title: 8005_Avonex_intermed_144

value: IM

value: 15 μg


title: ume6_Glucose_R1

status: Public on Jun 23 2026

type: SRA

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: Library name: dume6_F_Glucose_R1

library_source: transcriptomic

data_processing:
Processing is automated using the Tail-Tools pipeline, version 1.9 (https://github.com/Monash-RNA-Systems-Biology-Laboratory/tail-tools), and proceeds as follows: Reads are stripped of trailing poly(A) sequences. Reads are aligned using the STAR aligner. Any multi-mapping reads are assigned to one location at random. Counts per gene are produced with UMI deduplication. The UMI sequence can be found at the end of the read names in the FASTQ files. UMIs where the reads had an observed poly(A) tail of length at least 13 are also counted, and the average tail length from these UMIs is calculated. As 3'UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene but not proceeding into another gene on the same strand are counted towards that gene.
Assembly: Candida auris B8441, downloaded 22 June 2020 from candidagenome.org.
Supplementary files format and content: CSV file containing counts of UMIs, counts of UMIs with a tail, and average tail lengths associated with each gene.

molecule: total RNA

organism: Candidozyma auris

source_name: Candida auris cells

growth_protocol: Wild type and 3 transcription factor mutants grown in media containing either glucose or lactate as a carbon source. After 2 days growth on YP+2% Glucose and YP+2% Lactate plates at 30°C, cells were harvested directly from plates, washed in ice-cold ddH2O and pellets were stored at -80°C prior to RNA extraction.

extract_protocol:
Hot Phenol method: 1 ug of DNase treated Total RNA was used as library input.
Beilharz Lab Pooled PAT Seq  method

tag: cell type

value: Candida auris cells

tag: genotype

value: 470140  background

tag: treatment

value: Grown in Glucose media


title: PDX244_988_20_RAD_11R

city: Barcelona

first: Alba

last: Mas Malavila

address: Saturnino Calleja 11-13

country: Spain

institute: VHIO

description:
Library name: 23
23 is a replicate of a sample treated with EP0062 from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt

data_processing:
Raw reads were mapped to the human reference genome (Gencode, release 38) and counted at the gene level using STAR version 2.55.3a and parameters '--outSAMunmapped None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts'.
Differential expression analysis was performed in the R (version 4.0.0)/ Bioconductor environment, using the DESeq2 package version 1.28.1
Assembly: RNA-seq reads were mapped against the human reference genome (Gencode 38) with STAR 2.5.3a using ENCODE parameters.
Supplementary files format and content: DESeq2 normalized counts in txt format

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast cancer Patient Derived Xenograft

extract_protocol:
RNeasy Mini Kit (#74106, Qiagen)
KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche)

tag: tissue

value: Breast cancer Patient Derived Xenograft

tag: condition

value: Treated

tag: sensitivity

value: Resistant

tag: batch


title: 8005_Avonex_intermed_120

type: protein

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

country: USA

institute: U.S. FDA

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

source_name: EDTA plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol: EDTA plasma from whole blood

treatment_protocol: Subjects were randomized between IFNβ-1a (15 µg) and pegIFNβ-1a (62.5 µg).

tag: drug group

tag: delivery

tag: dose

tag: timepoint


title: PDX244_988_20_RAD_12R

description:
Library name: 244_R2
244_R2 is a replicate of a sample treated with EP0062 from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: irf1_Glucose_R2

description: Library name: dirf1_F_Glucose_R2


title: 8005_Avonex_intermed_96

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: brg1_Glucose_R2

description: Library name: dbrg1_F_Glucose_R2


title: PDX244_988_20_RAD_12L

description:
Library name: 244_R1
244_R1 is a replicate of a sample treated with EP0062 from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: 8005_Avonex_intermed_72

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: brg1_Glucose_R1

description: Library name: dbrg1_F_Glucose_R1


title: PDX244_988_20_Control_4L

description:
Library name: 253
253 is a replicate of a control sample from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt

value: Control


title: Wild_Type_Glucose_R3

description: Library name: 470140_F_Glucose_R3


title: Wild_Type_Glucose_R2

description: Library name: 470140_F_Glucose_R2


title: 8005_Avonex_intermed_48


title: 8005_Avonex_intermed_32


title: irf1_Glucose_R1

description: Library name: dirf1_F_Glucose_R1


title: B11205_Casamino_acid_R3

description: Library name: B11205_Casamino_acid_R3

growth_protocol: Five C. auris clinical isolates' were grown on YP+2% Glucose, YP+2% Lactate, and YP+2% Casamino acid plates at 30°C.  After 2 days, cells were harvested directly from plates, washed in ice-cold ddH2O and pellets were stored at -80°C prior to RNA extraction.

value: B11205 background

value: Grown in Casamino acid media


title: brg1_Glucose_R3

description: Library name: dbrg1_F_Glucose_R3


title: PDX244_988_20_Control_3L

description:
Library name: 244_C1
244_C1 is a replicate of a control sample from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: 8005_Avonex_intermed_16


title: B11205_Casamino_acid_R1

description: Library name: B11205_Casamino_acid_R1


title: B11205_Casamino_acid_R2

description: Library name: B11205_Casamino_acid_R2


title: K-CDX-C36-40-rep3

city: Shanghai

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

data_processing:
Illumina PE150 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2(version 2.2.0).
The number of reads falling in the exons were calculated using featureCounts (version v1.5.3) and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

source_name: Karpas422-derived xenograft tissues

growth_protocol: We built Karpas422 cell-derived xenograft models in mice. Karpas422 cells were washed and resuspended in cold PBS, mixed with Matrigel at 1:1 (v/v) to reach 1 × 107 cells per 200 μL, and then the tumor cell mixtures were injected subcutaneously into the left flank of female Balb/c nude mice at 200 μL per mice (5-6 weeks of age).

extract_protocol:
RNA were harvested using Trizol reagent. 200 ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis 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 ligated to prepare for was of DNA fragments, Adaptor with hairpin loop structure hybridization. In order to select cDNA fragments of preferentially 370 420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). 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: When tumor volume reached ~150 mm3, mice were randomly assigned into groups. C36 was resolved and suspended in water with 0.5% HPMC and 0.5% Tween-20. The mice were administered orally by gavage at a dose volume of 40 ml/kg twice daily or an equivalent volume of vehicle as a control. At the last day, tumors were collected 3 h post treatment and frozen immediately in liquid nitrogen.

value: Karpas422-derived xenograft tissues

value: Wild type

value: 40 mg/kg C36


title: LIMD1 Het C8 (IP)

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: IP_LIMD1_Het_C8

data_processing:
Initial processing and analysis was performed by Eclipsebio (https://eclipsebio.com/) with a proprietary analysis pipeline v1 developed from several published eCLIP publications: [10.1101/2022.02.13.480296]; [PMID 27018577]; [PMID 28766298]. The original bioinformatic pipelines are available (https://github.com/yeolab/eclip; https://github.com/YeoLab/chim-eCLIP). Briefly, UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome (UCSC version GRCh38/hg38) using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). AGO2 eCLIP peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1) (55). For each peak, IP versus input fold enrichments and p-values were calculated. miRNAs from miRBase (v22.1) were "reverse mapped" to any reads that did not map to repetitive elements or the genome using bowtie (v1.2.3). The miRNA portion of each read was then trimmed, and the remainder of the read was mapped to the genome using STAR (v2.7.7a). PCR duplicates were resolved using umi_tools (v1.1.1), and miRNA target clusters were identified using CLIPper (v2.0.1). Each cluster was annotated with the names of miRNAs responsible for that target. Peaks were annotated using transcript information from GENCODE release 41 (GRCh38.p13) with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron). AGO2 clusters identified in the IP sample were then normalized against a paired input sample, with AGO2 peaks defined as a cluster with log2 fold enrichment ≥ 3 and p-value ≤ 0.001. Reproducible peaks were identified using IDR (Irreproducible Discovery Rate) analysis. Reproducible chimeric AGO2:miRNA-target peaks peaks were identified by filtering for peaks where each replicate contained at least three chimeric reads with miRNAs of the same miRNA seed family overlapping the peak. From here, AGO2- and chimeric peak data, stratified by genomic coordinate, gene, feature (RNA region), enrichment/chimeric read count per peak, and differences (fold change and p-values) between samples were further analysed using conventional methods (Microsoft Excel and GraphPad Prism v9.5.1). Further details on chimeric miR-eCLIP analysis can be obtained upon request.
Assembly: hg38
Supplementary files format and content: bigWig files
Library strategy: iCLIP

source_name: hSAEC

growth_protocol: SAEC cells were cultured at 37C at 5% CO2 and maintained in SAEC basal growth medium (with supplements) (antibiotic free).

