes was used to perform principal component analysis (PCA). The top 50 principal components were chosen for further analysis, including clustering to identify cell populations. UMAPs were calculated by RunUMAP function in Seurat package using top 50 PCs
Assembly: GRCm38
Supplementary files format and content: Raw counts

source_name: fetal ovarian somatic cells

growth_protocol: Ovarian somatic cells for each corresponding lot were obtained from E12.5 mice from ten pregnant female CD1(Charles River, Strain code: 022) mice. Gonads, which included the mesonephros and ovaries, were collected into cell culture plates filled with MEF media on ice. Gonads were transferred into glass plates containing MEF media and mesonephros were removed using surgical blade and fine forceps under a SZX16 (Olympus) microscope. Ovaries were collected into a well of a 4-well plate containing MEF media and DNase I.  Ovaries were washed twice by transferring them into wells containing PBS. Dissociation of ovaries was performed in 0.05% Trypsin for 10 minutes at 37C. MEF media was used to quench and tissues were dissociated by vigorous pipetting. Cells were strained using a 70uM cell strainer and then washed using MEF media. The ovarian somatic cell pellet was then resuspended in MACs Buffer and incubated with the MACs antibodies SSEA1 and CD31 at 4C for 30 minutes. Afterwards labeled cells were washed by adding MACS buffer and spinning for 5 minutes at 1,600rpm. The cell pellet was resuspended in 500uL MACS buffer and then loaded into a MS column held by a MiniMACS™ Separator magnet. Flow through was collected, including the MACS media added for washes. The number of cells collected was counted and aliquots of 300,000 cells per vial were frozen down in Cell Banker 2 at -80C then transferred to Liquid nitrogen storage tanks for long term storage.

extract_protocol:
Single cell suspensions were prepared of the day 6 aggregates (n=4 samples) and the thawed FOSC lots (n=3 samples) using trypsin EDTA (Gibco Cat#25300-054). Single cells were washed three to five times in cold PBS supplemented with 0.04% BSA. Single cell suspensions were processed to 10X Genomics GEM formation and library preparation using the Chromium Single Cell 3’Reagent Kits v3 (10X Genomics Cat# PN-100075).
The libraries were made according to 10X Genomics protocols
10X Genomics

value: fetal ovarian somatic cells

value: Charles River, Strain code:022


title: DLD-1 cells, untreated, replicate 1


title: DLD-1 cells, oxaliplatin-treated, replicate 2

value: 6h oxaliplatin


title: 3543_OF1B_1-2-B11-E4

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: E12point5-FOLC-Lot-26


title: E12point5-FOLC-Lot-29


title: A549_shNC_3

city: Chengdu

first: Xinyue

last: Zhang

address: Renmin South Road, Wuhou District,、

country: China

institute: Sichuan University

data_processing:
Hisat2 v2.0.5
Reads obtained from the sequencing machines includes raw reads containing adapters or low   quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing more than 10% of unknown nucleotides(N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2(version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 v2.0.5 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM(fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: Non-small cell lung cancer

value: WT-knockdown control


title: Slbp siRNA Day3 TGF repeat1

value: Slbp KD


title: Flash siRNA Day3 TGF repeat2

value: Flash KD


title: A549_shNC_2


title: 3543_OF1B_1-2-B11-E3

value: Female

value: nuclear RNA + genomic DNA


title: Flash siRNA Day3 TGF repeat1

value: pancreas


title: Mice orally gavaged with PBS at day 7 and 10 of life Sample 22

city: Seattle

first: Donald

last: Nyangahu

state: Washington

address: 307 Westlake Ave N

institute: Seattle Children's Research Institute

data_processing:
Quality filtering was performed using fastp. Reads were mapped onto the human transcriptome by salmon. Quant.sf files were imported into R and processed by tximport package to obtain raw count data file.
Count file was then used for differential gene expression testing by DESEq2.
comma separated file containing gene counts across all samples

source_name: Mouse colonic cells

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).
RNA sequencing libraries were prepared using NEBNext Ultra II RNA library prep kit for illumina following manufacturer's instructions

