title: cpxS_noPT_60min_4

city: Großhansdorf

first: Espen

middle: E

last: Groth

address: Wöhrendamm 80

department: Department of Pulmonology

institute: LungenClinic Grosshansdorf

description:
Library name: H27490-L1_S48_L002_R1_001
cpxS_noPT_60min_4.rpkm_0

data_processing:
Reads were trimmed with Trimmomatic (v0.39, settings phredThreshold=phred33, seedMismatches=2, palindromeClipThreshold=10, lengthMin=36).
The reference genome for UCBPP-PA14 was retrieved from GenBank (NCBI Reference Sequence NC_008463.1) and for the Cpx T163P mutant, the genome was adapted via a custom R script to include the mutation.
Reads were followingly mapped to the respective genomes using EDGEpro (v1.3.1), substituting the bundled Bowtie package with the newest available at the time of mapping (Bowtie2 v2.4.1).
Assembly: NCBI Reference Sequence NC_008463.1
Supplementary files format and content: Tab-delimited text file contains RPKMs for each sample.

organism: Pseudomonas aeruginosa PA14

source_name: Pseudomonas aeruginosa PA14

growth_protocol: To generate exponential phase cells, an overnight culture was diluted 1:200 in M9 (plus supplements if indicated) and incubated at 37 °C until an OD600 of 0.06 – 0.07 was reached. At this point, the culture was split into 5 mL portions.

extract_protocol:
Cells were collected by centrifugation (3220 x g, 10 min, 4 °C) and total RNA was isolated using a TRIzol lysis and the NucleoSpin miRNA kit (Macherey-Nagel). RNA was eluted in TE buffer and stored at -80 °C
rRNA depletion (RiboZero Bacterial Kit), library preparation (TruSeq stranded total RNA) and sequencing (Illumina, HiSeq4000, 1 x 50 bp).

treatment_protocol: The pre-treatment drug (the beta-lactam antibiotic carbenicillin) was added at sub-MIC level (50 mg/L). A mock treatment not containing antibiotic served as control. After 30 min, cells were resuspended in antibiotic-free medium and followingly harvested at three sequential time points (0, 30 and 60 min) to investigate the expression dynamics induced by short-term carbenicillin/Beta-lactam pretreatment that could explain induced sensitivity towards other antibiotics when administered subsequently.

value: Pseudomonas aeruginosa PA14

value: CpxS T163P mutant

tag: pretreatment

value: Control

tag: time point_rna_isolation_(min)

tag: replicate


title: cpxS_CAR_60min_4

status: Public on Feb 13 2026

type: SRA

country: Germany

description:
Library name: H27488-L1_S46_L002_R1_001
cpxS_CAR_60min_4.rpkm_0

library_source: transcriptomic

molecule: total RNA

tag: cell line

tag: genotype

value: CAR


title: WT_noPT_60min_4

description:
Library name: H27489-L1_S47_L002_R1_001
WT_noPT_60min_4.rpkm_0

value: PA14 wildtype


title: WT_CAR_60min_4

description:
Library name: H27487-L1_S45_L002_R1_001
WT_CAR_60min_4.rpkm_0


title: Thy6-abTCR

city: Chicago

first: Erin

middle: J

last: Adams

state: IL

country: USA

institute: University of Chicago

description:
10X Genomics
Thy6_abTCR

library_source: other

data_processing:
Sequences were deconvoluted using Cellranger software v.7.1 and imported into R. Initial QC and gene expression and clustering analysis was conducted using the standard Seurat v5 pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

organism: Homo sapiens

source_name: Vδ1 thymocytes

extract_protocol:
Thymic fragments were incubated in DMEM-F12 with rotation for 20min and thymocytes were collected from supernatant.Dead cells were separated using Ficoll density gradient and thymocytes were counted and frozen in FBS + 10% DMSO until thawing for staining and sequencing.
Samples were processed for sequencing using the 10X Genomics 5’ Single Cell Immune Profiling workflow. γδ TCR libraries were generated using the 10X universal forward primers and nested custom reverse primers (TRG outer Reverse: AGTCTTCATGGTGTTCCCCTCC, TRG inner Reverse: AAAATAGTGGGCTTGGGGGA, TRD outer Reverse GTCGTGTTGAACTGAACATGTCAC, TRD inner Reverse CAGACAAGCGACATTTGTTCCA). Libraries for all samples were pooled and sequenced on a NovaSeq6000 or NovaX (Illumina) and resultant FASTQs were demultiplexed by the University of Chicago Genomics Facility.
scRNA-seq, CITE-seq, and VDJ libraries

tag: tissue

value: thymus

tag: Sex

value: F

tag: library type

value: abTCR VDJ

tag: age

value: 4 day


title: si-dnmt + TNF, biological replicate 3

city: Charlottesville

first: Andrew

middle: C

last: Dudley

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

description: Library name: F3

data_processing:
cutadapt/4.9:  Trim adapters (P5, P7, and universal Illumina motif). P5 adapter：P5→P7’(5’→3 ’)
AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT
P7 adapter：P5→P7’(5’→3’)
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG
fastqc/0.12.1
multiqc/1.27.1
Assembly: star/2.7.11b followed by featureCounts, and the DESeq2

organism: Mus musculus

source_name: Veravec

growth_protocol: Mouse lung ECs were seeded at 1×105 cells/mL in 6-well plates and cultured overnight at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated using a column-based RNA extraction kit (Zymo Research) according to the manufacturer’s instructions.
Libraries were prepared and sequenced by Novogene for bulk RNA-seq analysis.

treatment_protocol: The next day, cells were transfected with either control siRNA or DNMT1-targeting siRNA (BLOCK-iT oligos; Invitrogen) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM I Reduced Serum Medium for 4 h, following the manufacturer’s instructions. A BLOCK-iT Alexa Fluor Red fluorescent oligo (Invitrogen) was used in parallel wells to monitor transfection efficiency. After 4 hrs, the transfection medium was replaced with growth medium containing 20% serum, and the cells were cultured for 24 hrs at 37 °C, humidified 5% CO₂. A second siRNA transfection was performed 24 h later to reinforce the knockdown. Cells were then treated with TNFa (10 ng/mL) or IFNg (1,000 U/mL) for 16 hrs.

value: Veravec

tag: cell type

value: lung endothelial cells

tag: treatment

value: si-dnmtl + TNF


title: cpxS_noPT_30min_4

description:
Library name: H27486-L1_S44_L002_R1_001
cpxS_noPT_30min_4.rpkm_0


title: si-dnmt + TNF, biological replicate 2

description: Library name: F2


title: WT_noPT_30min_4

description:
Library name: H27485-L1_S43_L002_R1_001
WT_noPT_30min_4.rpkm_0


title: cpxS_CAR_30min_4

description:
Library name: H27484-L1_S42_L002_R1_001
cpxS_CAR_30min_4.rpkm_0


title: Thy4-Sur

description:
10X Genomics
Thy4_barcodes.tsv.gz
Thy4_features.tsv.gz
Thy4_matrix.mtx.gz
Thy4_ADT

molecule: protein

value: M

value: ADT

value: 3 month

tag: adt


title: WT_CAR_30min_4

description:
Library name: H27483-L1_S41_L002_R1_001
WT_CAR_30min_4.rpkm_0


title: Thy6-gdTCR

description:
10X Genomics
Thy6_gdTCR

value: gdTCR VDJ


title: si-dnmtl + TNF, biological replicate 1

description: Library name: F1


title: Thy6-5GE

description:
10X Genomics
Thy6_barcodes.tsv.gz
Thy6_features.tsv.gz
Thy6_matrix.mtx.gz
Thy6_GEX

library_source: transcriptomic single cell

value: gene expression


title: cpxS_noPT_0min_4

description:
Library name: H27482-L1_S40_L002_R1_001
cpxS_noPT_0min_4.rpkm_0

value: Pseudomonas aeruginosa PA14


title: WT_noPT_0min_4

description:
Library name: H27481-L1_S39_L002_R1_001
WT_noPT_0min_4.rpkm_0


title: RNA-Seq of HRECs transduced with a LRP5-targeting shRNA lentivirus-replication 2

city: Chengdu

first: Shujin

last: Li

state: Sichuan

address: Chengdu, Sichuan province, China, first-ring road, No.34

country: China

institute: Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences

description: Library name: LRP5_KD_2

data_processing:
Data quality control was performed using fastp to remove reads with adapters.Paired reads were removed under the following conditions:when the the number of N in any sequencing read exceeded 10%of the length of that read,and when any sequencing read contained low-quality bases(Q<=20) exceeding 50% of the length of that read.Subsequent analyses were based on clean reads. The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index,and clean reads were aligned to the reference genome. Gene expression levels were quantified using feature Counts to calculate gene alignment statistics. Subsequently, FPKM (Fragments Per Kilobase Million) values for each gene were computed based on gene length. FPKM is currently the most used method for estimating gene expression levels.
Assembly: GRCh38.109.
Supplementary files format and content: FPKM for beta-catenin signaling.txt contains fpkm values for each gene of biosample SAMN50221966-SAMN50221980.
Supplementary files format and content: KIF11_KD_symbol_fpkm.txt contains fpkm values for each gene of biosample SAMN50221981-SAMN50221986.
Supplementary files format and content: PRDX1_KD_symbol_fpkm.txt contains fpkm values for each gene of biosample SAMN50221987-SAMN50221992.

molecule: polyA RNA

source_name: retina

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNAqualitywas determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDropTechnologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
mRNA is enriched by Oligo(dT) magnetic beads to selectively capture mRNAs with poly(A) tails. A fragmentation buffer is then added to shear the RNA into short fragments. Using these fragments as a template, first-strand cDNA is synthesized with random hexamers. Subsequently, a buffer, dNTPs, and DNA polymerase are added for second-strand cDNA synthesis, and the resulting double-stranded cDNA is purified using DNA purification magnetic beads. The purified double-stranded cDNA then undergoes end repair, A-tailing, and adapter ligation. Following these steps, DNA purification magnetic beads are used for fragment size selection, and the final cDNA library is obtained through PCR enrichment. The experimental workflow is shown in the figure below.

value: retina


title: cpxS_CAR_0min_4

description:
Library name: H27480-L1_S38_L002_R1_001
cpxS_CAR_0min_4.rpkm_0

value: CpxS T163P mutant


title: Thy4-gdTCR

description:
10X Genomics
Thy4_gdTCR


title: si-dnmt, biological replicate 3

description: Library name: E3

value: si-dnmt


title: Thy2-Sur

description:
10X Genomics
Thy2_barcodes.tsv.gz
Thy2_features.tsv.gz
Thy2_matrix.mtx.gz
Thy2_ADT


title: Thy4-5GE

description:
10X Genomics
Thy4_barcodes.tsv.gz
Thy4_features.tsv.gz
Thy4_matrix.mtx.gz
Thy4_GEX


title: si-dnmt, biological replicate 4

description: Library name: E4


title: WT_CAR_0min_4

description:
Library name: H27479-L1_S37_L002_R1_001
WT_CAR_0min_4.rpkm_0

value: PA14 wildtype

value: CAR


title: Thy4-abTCR

description:
10X Genomics
Thy4_abTCR

value: thymus


title: si-dnmt, biological replicate 1

description: Library name: E1


title: SH Cell_P35 VC_rep3

type: RNA

city: Subang Jaya

first: Bin Seng

last: Low

state: Selangor

address: No 1, Jalan Taylor's,

department: School of Medicine

country: Malaysia

institute: Taylor's University

description: Gene expression data from SH-SY5Y human neuroblastoma cells with vehicle control at passage 33

hyb_protocol: The single-stranded sense cDNA synthesis which was later fragmented, labeled, and hybridized toHuman Clariom S Array for 16 hours at 45°C with rotation at 60 rpm. GeneChips were washed and stained using the FS450_0007 fluidics protocol.