extract_protocol:
2 x 1.25m cells per replicate (n=4) per sample group were seeded per 15 cm dish and grown to ~80% confluence (2 x 10m cells each) before UV-crosslinking on ice at 254 nm (400 mJ/cm²). Cells were scraped, pelleted at 300 g, flash-frozen in liquid nitrogen, and stored at –80 °C. Pellets were lysed in cold eCLIP buffer containing protease and RNase inhibitors, then sonicated on a QSonica Q800R (75% amplitude, 30 s on/off for 10 cycles). Lysates were adjusted to fragment RNA with RNase I according to sample RIN, clarified by centrifugation, and aliquoted to yield 20 µg RNA per IP.
For miR-eCLIP experiments, the standard eCLIP protocol [PMID 27018577] was modified to enable chimeric ligation of miRNA and mRNA pairs associated with AGO2 according to bioRxiv preprint by Manakov et al, 2022 [10.1101/2022.02.13.480296]. AGO2 immunoprecipitation was carried out overnight at 4 °C with AGO2 antibody (Santa-Cruz, sc-53521)–coated magnetic beads (M280 Sheep Anti-Mouse IgG Dynabeads, Thermo Fisher 11202D), which were then washed under stringent high-salt and no-salt conditions. Beads were sequentially treated with PSP and PNK enzymes to repair RNA ends, and chimeric miRNA–mRNA ligation was performed on-bead using T4 RNA ligase. After additional washes, 3′ RNA adapters were ligated on-bead and RNA was released by proteinase K digestion. Matched Input RNA samples were processed in parallel: column cleanup, PSP/PNK end repair, and 3′ adapter ligation. Both IP and Input RNAs were reverse-transcribed using a chimera-specific primer, and the resulting cDNA underwent end repair by nuclease treatment and mild alkaline hydrolysis with bead-based cleanup. Overnight ligation of a single-stranded cDNA adapter was followed by PCR amplification using Illumina i7/i5 index primers, with cycle numbers determined by qPCR. Final libraries were purified with AMPure XP beads, quality-checked on an Agilent TapeStation, pooled equimolarly, and sequenced single-end (100 bp) on an Illumina platform, targeting ~50 million reads per IP sample and ~40 million reads per Input sample. Further details on chimeric miR-eCLIP protocol can be obtained upon request.

treatment_protocol: Early passage WT SAECs were edited using the Dharmacon Edit-R CRISPR–Cas9 platform comprising EGFP–Cas9 mRNA, Edit-R tracrRNA, and a predesigned crRNA targeting exon 1 of LIMD1 (guide #3; 5′-CCGAGTTTGAGGAAACTCGC-3′) or a non-targeting synthetic sgRNA negative control.

tag: cell line

value: hSAEC

value: LIMD1 Het

value: IP AGO2


title: LIMD1 Het C6 technical replicate 1 (IP)

description: Library name: IP_LIMD1_Het_C6_tr1


title: 8005_Avonex_intermed_8

value: IM


title: B8441_Casamino_acid_R3

description: Library name: B8441_Casamino_acid_R3

value: B8441 background


title: B8441_Casamino_acid_R2

description: Library name: B8441_Casamino_acid_R2

value: Candida auris cells


title: 8008_Avonex_intermed_3

value: 15 μg


title: PDX244_988_20_Control_3R

description:
Library name: 244_C2
244_C2 is a replicate of a control sample from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: K-CDX-C36-40-rep2


title: B8441_Casamino_acid_R1

description: Library name: B8441_Casamino_acid_R1


title: 8007_Pleg_intermed_312

value: SC


title: Wild_Type_Glucose_R1

description: Library name: 470140_F_Glucose_R1

value: 470140  background

value: Grown in Glucose media


title: 8005_Avonex_intermed_3


title: 470121_Casamino_acid_R3

description: Library name: 470121_Casamino_acid_R3

value: 470121 background


title: 470121_Casamino_acid_R2

description: Library name: 470121_Casamino_acid_R2


title: 8005_Avonex_intermed_0


title: 470121_Casamino_acid_R1

description: Library name: 470121_Casamino_acid_R1


title: K-CDX-C36-40-rep1


title: 8007_Pleg_intermed_144


title: K-CDX-V-rep3

value: Vehicle


title: Cas9 control C2 (input)

description: Library name: input_Cas_C2

value: Cas9 control


title: 470140_Wrinkled_Casamino_acid_R3

description: Library name: 470140_F_Casamino_acid_R3

value: 470140 Wrinkled background

value: Grown in Casamino acid media


title: COVID-19 covalescent plasma 2

description:
(BioIVT) HMN373533-K21
F00373533

value: Covid-19 covalescent plasma


title: Cas9 control C3 (input)

description: Library name: input_Cas9_C3


title: 470140_Wrinkled_Casamino_acid_R2

description: Library name: 470140_F_Casamino_acid_R2


title: K-CDX-V-rep2

value: Karpas422-derived xenograft tissues

value: Wild type


title: 470140_Wrinkled_Casamino_acid_R1

description: Library name: 470140_F_Casamino_acid_R1


title: K-CDX-V-rep1


title: 470140_Smooth_Casamino_acid_R3

description: Library name: 470140_A_Casamino_acid_R3

value: 470140 Smooth background


title: 470140_Smooth_Casamino_acid_R2

description: Library name: 470140_A_Casamino_acid_R2


title: COVID-19 covalescent plasma 1

description:
(BioIVT) HMN373532-K21
F00373532


title: HS_22

type: genomic

city: Basel

first: Baptiste

last: Ameline

address: Schoenbeinstrasse 40

department: Pathology

country: Switzerland

institute: University hospital basel

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using minfi and the normalization function : processIllumina()
[processed value definition] Beta values, calculated with minfi using the Illumina method

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Histiocyc sarcoma

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

value: Histiocyc sarcoma

tag: gender

value: female

tag: site

value: M. gluteus

tag: age


title: B11205_Lactate_R3

description: Library name: B11205_Lactate_R3

value: Candida auris cells

value: B11205 background

value: Grown in Lactate media


title: HS_21

value: male

value: M. vastus medialis


title: Comb_3

city: Houston

first: Priyanka

last: Sharma

state: Texas

address: 1515 Holcombe Blvd.

department: Department of Leukemia

institute: University of Texas MD Anderson Cancer Center

data_processing:
Paired end sequencing reads were trimmed to remove adapter sequences. Low quality reads were filtered.
Reads were aligned to hg38 geneome sequnces using HISAT2.
Read counts were calculated using htseq-counts function.
Read counts from each sample were tabulted into a tab delimted text file using Tydiverse in R programming environment.
Data was normalized and differential expression analysis was performed using Deseq2 package.
Assembly: Hg38
Supplementary files format and content: Raw read counts table was submitted as tab delimted text file. Rows represent genes and columns represent samples.