value: Mouse colonic cells

tag: day of_necropsy


title: A549_shNC_1

tag: treatment


title: 3543_OF1B_1-2-B11-F3

tag: brain region


title: Mice orally gavaged with PBS at day 7 and 10 of life Sample 21


title: Non-transfected Day3 TGF repeat 2

value: epithelial cancer

value: WT


title: A549_shNR0B1_3

value: NR0B1 knockdown


title: Mice orally gavaged with PBS at day 7 and 10 of life Sample 20


title: 3543_OF1B_1-2-B11-E15

tag: age


title: blood, PBS injected, scRNA

description:
10X 3' chemistry
BL_BL_PBS

value: blood

value: PBS injected


title: Npat siRNA Day3 repeat1

value: Npat KD

value: no treatment


title: A549_OEC_3

value: WT-overexpression control


title: 3543_OF1B_1-2-B11-D15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: Sex


title: 3543_OF1B_1-2-B11-D4

tag: molecule subtype


title: A549_shNR0B1_2

value: Non-small cell lung cancer


title: 3543_OF1B_1-2-B11-D16


title: Slbp siRNA Day3 TGF repeat2

value: TGFbeta


title: Mice orally gavaged with PBS at day 7 and 10 of life Sample 18


title: A549_shNR0B1_1


title: Mice orally gavaged with PBS at day 7 and 10 of life Sample 19


title: Npat siRNA Day3 repeat2


title: Mice orally gavaged with PBS at day 7 and 10 of life Sample 17


title: 3543_OF1B_1-2-B11-D3


title: A549_OEC_2


title: Slbp siRNA Day3 repeat2

value: Slbp KD


title: A549_OEC_1


title: Slbp siRNA Day3 repeat1


title: Mice orally gavaged with heat-killed B. infantis at day 7 and 10 of life Sample 15


title: Mice orally gavaged with heat-killed B. infantis at day 7 and 10 of life Sample 16


title: Mice orally gavaged with heat-killed B. infantis at day 7 and 10 of life Sample 14


title: A549_NR0B1 OE_3

value: NR0B1 overexpression


title: 3543_OF1B_1-2-B11-C4

value: Female


title: 3543_OF1B_1-2-B11-C3

value: nuclear RNA + genomic DNA


title: Flash siRNA Day3 repeat2

value: pancreas

value: Flash KD


title: Flash siRNA Day3 repeat1

value: epithelial cancer


title: A549_NR0B1 OE_2


title: 3543_OF1B_1-2-B11-E16


title: Mice orally gavaged with heat-killed B. infantis at day 7 and 10 of life Sample 13

value: Mouse colonic cells


title: Non-transfected Day3 TGF repeat 1

value: WT


title: 3543_OF1B_1-2-B11-C15


title: Mice orally gavaged with Bacteroides thetaiotaomicron at day 7 and 10 of life Sample 12


title: A549_NR0B1 OE_1


title: Non-transfected Day3 repeat 2


title: PATIENT_tgfb1_2 [UDN_T2A]

city: boston

first: christian

last: lino cardenas

state: Massachusetts

address: 185 Cambridge st Room 3224

department: cardiology

institute: Massachusetts General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38.p1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38.p1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: SKIN FIBROBLASTS

growth_protocol: Cell lines. Primary human aortic vascular smooth muscle cells (VSMC) were purchased from Cell Applications Inc. (354K-05a), California, USA. To preserve cell identity all experiments were carried out at passages 1-5, and cell identity (contractile phenotype) was assessed by immunofluorescence staining of contractile markers including SM22α, α-SMA, MYH11 and cytoskeleton integrity by F-actin staining. Human fibroblasts from healthy and patient individuals were obtained. Tissue biopsies were dissected into small blocks and placed in appropriate culture dishes and supplemented with growth media. Tissue was cultured for 2-3 weeks until a single cell monolayer covered the surface of the dish followed by passage of cells to perform experiments.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: TGFB 10ng/mL

value: SKIN FIBROBLASTS

value: PRIMARY

value: FIBROBLASTS

value: MUTANT


title: PATIENT_tgfb1_3 [UDN_T3A]


title: Non-transfected Day3 repeat 1

value: no treatment


title: 3543_OF1B_1-2-B11-B3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Mice orally gavaged with Bacteroides thetaiotaomicron at day 7 and 10 of life Sample 11


title: PATIENT_3 [UDN_C3A]

value: DMSO


title: 3543_OF1B_1-2-B11-B16


title: Patient 14, NSCLC tumor-draining lymph node, LN1

last: KHALIFA

address: IUCT-Oncopole 1 avenue Irène-Joliot Curie

institute: Institut Universitaire du Cancer de Toulouse - Oncopole

data_processing:
For each sample, FASTQ raw files were trimmed with Trimgalore then aligned to hg38 genome with STAR. MarkDuplicates (PicardTools) was used to remove PCR duplicates. Htseq-count (HTSeq) was used to quantify genes and counts were normalized in TPM (Transcript Per Million).
Assembly: hg38