scan_protocol: GeneChips were scanned using an Applied Biosystems™ GeneChip™ Scanner 3000 7G..

data_processing: The data were imported to Transcriptome Analysis Console (TAC, Affymetrix, Inc., U.S.) for gene expression analysis.

label: biotin

source_name: SH-SY5Y human neuroblastoma cells with VC at passage 35

label_protocol: Biotinylated cDNA were preparedfrom 100 ng total RNA according to the standard Affymetrix protocol (Manual Target Preparation for GeneChip™ Whole Transcript (WT)  Expression Arrays, 2020, Thermo Fisher Scientific Inc.).

growth_protocol: The SH-SY5Y human neuroblastoma cell line (purchased from ATCC, CRL-2266™, Manassas, Virginia, U.S.), cultured in DMEM with 1% penicillin-streptomycin and 15% (v/v) heat-inactivated FBS, and incubated in a 37 ºC incubator with 5% CO2 and 95% humidity

extract_protocol: Total RNA extraction was performed according to the manufacturer’s protocol (Promega Corporation 2021).

treatment_protocol: SH-SY5Y cells induced by the differentiation agent, atRA over 96 hours of treatment with the concentrations of bioactive compound at 15 μM was administered

value: SH-SY5Y human neuroblastoma cells


title: Thy2-5GE

description:
10X Genomics
Thy2_barcodes.tsv.gz
Thy2_features.tsv.gz
Thy2_matrix.mtx.gz
Thy2_GEX

value: 4 day


title: si-control + TNF + IFN, biological replicate 4

description: Library name: D4

value: Veravec

value: si-control + TNF + IFN


title: WT_noPT_60min_3

description:
Library name: H27477-L1_S35_L002_R1_001
WT_noPT_60min_3.rpkm_0

value: Control


title: SH Cell_P34 VC_rep2

source_name: SH-SY5Y human neuroblastoma cells with VC at passage 34


title: si-control + TNF + IFN, biological replicate 3

description: Library name: D3

value: lung endothelial cells


title: cpxS_CAR_60min_3

description:
Library name: H27476-L1_S34_L002_R1_001
cpxS_CAR_60min_3.rpkm_0


title: SH Cell_P35 15EN_rep3

description: Gene expression data from SH-SY5Y human neuroblastoma cells treated with 15EN at passage 33

source_name: SH-SY5Y human neuroblastoma cells treated with 15EN at passage 35


title: Thy2-gdTCR

description:
10X Genomics
Thy2_gdTCR

value: M


title: Thy2-abTCR

description:
10X Genomics
Thy2_abTCR

value: abTCR VDJ


title: si-control + TNF + IFN, biological replicate 2

description: Library name: D2


title: cpxS_noPT_60min_3

description:
Library name: H27478-L1_S36_L002_R1_001
cpxS_noPT_60min_3.rpkm_0


title: WT_CAR_60min_3

description:
Library name: H27475-L1_S33_L002_R1_001
WT_CAR_60min_3.rpkm_0


title: SH Cell_P33 VC_rep1

source_name: SH-SY5Y human neuroblastoma cells with VC at passage 33


title: SH Cell_P33 15EN_rep1

source_name: SH-SY5Y human neuroblastoma cells treated with 15EN at passage 33


title: K562 + R-Exo4

city: Guangzhou

first: Fei

state: Guangdong

address: 135 Xingang West Road, Haizhu District

institute: Sun Yat-sen University

description: Library name: REXO4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: human NCBI genome build 36
Supplementary files format and content: Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: Peripheral blood

growth_protocol: CML cells were treated with or without Exo and cultured in 10%FBS RPMI medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: CML cells were treated with or without Exo for 48h

value: Peripheral blood

value: Chronic myeloid leukemia cells

value: R-Exo treatment


title: cpxS_noPT_30min_3

description:
Library name: H27474-L1_S32_L002_R1_001
cpxS_noPT_30min_3.rpkm_0

value: Pseudomonas aeruginosa PA14


title: HD3, DIF-WT, CTCT, rep1

city: Mexico City

first: Gustavo

last: Tapia

state: CDMX

address: Cto. Exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

description: Library name: Sample 3

library_source: genomic

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trim Galore
Trimmed sequencing reads were mapped to GRCg6a/galGal6 using Bowtie2
Read filtering and peak calling were performed using NGSUtils and MACS2, respectively
Assembly: galGal6
Supplementary files format and content: Peaks in a tabular-delimited file

molecule: genomic DNA

organism: Gallus gallus

source_name: Hematopoietic

growth_protocol: HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cells were crosslinked with 1% paraformaldehyde for 10 minutes and quenched with 0.125M Glycine. Nuclei were extracted and lysed, and chromatin was sonicated in a Covaris M220 sonicator to an average of 300 bp fragments. Immunoprecipitation was performed overnight with the CTCF antibody at 4°C. Immunoprecipitated chromatin was the incubated with magnetic beads, washed, TAGmented with Tn5 transposase and eluted from beads. Then, chromatin was decrosslinked and DNA was purified using MinElute kit (Qiagen)
Preparation of ChIPmentation libraries was performed as described for ATAC-seq assays in Buenrostro et al., (2015)

treatment_protocol: Cells were treated with H7 (20 μM, Sigma) and 10 mM Hepes pH 8.0 in HD3 cell medium in 1% CO2 athmosphere at 42°C for 24 h

value: Hematopoietic

value: Chicken erythroblasts

value: 20μM H7 (Sigma), 10mM Hepes pH 8, 42°C, 1% CO2


title: WT_noPT_30min_3

description:
Library name: H27473-L1_S31_L002_R1_001
WT_noPT_30min_3.rpkm_0

value: PA14 wildtype


title: K562 + R-Exo3

description: Library name: REXO3


title: HD3, DIF-WT, CTCT, rep2

description: Library name: Sample 4

value: 20μM H7 (Sigma), 10mM Hepes pH 8, 42°C, 1% CO3


title: K562 + R-Exo2

description: Library name: REXO2


title: si-control + TNF + IFN, biological replicate 1

description: Library name: D1


title: cpxS_CAR_30min_3

description:
Library name: H27472-L1_S30_L002_R1_001
cpxS_CAR_30min_3.rpkm_0

value: CpxS T163P mutant

value: CAR


title: si-control + IFN, biological replicate 3

description: Library name: C3

value: Veravec

value: si-control + IFN


title: HD3, WT, CTCF, rep2

description: Library name: Sample 2


title: HD3, WT, CTCF, rep1

description: Library name: Sample 1


title: BMD STING-seq full GDO 6

city: Toronto

first: John

middle: A

last: Morris

state: Ontario

address: 160 College Street

department: Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

description: Library name: Full-GDO-6

data_processing:
We generated UMI count matrices for all single-cell sequencing libraries using 10X Cell Ranger v8.0.1. We produced cDNA UMI count matrices aligned to hg38 (refdata-gex-GRCh38-2024-A), gRNA UMI count matrices, and hashtag UMI count matrices for the pilot and full experiments.
Assembly: hg38
Supplementary files format and content: UMI count matrices before quality control

source_name: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2

extract_protocol:
We performed single-cell RNA-seq using 10X Genomics Chromium Next GEM Single Cell 5′ Reagent Kits v2 (dual index) on cells detached from culture plates. We labeled cells from each state with different hashtag antibodies targeting cell surface proteins (BioLegend TotalSeq 394661, 394663, 394665, 394667) following the manufacturer’s recommendations. We then pooled equal numbers of cells from each state into a single sample and aliquoted them into as many reactions as needed to capture approximately 200,000 cells in total. We used 2 microfluidics channels for the pilot experiment and 6 channels for the full experiment.
We constructed sequencing libraries for the three different barcoded nucleic acids for each reaction according to 10X Genomics protocols and pooled them disproportionately so that mRNA-derived cDNA libraries represented ~90% of the sample, with gRNA and hashtag libraries comprising the remaining 10%. We sequenced the pooled library to a depth of approximately 20,000 mRNA/cDNA reads per cell on an Illumina NextSeq 500 sequencing platform for the pilot experiment and on an Illumina NovaSeq X for the full experiment.


title: si-control + IFN, biological replicate 2

description: Library name: C2


title: si-control + IFN, biological replicate 4

description: Library name: C4


title: WT_CAR_30min_3

description:
Library name: H27471-L1_S29_L002_R1_001
WT_CAR_30min_3.rpkm_0


title: K562 + R-Exo1

description: Library name: REXO1


title: BMD STING-seq full HTO 6

description: Library name: Full-HTO-6

data_processing:
We generated UMI count matrices for all single-cell sequencing libraries using 10X Cell Ranger v8.0.1. We produced cDNA UMI count matrices aligned to hg38 (refdata-gex-GRCh38-2024-A), gRNA UMI count matrices, and hashtag UMI count matrices for the pilot and full experiments.
Assembly: hg38
Supplementary files format and content: UMI count matrices before quality control
Library strategy: CITE-seq