extract_protocol:
RNA was isolated using RNAeasy kit with on-column DNA digestion.
Paired end sequencing

value: AML

value: ABT199 + ERKi

tag: replicate


title: 470140_Smooth_Casamino_acid_R1

description: Library name: 470140_A_Casamino_acid_R1


title: B11205_Lactate_R2

description: Library name: B11205_Lactate_R2


title: B11205_Lactate_R1

description: Library name: B11205_Lactate_R1


title: B8441_Lactate_R3

description: Library name: B8441_Lactate_R3

value: B8441 background


title: Comb_2


title: HS_20

value: Mandibula


title: 8007_Pleg_intermed_32

value: SC


title: B8441_Lactate_R2

description: Library name: B8441_Lactate_R2


title: Comb_1


title: B8441_Lactate_R1

description: Library name: B8441_Lactate_R1


title: HS_19

value: Spleen


title: ERKi_3

value: ERKi (compound 27)


title: PDX244_988_20_Palbo_42L

description:
Library name: 269
269 is a replicate of a sample treated with palbociclib from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt

value: Breast cancer Patient Derived Xenograft

value: Treated

value: Palbociclib

value: Resistant


title: 470121_Lactate_R3

description: Library name: 470121_Lactate_R3

value: 470121 background


title: HS_18_duplicate

description: Repetition with FFPE Restoration kit Illumina

value: Histiocyc sarcoma

value: female


title: ERKi_2


title: 16JB_pos_0_250305_invitro12hr

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

description: Library name: Sample 25

data_processing:
Transcript abundance was determined from FASTQ files using Salmon (v1.8.0) and the Ensembl reference transcript sequences. Transcript per million (TPM) values and gene level counts were calculated using the tximport R Bioconductor package (v1.22.0). Differential gene expression analysis was performed with the DESeq2 R Bioconductor package (v 1.44.0) .
Assembly: hg38
Supplementary files format and content: raw counts from DESeq2

extract_protocol:
RNA was harvested using the trizol-chloroform technique followed by the Qiagen Rneasy micro kit.
100ng of total RNA was used to generate RNA-Seq libraries using Illumina stranded mRNA kit (Catalog#: 20040534), following the manufactures protocol.   Libraries prepared with unique dual indexes were pooled at equal molar ratios.

treatment_protocol: Human abdominal subcutaneous adipose tissue was collected 7-10 days before, or 3-hours following, a graded exercise test on a treadmill. In vitro adipocytes were collected 12-hours following incubation with plasma collected either in the resting (no exercise) state, or with plasma collected immediately following sprint-interval exercise or moderate-intensity exercise.

value: HprAD - Human Subcutaneous Preadipocyte

value: Adipocyte

value: MIE Plasma


title: 470121_Lactate_R2

description: Library name: 470121_Lactate_R2

value: Candida auris cells

value: Grown in Lactate media


title: 470121_Lactate_R1

description: Library name: 470121_Lactate_R1


title: ERKi_1

value: AML


title: 470140_Wrinkled_Lactate_R3

description: Library name: 470140_F_Lactate_R3

value: 470140 Wrinkled background


title: HS_18


title: 470140_Wrinkled_Lactate_R2

description: Library name: 470140_F_Lactate_R2


title: HS_17_duplicate

value: male


title: 470140_Smooth_Lactate_R3

description: Library name: 470140_A_Lactate_R3

value: 470140 Smooth background


title: 470140_Wrinkled_Lactate_R1

description: Library name: 470140_F_Lactate_R1


title: HS_17

value: Spleen


title: ABT199_3

value: ABT199 (venetoclax)


title: ume6_Glucose_R3

description: Library name: dume6_F_Glucose_R3

value: 470140  background

value: Grown in Glucose media


title: 470140_Smooth_Lactate_R1

description: Library name: 470140_A_Lactate_R1


title: 470140_Smooth_Lactate_R2

description: Library name: 470140_A_Lactate_R2


title: HS_16_duplicate

value: Back (skin)


title: ABT199_1


title: HS_16


title: ABT199_2


title: B11205_Glucose_R2

description: Library name: B11205_Glucose_R2

value: B11205 background


title: B11205_Glucose_R1

description: Library name: B11205_Glucose_R1


title: lib25_round1-R5

city: Hangzhou

first: Han

last: Guo

state: Zhejiang

address: Xiasha

department: Aptamer Selection Center

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

description:
Library name: lib25_round1-R5
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

library_source: other

data_processing:
Raw reads were quality-checked using FastQC. Adapter sequences and low-quality bases (Phred score < 20) were trimmed using Cutadapt. Reads shorter than 220 bp after trimming were discarded. Barcode and SELEX primer sequences were removed from the reads using custom scripts. Reads were demultiplexed based on round-specific barcodes. Clean reads were collapsed into unique sequences using fastx-collapser. The abundance of each unique aptamer sequence was counted across all target proteins. Read counts were normalized to reads per million (RPM) across samples.
FASTQ files named with the suffix round1-R5 contain sequencing data of aptamer libraries enriched against each target protein in round 5 of the preliminary screening process (round 1-R5). Each file corresponds to 24 protein targets derived from the same initial random library. We summed the read counts of each unique sequence across all sub-libraries and sorted the results in descending order. Unique sequences with prominent total read counts indicating significant enrichment were retained. The CSV files labeled raw_counts_round1-R5 document the read counts of these selected sequences in each individual sub-library.
FASTQ files named with round2-R2 contain sequencing data of aptamer libraries enriched against each target protein in round 2 of the secondary screening process (round 2-R2). Each file corresponds to 24 protein targets derived from the same top 3000 enriched library. Read counts of the original 3000 unique sequences across all sub-libraries were extracted and compiled into CSV files named raw_read_counts_round2-R2. Fewer than 3000 unique sequences were detected in each file. The missing sequences are likely false positives caused by matrix adsorption during the preliminary screening process, or result from limited sequencing throughput.
Total read counts of the 3000 unique sequences across 24 target-enriched libraries were normalized. For each unique sequence, we calculated the sum of read counts across 24 target libraries, and then computed the relative abundance ratio by dividing the read count of each library by the total read count. All results are presented in CSV files named relative_abundance_ratio_round2-R2. The relative abundance ratio reflect the binding capacity of each unique sequence to different target proteins and characterize sequence binding specificity.
Assembly: Not applicable.
Supplementary files format and content: All processed data are provided as CSV files. Files named with raw_count contain read counts of unique sequences in enriched libraries against each protein target. Files named with relative_abundance_ratio record the relative abundance ratios of corresponding read counts. Lib10, lib13, lib18 and lib25 represent four distinct random ssDNA libraries with different primer regions. Each library was used for aptamer selection against 24 protein targets. In these files, each row corresponds to one unique sequence, and each column represents one protein target. For round1-R5, since sample IDs in FASTQ files do not match protein names in CSV files, a supplementary file named round1-R5_fastq_SampleID_to_csv_Protein_Name_mapping is supplied to clarify the correspondence between sample IDs and protein names. Detailed data processing procedures are described in the Data Processing Steps section.

molecule: other

organism: synthetic construct

source_name: in vitro synthetic nucleic acid library; SELEX aptamer library, no native biological cell/tissue origin

growth_protocol: Not applicable. No biological cells or tissues were used in this study. All experoments were performed in vitro using synthetic oligonucleotide libraries and purified proteins.

extract_protocol:
Nucleotide sequences bound to target proteins were eluted using 100 μL of ddH2O by heating at 95 ℃ for 10 min.
Enriched ssDNA pools from each SELEX round were end-repaired, A-tailed, and ligated with sequencing adapters following standard Illumina library preparation protocols. Barcodes were incorporated for multiplexed sequencing. Libraries were amplified by limited-cycle PCR and purified to remove primer dimers and non-specific products before sequencing.