source_name: Lymph node

extract_protocol:
Lymph node tissues were obtained from the pathological specimens of LN dissection. Rapidly after resection, lymph nodes were placed in 10% neutral buffered formalin solution, fixed at room temperature and embedded in paraffin blocks (FFPE). FFPE blocks were sliced into 4 µm unstained sections on glass slides for RNA extraction. RNA was extracted using the RNeasy FFPE kit (Qiagen) following scraping of LN tissues with a razor blade from 15 glass slides per sample and de-paraffinization using the Deparaffinization Solution (Qiagen). RNA concentration was quantified by spectrophotometry (NanoDrop™ One, Thermo Scientific) and fluorometry (Qubit™, Invitrogen), and RNA quality (DV200) was assessed using the Fragment Analyzer 5200 System (Agilent) and the DNF-472 HS RNA (15nt) kit (Agilent).
Total RNA libraries were prepared using Illumina stranded Total RNA prep ligation with Ribo-Zero Plus kit (Illumina) starting with an input amount of 187-200 ng total RNA. The size and quality of the libraries were evaluated with the Fragment Analyzer 5200 System and the DNF-474 HS NGS Fragment kit (1-6000bp) (Agilent). The KAPA Library Quantification kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify the libraries. Samples were pooled in equimolarity. The double indexed libraries were sequenced on a NextSeq 550 instrument (Illumina) using 74 base-length read chemistry in paired-end mode.

value: Lymph node


title: Patient 15, NSCLC tumor-draining lymph node, LN1


title: Mice orally gavaged with Bacteroides thetaiotaomicron at day 7 and 10 of life Sample 9


title: Mice orally gavaged with Bacteroides thetaiotaomicron at day 7 and 10 of life Sample 10


title: Patient 13, NSCLC tumor-draining lymph node, LN3

value: Neoadjuvant chemoradiotherapy


title: 3543_OF1B_1-2-B11-B4


title: PATIENT_2 [UDN_C2A]


title: Mice orally gavaged with Bacteroides thetaiotaomicron at day 7 and 10 of life Sample 7


title: 3543_OF1B_1-2-B11-A4


title: 3543_OF1B_1-2-B11-B15


title: Mice orally gavaged with Bifidobacterium infantis at day 7 and 10 of life Sample 6


title: PATIENT_1 [UDN_C1A]


title: 3543_OF1B_1-2-B11-A3


title: 3543_OF1B_1-2-B11-C16


title: PATIENT_tgfb1_1 [UDN_T1A]


title: Mice orally gavaged with Bifidobacterium infantis at day 7 and 10 of life Sample 5


title: Patient 16, NSCLC tumor-draining lymph node, LN1


title: 3543_OF1B_1-2-B11-A15


title: Mice orally gavaged with Bacteroides thetaiotaomicron at day 7 and 10 of life Sample 8


title: 3543_OF1B_1-2-B11-A16


title: 3543_OF1B_1-1-B11-P1


title: 3543_OF1B_1-1-B11-P14


title: Patient 11, NSCLC tumor-draining lymph node, LN2


title: Patient 13, NSCLC tumor-draining lymph node, LN1


title: CONTROL3_TGFB_3 [T3A_3]

value: WILDTYPE


title: CONTROL3_TGFB_1 [T3A_1]


title: CONTROL2_TGFB_2 [T2A_2]


title: CONTROL2_TGFB_3 [T2A_3]


title: Patient 13, NSCLC tumor-draining lymph node, LN2


title: CONTROL3_TGFB_2 [T3A_2]


title: Patient 12, NSCLC tumor-draining lymph node, LN1


title: 3543_OF1B_1-1-B11-O2

value: Female


title: Mice orally gavaged with Bifidobacterium infantis at day 7 and 10 of life Sample 3


title: Mice orally gavaged with Bifidobacterium infantis at day 7 and 10 of life Sample 1


title: 3543_OF1B_1-1-B11-P13

value: nuclear RNA + genomic DNA


title: Patient 10, NSCLC tumor-draining lymph node, LN1


title: CONTROL2_TGFB_1 [T2A_1]


title: 3543_OF1B_1-1-B11-O1


title: Olfr78 KO colon cells

city: Anderlecht

first: Gilles

last: Dinsart

address: 808 route de lennik

country: Belgium

institute: Université Libre de Bruxelles

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Barcodes, Features and Matrix files