value: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2


title: si-control + IFN, biological replicate 1

description: Library name: C1

value: lung endothelial cells


title: cpxS_noPT_0min_3

description:
Library name: H27470-L1_S28_L002_R1_001
cpxS_noPT_0min_3.rpkm_0

value: Control


title: K562 + S-Exo2

description: Library name: SEXO2

value: S-Exo treatment


title: si-control + TNF, biological replicate 4

description: Library name: B4

value: si-control + TNF


title: WT_noPT_0min_3

description:
Library name: H27469-L1_S27_L002_R1_001
WT_noPT_0min_3.rpkm_0


title: K562 + S-Exo1

description: Library name: SEXO1

value: Peripheral blood

value: Chronic myeloid leukemia cells


title: si-control + TNF, biological replicate 3

description: Library name: B3


title: BMD STING-seq full GDO 5

description: Library name: Full-GDO-5


title: K562 + H-Exo3

description: Library name: HEXO3

value: H-Exo treatment


title: SH Cell_P34 15EN_rep2

source_name: SH-SY5Y human neuroblastoma cells treated with 15EN at passage 34

value: SH-SY5Y human neuroblastoma cells


title: si-control + TNF, biological replicate 2

description: Library name: B2


title: BMD STING-seq full cDNA 6

description: Library name: Full-cDNA-6


title: BMD STING-seq full HTO 5

description: Library name: Full-HTO-5


title: WT_CAR_0min_3

description:
Library name: H27467-L1_S25_L002_R1_001
WT_CAR_0min_3.rpkm_0

value: Pseudomonas aeruginosa PA14


title: cpxS_noPT_60min_2

description:
Library name: H27466-L1_S24_L001_R1_001
cpxS_noPT_60min_2.rpkm_0


title: si-dnmt, biological replicate 2

description: Library name: E2

value: si-dnmt


title: K562 + H-Exo1

description: Library name: HEXO1


title: si-control, biological replicate 4

description: Library name: A4

value: si-control


title: si-control + TNF, biological replicate 1

description: Library name: B1


title: BMD STING-seq full GDO 4

description: Library name: Full-GDO-4


title: WT_noPT_60min_2

description:
Library name: H27465-L1_S23_L001_R1_001
WT_noPT_60min_2.rpkm_0

value: PA14 wildtype


title: cpxS_CAR_0min_3

description:
Library name: H27468-L1_S26_L002_R1_001
cpxS_CAR_0min_3.rpkm_0

value: CpxS T163P mutant


title: K562 + H-Exo2

description: Library name: HEXO2


title: si-control, biological replicate 3

description: Library name: A3


title: K562 NC2

description: Library name: CTL2

value: WT

value: NC


title: cpxS_CAR_60min_2

description:
Library name: H27464-L1_S22_L001_R1_001
cpxS_CAR_60min_2.rpkm_0

value: CAR


title: K562 NC3

description: Library name: CTL3


title: si-control, biological replicate 2

description: Library name: A2

value: Veravec


title: BMD STING-seq full cDNA 4

description: Library name: Full-cDNA-4

value: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2


title: K562 NC1

description: Library name: CTL1


title: WT_CAR_60min_2

description:
Library name: H27463-L1_S21_L001_R1_001
WT_CAR_60min_2.rpkm_0


title: BMD STING-seq full GDO 3

description: Library name: Full-GDO-3


title: BMD STING-seq full HTO 4

description: Library name: Full-HTO-4


title: WT_noPT_30min_2

description:
Library name: H27461-L1_S19_L001_R1_001
WT_noPT_30min_2.rpkm_0

value: Control


title: PBMC, CMS_3

city: Palakkad

first: Jagadeesh

last: Bayry

state: Kerela

address: IIT Palakkad

country: India

institute: IIT palakkad

description: Library name: Sample 6

data_processing:
DESeq2 package (DESeq2_1.42.1) is used to determine the proportion of differentially expressed genes between two conditions.We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function), with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustement, and genes with at least 10 reads in at least 3 different samples). Following the package recommendations, we used the Wald test with the contrast function and the Benjamini-Hochberg FDR control procedure to identify the differentially expressed genes. R scripts and parameters are availables on the plateform, https://github.com/GENOM-IC-Cochin/RNA-Seq_analysis
Assembly: Ensembl 109
Supplementary files format and content: all_samples.csv

source_name: PBMC

extract_protocol:
Buffy coats of healthy donors obtained from Etablissement Français du Sang, Rungis, France (Institut National de la Santé et de la Recherche-EFS ethical committee convention 18/EFS/033) were subjected  to Ficoll density gradient centrifugation to isolate PBMCs. Monocytes were positively selected using CD14 Microbeads (Miltenyi Biotec) and cultured in the presence of granulocyte-macrophage colonystimulating factor (GM-CSF, 1000 IU/10^6  cells) (Miltenyi Biotec) and IL-4 (500 IU/10^6  cells) (Miltenyi Biotec) in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin135 streptomycin for 5 days to generate immature DCs.
Fastq files were then aligned using STAR algorithm (version 2.7.11b), on the Ensembl release 109 reference.Reads were then count using RSEM (v1.3.3) and the statistical analyses on the read counts were performed with R (version 4.3.1)

value: PBMC

value: Dendritic cells

value: Carbohydrate fatty acid monosulphate ester

tag: batch


title: PBMC, CMS_1

description: Library name: Sample 4


title: low_stiffness_0_2kPa

city: Rochester

first: Schwarz

last: Edward

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center

description: Library name: low_stiffness_0_2kPa

data_processing:
Demultiplexing with bcl2fastq v2.20.0
Quality control and adapter trimming using FastP v0.23.1
Alignment to reference genome using STAR v2.7.9a
Gene-level read quantification using featureCounts (Subread v2.0.1)
Differential expression analysis with DESeq2 v1.34.0
Assembly: Mouse: GRCm39 / GENCODE M31
Supplementary files format and content: Unsorted BAM files (from STAR alignment) Gene count matrix (raw counts from featureCounts) Normalized expression matrix (e.g., rLog or vst from DESeq2) Plots and figures: PCA plots, heatmaps, volcano plots, dot plots (in PDF or image format) GO enrichment result tables (from EnrichR, usually CSV or Excel)

source_name: ankle synovium

growth_protocol: FACS-purified tdTomato⁺ cells from Efhd1CreER; Ai9 mice were cultured in complete DMEM supplemented with F12 nutrient mix. Cells were maintained under standard conditions (37 °C, 5% CO₂), with media changes every 3 days unless otherwise specified.

extract_protocol:
Qiagen RNeasy Plus Kit
Illumina TruSeq Stranded mRNA

treatment_protocol: Synovial tissues were dissected from mouse ankle joints under a surgical microscope and digested in 1.5 mL enzyme mix containing 400 µg/mL Collagenase IV, 400 µg/mL Liberase, and 400 µg/mL DNase I in DMEM (serum-free). Tissues (up to 2 synovia/tube) were incubated at 37 °C for 30–35 min with vigorous vortexing at 0, 15, and 30 minutes. Digestion was stopped by adding 2 mL FACS buffer (PBS with 2% FBS, 5 mM EDTA), filtered through a 30 µm MACS SmartStrainer, and mechanically disrupted. Cells were pelleted (1000 rpm, 5 min, 4 °C), red blood cells lysed using ammonium chloride, and washed again in FACS buffer. Resulting single-cell suspensions processed for FACS of tdTomato+ Efhd1 expressing cells.

value: ankle synovium

value: telocytes

value: Efhd1CreER; Ai9

value: cultured on collagen-coated CytoSoft® plates of varying stiffness (0.2kPa)


title: BMD STING-seq full HTO 3

description: Library name: Full-HTO-3


title: BMD STING-seq full cDNA 3

description: Library name: Full-cDNA-3


description:
Library name: 09/06/24 Efhd1-tdT knee synovial scRNA seq L006
Samples demultiplexed using Cell Ranger mkfastq.gz and analyzed with Cell Ranger count v8.0.0. Gene expression quantified with 10X Genomics Single Cell 3' v3 chemistry, alignment to GRCh38 or GRCm39 reference genome. Sequencing saturation: 91.3%, Median genes per cell: 3,024, Estimated cells: 5,259.

data_processing:
cellranger-8.0.0
Seurat version 5.0.1
Assembly: Mouse: GRCm39 / GENCODE M31
Supplementary files format and content: matrix.mtx.gz; features.tsv; barcodes.tsv

source_name: knee synovium

extract_protocol:
Qiagen RNeasy Plus Kit
10x Genomics Chromium Single Cell 3’ v3.1 Kit

treatment_protocol: Synovial tissues were dissected from mouse knee joints and digested in 1.5 mL enzyme mix containing Collagenase IV, Liberase, and DNase I in serum-free DMEM. Tissues were incubated at 37 °C for 30–35 minutes with intermittent vortexing. Digestion was stopped by adding FACS buffer (PBS with 2% FBS and 5 mM EDTA). The suspension was filtered through a 30 µm strainer and mechanically disrupted. Cells were centrifuged, red blood cells lysed with ammonium chloride, washed, and resuspended in FACS buffer for downstream processing.

value: knee synovium


title: si-control, biological replicate 1

description: Library name: A1

value: lung endothelial cells

value: si-control


title: mid_stiffness_8kPa

description: Library name: mid_stiffness_8kPa

value: cultured on collagen-coated CytoSoft® plates of varying stiffness (8 kPa)


title: WT_CAR_30min_2

description:
Library name: H27459-L1_S17_L001_R1_001
WT_CAR_30min_2.rpkm_0

value: Pseudomonas aeruginosa PA14

value: PA14 wildtype


title: cpxS_CAR_30min_2

description:
Library name: H27460-L1_S18_L001_R1_001
cpxS_CAR_30min_2.rpkm_0

value: CpxS T163P mutant

value: CAR


title: PBMC, CMS_2

description: Library name: Sample 5


title: PBMC, control_3

description: Library name: Sample 3

value: No treatment


title: BMD STING-seq full GDO 2

description: Library name: Full-GDO-2

value: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2


title: high_stiffness_64kPa

description: Library name: high_stiffness_64kPa

value: cultured on collagen-coated CytoSoft® plates of varying stiffness (64 kPa)


title: cpxS_noPT_0min_2

description:
Library name: H27458-L1_S16_L001_R1_001
cpxS_noPT_0min_2.rpkm_0

value: Control


title: BMD STING-seq full HTO 2

description: Library name: Full-HTO-2


title: PBMC, control_2

description: Library name: Sample 2

value: PBMC

value: Dendritic cells


title: IEC - Transgenic - DSS - Replicate 6

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description: Library name: DSS_Seq2_29

data_processing:
The two sets of samples (Casp3/7 villin mice colon tissue and Casp3/7 villin mice colon IECs) were sequenced using paired end Illumina sequencing (150 nt). The set of Casp3/7 villin mice colon IEC samples (4 WT - control, 4 transgenic - control, 6 WT - DSS, 6 transgenic - DSS) was processed by trimming the reads using Trimmomatic (v0.39) with the following parameter settings: ILLUMINACLIP:"adapters.fa":3:30:10:2:True, SLIDINGWINDOW:5:20, MINLEN:36. The adapter sequences in the fasta file are F: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT and R:GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATGACTATCTCGTATGCCGTCTTCTGCTTG.
Read mapping was performed using STAR  (v2.7.8a) on the GRCm39 mouse genome. Only uniquely mapped reads were kept by setting --outFilterMultimapNmax 1.
BAM files were read into an R (v4.4) environment and a count table was made using the summarizeOverlaps function (mode = "Union") of the GenomicAlignments  package and the GRCm39 gene annotation of Ensembl version 106. One WT – DSS and one transgenic – DSS (DSS_Seq1_12 and DSS_Seq1_15) sample were excluded based on principal component analysis.
The set of Casp3/7 villin mice colon tissue samples (5 Day 0 - WT, 6 Day 0 - transgenic, 5 Day 8 - WT, 6 Day 8 - transgenic) were processed similarly with the following changes: the trimming step was omitted and DESeq2 analysis was done per time point rather than on all samples at once.
Assembly: GRCm39
Supplementary files format and content: count tables

source_name: intestinal epithelial cells

growth_protocol: Mice were bred in-house using heterozygous breeding pairs to obtain wild-type littermate controls in the VIB Center for Inflammation Research under specific pathogen-free (SPF) conditions. C57BL6/N wildtype mice were purchased from JANVIER LABS and acclimated for at least 1 week before the start of any experiment. All experiments on mice were conducted according to institutional, national, and European animal regulations. Animal protocols were approved by the ethics committee of Ghent University, (EC_LP0024_PVA_2022, EC2025-003). Sex-matched and age-matched co-housed littermates were used through the entire study, except further indicated.

extract_protocol:
For colon tissue RNA extraction, 5mm distal colon was placed in a 2 ml microcentrifuge tube containing one stainless steel bead (5mm mean diameter), add 150 μl Buffer RLT per tube and operate the TissueLyser II for 5 min at 20 Hz to generate tissue homogenate. Keep on ice for 10mins, centrifuge at 12000 g for 10 min at 4 °C, collect supernatant. For IECs, directly lysis with 150 μl Buffer RLT. Next, total RNA was isolated by using the RNeasy Micro Kit (74004, Qiagen) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. 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.

treatment_protocol: DSS treatment pertaining to the colon tissue samples was performed by adding 3% DSS in the drinking water for 5 days followed by 3 days of no DSS drinking water. The DSS treatment pertaining to the IEC samples was performed by adding 3% DSS for 3 days to the drinking water of the mice.