treatment_protocol: The preliminary screening procedure (round 1-R1 to round 1-R5) was conducted according to the classic magnetic bead-based SELEX process. For each target protein, an initial, artificially synthesized random ssDNA library, comprising approximately 10^15 molecules (1 OD), was employed. These ssDNA libraries were dissolved, denatured at 95 ℃ for 10 min, and cooled to 4 ℃ for 5 min to ensure optimal structural conformation. The prepared libraries were added into the histidine peptide-coupled plate for a 1 h counter selection process to eliminate the nonspecific binding. The supernatant was then transferred to the target protein-coupled plate and incubated for 1 h. To further reduce nonspecific binding through competitive interactions, BSA, HsDNA and histidine peptide were incorporated during the positive selection phase. The concentration of these agents was increased to augment selection pressure in subsequent rounds. Following this, unbound sequences present in the supernatant were discarded, and the plate was washed for four times with 200 μL of DPBS-T. Sequences bound to target proteins were eluted using 100 μL of ddH2O by heating at 95 ℃ for 10 min. The eluted ssDNA was then amplified and collected for the next round of selection. In the secondary screening procedure, the initial libraries comprised the corresponding 3000 sequences (top 3000 sequences). These top3000 sequences were derived from the NGS results of the round 1-R5, representing sequences that were significant enriched in the prior screening. Utilizing chip printing technology, the top 3000 sequences of the four libraries (a total of 12000 sequences) were synthesized in batches. Subsequently, emulsion PCR was performed using the corresponding primers to obtained uniformly amplified initial libraries for the secondary screening. The subsequent steps paralleled those of the preliminary screening.

value: lib25 ssDNA library, round 5 of the preliminary screening process


title: DMSO_3

value: DMSO


title: DMSO_2


title: B8441_Glucose_R3

description: Library name: B8441_Glucose_R3

value: B8441 background


title: HS_15

value: Histiocyc sarcoma


title: lib18_round1-R5

description:
Library name: lib18_round1-R5
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

value: in vitro synthetic nucleic acid library; SELEX aptamer library, no native biological cell/tissue origin

value: lib18 ssDNA library, round 5 of the preliminary screening process


title: HS_13_duplicate


title: DMSO_1


title: HS_12

value: female

value: Brain


title: HS_13


title: B8441_Glucose_R1

description: Library name: B8441_Glucose_R1

value: Candida auris cells


title: Tumor, conventional 7x19 CAR-T, 3

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

description:
Library name: 7x19.CART_3.bam
Column name in count matrix.txt: 7x19.CART_3

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.12.1).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to AmpliSeq_Mouse_Transcriptome_V1 using software provided with the Ion Torrent Proton sequencer (ampliSeqRNA v5.12.0.1).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (ampliSeqRNA v5.12.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Tumor

growth_protocol: C57BL/6N mice were inoculated with MC38-human CD20 cells for the in vivo study.

extract_protocol:
CD45+ cells were enriched using the CD45 EasySep positive selection kit, followed by depletion of CD90.1+ cells. Total RNA was extracted from the remaining recipient immune cells.
RNA libraryies for RNA-seq were prepared using Ion Ampliseq Transcriptome Mouse Gene Expression Kit following manufacturer's protocols.

treatment_protocol: CAR-T cells were infused via the tail vein.

value: Tumor

value: Mouse immune cells

value: CD45+ cells

value: Wild type

value: 7x19 CAR-T


title: 470121_Glucose_R3

description: Library name: 470121_Glucose_R3

value: 470121 background

value: Grown in Glucose media


title: lib10_round1-R5

description:
Library name: lib10_round1-R5
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

value: lib10 ssDNA library, round 5 of the preliminary screening process


title: Tumor, conventional 7x19 CAR-T, 2

description:
Library name: 7x19.CART_2.bam
Column name in count matrix.txt: 7x19.CART_2


title: 470121_Glucose_R2

description: Library name: 470121_Glucose_R2


title: SDPo35,90 days postoperative SDT

first: Zhongyu

last: Wu

state: Zhejiang Province

address: 3 East Qingchun Road

department: Sir RunRun Shaw Hospital,School of Medicine

institute: Zhejiang University

description: Library name: SDPo35

library_source: genomic

data_processing:
Relative abundance: Top 20 taxa of each sample at each taxonomic ranks (Phylum, Class, Order, Family, Genus, Species) were selected to plot the distribution histogram of relative abundance in Perl through SVG function. Alpha and Beta Diversity: For analyzing community diversity, richness, and evenness, alpha diversity was calculated using Shannon and Simpson indices in QIIME2. Beta diversity was performed with Principal Coordinates Analysis (PCoA) and Adonis analysis. Community difference analysis: T-test, and linear discriminant analysis effect size (LEfSe) were conducted to characterize community structure differentiation. Function Prediction: PICRUSt2 (V2.3.0) was applied to predict metagenomic functions based on marker genes. Canonical correspondence analysis (CCA) were used to explore interspecies symbiosis and environmental impacts on community structure, reflecting correlations between environmental factors and genus/species abundance.
Continuous variables were expressed as mean with standard deviation and compared using the Student’s T test. Categorical data, on the other hand, were represented as frequencies and percentages, and comparisons were made using the Pearson χ2 test or the Fisher exact test, depending on suitability. A two-sided p value less than 0.05 was considered statistically significant. All data analyses were conducted using the R software package (version 4.0).
Assembly: 16S rRNA gene reference database(Silva 138.1)
Supplementary files format and content: Processed data are ASV feature count matrix (tab-delimited TSV format). Rows represent individual ASVs, columns correspond to sample IDs, and values denote raw sequencing read counts of each ASV across all fecal samples. Taxonomic classification results assigned against SILVA 138.1 database are also provided in the feature table.
Library strategy: 16S rRNA-seq

organism: human feces metagenome

source_name: feces

extract_protocol:
16S rRNA genes of distinct regions (16SV3-V4) were amplified used specific primer with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 0.2µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30s and 72℃ for 5 min. The PCR products were purified using magnetic bead purification. Samples were mixed in equidensity ratios based on the concentration of PCR products.
After thorough mixing, the PCR products were detected and target bands were recovered. Sequencing libraries were generated and indexes were added. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: feces