source_name: Colon

extract_protocol:
Colon tissues from one wild type and one Olfr78GFP KO mice (respectively 8 and 6 months-old) were cut in small pieces and put to digest in collagenase I at 0,5 mg/ml for 25 min at 37°C under agitation at 75 RPM. Ups-and-downs were performed with a 10 ml pipette and the samples were put back 20 min at 37°C and 75 RPM. Equal volume of PBS-5 mM EDTA was added and cells were centrifuged 10 min at 50 g. The supernatant was removed and 5 ml of Trypsin were then added for 25 min at 37°C and 75 RPM. Cells were pipetted up and down, passed through a 40 µm filter and pelleted at 50 g for 10 min. The pellet was washed 3 times with PBS-BSA 0.04% (w/v).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Colon

value: All colon cell types

value: Olfr78 KO

value: No


title: Patient 12, NSCLC tumor-draining lymph node, LN2


title: Mice orally gavaged with Bifidobacterium infantis at day 7 and 10 of life Sample 4

value: Mouse colonic cells


title: CONTROL1_TGFB_3 [T1A_3]

value: SKIN FIBROBLASTS


title: Patient 9, NSCLC tumor-draining lymph node, LN2


title: 3543_OF1B_1-1-B11-O14

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq


title: CONTROL1_TGFB_2 [T1A_2]

value: PRIMARY


title: Epcam+ve/GFP+ve cells, homozygous, pool 2

data_processing:
The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) and sequences were produced using a 200 Cycles Kit. Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software to generate read alignments for each sample. Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org.
Assembly: mm10
Supplementary files format and content: files include RP20M values for each sample

extract_protocol:
RNA was extracted using Rneasy mini kit or miRNeasy microkit for crypts and sorted cells, respectively, following manufacturer's instructions.
Indexed cDNA libraries were obtained using the Ovation Solo RNAseq systems (Tecan) following manufacturer recommendations.

value: Epithelial cells

tag: cell subtype

value: enteroendocrine


title: Patient 10, NSCLC tumor-draining lymph node, LN2


title: Patient 11, NSCLC tumor-draining lymph node, LN1


title: Epcam+ve/GFP+ve cells, homozygous, pool 1


title: Patient 7, NSCLC tumor-draining lymph node, LN1


title: Olfr78 WT colon cells

description: 10X Genomics

value: WT


title: 3543_OF1B_1-1-B11-N2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1B_1-1-B11-N1


title: Patient 8, NSCLC tumor-draining lymph node, LN1


title: Patient 6, NSCLC tumor-draining lymph node, LN2


title: CONTROL3_3 [C3A_3]

value: FIBROBLASTS

value: DMSO


title: 3543_OF1B_1-1-B11-N14


title: CONTROL3_1 [C3A_1]


title: Patient 9, NSCLC tumor-draining lymph node, LN1

value: Lymph node


title: Epcam+ve/GFP+ve cells, heterozygous, pool 2

value: HE


title: Epcam+ve/GFP-ve cells, mouse 1 sample 2


title: Patient 6, NSCLC tumor-draining lymph node, LN1


title: 3543_OF1B_1-1-B11-N13

value: Female


title: CONTROL2_3 [C2A_3]

value: WILDTYPE


title: Epcam+ve/GFP-ve cells, mouse 1 sample 1

value: Colon


title: 3543_OF1B_1-1-B11-M2

value: nuclear RNA + genomic DNA


title: Mice orally gavaged with Bifidobacterium infantis at day 7 and 10 of life Sample 2


title: Epcam+ve/GFP+ve cells, heterozygous, pool 1


title: CONTROL2_2 [C2A_2]


title: Colon crypts Knockout, mouse 5

value: Crypts

value: all epithelium

value: Olfr78 KO


title: CONTROL1_TGFB_1 [T1A_1]

value: SKIN FIBROBLASTS


title: CONTROL3_2 [C3A_2]

value: PRIMARY


title: Patient 4, NSCLC tumor-draining lymph node, LN2


title: Patient 5, NSCLC tumor-draining lymph node, LN1


title: Patient 4, NSCLC tumor-draining lymph node, LN1


title: 3543_OF1B_1-1-B11-M1


title: Colon crypts Knockout, mouse 3


title: CONTROL2_1 [C2A_1]