value: intestinal epithelial cells

value: Casp3/7 Tg

value: DSS


title: PBMC, control_1

description: Library name: Sample 1


title: IEC - Transgenic - DSS - Replicate 5

description: Library name: DSS_Seq2_27


title: BMD STING-seq full cDNA 2

description: Library name: Full-cDNA-2


title: K562 + S-Exo3

description: Library name: SEXO3

value: Peripheral blood

value: Chronic myeloid leukemia cells

value: S-Exo treatment


title: cpxS_CAR_0min_2

description:
Library name: H27456-L1_S14_L001_R1_001
cpxS_CAR_0min_2.rpkm_0

source_name: Pseudomonas aeruginosa PA14


title: WT_noPT_0min_2

description:
Library name: H27457-L1_S15_L001_R1_001
WT_noPT_0min_2.rpkm_0


title: WT_CAR_0min_2

description:
Library name: H27455-L1_S13_L001_R1_001
WT_CAR_0min_2.rpkm_0


title: IEC - Wild_type - DSS - Replicate 6

description: Library name: DSS_Seq2_22

value: Casp3/7 WT


title: OT1 CD8+ T cell, OE PTMA, stimulate for 48h,rep3

city: shanghai

first: keling

last: huang

address: south chongqing road

institute: shanghaijiaotong university

description: Library name: Pt_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
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 FPKM values for each Sample

source_name: CD8+ T cell

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 Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8+ T cell

value: WT

value: OVA peptide stimulate for 48h


title: BMD STING-seq full HTO 1

description: Library name: Full-HTO-1


title: OT1 CD8+ T cell, OE PTMA, stimulate for 48h,rep2

description: Library name: Pt_2


title: IEC - Wild_type - DSS - Replicate 5

description: Library name: DSS_Seq2_21


title: BMD STING-seq full GDO 1

description: Library name: Full-GDO-1


title: OT1 CD8+ T cell, OE PTMA, stimulate for 48h,rep1

description: Library name: Pt_1


title: cpxS_noPT_60min_1

description:
Library name: H27454-L1_S12_L001_R1_001
cpxS_noPT_60min_1.rpkm_0

value: Pseudomonas aeruginosa PA14

value: CpxS T163P mutant


title: IEC - Transgenic - DSS - Replicate 4

description: Library name: DSS_Seq1_18


title: WT_noPT_60min_1

description:
Library name: H27453-L1_S11_L001_R1_001
WT_noPT_60min_1.rpkm_0

value: PA14 wildtype


title: BMD STING-seq full cDNA 1

description: Library name: Full-cDNA-1

value: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2


title: HepG2/C3A_PFOS_3

city: Gainesville

first: Chanhee

last: Kim

state: Florida

address: 2187 Mowry Road

department: Physiological sciences

institute: University of Florida

description: Library name: Sample 6

data_processing:
After data acquisition (raw fastq.gz files), read quality were checked using FASTQC tools. A Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MaGeCK) was then used to demultiplex raw fastq data files, which were further processed to generate reads containing only the unique 20 bp guide sequences. The resulting read counts from different samples of PFOS exposure and corresponding control were then normalized to adjust for the effect of library sizes and read count distributions.
Assembly: GRCh38
Supplementary files format and content: .xlsx / individual sgRNA counts of each sample condition (not normalized)
Library strategy: CRISPR Screen

source_name: Liver

growth_protocol: Grow HepG2/C3A cells in 37C in T225 flasks for each sample condition

extract_protocol:
Genomic DNA was extracted from 1.6x106 cells (400X coverage) of each sample using the Quick-DNA Midiprep Plus Kit (ZYMO Research) following the manufacturer’s protocols
PCR amplicons for generating NGS Illumina sequencing library using the pairs of universal CRISPR-FOR1 forward primer and various CRISPR-REV# reverse primers (#: 1 to 48) specific for each sample for multiplexing.

treatment_protocol: control vs. PFOS treatment at 192 uM  for 10 doubling times (=18 days)

value: Liver

value: epithelial-like

value: mutant pool

value: PFOS 192 uM


title: OT1 CD8+ T cell, OE vector, stimulate for 48h,rep3

description: Library name: CTR_3


title: IEC - Transgenic - DSS - Replicate 3

description: Library name: DSS_Seq1_17

value: intestinal epithelial cells

value: Casp3/7 Tg


title: HepG2/C3A_PFOS_2

description: Library name: Sample 5


title: IEC - Transgenic - DSS - Replicate 2

description: Library name: DSS_Seq1_16

value: DSS


title: cpxS_CAR_60min_1

description:
Library name: H27452-L1_S10_L001_R1_001
cpxS_CAR_60min_1.rpkm_0

value: CAR


title: OT1 CD8+ T cell, OE vector, stimulate for 48h,rep2

description: Library name: CTR_2


title: BMD STING-seq full cDNA 5

description: Library name: Full-cDNA-5


title: WT_CAR_60min_1

description:
Library name: H27451-L1_S9_L001_R1_001
WT_CAR_60min_1.rpkm_0


title: HepG2/C3A_PFOS_1

description: Library name: Sample 4


title: OT1 CD8+ T cell, OE vector, stimulate for 48h,rep1

description: Library name: CTR_1


title: IEC - Transgenic - DSS - Replicate 1

description: Library name: DSS_Seq1_15


title: HepG2/C3A_Control_3

description: Library name: Sample 3

value: wild-type

value: control


title: cpxS_noPT_30min_1

description:
Library name: H27450-L1_S8_L001_R1_001
cpxS_noPT_30min_1.rpkm_0

value: Control


title: WT_noPT_30min_1

description:
Library name: H27449-L1_S7_L001_R1_001
WT_noPT_30min_1.rpkm_0


title: Raw264.7 cell, treated with HE4-Fc protein [L1MKK]

first: Bo

last: Zeng

address: No.4, Section 2, North Jianshe Road, Chengdu

department: school of medicine

institute: University of Electronic Science and Technology of China

description:
Library name: HE4-Fc
performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)

data_processing:
The sequencing data were analyzed via an online platform (https://cloud.majorbio.com/).
Assembly: Mus musculus
Supplementary files format and content: TPM

source_name: macrophage

extract_protocol:
After washing twice with ice-cold PBS, total RNA was extracted and reverse-transcribed into cDNA.
Library construction and sequencing were conducted via the MGI DNBSEQ-T7 platform (MGI-Tech, Shenzhen, China) at Majorbio Biopharm Technology Co., Ltd. (Shanghai, China).

treatment_protocol: Raw264.7 cells were seeded in 6-well plates at a density of 5 × 105 cells/well and then stimulated with either HE4-Fc (20 μg/mL), IFN-γ (1 μg/mL), or HE4-Fc (1 μg/mL) plus IFN-γ (1 μg/mL) for 3 h.

value: macrophage

value: HE4-Fc protein

value: WT


title: HepG2/C3A_Control_2

description: Library name: Sample 2


title: cpxS_CAR_30min_1

description:
Library name: H27448-L1_S6_L001_R1_001
cpxS_CAR_30min_1.rpkm_0

value: Pseudomonas aeruginosa PA14

value: CpxS T163P mutant


title: IEC - Wild_type - DSS - Replicate 3

description: Library name: DSS_Seq1_13

value: Casp3/7 WT


title: Raw264.7 cell, treated with HE4-Fc plus IFN-γ (HE4-Fc : IFN-γ=1 : 1) [L1MKK]

description:
Library name: HF1
performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)

value: HE4-Fc plus IFN-γ (HE4-Fc :IFN-γ=1 :1)


title: IEC - Wild_type - DSS - Replicate 4

description: Library name: DSS_Seq1_14


title: cpxS_noPT_30min_2

description:
Library name: H27462-L1_S20_L001_R1_001
cpxS_noPT_30min_2.rpkm_0


title: HepG2/C3A_Control_1

description: Library name: Sample 1

value: Liver

value: epithelial-like


title: Raw264.7 cell, treated with IFN-γ [L1MKK]

description:
Library name: IFN-γ
performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)

value: IFN-γ


title: IEC - Wild_type - DSS - Replicate 2

description: Library name: DSS_Seq1_12

value: intestinal epithelial cells


title: MV-11

description:
10X Genomics
Thy9_abTCR

source_name: Vδ1 thymocytes

value: thymus

value: F

value: abTCR VDJ

value: 5 months


title: WT_CAR_30min_1

description:
Library name: H27447-L1_S5_L001_R1_001
WT_CAR_30min_1.rpkm_0

value: PA14 wildtype

value: CAR


title: Raw264.7 cell, treated with PBS [L1MKK]

description:
Library name: PBS
performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)

value: macrophage

value: PBS


title: MV-15

description:
10X Genomics
Thy9_gdTCR

value: gdTCR VDJ


title: MV-14

description:
10X Genomics
Thy6_gdTCR_rep2

value: 4 day


title: WT_noPT_0min_1

description:
Library name: H27445-L1_S3_L001_R1_001
WT_noPT_0min_1.rpkm_0

value: Pseudomonas aeruginosa PA14

value: Control


title: MV-10

description:
10X Genomics
Thy6_abTCR_rep2


title: IEC - Transgenic - Control - Replicate 4

description: Library name: DSS_Seq1_8

value: Casp3/7 Tg


title: Subcutaneous LLC tumors+con IgG-#1

description:
Library name: con_1
MGI DNBSEQ-T7 platform

data_processing:
Reads were processed using the dnbc4 tools v2.1.2 pipeline with default and recommended parameters. FASTOs generated from lllumina sequencing output were aligned to the mice genome, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMls and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v4.11) R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were rum with default parameters, unless specified otherwise. We first filtered the matrices to exclude low-quality cells using a standard panel of three quality criteria: (1) number of detected transcripts (number of unique molecular identifiers); (2) detected genes; and (3) percent of reads mapping to mitochondrial genes The expression of mitochondria genes was calculated using Percentage Feature Set function of the seurat package. The normalized data (Normalize Data function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying 'anchors’ between datasets using Find Integration Anchors and Integrate Data in the seurat package. Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
preprocessing of scRNA-seq data, integration, dimensionality reduction and clustering were performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)
Assembly: Mus musculus
Supplementary files format and content: .tsv and .mtx, respectively

source_name: tumor

extract_protocol:
Subcutaneous LLC tumors were harvested on the day after the last administration of the mAbs. Tissues were minced on ice and then digested at 37°C with a shaking speed of 50 rpm or 30 min. Cell suspensions were filtered through a 40-μm strainer, and the cell pellet was resuspended in red blood cell lysis solution and incubated on ice for 5 min. The cell pellet was washed and resuspended in PBS containing 0.5% FBS, followed by the evaluation of cell viability.
The samples were then sent to Majorbio Biopharm Technology Co., Ltd. (Shanghai, China), for further sequencing and bioinformatic analysis. Briefly, library construction was performed according to the manufacturer’s protocol (DNBelab C TaiM4 V3.0) and quantified via a high-sensitivity DNA chip on a Bioanalyzer 2100 and a Qubit high-sensitivity DNA assay (Thermo Fisher Scientific). Libraries were sequenced on the MGI DNBSEQ-T7 platform (MGI-Tech, Shenzhen, China).