title: snATAC_Athaliana_root1

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

description: Library name: NYZYG-NYZYH-NYZYN-NYZYO_Athaliana_Ath-root-atac

library_source: genomic single cell

data_processing:
We used the Cell Ranger-ATAC version 2.1.0 count command to filter and map reads to each reference, and generate the fragments file containing a unique ATAC-seq fragment created by two separate transposition events. We then used SnapATAC2 v2.50 to process the fragment files to downstream analyses from cell filtering to cell type annotation. To keep high-quality cells we required a minimum of 3000 fragments per cell and a 3-fold enrichment around the TSS. We separated the data into 500 bp windows across the genome and created a cell by bin count matrix. We used the scrublet algorithm to identify potential doublets and remove them afterwards. We then combined replicates using the MNN-Correct algorithm in SnapATAC2 for batch correction. For visualization purposes we created a UMAP of each atlas. Pseudo-bulk profiles generated from our snATAC-seq data aligned well with published whole-tissue open chromatin profiles (Pearson r2 0.58). We used gene accessibility scores as a proxy for gene expression to annotate cells with cell types from our snRNA-seq atlases. We calculated gene accessibility scores using the ‘pp.make_gene_matrix()’ function in snapATAC2. Briefly, this function assigns genomic bins to nearby genes, counts the transposase insertion events associated with each gene, and creates a matrix of accessibility scores for a particular gene and cell. Using the gene accessibility matrix, we integrated the snATAC-seq and the snRNA-seq datasets selecting the top 1000 most variable genes from our snATAC-seq data. We used scVI integrated in SnapATAC2 to transfer cell type labels from the snRNA-seq atlas to the snATAC-seq atlas. To do this, we trained models using as covariate the batch information, negative binomial distribution (“nb”) as the gene likelihood statistic, and a maximum number of epochs of 1000. After assigning cell type labels, we called peaks using MACS3 integrated into snapATAC2 independently for each cell type. We then merged peaks that were in close proximity (250 bp to either edge) to make comparisons across different cell types possible. To calculate the differentially accessible regions (DARs) we sampled random cells per cell type, excluding the cell type being tested, and combined them to create a background using the regression-based test from snapATAC2 “snap.tl.diff_test()”, to identify regions more likely to be open in a given cell type than the background set of cells. We defined DARs as peaks with an adjusted p< 0.01.
Assembly: Arabidopsis thaliana Col-0 TAIR/Araport via Phytozome
Assembly: Arabidopsis lyrata MN47 Phytozome v2.1
Assembly: Brassica oleracea TO1000DH3 NCBI RefSeq GCF_000695525.1
Assembly: Capsella rubella Monte_Gargano Phytozome v1.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Arabidopsis thaliana

source_name: seedling root

growth_protocol: A. thaliana, A. lyrata, C. rubella, and B. oleracea seeds were surface sterilized before planting vertically on agar plates containing 3mM Ca(NO3)2, 1.5mM MgSO4, 1.25mM NH4H2PO4, 1mM KCl, and 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. The seeds were sterilized by soaking in 75% ethanol for 1 minute and 50% bleach for 5 minutes, 25% bleach with 0.2% Triton X-100 (Sigma-Aldrich 93443) for 4 minutes, then rinsed with sterile water 8 times. After sterilization, seeds in the 2 mL Eppendorf tube were wrapped in aluminum foil and put into a 4°C fridge for cold stratification. Seeds were left in the fridge for 3 days for A. thaliana and C. rubella, or 5 days for A. lyrata. Cold stratification was not needed for efficient germination of B. oleracea seeds. We staggered the planting of different species to account for different germination times of the four plant species, allowing us to harvest seedling root and shoot tissues of plants at the same 5-7 day old growth stage of all species on the same day. A. lyrata was planted on the agar plates 3 days before A. thaliana, C. rubella was planted 1 day after A. thaliana, and B. oleracea seeds without cold stratification were planted 2 days after A. thaliana. The conditions of the growth chamber (Percival Scientific) were set to 16 hours light at 22°C and 8 hours dark at 19°C, with the light turning on at 5am and turning off at 9pm. Root, shoot, and whole seedlings were sampled between 10am and 12pm for all experiments.

extract_protocol:
Freshly harvested samples were used for all snATAC-seq libraries. Nuclei isolation from tissues was performed as follows. Buffer 1 (lysis buffer) consisted of 0.275 M sorbitol (Sigma-Aldrich S6021), 0.1% Triton X-100 (Sigma-Aldrich 93443), 0.01 M MgCl2 (Ambion AM9530G), 1x protease inhibitor cocktail (Sigma-Aldrich 4693132001), 0.3 U/μl RNase inhibitor (Roche 03335399001), and 1 mM DTT (Teknova D9750). Buffer 2 (wash and resuspension buffer) consisted of 1x phosphate buffer saline (without Mg and Ca), 1% BSA, 0.4 U/μl RNase inhibitor, and 1 mM DTT. For isolation of nuclei from mature leaves containing high levels of chloroplasts, an extra modified wash and resuspension buffer (buffer 3) was used to eliminate chloroplasts before the final wash and resuspension step by buffer 2. It consisted of 0.275 M sorbitol, 0.2% Triton X-100, 0.2% NP40 (Thermo Fisher Scientific PI28324), 0.01 M MgCl2, 1x protease inhibitor cocktail, and 1 mM DTT. All nuclei isolation steps were carried out in a cold room at 4°C. For each sample, 20-100 mg fresh or frozen tissue was chopped for 3 minutes using a razor blade on a glass plate with 100-200 μl buffer 1, then transferred to a petri dish with 1.5 mL cold buffer 1 and allowed to rest on ice with gentle shaking for 2 minutes. For multiplexed samples, tissues from different species were weighed separately before being combined and chopped together. The samples were then transferred to a 48-well filter plate (25 μm, 4mL, Agilent, 201003-100), which was pre-wet with 1 mL cold buffer 1 before it was placed on the receiving plate attached to a QIAvac96 (Qiagen). Pressure was maintained below 100 bar during filtration. The filtered nuclei solution was centrifuged at 500x g for 10 minutes at 4°C to pellet the nuclei, after which the supernatant was discarded. For samples with low or no chloroplast content: The pellet was resuspended by gentle flicking and pipetting, washed with 2 mL cold buffer 2, centrifuged at 500x g for 5 minutes, and the supernatant was discarded. For nuclei isolation from mature leaves with high chloroplast content: The pellet was resuspended by gentle flicking and pipetting and 10 mL cold buffer 3 was added, centrifuged at 500x g for 5 minutes, and the supernatant was discarded. The pellet was washed with 2 mL cold buffer 2, centrifuged at 500x g for 10 minutes, and the supernatant was discarded. For both protocols, pellets from the final centrifugation were resuspended in 100 μl cold buffer 2 for snRNA-seq, or cold 1x nuclei buffer (10X Genomics PN-2000207) for snATAC-seq. Nuclei quality and quantity were assessed by flow cytometry and microscopy before continuing to the single nuclei partitioning and barcoding step. A BD Accuri C6 plus flow cytometer was used to analyze the quality and quantity of nuclei stained by propidium iodide (Sigma-Aldrich P4864), added to a final concentration of 50 μg/mL. The stained samples were incubated on ice in darkness for 5-10 min prior to analysis. The analysis was conducted using light-scatter and fluorescence signals produced by a 20 mW laser illumination at 488 nm. Signals corresponding to forward-angle scatter (FSC), 90° side scatter (SSC), and fluorescence were collected. Fluorescence signals (pulse area measurements) were screened using the following filter configurations: (a) FL-2, with a 585/40 nm band-pass filter, and (b) FL-3, with a 670 nm long-pass filter. Threshold levels were set empirically at 80,000 for FSC-H to exclude debris commonly found in plant homogenates. Templates for uni- (FL2-A and number of nuclei) and bi-parametric (FL2-A and FL3-A) frequency distributions were established. Upon identifying the region corresponding to nuclei, data was collected to a total count of 5,000–10,000 nuclei. The flow cytometer was operated at the Slow Flow Rate setting (14 μl sample/minute), with data acquisition for a single sample typically taking 3–5 minutes. Different plant species exhibited varying patterns of somatic endoreduplication within most of their tissues and organs. For example, in young A. thaliana roots and cotyledons, this variation is reflected in the form of multiple clusters within the distribution, corresponding to nuclei forming a 2C, 4C, 8C, 16C, etc., of the endoreduplicative series61. All the nuclei of all the endoreduplicative series were counted and divided by the actual volume analyzed in the flow cytometer to obtain the concentration of the nuclei. An EVOS M5000 microscope was also used for validation of nuclei quality and quantity by analyzing 7 μl diluted nuclei sample stained by 1 µl of diluted SYBR Green dye (Thermo Fisher Scientific S7585 diluted 1:10,000 in water) using a C-Chip Disposable Hemocytometer. For nuclei prepared from fresh tissue samples, most of the nuclei in each sample showed well-resolved edges without obvious evidence of blebbing. In the case of nuclei prepared from frozen samples, where cell debris around the nuclei can interfere with these microscopy observations, nuclei quality was primarily assessed by comparing to fresh nuclei’s distribution and the endoreduplicative series pattern on the flow cytometer.
The nuclei suspension was then diluted to concentration of 700-1000 nuclei/μl using cold buffer 2 for snRNAseq or cold 1x nuclei buffer (10x Genomics PN-2000207) for snATAC-seq. Single nuclei were partitioned and barcoded using a Chromium system (10x Genomics) with the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) for snRNAseq or Chromium Single Cell ATAC Reagent Kits v2 for snATAC-seq. Approximately 20,000 nuclei in total were loaded for single species samples, and up to 60,000 nuclei for multiplexed species samples. Library creation was carried out following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell or NovaSeq X plus 10B or 25B flow cell, using 2x150 bp paired-end sequencing, targeting 200M fragments per species for RNA-seq samples and 250M fragments per species for mixed-species ATAC-seq samples, with higher coverage for A. thaliana seedling samples (900M fragments and 1800M fragments for root and shoot respectively).