title: Patient 3, NSCLC tumor-draining lymph node, LN1

value: Neoadjuvant chemoradiotherapy


title: 3543_OF1B_1-1-B11-O13


title: 3543_OF1B_1-1-B11-M14


title: 3543_OF1B_1-1-B11-L2


title: CONTROL1_3 [C1A_3]


title: Patient 2, NSCLC tumor-draining lymph node, LN2


title: Colon crypts Knockout, mouse 2


title: CONTROL1_1 [C1A_1]


title: Colon crypts Knockout, mouse 4


title: Patient 2, NSCLC tumor-draining lymph node, LN1


title: Colon crypts Knockout, mouse 1


title: CONTROL1_2 [C1A_2]


title: 3543_OF1B_1-1-B11-L1


title: M29, MDA5 KD, Mock, 48h

city: Worcester

first: Ozkan

last: Aydemir

address: 366 Plantation Street, Paul J. DiMare Center  N4-1085

institute: UMass Medical School

description:
genes_expression_expected_count_hg38.tsv
genes_expression_expected_count_hg38_HIV.tsv

data_processing:
Reads were aligned to human genome assembly hg38  (Gencode v34 transcript set) and gene expression was quantified via RSEM (v1.3.1) software's rsem-calculate-expression command, utilizing STAR aligner (v2.6.1)  with default parameters to create the "expected gene counts" files.
Reads were aligned to human genome assembly hg38  (Gencode v34 transcript set) concatenated to HIV genome plasmid (pUC57mini_NLBN_dEnv_GFP) and human and HIV genes were quantified via RSEM (v1.3.1) software's rsem-calculate-expression command, utilizing STAR aligner (v2.6.1)  with default parameters to create the "expected gene counts" files.
Assembly: hg38
Supplementary files format and content: Matrix table with raw (expected) gene counts for every gene and every sample

source_name: Monocyte-derived dendritic cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from leukopaks by gradient centrifugation on Lymphoprep. To generate dendritic cells, CD14+ mononuclear cells were enriched by positive selection using anti-CD14 antibody microbeads. Enriched CD14+ cells were plated in RPMI-1640, supplemented with 5% heat-inactivated human AB+ serum, 20 mM GlutaMAX, 1 mM sodium pyruvate, 1x MEM non-essential amino acids and 25 mM HEPES pH 7.2 (RPMI−HS complete), at a density of 2 x 10^6 cells/ml. To differentiate CD14+ cells into dendritic cells, 1:100 human granulocyte-macrophage colony stimulating factor (hGM-CSF) and 1:100 human interleukin-4 (hIL-4)-conditioned media was added. Cells were cultured in humidified, 5% CO2 incubators at 37°C.

extract_protocol:
Cells were lysed and RNA from these samples was isolated by using Rneasy Plus Mini kit (Qiagen) following manufacturer's protocol.
Poly(A)-selected RNA-seq libraries were generated by Genewiz, using standard Illumina protocol.

treatment_protocol: CD14+ mononuclear cells, isolated from 3 different human blood donors, were transduced with shRNA-encoding lentivectors targeting either Luc or MDA5. Upon differentiation into MDDCs, cells were either challenged with HIV-1 for 48 hours, or left uninfected.

value: Monocyte-derived dendritic cells

tag: donor number

value: MDA5 KD

tag: infection

value: Mock


title: 3543_OF1B_1-1-B11-L14

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Colon crypts Wildtype, mouse 2

tag: tissue

value: WT


title: M29, MDA5 KD, HIV1, 48h


title: Colon crypts Wildtype, mouse 1


title: M29, Luc KD, HIV1, 48h

value: control


title: RpoD_ChIP-seq WT mid-log phase rep 2

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

institute: UNIST

description: Escherichia coli str. K-12 substr. MG1655 RpoD ChIP-seq mid-log phase replicate 2

data_processing:
The sequencing was performed on Miseq (Illumina).
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
In-house python script was used to generate gff files from BAM files. No peak calling was performed.
Genome_build: E.coli genome(NC_000913.2)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

source_name: Bacteria

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. M9 minimal media was also supplemented with 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with sigma factor 70 antibody (cat# WP004, neoclone).
ChIP-seq experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

value: wild type

tag: chip antibody

value: sigma factor 70 (cat# WP004, neoclone)