value: tumor

value: LLC

value: female

value: wild-type

value: con IgG


title: Subcutaneous LLC tumors+con IgG-#2

description:
Library name: con_2
MGI DNBSEQ-T7 platform


title: Subcutaneous LLC tumors+con IgG-#3

description:
Library name: con_3
MGI DNBSEQ-T7 platform


title: cpxS_noPT_0min_1

description:
Library name: H27446-L1_S4_L001_R1_001
cpxS_noPT_0min_1.rpkm_0

data_processing:
Reads were trimmed with Trimmomatic (v0.39, settings phredThreshold=phred33, seedMismatches=2, palindromeClipThreshold=10, lengthMin=36).
The reference genome for UCBPP-PA14 was retrieved from GenBank (NCBI Reference Sequence NC_008463.1) and for the Cpx T163P mutant, the genome was adapted via a custom R script to include the mutation.
Reads were followingly mapped to the respective genomes using EDGEpro (v1.3.1), substituting the bundled Bowtie package with the newest available at the time of mapping (Bowtie2 v2.4.1).
Assembly: NCBI Reference Sequence NC_008463.1
Supplementary files format and content: Tab-delimited text file contains RPKMs for each sample.

value: CpxS T163P mutant


title: WT_CAR_0min_1

description:
Library name: H27443-L1_S1_L001_R1_001
WT_CAR_0min_1.rpkm_0


title: IEC - Transgenic - Control - Replicate 3

description: Library name: DSS_Seq1_7

value: intestinal epithelial cells


title: IEC - Transgenic - Control - Replicate 2

description: Library name: DSS_Seq1_6


title: cpxS_CAR_0min_1

description:
Library name: H27444-L1_S2_L001_R1_001
cpxS_CAR_0min_1.rpkm_0


title: IEC - Transgenic - Control - Replicate 1

description: Library name: DSS_Seq1_5


title: MV-13

description:
10X Genomics
Thy5_gdTCR

data_processing:
Sequences were deconvoluted using Cellranger software v.7.1 and imported into R. Initial QC and gene expression and clustering analysis was conducted using the standard Seurat v5 pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

value: thymus

value: F

value: 3 weeks


title: Subcutaneous LLC tumors+anti-HE4-#3

description:
Library name: aHE4_3
MGI DNBSEQ-T7 platform

value: anti-HE4 mAb


title: 10_SNU719-H2A.Z-B_ChIP

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 10_SNU719-H2AZ-B_ChiP_S10

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome and human gammaherpesvirus 4 (HHV4) NC_007605.1 genome assembly using bowtie2.
MACS2 software package was used to call peaks in pull-down samples compared to input samples.
Assembly: hg19 and NC_007605.1 version of EBV
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1) for both hg19 and NC_007605.1 version of EBV genome. Score represents the normalized coverage of DNA fragment at a given coordinate.

growth_protocol: RPMI1640 media supplemented with 10% fetal bovine serum, 1X Glutamax, and 100 μg/ml streptomycin, and 100U/ml penicillin, cells were incubated at 37°C with 5% CO2

extract_protocol:
fixed with 1% formaldehyde for 15 min and fragmented using Covaris ME220
Libraries for sequencing were made using the NEBNext Ultra II DNA Library Prep Kit. Libraries were amplified using 10 cycles on the thermocycler. Post amplication libraries were size selected at 250-250bp in length using AMPure XP beads from Beckman Coulter.

value: Gastric Cancer cell line

tag: chip antibody


title: IEC - Wild_type - Control - Replicate 4

description: Library name: DSS_Seq1_4

value: Casp3/7 WT


title: MV-9

description:
10X Genomics
Thy5_abTCR

value: abTCR VDJ


title: 9_SNU719-H2A.Z-A_ChIP

description: Library name: 9_SNU719-H2AZ-A_ChiP_S9


title: MV-16

description:
10X Genomics
Thy10_gdTCR

value: M

value: gdTCR VDJ

value: 5 days


title: 8_SNU719-INPUT_ChIP

description: Library name: 8_SNU719-INPUT_ChiP_S8


title: IEC - Wild_type - DSS - Replicate 1

description: Library name: DSS_Seq1_11

value: DSS


title: Subcutaneous LLC tumors+anti-HE4-#1

description:
Library name: aHE4_1
MGI DNBSEQ-T7 platform

value: tumor

value: LLC


title: MV-12

description:
10X Genomics
Thy10_abTCR


title: IEC - Wild_type - Control - Replicate 3

description: Library name: DSS_Seq1_3

value: Control


title: Subcutaneous LLC tumors+anti-HE4-#2

description:
Library name: aHE4_2
MGI DNBSEQ-T7 platform

value: female

value: wild-type


title: Raw264.7 cell, treated with HE4-Fc protein

description:
Library name: HE4-Fc
performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)

data_processing:
The sequencing data were analyzed via an online platform (https://cloud.majorbio.com/).
Assembly: Mus musculus
Supplementary files format and content: .fastq

treatment_protocol: Raw264.7 cells were seeded in 6-well plates at a density of 5 × 105 cells/well and then stimulated with either HE4-Fc (20 μg/mL) or IFN-γ (100 ng/mL) for 3 h.

value: macrophage

value: HE4-Fc protein

value: WT


title: IEC - Wild_type - Control - Replicate 2

description: Library name: DSS_Seq1_2

value: intestinal epithelial cells


title: 7_SNU719-EBNA1-B_ChIP

description: Library name: 7_SNU719-EBNA1-B_ChiP_S7


title: Raw264.7 cell, treated with Fc protein

description:
Library name: Fc
performed by Majorbio Biopharm Technology Co., Ltd. (Shanghai, China)

value: Fc protein


title: IEC - Wild_type - Control - Replicate 1

description: Library name: DSS_Seq1_1


title: MV-3

description:
10X Genomics
Thy9_barcodes.tsv.gz
Thy9_features.tsv.gz
Thy9_matrix.mtx.gz
Thy9_GEX

value: thymus

value: F

value: gene expression

value: 5 months


title: Tissue - Tg - Day 8 - Replicate 5

description: Library name: DSS11_48

source_name: colon tissue

value: colon tissue

value: Casp3/7 Tg


title: 6_SNU719-EBNA1-A_ChIP

description: Library name: 6_SNU719-EBNA1-A_ChiP_S6

value: Gastric Cancer cell line


title: 5_Mutu1-H2A.Z-B_ChIP

description: Library name: 5_Mutu1-H2AZ-B_ChiP_S5

value: Burkitt's lymphomacell line


title: Raw264.7 cell, treated with IFN-γ

value: IFN-γ


title: Raw264.7 cell, treated with PBS

value: PBS


title: Tissue - Tg - Day 8 - Replicate 4

description: Library name: DSS11_47

value: DSS


title: 4_Mutu1-H2A.Z-A_ChIP

description: Library name: 4_Mutu1-H2AZ-A_ChiP_S4


title: MV-7

description:
10X Genomics
Thy9_barcodes.tsv.gz
Thy9_features.tsv.gz
Thy9_matrix.mtx.gz
Thy9_ADT

value: ADT


title: MV-6

description:
10X Genomics
Thy6-2_barcodes.tsv.gz
Thy6-2_features.tsv.gz
Thy6-2_matrix.mtx.gz
Thy6_ADT_rep2

value: 4 day


title: 2_Mutu1-EBNA1-B_ChIP

description: Library name: 2_Mutu1-EBNA1-B_ChiP_S2


title: Tissue - WT - Day 8 - Replicate 6

description: Library name: DSS11_44

value: Casp3/7 WT


title: MV-1

description:
10X Genomics
Thy5_barcodes.tsv.gz
Thy5_features.tsv.gz
Thy5_matrix.mtx.gz
Thy5_GEX

value: 3 weeks


title: MV-5

description:
10X Genomics
Thy5_barcodes.tsv.gz
Thy5_features.tsv.gz
Thy5_matrix.mtx.gz
Thy5_ADT


title: 1_Mutu1-EBNA1-A_ChIP

description: Library name: 1_Mutu1-EBNA1-A_ChiP_S1


title: Tissue - WT - Day 8 - Replicate 5

description: Library name: DSS11_43


title: TIA 3d 2

city: München

first: Gemma

last: Llovera

address: Feodor-Lynen-Straße 17

institute: Institut für Schlaganfall- und Demenzforschung (ISD)

description: TIA 3d 2

hyb_protocol: The final hybridization reaction will contain the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet. Incubate hybridization assays for at least 12 hours at 65°C. Hybridizations should be left at 65°C until ready for processing.

scan_protocol: nCounter® SPRINT Profiler

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA)
Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane.

label: codeset probes

source_name: microglia

extract_protocol: Microglial total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied biosystems #KIT0204)

treatment_protocol: Mice were perfused transcardially with ice-cold saline containing Heparin (2U/mL). Brains were placed in HBSS (w/divalent cations Ca2+ and Mg2+) supplemented with actinomycin D (1:1000, 1mg/mL, Sigma, #A1410), and microglia was isolated with the Papain-based Neural Tissue Dissociation Kit (P) (# 130-092-628, MiltenyiBiotec B.V. & Co. KG) according to the manufacturer’s instructions. Cell suspension was enriched using 30% isotonic Percoll gradient. 1×103–1.5×103 live microglia cells from 3 mice per condition were sorted according to their surface marker CD45+CD11b+7-AAD negative (SH800S Cell Sorter, Sony Biotechnology).

value: microglia

value: TIA

tag: time course


title: MV-2

description:
10X Genomics
Thy6-2_barcodes.tsv.gz
Thy6-2_features.tsv.gz
Thy6-2_matrix.mtx.gz
Thy6_GEX_rep2

extract_protocol:
Thymic fragments were incubated in DMEM-F12 with rotation for 20min and thymocytes were collected from supernatant.Dead cells were separated using Ficoll density gradient and thymocytes were counted and frozen in FBS + 10% DMSO until thawing for staining and sequencing.
Samples were processed for sequencing using the 10X Genomics 5’ Single Cell Immune Profiling workflow. γδ TCR libraries were generated using the 10X universal forward primers and nested custom reverse primers (TRG outer Reverse: AGTCTTCATGGTGTTCCCCTCC, TRG inner Reverse: AAAATAGTGGGCTTGGGGGA, TRD outer Reverse GTCGTGTTGAACTGAACATGTCAC, TRD inner Reverse CAGACAAGCGACATTTGTTCCA). Libraries for all samples were pooled and sequenced on a NovaSeq6000 or NovaX (Illumina) and resultant FASTQs were demultiplexed by the University of Chicago Genomics Facility.
scRNA-seq, CITE-seq, and VDJ libraries

value: thymus


title: MV-4

description:
10X Genomics
Thy10_barcodes.tsv.gz
Thy10_features.tsv.gz
Thy10_matrix.mtx.gz
Thy10_GEX

value: M

value: 5 days


title: Vhcl_66_Hy

status: Public on Feb 14 2026

city: Neuherberg

first: Robert

middle: Michael

last: Gutgesell

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Center Munich

description: Library name: 25L001070

data_processing:
Quality control for the raw transcriptomics sequencing reads was performed using FastQC.
Transcripts were aligned and quantified to the GRCm38 reference genome using STAR with default parameters.
Transcript counts were imported into Python using scanpy and decoupler.
Gene expression was normalized using the median ratio method implemented in pyDESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing raw integer counts. Rows are Genes, Columns are Samples.

source_name: Hypothalamus

growth_protocol: Mice were double- or single-housed and fed ad libitum with either a regular chow (#1314, Altromin, Germany or #5L0D, LabDiet, USA) or a high-fat diet (58% fat, D12331, Research Diets, New Brunswick, USA). Animals were kept under constant ambient conditions of 22 ± 2°C with constant humidity (45–65%) and a 12h/12h light/dark cycle.