value: seedling root

tag: tissue condition

value: fresh

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


title: SDPo34,90 days postoperative SDT

description: Library name: SDPo34


title: snATAC_Athaliana_root2

description: Library name: NZYPA-NZYPB-NZYPC-NZYPG_Athaliana_Ath-root-atac-2


title: Tumor, conventional 7x19 CAR-T, 1

description:
Library name: 7x19.CART_1.bam
Column name in count matrix.txt: 7x19.CART_1

tag: cell type

tag: genotype

tag: treatment


title: 470121_Glucose_R1

description: Library name: 470121_Glucose_R1


title: snATAC_Athaliana_shoot1

description: Library name: NYZYP-NYZYS-NYZYT-NYZYU_Athaliana_Ath-shoot-atac

source_name: seedling shoot

tag: tissue

value: seedling shoot


title: Tumor, conventional CAR-T, 3

description:
Library name: Conv.CART_3.bam
Column name in count matrix.txt: Conv.CART_3

value: CAR-T


title: SDPo31,90 days postoperative SDT

description: Library name: SDPo31


title: B8441_Glucose_R2

description: Library name: B8441_Glucose_R2

value: B8441 background


title: 470140_Wrinkled_Glucose_R3

description: Library name: 470140_F_Glucose_R3

value: 470140 Wrinkled background


title: snATAC_Athaliana_shoot2

description: Library name: NZYPH-NZYPN-NZYPO-NZYPP_Athaliana_Ath-shoot-atac-2


title: Tumor, conventional CAR-T, 2

description:
Library name: Conv.CART_2.bam
Column name in count matrix.txt: Conv.CART_2


title: 470140_Wrinkled_Glucose_R2

description: Library name: 470140_F_Glucose_R2

value: Candida auris cells


title: SDPo28,90 days postoperative SDT

description: Library name: SDPo28


title: Tumor, conventional CAR-T, 1

description:
Library name: Conv.CART_1.bam
Column name in count matrix.txt: Conv.CART_1

value: Tumor


title: S.aureus, CP1_CFS-treated, 1%glucose, rep3

city: Dublin

first: Linda

last: Holland

address: Glasnevin

country: Ireland

institute: Dublin City University

description:
Library name: CP1_CSF3_TBS-1G
CFS 3 (1% Glucose)

data_processing:
Galaxy server (usegalaxy.eu), Bioconductor package EdgeR.
FastQC was used to assess read quality and ensure adapter and low-quality read removal.
Sequence reads were mapped to the reference genome Staphylococcus aureus NCTC 8325 (NC_007795.1) using Hisat2 (Galaxy Version 2.2.1+galaxy0). Aligned reads were sorted by coordinate.
Htseq-count (Galaxy Version 0.9.1+galaxy1) was used to count how many reads mapped to each feature.
A counts matrix was produced and imported in to RStudio where EdgeR of the Bioconductor package was used for differential gene expression analysis.
Assembly: NC_007795.1
Supplementary files format and content: counts_matrix.txt. Contains gene counts for each sample. Columns represent each sample and rows represent individual genes.

organism: Staphylococcus aureus

source_name: culture

growth_protocol: S. aureus biofilms were grown in 6-well nunclon plates (Thermo Fisher) in the conditions described above for 24 h under static conditions at 37°C.

extract_protocol:
Following 24 h of growth, biofilm cells were pelleted at 4°C and total bacterial RNA was extracted using the Qiagen RNeasy mini kit according to the manufacturer's instructions. To remove genomic DNA, RNase-Free DNase Set (Qiagen) was used according to the manufacturer's instructions. Input total RNA concentration was measured by nanodrop. Sample quality was assessed using the 2100 bioanalyzer (Agilent).
Library construction was carried out by Novogene. RNA library was formed by polyA capture (or rRNA removal) and reverse transcription of cDNA. Illumina PE150 technology was employed to sequence the samples.

tag: strain

value: S.aureus biofilm

value: culture

tag: time

value: 24 hour

value: co-culture with 50% Candida parapsilosis Cell-free supernatant in 1% glucose


title: SDPo26,90 days postoperative SDT

description: Library name: SDPo26


title: 470140_Wrinkled_Glucose_R1

description: Library name: 470140_F_Glucose_R1


title: Tumor, control, 3

description:
Library name: NT_3.bam
Column name in count matrix.txt: NT_3

value: Mouse immune cells

value: CD45+ cells

value: Wild type

value: Vehicle


title: SDPo25,90 days postoperative SDT

description: Library name: SDPo25

value: feces


title: S.aureus, CP1_CFS-treated, 1%glucose, rep2

description:
Library name: CP1_CSF2_TBS-1G
CFS 2 (1% Glucose)


title: 470140_Smooth_Glucose_R3

description: Library name: 470140_A_Glucose_R3

value: 470140 Smooth background

value: Grown in Glucose media


title: Tumor, control, 2

description:
Library name: NT_2.bam
Column name in count matrix.txt: NT_2


title: SDPo24,90 days postoperative SDT

description: Library name: SDPo24


title: S.aureus, CP1_CFS-treated, 1%glucose, rep1

description:
Library name: CP1_CSF1_TBS-1G
CFS 1 (1% Glucose)


title: 470140_Smooth_Glucose_R2

description: Library name: 470140_A_Glucose_R2


title: S.aureus, control, 1%glucose, rep3

description:
Library name: Control3_TBS-1G
control 3 (1% Glucose)

value: WT (S. aureus biofilm) in 1% glucose


title: SDPo16,90 days postoperative SDT

description: Library name: SDPo16


title: Tumor, control, 1

description:
Library name: NT_1.bam
Column name in count matrix.txt: NT_1


title: 470140_Smooth_Glucose_R1

description: Library name: 470140_A_Glucose_R1


title: S.aureus, control, 1%glucose, rep2

description:
Library name: Control2_TBS-1G
control 2 (1% Glucose)


title: SDPo04,90 days postoperative SDT

description: Library name: SDPo04


title: 470140_Wrinkled_Lactate_R3

description: Library name: R3_Lac

data_processing:
Processing is automated using the Tail-Tools pipeline, version 1.9 (https://github.com/Monash-RNA-Systems-Biology-Laboratory/tail-tools), and proceeds as follows: Reads are stripped of trailing poly(A) sequences. Reads are aligned using the STAR aligner. Any multi-mapping reads are assigned to one location at random. Counts per gene are produced. Reads where a poly(A) tail was found were also counted, and the average tail length from these reads was calculated. As 3'UTR annotations are not always accurate, reads up to 500 bases down-strand of a gene but not proceeding into another gene on the same strand are counted towards that gene.
Assembly: Candida auris B8441, downloaded 22 June 2020 from candidagenome.org.
Supplementary files format and content: CSV file containing counts of reads, counts of reads with a tail, and average tail lengths associated with each gene.