title: Patient 1, NSCLC tumor-draining lymph node, LN1

value: Lymph node


title: M29, Luc KD, Mock, 48h

tag: time


title: 3543_OF1B_1-1-B11-M13

value: Female

value: nuclear RNA + genomic DNA


title: ONC_cKO

data_processing:
FastQC (fastqc_v0.11.5) package was utilized to perform basic statistics on the quality of the raw reads. The resulting reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36).
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012).
The results of methylation extractor (bismark_methylation_extractor, --no_overlap) were transformed into bigWig format for visualization using IGV browser.
Assembly: GRCM38
Supplementary files format and content: bigWig (.bw)

source_name: Retina

extract_protocol:
DNA was harvested using Quick-DNA MiNIprep Kit (Zymo). 200 ng of total DNA was used for the construction of sequencing libraries.
Firstly, the genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treated to generate single strand DNA (ssDNA). During the bisulfite conversion, unmethylated cytosine were converted into uracil, while methylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. The library was ready after size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: Retinal ganglion cell

value: Retina

tag: strain


title: RpoD_ChIP-seq WT mid-log phase rep 1

description: Escherichia coli str. K-12 substr. MG1655 RpoD ChIP-seq mid-log phase replicate 1


title: 3543_OF1B_1-1-B11-K1


title: 3543_OF1B_1-1-B11-K2


title: 3543_OF1B_1-1-B11-K14


title: VD12_2

description: paired-end 150 bp sequencing

data_processing:
Novogene analysis pipline
Sequence reads were trimmed if contained adaptor sequence, low-quality sequence, and uncertain nucleotides constituting more than 10 percent of either read (N > 10%).
Trimmed sequence reads were mapped to Mus_musculus_Ensemble_94 using HISAT2 2.0.5
Read count extraction and normalization were performed using Stringtie 1.3.3b and featureCounts 1.5.0-p3.
Assembly: GRCM38
Supplementary files format and content: KOvsCtrl_DESeq_annoNovogene.csv

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (Zymo). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene.

tag: cell type

value: Retinal ganglion cells


title: HCA2_shFbxo22-senescence-3

city: Minato ku

first: Satotaka

last: Omori

state: tokyo

address: shirokanedai, 4-6-1

country: Japan

institute: the university of Tokyo

data_processing:
The libraries were sequenced on a Ion Proton System platform
The sequencing reads were aligned to the hg19/GRCh37 reference human genome using Bowtie2 (v2.0.0) and STAR (v2.3.0).
Data normalization and differential expression analysis were performed using a DESeq2 package (v1.14.1) in the R language (v3.2.2).
Genome_build: hg19

source_name: HCA2 (MJ90)

growth_protocol: Cells were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Rneasy mini kit (Qiagen)  according to the manufacturer’s instructions.
Ion Total RNA-Seq kit v2 (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: IR-irradiation (10 Gy)

tag: cell line

value: skin fibroblast

tag: cell condition

value: IR-irradiation


title: M29, Luc KD, Mock, 0h

value: Monocyte-derived dendritic cells

tag: genotype


title: 3543_OF1B_1-1-B11-K13

first: Joseph

tag: brain region


title: HCA2_shFbxo22-senescence-1


title: M28, MDA5 KD, HIV1, 48h

value: MDA5 KD


title: M28, MDA5 KD, Mock, 48h

value: Mock


title: VD15_1

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

description: paired-end 150 bp sequencing


title: 3543_OF1B_1-1-B11-J2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age


title: M28, Luc KD, HIV1, 48h

value: control


title: HCA2_shFbxo22-senescence-2


title: HCA2_shFbxo22-young-3

value: low passage


title: VD12_0

description: paired-end 150 bp sequencing


title: 3543_OF1B_1-1-B11-L13

tag: Sex


title: C035_0

description: paired-end 150 bp sequencing


title: C034_1

description: paired-end 150 bp sequencing


title: M28, Luc KD, Mock, 48h


title: 3543_OF1B_1-1-B11-J14

tag: molecule subtype


title: 3543_OF1B_1-1-B11-J1


title: HCA2_shFbxo22-young-1


title: ONC_CTRL


title: HCA2_shLuciferase-senescence-3


title: M28, Luc KD, Mock, 0h


title: 3543_OF1B_1-1-B11-J13


title: HCA2_shLuciferase-senescence-2


title: C033_1

description: paired-end 150 bp sequencing


title: M27, MDA5 KD, Mock, 48h


title: Substantia nigra, Tg-Mlkl+/+

city: Shanghai

first: Wenqing

last: Gao

address: Songhu Road, Yangpu District

institute: Fudan university

data_processing:
Single nuclei RNA-seq reads were aligned to the mm10 genome assembly using Cell Ranger version 3.1.0 following standard recommendation.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Substantia nigra