extract_protocol:
Total RNA was isolated using the RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
Sequencing libraries were generated from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit with poly-A enrichment, according to the manufacturer's instructions.

treatment_protocol: Mice were treated with either Vehicle, Lanifibranor, semaglutide, GLP-1:Lani, GLP-1:Tesa, GLP1:GIP, GLP-1:GIP:Tesa, GLP-1:GIP:Lani, or physical co-therapies of these combinations. Following treatment, specific tissues (e.g., Liver, WAT, etc.) were excised and processed for RNA extraction.

value: Hypothalamus

value: WT

value: Vhcl


title: TIA 3d 3

description: TIA 3d 3


title: TIA 24h 3

description: TIA 24h 3


title: 3_Mutu1-INPUT_ChIP

description: Library name: 3_Mutu1-INPUT_ChiP_S3


title: MV-8

description:
10X Genomics
Thy10_barcodes.tsv.gz
Thy10_features.tsv.gz
Thy10_matrix.mtx.gz
Thy10_ADT


title: Dnmt1iECKO EC

description:
Library name: Sample 2
10x Genomics

data_processing:
Demultiplexing, barcode processing, alignment to the mouse reference genome (mm10; refdata-gex-mm10-2020-A), filtering, and UMI counting were performed using Cell Ranger Multi (v9.0.1) via the 10x Genomics Cloud platform (10x Genomics). Default parameters were used unless otherwise specified.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

growth_protocol: Mice were injected subcutaneously into the shaved shoulder with 5 x105 YUMMER1.7 melanoma cells suspended in 100 μl of PBS. Mice were monitored for the appearance of tumors to begin caliper measurements.

extract_protocol:
YUMMER1.7 tumors from control and Dnmt1iECKO mice were harvested and enzymatically dissociated into single-cell suspensions using collagenase II, dispase, and DNase I, followed by mechanical dissociation. Red blood cells were lysed and cells were stained with viability dye and antibodies against CD31 and CD45. Live CD31⁺CD45⁻ tumor endothelial cells were sorted by flow cytometry, washed, and resuspended in PBS supplemented with 0.04% BSA prior to single-cell library preparation.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Gene Expression GEM-X v4 kit according to the manufacturer’s instructions. Briefly, sorted cells were loaded onto the Chromium Controller for partitioning into GEMs, followed by reverse transcription, cDNA amplification, and library construction. Libraries were sequenced on an Illumina NextSeq 2000 using the P2 XLEAP-SBS 100-cycle kit in paired-end mode, targeting approximately 20,000–25,000 reads per cell.

value: Tumor

value: Melanoma cells

value: 8-10 weeks old

value: female


title: Tissue - WT - Day 8 - Replicate 3

description: Library name: DSS11_41

value: colon tissue

value: DSS


title: TIA 3d 1

description: TIA 3d 1


title: 5xTFEB_HP_27

city: Incheon

first: Yeji

state: Yeonsu-gu

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology

country: South Korea

institute: Gachon University

description: Library name: 5xTFEB_HP_27

data_processing:
High-throughput sequencing was performed as paired-end 150 sequencing using NextSeq 2000 (Illumina, Inc., USA).
A quality control of raw sequencing data was performed using FastQC. Adapter and low quality reads were removed using Fastp
Then the trimmed reads were mapped to the reference genome using STAR. The quantification of reads was processed using Salmon.  The Read Counts were processed based on TMM + CPM normalization method using Python “conorm” pacakge.
Assembly: GRCm39
Supplementary files format and content: csv files include log2 (TMM+CPM Normalized RC+1) values for all sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from each sample using the Qiagen Rneasy mini kit according to manufacturer's instruction
Libraries were prepared from isolated mRNA using the CORALL RNA-Seq V2 Library Prep Kit (LEXOGEN, Inc., Austria). Subsequently, libraries were checked using the TapeStation4200 System (Agilent Technologies, Amstelveen, The Netherlands) or Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands) to evaluate the mean fragment size.

value: Hippocampus


title: Tissue - Tg - Day 8 - Replicate 2

description: Library name: DSS10_39

value: Casp3/7 Tg


title: TIA 24h 2

description: TIA 24h 2


title: TIA 24h 1

description: TIA 24h 1


title: S58_AS_12_Lung

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

description: Library name: S58_AS.12.Lung

data_processing:
Following sample demultiplexing via bcl2fastq2 v2.20, raw sequenced reads were quality assessed with FastQC v0.11.9. Reads were subsequently trimmed for ambiguous base calling, retained Illumina adaptors, and minimum read lengths with Trimmomatic v0.39 using the following parameters: “ILLUMINACLIP:TruSeq3.fa:2:30:10:2:TRUE”, “SLIDINGWINDOW:4:20”, “MINLEN:28”, “LEADING:3”, and “TRAILING:3”.
Retained trimmed reads were mapped and indexed to the sheep reference genome assembly ARS-UI_Ramb_v3.0 (Ovis aries) with HISAT2 v2.2.1 utilizing default parameters.
Prior to transcript assembly, Sequence Alignment Map (.sam) files generated from HISAT2 were converted to Binary Alignment Map (.bam) files via Samtools v1.14, utilizing default parameters. Transcript assembly and relative gene-level expression estimation was performed via StringTie2 v2.2.0, with default parameters. Following merged Gene Transfer Format (.gtf) file generation of expression estimates for each sample, post-processing for the appending of ambiguous gene-level identifications (“MSTRG” tags) was performed with a custom Perl script.
Assembly: GCF_016772045.2
Supplementary files format and content: Tab-delimited file of raw gene count data for each sample.

organism: Ammotragus lervia

source_name: Lung

extract_protocol:
Total RNA was collected from approximately 20mg of sterilely dissected frozen tissue via Rneasy Plus Mini Kits (Qiagen) using manufactorer's instruction.
mRNA library preparation was performed with the Stranded mRNA Library Kit (Illumina) using manufactorer's instruction.

value: Lung

tag: animal id

tag: mycoplasma ovipneumoniae_presence

value: No

tag: pasteruella multocida_presence

value: Yes

tag: bibersteinia trehalosi_presence

tag: mannheimia haemolytica_presence

tag: trueperella pyogenes_presence


title: S56_AS_11_Lung

description: Library name: S56_AS.11.Lung


title: Tissue - Tg - Day 8 - Replicate 1

description: Library name: DSS10_36

tag: genotype


title: S57_AS_11_LN

description: Library name: S57_AS.11.LN

source_name: Lymph node

tag: tissue

value: Lymph node


title: Sham 3

description: Sham 3

value: microglia

value: Sham


title: Tissue - Tg - Day 8 - Replicate 3

description: Library name: DSS11_46


title: 5xTFEB_HP_8

description: Library name: 5xTFEB_HP_8


title: 5xTFEB_HP_2

description: Library name: 5xTFEB_HP_2


title: Tissue - WT - Day 8 - Replicate 2

description: Library name: DSS10_34

value: Casp3/7 WT


title: Tissue - WT - Day 8 - Replicate 1

description: Library name: DSS10_33


title: Sham 2

description: Sham 2


title: S53_AS_8_Lung

description: Library name: S53_AS.8.Lung


title: Tissue - Tg - Day 0 - Replicate 6

description: Library name: DSSIEC2_16

value: Control


title: S54_AS_9_Lung

description: Library name: S54_AS.9.Lung


title: 5xFAD_HP_31

description: Library name: 5xFAD_HP_31


title: Tissue - Tg - Day 0 - Replicate 5

description: Library name: DSSIEC2_15


title: Sham 1

description: Sham 1


title: 5xFAD_HP_3

description: Library name: 5xFAD_HP_3


title: 5xFAD_HP_36

description: Library name: 5xFAD_HP_36


title: Tissue - Tg - Day 0 - Replicate 4

description: Library name: DSSIEC2_14


title: S52_AS_7_Lung

description: Library name: S52_AS.7.Lung


title: S46_DBS_14_Lung

description: Library name: S46_DBS.14.Lung

organism: Ovis canadensis


title: directRNA_ercc

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: Library name: Sample2

data_processing:
Reads were demultiplexed and concatenated into FASTQ by MinKNOW. • PCR-cDNA reads: adapter trimming and orientation correction with pychopper v2.7.10; discard <50 bp reads. • Alignment with minimap2 v2.28 (spliced alignment mode, k=14, canonical splice sites). • Direct RNA reads aligned directly without trimming. • ERCC quantification: featureCounts (Subread v2.0.6). • Transcript quantification: bambu v3.6.0 (discovery mode = false). • Coverage analysis: RSeQC v5.0.4. • Differential gene expression: DESeq2 v1.44.0 (FDR 5%), variance stabilising transformation for normalisation. • Pathway enrichment: GSVA v2.0.0 with MSigDB hallmark sets. • Differential transcript usage: DRIMSeq v1.52.0 → DEXSeq v1.52.0 → StageR v1.28.0 (all with FDR 5%). • Visualisation: R 4.4.1 with ggplot2, ggpubr, ggvenn, ggtranscript, ggalluvial, pheatmap.
Assembly: GRCh38.p14 (GENCODE v46 annotation). ERCC spike-in transcripts also used.
Supplementary files format and content: Commer seperated counts matrix

organism: synthetic construct

source_name: ERCC synthetic spike-ins

extract_protocol:
RNA concentration was measured on a NanoPhotometer NP80 (Implen, Germany), and RNA integrity was assessed using the Agilent 4150 TapeStation. RIN scores were 9.7–9.8.
PCR-cDNA: Libraries were prepared using the ONT PCR-cDNA Barcoding Kit (SQK-PCB111.24), with 200 ng of SKMM2 RNA or 16 ng ERCC spike-in. SKMM2 samples underwent 14 PCR cycles; ERCC samples 16 cycles. Libraries were quantified on Qubit 2.0 and quality-checked on Agilent 4150 TapeStation. Sequencing was on PromethION R9.4.1 flow cells (FLO-PRO002) for 72 h, base-called with Dorado (v7.4.14). Direct RNA: Libraries were prepared using the ONT Direct RNA Sequencing Kit (SQK-RNA004) from 1 µg RNA (cells) or ~150 ng ERCC RNA. Entire libraries were loaded onto PromethION RNA Flow Cells (FLO-PRO004RA) and sequenced on PromethION 24 for 72 h with Dorado RNA high-accuracy base-calling (v7.4.14).