growth_protocol: C. auris 470140 cells were grown on either YP+2% Glucose and YP+2% Lactate plates at 30°C for 2 days. A single smooth or Wrinkled colony from each plate was harvested, washed in ice-cold ddH2O and pellets were stored at -80°C prior to RNA extraction.

extract_protocol:
Hot Phenol method: 1 microgram of Total RNA was used as library input.
Beilharz Lab Pooled PAT Seq  method

value: 470140 Wrinkled Background

value: Grown in Lactate media


title: miRNA from serum of Tn- tumor-bearing mice (sample 1)

type: RNA

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

description: 30 ng of miRNA were loaded into the platform.

hyb_protocol: miRNAv3 NanoString® cartridges (NanoString® Technologies, cat. CSO-MIR3-12) were loaded with the mix per sample and sealed.

scan_protocol: For data collection, we transferred samples to an nCounter® Digital Analyzer device (NanoString® Technologies).

data_processing:
After expression profiling, the data were analyzed using the nCounter® Advanced Analysis Software. Normalization of all available mouse miRNA regions was performed by subtracting the geometric mean of the negative probes, normalized using the geometric mean of the positive probes, and content set normalization was run considering the most stable regions (coefficient of variation <15%). After, normalized values were exported in comma-separated values (CSV) format and handled in R v.4.4 (The R Foundation for Statistical Computing)
Data were exported in comma-separated value (*.csv) format for further analysis.

label: miRNA reported and capture probes

source_name: serum of Tn- tumor-bearing mice

label_protocol: ~30 ng of cf-miRNA were hybridized for 16.5 hours with molecular barcoding for 527 experimentally validated mouse miRNAs (from miRBase) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012).

growth_protocol: The murine TNBC cell line 4T1 was obtained from ATCC and cultured in DMEM with glutamine (Capricorn, Germany or Gibco, USA) supplemented with 10% inactivated fetal bovine serum (Capricorn, Germany) and antibiotic–antimycotic (Thermo Fisher) at a final concentration of 100 units/mL of penicillin, 100 µg/mL of streptomycin, and 0.25 µg/mL of Gibco Amphotericin B (complete culture medium). The 4T1/Tn+ cell line was generated by CRISPR/Cas9 guide targeted to Ccosmc gene exon 2 170 s (GATATCTCGAAAATTTCAG) cloned in pBS-U6sg plasmid (Tacgene, France) and GFP-tagged Cas9-PBKS plasmid (Addgene), as previously described21. Cells were maintained at 37 °C in a humidified atmosphere of 5% CO2 and  harvested by washing with phosphate-buffered saline (PBS) pH 7.4 and incubation with trypsin (0.1%) and EDTA (0.04%) in PBS.

extract_protocol: Total RNA, including miRNAs, was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (Qiagen, Cat. No. 217204), following the manufacturer’s protocol. RNA was eluted in a final volume of 20 µL. Given the limited volume of biological material available per animal, serum samples were pooled by the experimental group based on the Tn status (Tn+ or Tn−) to ensure sufficient RNA yield. For the Nanostring nCounter miRNA expression analysis, we included three pooled samples: two from Tn+ cases and one from Tn−.

treatment_protocol: Six-to eight-week-old female BALB/c mice were purchased from DILAVE Laboratories (Uruguay), or URBE (Facultad de Medicina, UdelaR, Uruguay). Animals were kept in the animal house (URBE) with water and food supplied ad libitum. Mouse handling and experiments were carried out in accordance with strict guidelines from the National Committee on Animal Research (CNEA, Uruguay). All procedures involving animals were approved by the Universidad de la República’s Committee on Animal Research (CHEA Protocols N° 070153–000732-17). Cells were harvested at 60–70% confluence, washed, counted and inoculated in the 4th right mammary fat pad with 100,000 4T1 cells resuspended in 50 μl of phosphate saline buffer (PBS). Fifteen days after cell implantation, 100% mice showed palpable tumors. Tumor size was measured from the day of first appearance every 2–3 days, and tumor volume was calculated as V = 4/3.π.(r1.r22), being r1 the largest ratio. Animals were sacrificed at day 28 and tumors were weighted and processed for analyses. At least eight mice were used per group in each study.

value: serum

tag: group

value: Tn-

tag: molecule subtype

value: miRNA


title: S.aureus, control, 1%glucose, rep1

description:
Library name: Control1_TBS-1G
control 1 (1% Glucose)

value: S.aureus biofilm


title: SDPo02,90 days postoperative SDT

description: Library name: SDPo02


title: miRNA from serum of Tn+ tumor-bearing mice (sample 2)

source_name: serum of Tn+ tumor-bearing mice

value: Tn+


title: 470140_Wrinkled_Lactate_R2

description: Library name: R2_Lac

value: Candida auris cells


title: miRNA from serum of Tn+ tumor-bearing mice (sample 1)


title: S.aureus, CP1_CFS-treated, 0.2%glucose, rep3

description:
Library name: CP1_CSF3_TBS-0.2G
CFS 3 (0.2% Glucose)

value: culture

value: 24 hour

value: co-culture with 50% Candida parapsilosis Cell-free supernatant in 0.2% glucose


title: 470140_Wrinkled_Lactate_R1

description: Library name: R1_Lac


title: SDPo01,90 days postoperative SDT

description: Library name: SDPo01


title: AVP-treated GT1-7 cells biol rep 3

city: Dallas

first: Ran

last: Tao

state: TX

address: 3302 Gaston Avenue

department: Biomedical Sciences

institute: Texas A&M University College of dentistry

description:
Library name: AVP3
GT1-7 cells treated with 200 pg/mL AVP for 6 h, biological replicate 3

data_processing:
Raw sequencing reads were filtered to remove low-quality reads and adaptor sequences.
Assembly: Mus musculus reference genome mm10/GRCm38

source_name: Cell line

growth_protocol: GT1-7 cells were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from GT1-7 cells using TRIzol reagent according to the manufacturer’s instructions. RNA quality was assessed before library preparation.
RNA-seq libraries were prepared from total RNA and sequenced on the Illumina HiSeq X Ten platform.

value: Cell line

value: GnRH neuron-like cell

value: wild type

value: AVP, 200 pg/mL, 6 h

tag: batch

value: batch 1


title: S.aureus, CP1_CFS-treated, 0.2%glucose, rep2

description:
Library name: CP1_CSF2_TBS-0.2G
CFS 2 (0.2% Glucose)


title: B11205_Glucose_R3

description: Library name: B11205_Glucose_R3

value: B11205 background

value: Grown in Glucose media


title: ILPo45,90 days postoperative ILE

description: Library name: ILPo45

value: feces


title: AVP-treated GT1-7 cells biol rep 2

description:
Library name: AVP2
GT1-7 cells treated with 200 pg/mL AVP for 6 h, biological replicate 2

tag: cell line


title: S.aureus, CP1_CFS-treated, 0.2%glucose, rep1

description:
Library name: CP1_CSF1_TBS-0.2G
CFS 1 (0.2% Glucose)


title: 470140_Smooth_Lactate_R3

description: Library name: S3_Lac

value: 470140 Smooth Background

value: Grown in Lactate media


title: ILPo43,90 days postoperative ILE

description: Library name: ILPo43


title: 470140_Smooth_Lactate_R2

description: Library name: S2_Lac


title: AVP-treated GT1-7 cells biol rep 1

description:
Library name: AVP1
GT1-7 cells treated with 200 pg/mL AVP for 6 h, biological replicate 1


title: S.aureus, CP1_cells-treated, 0.2%glucose, rep3

description:
Library name: CP1_cells3_TBS-0.2G
Cells 3 (0.2% Glucose)