extract_protocol:
All procedures were carried out on the ice or at 4 °C. Briefly, the frozen substantia nigra brain tissue was homogenized in 2 ml Homogenization Buffer (10 mM Tris-HCl, pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X-100, 250 mM sucrose, 0.5 U/μl SuperRNase inhibitor, and 0.5 U/μl RNAse inhibitor), using a Wheaton Dounce Tissue Grinder (10 strokes with the loose pestle and 15 strokes with the tight pestle). Then, tissue homogenate was overlaid onto 10% iodixanol and centrifuged with an SW32 rotor at 10,000g for 20 minutes at 4 °C. After ultracentrifugation, the supernatant was aspirated and discarded, and the remaining pellet was resuspended in 0.5 % BSA plus 50 ng/ul DAPI for nuclei isolation using a BD AriaFusion cell sorter (BD Biosciences).
RNA libraries were prepared for sequencing using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns PN-1000075
Single nuclei RNA-Seq

value: Substantia nigra

value: 10 month

value: hA53T transgenic mice


title: 10d HF 5

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: oesophageal-derived skin in vitro - 10 days

data_processing:
Quality checks, UMI identification, alignment to the mouse reference genome and cell calling were performed using the cellranger software (v3.1.0) with default parameters. Violin plots of the distribution of counts, features, mitochondrial and ribosomal RNA were created and upper and lower bounds were introduced to avoid data heterogeneity and exclude potentially problematic cells.
The data was normalised using the Seurat R package (v3.2.2). Dimensionality reductions (PCA and UMAP), as well as clustering were also performed using the Seurat R package, with the number of clusters being the optimal selected by the software. For the subsequent analysis, we focused on the 1000 most abundant genes. Markers for each cluster were identified by testing for differential gene expression, using the Seurat R package. The above steps were performed both for all the cells in the data, but also individually for each sample set (HF_3d, HF_10d, OE_3d, OE_10d).
Clustering stability was evaluated by a PAC analysis (https://doi.org/10.1038/srep06207). Enrichment analysis on the markers identified per cluster was performed using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.8). RNA velocity trajectory analysis was performed with the velocyto software (v0.17.17) and associated R package (v0.6). Pseudotime analysis was performed with the monocle3 R package (v0.2.3.0).  Further analysis was performed with the above tools, focused on sub-clusters of biological interest.
Cells marked with the fluorescent markers eGFP and tdTomato were identified through sequencing. The identity of the unlabelled cells was inferred by using a semi-supervised classifier based on random forests.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: Sparse matrix of raw abundances for each gene, per cell

source_name: Oesophageal epithelial cells

growth_protocol: 3D organotypic cultures were performed by combining oesophageal epithelium with either oesophageal stroma or skin stroma (tail dermis) in ThinCert™ Cell Culture Inserts (6-well plates with a pore diameter of 0.4μm, Greiner Bio-One), in DMEM High Glucose/DMEM:F12 (1:1) supplemented with FBS 5%, Insulin 5ug/ml, Adenine 25ug/ml and Apotransferrin 10ug/ml.

extract_protocol:
After 3 or 10days in culture, the oesophageal-derived epithelia were harvested and peeled off from the oesophageal stroma or dermis. The epithelial sheet was dissociated into a single cell suspension and FACS sorted to select live singlets. For each sample, 7,000-9,000 cells were submitted for  10X single cell GEX v3 library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols for 10X Single Cell GEX v3

tag: time point

value: 10 days

value: Tail skin dermis

tag: replicate


title: HCA2_shLuciferase-young-3


title: M27, MDA5 KD, HIV1, 48h

tag: donor number

tag: infection


title: Substantia nigra, Tg-Mlkl-/-

tag: tissue

value: hA53T transgenic mice plus Mlkl-/-


title: M27, Luc KD, HIV1, 48h


title: M27, Luc KD, Mock, 48h


title: 10d HF 4


title: HCA2_shFbxo22-young-2


title: HCA2_shLuciferase-young-2


title: M27, Luc KD, Mock, 0h


title: HCA2_shLuciferase-young-1


title: 3543_OF1B_1-1-B11-H2

city: La Jolla

source_name: OF1B human BA46

value: Female

value: nuclear RNA + genomic DNA


title: 10d HF 3


title: 10d HF 2


title: Cardiac fibroblast, TAC, 8 week, rep 3

city: Hwasun, Jeollanam-do

first: Young-Kook

address: 264, Seoyang-ro

department: Department of Biochemistry

data_processing:
The FastQC was used for the initial quality check of sequencing results.
The reads with low quality were removed with Trimmomatic (PMID: 24695404).
The expression counts of circRNAs were calculated using the STAR aligner (PMID: 23104886) and DCC algorithm (PMID: 26556385).
The expression counts were normalized by the total counts of circRNAs in each sample.
Assembly: mm10
Supplementary files format and content: Tab-delimited circRNA expression counts normalized by the total counts of circRNAs in each sample.