value: ERCC synthetic spike-ins

tag: seqtype

value: directRNA


title: cdna_erccpass

description: Library name: Sample1

value: cDNA


title: WT_HP_22

description: Library name: WT_HP_22

value: WT


title: S45_DBS_13_LN

description: Library name: S45_DBS.13.LN


title: S49_AS_4_Lung

description: Library name: S49_AS.4.Lung


title: S43_DBS_12_Lung

description: Library name: S43_DBS.12.Lung


title: WT_HP_11

description: Library name: WT_HP_11


title: Tissue - WT - Day 0 - Replicate 4

description: Library name: DSSIEC2_12


title: Tissue - WT - Day 0 - Replicate 3

description: Library name: DSSIEC2_11


title: S50_AS_5_Lung

description: Library name: S50_AS.5.Lung


title: S48_AS_3_Lung

description: Library name: S48_AS.3.Lung


title: Tissue - WT - Day 0 - Replicate 5

description: Library name: DSSIEC2_13


title: S41_DBS_11_Lung

description: Library name: S41_DBS.11.Lung


title: WT_HP_7

description: Library name: WT_HP_7


title: S42_DBS_11_LN

description: Library name: S42_DBS.11.LN


title: S51_AS_6_Lung

description: Library name: S51_AS.6.Lung


title: THP1 treated with 100sAb, replicate 3 (Batch 4710)

city: Rotselaar

first: Daan

last: Moechars

address: Catharinalaan 43

institute: KULeuven

description:
Library name: 4710_KK18
RNA-seq of THP1 cells treated with 100sAb

data_processing:
Low quality ends and adapter sequences were trimmed off from the sequenced reads  with Cutadapt 3.2. Subsequently, small reads (length < 35 bp), polyA-reads (more  than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads  (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read  equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.58.0 47.  With Bowtie2 2.4.5 we identified and removed reads that align to phix_illumina
The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference  genome of Homo sapiens (GRCh38.88). Default STAR aligner parameter settings  were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic -alignIntronMin 50 –alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’.  Using Samtools 1.15.1, reads with a mapping quality smaller than 20 were removed  from the alignments
Assembly: GRCh38.88
Supplementary files format and content: A comma delimited file  of of raw counts in gene x sample format.

growth_protocol: HP-1 cells (TIB-202, ATCC) were cultured in RPMI-1640 medium, supplemented with  10% FBS (15517589, FisherScientific), 1mM Sodium Pyruvate (11360070,  ThermoFisher Scientific) and 1x non-essential amino acids (12084947, FisherScientific)  at 37oC and 5% CO2. Cells were plated at 30000 cells/well in a 96-well plate  (PerkinElmer) or in a culture slide (NuncTM Lab-TekTM II Chamber SlideTM System) and  differentiated with RPMI-1640 supplemented with 50ng/ml phorbol 12-myristate 13acetate (PMA). After 48h, the medium was changed to RPMI-1640 without PMA. 5h  later

extract_protocol:
For each sample, 500 ng of total RNA was used as the starting material. Following the Illumina Stranded mRNA Sample Prep protocol, poly-A containing mRNA molecules were purified from the total RNA input using poly-dT oligo-attached magnetic beads.
Purified dual-indexed sequence-libraries of each sample were equimolarly pooled,  converted with the Adept PCR Plus kit (Element Biosciences) and sequenced on  Element Biosciences AVITI (two runs, 2x75 Cloudbreak High kit, single read 100 (10110-10-0))

treatment_protocol: the cells were incubated with different concentrations of Aβ42 for 48h.  Recombinant Aβ42 (rAβ42, rpeptide) or synthetic Aβ42 (sAβ42, ab120301, Abcam)  were prepared by dissolving in sterile H20 and sonicating for 2min. Similarly, Scrambled  Aβ42 (rPeptide) was prepared. For the fixed-cells experiments, cells were fixed after the  5-hour rest and before adding Aβ42 with 4% PFA in PBS.

tag: cell line

value: Macrophages


title: Tissue - Tg - Day 0 - Replicate 3

description: Library name: DSSIEC12_126

value: colon tissue


title: 5xTFEB_CX_8

description: Library name: 5xTFEB_CX_8

source_name: Cortex

value: Cortex


title: 5xTFEB_CX_27

description: Library name: 5xTFEB_CX_27


title: THP1 treated with 100sAb, replicate 2 (Batch 4710)

description:
Library name: 4710_KK17
RNA-seq of THP1 cells treated with 100sAb


title: THP1 treated with 100sAb, replicate 1 (Batch 4710)

description:
Library name: 4710_KK16
RNA-seq of THP1 cells treated with 100sAb


title: S40_DBS_9_LN

description: Library name: S40_DBS.9.LN


title: Tissue - Tg - Day 0 - Replicate 2

description: Library name: DSSIEC12_125


title: 5xFAD_CX_36

description: Library name: 5xFAD_CX_36


title: 5xTFEB_CX_2

description: Library name: 5xTFEB_CX_2


title: S39_DBS_8_Lung

description: Library name: S39_DBS.8.Lung


title: Tissue - Tg - Day 0 - Replicate 1

description: Library name: DSSIEC12_124


title: Tissue - WT - Day 0 - Replicate 1

description: Library name: DSSIEC12_122


title: THP1 treated with 30sAb, replicate 3 (Batch 4710)

description:
Library name: 4710_KK15
RNA-seq of THP1 cells treated with 30sAb


title: 5xFAD_CX_31

description: Library name: 5xFAD_CX_31


title: Sample 35

city: Liverpool

first: Francesco

last: Del Carratore

address: Crown Street

department: Department of Biochemistry, Cell and Systems Biology

institute: University of Liverpool

description: Library name: 4-4_2_S35

data_processing:
Fastq files containing the raw reads were processed with the BBDuk and BBMap bioinformatics tools (B. Bushnell, sourceforge.net/projects/bbmap/). On a first run, BBDuk was used to trim the adapter sequences from the reads. On a second run, BBDuk was used to perform a rRNA decontamination step. For this step the SILVA  database62 was modified by including the rRNA sequence from the strains considered in this study.
The BBMap tool was then used to map the remaining reads to the four concatenated genomes considered in this study. Reads with ambiguous matches across the four genomes were discarded.
The alignment data obtained together with the concatenated genomes were then processed using the Bioconductor packages Rsamtools, GenomicFeatures and GenomicAlignments to obtain the raw counts data table.
Assembly: The genome assemblies for the 4 isolates are available on JGI at the following links:
Assembly: https://genome.jgi.doe.gov/portal/Strsp32123_FD/Strsp32123_FD.info.html
Assembly: https://genome.jgi.doe.gov/portal/Strsp32113_FD/Strsp32113_FD.info.html
Assembly: https://genome.jgi.doe.gov/portal/Strsp32124_FD/Strsp32124_FD.info.html
Assembly: https://genome.jgi.doe.gov/portal/Strsp3213_FD/Strsp3213_FD.info.html
Supplementary files format and content: Processed data are contained in the file named raw_counts.csv. The file contains the raw counts measured for all genes in the 4 concatenated genomes. Colums represent the samples as described above

organism: unclassified Streptomyces

source_name: unclassified Streptomyces

growth_protocol: strains were incubated on SFM or ISP2 agar at 30 °C, conjugations were performed on SFM agar. All interaction, molecular profiling and desferrioxamine experiments were performed on ISP2 agar. SFM was prepared per litre tap water: 20 g soya flour (Holland & Barrett), 20 g mannitol (Fisher), 20 g agar (Fisher). ISP2 was prepared per litre distilled water:  4 g yeast extract (Oxoid), 10 g malt extract (Difco), 4 g d-glucose (Fisher), optionally 20 g agar, with the pH adjusted to 7.2 by strong NaOH. To culture the interacting bacteria for molecular profiling analysis, spores of each strain had first been standardised and aliquoted at 1 x 109 CFU ml-1 in 20% glycerol. Before use, these were diluted 10-fold to 1 x 108 CFU ml-1 in ISP2 broth, and 4 µl inoculated 1 cm apart in pairs on ISP2 agar. Each pairing was prepared in quadruplicate for each of the 5 timepoints (n=20 total for each pairing), to allow for the metabolite and RNA sampling in triplicate daily (with one spare). One set of quadruplicate plates was chosen at random to be photographed daily, such that the same four plates were imaged to capture phenotypes, considering our sampling on earlier timepoints is destructive. Images were captured daily on days 2 through to 6 of the quadruplicate set.

extract_protocol:
Streptomyces mycelia was scraped from the agar surface with a spatula, and frozen in liquid nitrogen before storage at -80 °C. Frozen cells were transferred to Lysing Matrix E 2ml tubes (MP Biomedicals LLC) before lysis with a FastPrep bead homogeniser (MP Biomedicals LLC) set to 6.0 m/s for 20 s. Trizol (1ml, ThermoFisher) was added to each tube, mixed by hand inversion and incubated for 5 minutes to allow dissociation of the nucleoproteins complex. Samples were centrifuged at 16,000 x g for 10 min, and 700 µl of supernatant was collected. To each, 140 µl of chloroform was added with incubation at room temperature for 3 min with occasional mixing by hand. After centrifugation for 15 min at 12,000 x g at 4 °C, samples separate to a lower red phenol-chloroform, interphase and colourless upper aqueous phase. The aqueous phase (2 x 140 µl) containing the RNA was transferred to a fresh tube, before removal of 200 µl with the tube tilted to avoid any contamination of the other phases. An equal volume of 200 µl 100% ethanol was added to each. RNA isolation from the resulting samples was performed using the Direct-zol RNA Miniprep kit (Zymo Research) with the manufacturer’s protocol, omitting the on-column DNAse treatment (that had proven ineffective in this experiment as indicated by qPCR). Samples were eluted in 50 µl autoclaved milli-Q water and concentration monitored by Qubit HS and BR RNA assay kits (Thermofisher). To remove residual gDNA in 50 µl samples, the manufacturer’s protocol was followed for TURBO DNase kit (Ambion), with 1 µl DNase per 50 µl input sample, including the DNase removal steps by kit reagent and centrifugation. RNA integrity was measured by recording RINs with a Bioanalyzer 2100 (Agilent).
Library preparation and sequencing was performed by Source Bioscience. The libraries were prepared with the NEBNext rRNA Depletion Kit for Bacteria (NEB) according to the manufacturer’s protocol. During this process, the libraries were indexed with NEBNext Multiplex Oligos for Illumina (NEB). Illumina sequencing was performed at depth 30 million read pairs per sample as 150 b.p. paired end reads. RNA samples were multiplexed before library generation and subsequent sequencing. To confirm our assertion that all four strains could be multiplexed without significant data loss, preliminary RNA-seq was performed with samples from strains B and C run individually, compared with the same samples mixed with each other and all four strains. No significant changes were observed in gene expression due to multiplexing, and therefore this strategy was applied to all further RNA-seq.