source_name: heart

growth_protocol: Adult male C57BL/6J mice (8-10 weeks old) were purchased from Damul Science (Damul Science, Dajeon,Korea). All animal experiments were approved by the Institutional Review Board of Chonnam National University Medical School Research Institutional Animal Care and Use Committee (CNU-IACUC-H-2021-39 and CNU-IACUC-H-2022-11) and followed the ‘Guide for the Care and Use of Laboratory Animals’ (8th edition, National academies Press, Washington, DC, USA, 2011).

extract_protocol:
TRI Reagent (Molecular Research Center) was used to isolate total RNA in accordance with the manufacturer's protocol. DNase I (Takara) was used to remove residual DNA in RNA samples.
Total RNA was treated with Ribo-Zero Gold rRNA Removal Kit (Illumina) to remove the ribosomal RNAs and applied to TruSeq Stranded Total RNA Kit (Illumina) to construct RNA-seq library.
The library was sequenced by HiSeq 2500 (Illumina) in the paired-end mode with 100 sequencing cycles.

treatment_protocol: Eight-week-old male C57BL/6J mice were anaesthetized by Avertin. The mice were then ventilated and the chest was opened to expose the thymus and aortic arch. A 7-0 silk suture were placed between the innominate and left carotid arteries. A 27-gauge needle put parallel to the transverse aorta and the suture was tied. After ligation, the needle was removed and the rib cage was closed using 4-0 silk suture.

value: heart

value: cardiac fibroblast

tag: treatment

value: transverse aortic constriction

tag: treatment time

value: 8 week


title: 10d HF 1


title: 3543_OF1B_1-1-B11-H1


title: siNC_2

city: Hangzhou

first: Shuangshuang

last: Li

address: Qingchun Road

institute: the first affiliated hospital of Zhejiang University

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include read count and FPKM values for each Sample

source_name: Human HCC cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: HCC

value: siRNA-NC 50nM


title: Cardiac fibroblast, TAC, 8 week, rep 2

institute: Chonnam National University Medical School


title: 3543_OF1B_1-1-B11-I1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1B_1-1-B11-I2


title: 3543_OF1B_1-1-B11-H14


title: siNC_1


title: 3543_OF1B_1-1-B11-H13


title: siEIF4G2_3

value: siRNA-EIF4G2 50nM


title: 72h HF 2

description: oesophageal-derived skin in vitro - 3 days

value: 3 days


title: 3543_OF1B_1-1-B11-G2


title: 72h HF 3


title: 3543_OF1B_1-1-B11-I13


title: Cardiac fibroblast, sham, 8 week, rep 4

value: sham


title: 3543_OF1B_1-1-B11-G1


title: 72h HF 1


title: 3543_OF1B_1-1-B11-I14


title: HCA2_shLuciferase-senescence-1

value: skin fibroblast

value: IR-irradiation


title: siEIF4G2_1


title: Cardiac fibroblast, sham, 8 week, rep 3


title: siNC_3


title: siEIF4G2_2


title: 10d OE 3

description: oesophagus in vitro - 10 days

value: 10 days

value: Oesophageal stroma


title: 3543_OF1B_1-1-B11-G14

value: Female


title: atp22R3

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

description: atp22Δ cells collected during standard log phase growth

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. glabrata CBS138 reference genome using the hisat2 version 2.1.0.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the edgeR version 3.24.3 package. Genes with a p-value < 0.05 and a log2 fold change value > 1 were considered to represent significantly differentially expressed genes (DEGs). The GO analysis of DEGs was performed using the clusterProfiler version 4.7.1 package.
Assembly: C. glabrata CBS138 (GCF_000002545.3)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Nakaseomyces glabratus

source_name: C. glabrata cells

extract_protocol:
Total RNA was extracted using the hot phenol method
Illumina library preparation and sequencing were then performed by Singapore Immunology Network (SIgN) on samples from three independent experiments following standard operating procedures

value: C. glabrata cells

value: ATP22 knockout