value: unclassified Streptomyces

tag: day

tag: sits-a partner

value: SITS-D

tag: sits-b partner

value: SITS-C

tag: sits-c partner

tag: sits-d partner

value: SITS-B


title: THP1 treated with 30sAb, replicate 2 (Batch 4710)

description:
Library name: 4710_KK14
RNA-seq of THP1 cells treated with 30sAb

tag: cell type

tag: treatment

tag: batch


title: Tissue - WT - Day 0 - Replicate 2

description: Library name: DSSIEC12_123

data_processing:
The two sets of samples (Casp3/7 villin mice colon tissue and Casp3/7 villin mice colon IECs) were sequenced using paired end Illumina sequencing (150 nt). The set of Casp3/7 villin mice colon IEC samples (4 WT - control, 4 transgenic - control, 6 WT - DSS, 6 transgenic - DSS) was processed by trimming the reads using Trimmomatic (v0.39) with the following parameter settings: ILLUMINACLIP:"adapters.fa":3:30:10:2:True, SLIDINGWINDOW:5:20, MINLEN:36. The adapter sequences in the fasta file are F: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT and R:GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATGACTATCTCGTATGCCGTCTTCTGCTTG.
Read mapping was performed using STAR  (v2.7.8a) on the GRCm39 mouse genome. Only uniquely mapped reads were kept by setting --outFilterMultimapNmax 1.
BAM files were read into an R (v4.4) environment and a count table was made using the summarizeOverlaps function (mode = "Union") of the GenomicAlignments  package and the GRCm39 gene annotation of Ensembl version 106. One WT – DSS and one transgenic – DSS (DSS_Seq1_12 and DSS_Seq1_15) sample were excluded based on principal component analysis.
The set of Casp3/7 villin mice colon tissue samples (5 Day 0 - WT, 6 Day 0 - transgenic, 5 Day 8 - WT, 6 Day 8 - transgenic) were processed similarly with the following changes: the trimming step was omitted and DESeq2 analysis was done per time point rather than on all samples at once.
Assembly: GRCm39
Supplementary files format and content: count tables


title: THP1 treated with 30sAb, replicate 1 (Batch 4710)

description:
Library name: 4710_KK13
RNA-seq of THP1 cells treated with 30sAb


title: Sample 36

description: Library name: 4-4_3_S36


title: WT_CX_11

description: Library name: WT_CX_11


title: Sample 34

description: Library name: 4-4_1_S34


title: 5xFAD_CX_3

description: Library name: 5xFAD_CX_3


title: THP1 treated with 0sAb, replicate 3 (Batch 4710)

description:
Library name: 4710_KK12
RNA-seq of THP1 cells treated with 0sAb


title: Sample 33

description: Library name: 4-3_3_S33

value: SITS-A


title: WT_CX_22

description: Library name: WT_CX_22


title: THP1 treated with 0sAb, replicate 2 (Batch 4710)

description:
Library name: 4710_KK11
RNA-seq of THP1 cells treated with 0sAb


title: Kidney, ICI-Cyt 3

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: GEX_sample32
10x Genomics

data_processing:
All primary data was analyzed using 10x Genomics Cell Ranger and Loupe Browser software packages. Secondary analysis was performed at Mayo Clinical Sequencing Core with 10X Genomics Platform. The fastq files were processed with Cell Ranger v7 for quality control, read mapping and cell profiling. Output then analyzed with Seurat V5.
Assembly: mm10
Supplementary files format and content: Filtered feature-barcode matrix from Cell Ranger pipeline.

source_name: kidney

extract_protocol:
Whole live cells were isolated from kidney samples. Cell suspension was washed twice, resuspended in 1x PBS + 0.04% BSA, and immediately submitted to the Genome Analysis Core for Single Cell partitioning. The cells were counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter). The barcoded Gel Beads were thawed from -80C and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).1 Based on the desired number of cells to be captured for each sample, a volume of live cells was mixed with the cDNA master mix.  A per sample concentration of 500,000 cells per milliliter or better is required for the standard targeted cell recovery of up to 10,000 cells. The stock concentration requirements would not change for higher cell recovery numbers.
The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Next GEM G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contains a pool of uniquely barcoded molecules. A portion of the cleaned and measured pooled cDNA continues to library construction, where standard Illumina sequencing primers and a unique sample index (Dual Index Kit TT-Set A; 10x Genomics) were added to each cDNA pool, creating gene expression libraries. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific) and Agilent Bioanalyzer High Sensitivity chips (Agilent).   Libraries were sequenced at 50,000 fragment reads per cell following Illumina’s standard protocol using the Illumina NovaSeq X Plus™. The flow cells were sequenced as 100x2 paired end reads using NovaSeq X Plus sequencing reagents and software.

treatment_protocol: Control, Immune checkpoint inhibitors alone, and Immune checkpoint inhibitors plus Cytokines

value: kidney

value: Hu PD1/PDL1

value: ICI-Cyt

tag: age

value: 8-12 weeks old


title: Kidney, ICI-Cyt 2

description:
Library name: GEX_sample21
10x Genomics


title: THP1 treated with 0sAb, replicate 1 (Batch 4710)

description:
Library name: 4710_KK10
RNA-seq of THP1 cells treated with 0sAb


title: Sample 31

description: Library name: 4-3_1_S31


title: WT_CX_7

description: Library name: WT_CX_7


title: Kidney, ICI-Only 3

description:
Library name: GEX_sample26
10x Genomics

value: ICI-Only


title: Sample 30

description: Library name: 4-2_3_S30


title: Sample 32

description: Library name: 4-3_2_S32


title: THP1 treated with 100Ab, replicate 2 (Batch 4427)

description:
Library name: 4427_KK8
RNA-seq of THP1 cells treated with 100Ab


title: Parental 4T1 CD45

city: Lebanon

first: Brock

last: Christensen

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

description:
Library name: Sample12
10x Genomics

data_processing:
FASTQ files were generated using Cell Ranger mkfastq (v7.1.0).
Reads were aligned to the mm10-2020-A genome using Cell Ranger count to generate raw gene-barcode matrices.
Assembly: mm10-2020-A
Supplementary files format and content: Filtered gene expression matrices (genes × cells) and corresponding cell metadata are provided as tab-separated (.tsv) files for each sample.

source_name: Mammary fat pad

growth_protocol: 4T1-derived clonal cells were cultured in RPMI 1640 with 10% FBS and 1% penicillin-streptomycin at 37°C and 5% CO₂ before orthotopic implantation into BALB/c mice.

extract_protocol:
Tumors were digested in RPMI with 2 mg/mL collagenase A and 100 U/mL hyaluronidase at 37°C for 2 hours, filtered through 70 μm and 40 μm strainers, treated with RBC lysis buffer, and separated into CD45+ and CD45- fractions using CD45 magnetic beads (Miltenyi).
Single cells were fixed using the Chromium Next GEM Fixed RNA Sample Prep Kit (10x Genomics) and libraries were constructed using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 following manufacturer’s protocol.

value: Mammary fat pad

value: Breast tumor cells

value: 9-11 weeks old

tag: Sex

value: female

tag: host strain

value: BALB/c


title: Parental 4T1 Total

description:
Library name: Sample11
10x Genomics


title: Kidney, ICI-Cyt 1

description:
Library name: GEX_sample18
10x Genomics


title: Sample 29

description: Library name: 4-2_2_S29


title: Sample 28

description: Library name: 4-2_1_S28


title: THP1 treated with 100Ab, replicate 1 (Batch 4427)

description:
Library name: 4427_KK7
RNA-seq of THP1 cells treated with 100Ab

value: Macrophages


title: Kidney, ICI-Only 1

description:
Library name: GEX_sample11
10x Genomics


title: Kidney, ICI-Only 2

description:
Library name: GEX_sample14
10x Genomics


title: Clone M Total

description:
Library name: Sample9
10x Genomics


title: Kidney, Control 3

description:
Library name: GEX_sampleM06
10x Genomics

value: Control


title: Sample 27

description: Library name: 4-1_3_S27

value: unclassified Streptomyces


title: THP1 treated with 30Ab, replicate 3 (Batch 4427)

description:
Library name: 4427_KK6
RNA-seq of THP1 cells treated with 30Ab


title: Kidney, Control 2

description:
Library name: GEX_sampleM05
10x Genomics


title: Clone EM3 CD45

description:
Library name: Sample8
10x Genomics


title: THP1 treated with 100Ab, replicate 3 (Batch 4427)

description:
Library name: 4427_KK9
RNA-seq of THP1 cells treated with 100Ab


title: THP1 treated with 30Ab, replicate 2 (Batch 4427)

description:
Library name: 4427_KK5
RNA-seq of THP1 cells treated with 30Ab


title: Sample 26

description: Library name: 4-1_2_S26

value: SITS-D


title: THP1 treated with 30Ab, replicate 1 (Batch 4427)

description:
Library name: 4427_KK4
RNA-seq of THP1 cells treated with 30Ab


title: Kidney, Control 1

description:
Library name: GEX_sampleM04
10x Genomics


title: Sample 25

description: Library name: 4-1_1_S25

value: SITS-C


title: Clone M CD45

description:
Library name: Sample10
10x Genomics


title: RNA-Seq_MCF7_siESRRA-E2

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

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

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR version 2.7.10.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using the Eastep Super Total RNA Extraction Kit following the manufacturer’s protocol. DNase I was included in the column digestion to ensure RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed using an Illumina HiSeq 3000 system.

treatment_protocol: MCF7 cells were transfected with control siRNA (siCTL) or siRNA specifically targeting ESRRA (siESRRA) in stripping medium for three days, and then treated of either 10-7 M 17-β-estrodial (E2) or ethanol for 6h.


title: THP1 treated with 0Ab, replicate 3 (Batch 4427)

description:
Library name: 4427_KK3
RNA-seq of THP1 cells treated with 0Ab


title: RNA-Seq_MCF7_siESRRA-CTL

value: siESRRA-CTL


title: Sample 24

description: Library name: 3-4_4_S24

value: SITS-B


title: THP1 treated with 0Ab, replicate 2 (Batch 4427)

description:
Library name: 4427_KK2
RNA-seq of THP1 cells treated with 0Ab


title: Clone EM2 Total

description:
Library name: Sample5
10x Genomics


title: Sample 23

description: Library name: 3-3_3_S23

value: SITS-A


title: Clone EM3 Total

description:
Library name: Sample7
10x Genomics


title: Clone EM1 CD45

description:
Library name: Sample4
10x Genomics


title: RNA-Seq_MCF7_siCTL-CTL

value: siCTL-CTL


title: Clone EM2 CD45

description:
Library name: Sample6
10x Genomics


title: human-derived periodontal ligament cell, DEIX treatment, rep3

city: Jeonbuk

first: JungChae

last: Lee

address: 567, Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

institute: Jeonbuk National University

description: Library name: C4-III

data_processing:
Skewer ver 0.2.2 was used for trmming adaptor sequence.
Trimmed sequence reads were mapped to hg19 using STAR aligner ver 2.6
Read count extraction and normalization were performed using Cufflinks ver 2.2.1
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Human-originated periodontal ligament cells

extract_protocol:
The 1 ug of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacture's protocols.

value: DEIX treatment


title: Clone EM1 Total

description:
Library name: Sample3
10x Genomics


title: Clone E CD45

description:
Library name: Sample2
10x Genomics


title: RNA-Seq_MCF7_siCTL-E2


title: human-derived periodontal ligament cell, DEIX treatment, rep2

description: Library name: C4-II

value: Human-originated periodontal ligament cells


title: Sample 20

description: Library name: 3-2_3_S20


title: ChIP-Seq_MCF7_ESRRA_CTL

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed by 1% formaldehyde (Sigma), then the fixed reaction was stopped by the addition of glycine (0.125 M), followed by washing with cold PBS three times. Chromatin DNA was sheared to 200–500 bp average in size.The resultant protein was immunoprecipitated with anti-ESRRA antibody (5 ug) overnight at 4 °C, followed by incubation with protein G magnetic beads (0.8 mg/mL) for an additional 4 h. After washing, the protein-DNA complex was reversed by heating at 65 °C overnight.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: MCF7 cells were maintained in phenol red free DMEM (stripping medium) supplemented with 5% charcoal-treated FBS for three days, followed by treatemnt of either 10-7 M 17-β-estrodial or ethanol for 1 h.

value: CTL


title: ChIP-Seq_MCF7_ESRRA_E2


title: Clone E Total

description:
Library name: Sample1
10x Genomics

value: Mammary fat pad


title: THP1 treated with 0Ab, replicate 1 (Batch 4427)

description:
Library name: 4427_KK1
RNA-seq of THP1 cells treated with 0Ab


title: human-derived periodontal ligament cell, DEIX treatment, rep1

description: Library name: C4-I


title: Sample 21

description: Library name: 3-3_1_S21


title: Sample 22

description: Library name: 3-3_2_S22