value: co-culture with Candida parapsilosis cells in 0.2% glucose


title: ILPo42,90 days postoperative ILE

description: Library name: ILPo42


title: Control GT1-7 cells biol rep 3

description:
Library name: CON3
Untreated control GT1-7 cells, biological replicate 3

value: vehicle control


title: 470140_Smooth_Lactate_R1

description: Library name: S1_Lac


title: ILPo41,90 days postoperative ILE

description: Library name: ILPo41


title: S.aureus, CP1_cells-treated, 0.2%glucose, rep2

description:
Library name: CP1_cells2_TBS-0.2G
Cells 2 (0.2% Glucose)

value: S.aureus biofilm


title: 470140_Wrinkled_Glucose_R3

description: Library name: R3_Glu

value: Candida auris cells

value: 470140 Wrinkled Background


title: S.aureus, CP1_cells-treated, 0.2%glucose, rep1

description:
Library name: CP1_cells1_TBS-0.2G
Cells 1 (0.2% Glucose)

value: culture

value: 24 hour


title: Control GT1-7 cells biol rep 2

description:
Library name: CON2
Untreated control GT1-7 cells, biological replicate 2

value: Cell line


title: ILPo40,90 days postoperative ILE

description: Library name: ILPo40


title: 470140_Wrinkled_Glucose_R2

description: Library name: R2_Glu


title: lib13_round1-R5

description:
Library name: lib13_round1-R5
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

value: in vitro synthetic nucleic acid library; SELEX aptamer library, no native biological cell/tissue origin

value: lib13 ssDNA library, round 5 of the preliminary screening process


title: Control GT1-7 cells biol rep 1

description:
Library name: CON1
Untreated control GT1-7 cells, biological replicate 1

value: GnRH neuron-like cell

value: wild type


title: ILPo39,90 days postoperative ILE

description: Library name: ILPo39


title: 470140_Wrinkled_Glucose_R1

description: Library name: R1_Glu


title: S.aureus, control, 0.2%glucose, rep2

description:
Library name: Control2_TBS-0.2G
control 2 (0.2% Glucose)

value: WT (S. aureus biofilm) in 0.2% glucose


title: S.aureus, control, 0.2%glucose, rep3

description:
Library name: Control3_TBS-0.2G
control 3 (0.2% Glucose)


title: Donor8 CD14+ classical monocyte LPS

city: Heidelberg

first: Micahel

last: Hertwig

country: Germany

institute: Universitätsklinikum Heidelberg

hyb_protocol: Hybridization was performed according to the Illumina HumanHT-12 v4 Expression BeadChip manufacturer protocol.

scan_protocol: Arrays were scanned according to the Illumina HumanHT-12 v4 standard protocol.

data_processing: Raw expression data were background corrected and normalized using built-in negative and positive control probes according to standard Illumina procedures. Differential expression analysis was performed using the limma package in R. P-values were adjusted using the Benjamini-Hochberg method.

source_name: human peripheral blood monocytes

label_protocol: RNA labeling was performed according to the Illumina HumanHT-12 v4 Expression BeadChip manufacturer protocol.

growth_protocol: Peripheral blood mononuclear cells were isolated from healthy donors. Slan+ non-classical monocytes and CD14+ classical monocytes were isolated and cultured under standard conditions at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from purified monocyte populations according to standard laboratory procedures. RNA quality and quantity were assessed prior to hybridization.

treatment_protocol: Cells were incubated for 4 h on untreated plastic, immobilized immune complexes, or with 10 ng/mL lipopolysaccharide (LPS) at 37°C and 5% CO2.

tag: donor

value: CD14+ classical monocytes

value: LPS


title: 470140_Smooth_Glucose_R3

description: Library name: S3_Glu

value: 470140 Smooth Background

value: Grown in Glucose media


title: S.aureus, control, 0.2%glucose, rep1

description:
Library name: Control1_TBS-0.2G
control 1 (0.2% Glucose)


title: Donor8 CD14+ classical monocyte immune complexes

value: immobilized Immune Complexes


title: ILPo38,90 days postoperative ILE

description: Library name: ILPo38

value: feces


title: ILPo37,90 days postoperative ILE

description: Library name: ILPo37


title: Donor8 slan+ non-classical monocyte LPS

value: slan+ non-classical monocytes


title: Donor8 CD14+ classical monocyte untreated

value: untreated


title: 470140_Smooth_Glucose_R1

description: Library name: S1_Glu

value: Candida auris cells


title: ILPo36,90 days postoperative ILE

description: Library name: ILPo36


title: ILPo35,90 days postoperative ILE

description: Library name: ILPo35


title: BRCA_tumor_P20

first: Xiaofeng

last: Zheng

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: Library name: P20

data_processing:
RNA-seq reads were aligned using Kallisto > v0.42.4 to GENCODE v23 transcripts with default parameters.
The protein-coding transcripts, immunoglobulin heavy, kappa and lambda light chains, and TCR-related transcripts were retained.
Noncoding RNA, histone, and mitochondria- related transcripts were removed, resulting in 20,062 protein coding genes.
Gene expression was quantified as the sum of the transcripts and re-normalized per million (TPM) and log2- transformed.
Assembly: GRCh38
Supplementary files format and content: CSV file includes the log2 TMP for each sample

source_name: mammary gland tumor

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA)
Agilent SureSelect XTHS2 RNA kit (Agilent Technologies, Santa Clara, CA). Probes: Agilent V8 + UTR (RNA).

value: mammary gland tumor


title: ILPo34,90 days postoperative ILE

description: Library name: ILPo34


title: Donor8 slan+ non-classical monocyte immune complexes


title: ILPo33,90 days postoperative ILE

description: Library name: ILPo33


title: Donor7 CD14+ classical monocyte LPS


title: BRCA_tumor_P18

description: Library name: P18


title: ILPo32,90 days postoperative ILE

description: Library name: ILPo32


title: BRCA_tumor_P19

description: Library name: P19


title: Donor8 slan+ non-classical monocyte untreated


title: BRCA_tumor_P17

description: Library name: P17


title: Donor7 CD14+ classical monocyte untreated


title: ILPo31,90 days postoperative ILE

description: Library name: ILPo31


title: Donor7 CD14+ classical monocyte immune complexes


title: BRCA_tumor_P15

description: Library name: P15


title: ILPo30,90 days postoperative ILE

description: Library name: ILPo30


title: BRCA_tumor_P14

description: Library name: P14


title: Donor7 slan+ non-classical monocyte LPS


title: ILPo29,90 days postoperative ILE

description: Library name: ILPo29


title: BRCA_tumor_P13

description: Library name: P13


title: ILPo28,90 days postoperative ILE

description: Library name: ILPo28


title: Donor7 slan+ non-classical monocyte untreated


title: ILPo27,90 days postoperative ILE

description: Library name: ILPo27


title: Donor7 slan+ non-classical monocyte immune complexes


title: BRCA_tumor_P12

description: Library name: P12


title: Donor2 CD14+ classical monocyte LPS


title: ILPo17,90 days postoperative ILE

description: Library name: ILPo17


title: BRCA_tumor_P10

description: Library name: P10


title: Donor2 CD14+ classical monocyte immune complexes


title: ILPo10,90 days postoperative ILE

description: Library name: ILPo10


title: BRCA_tumor_P09

description: Library name: P09


title: BRCA_tumor_P08

description: Library name: P08


title: Donor2 CD14+ classical monocyte untreated


title: ILPo02,90 days postoperative ILE

description: Library name: ILPo02


title: BRCA_tumor_P07

description: Library name: P07


title: ILPo01,90 days postoperative ILE

description: Library name: ILPo01


title: Donor2 slan+ non-classical monocyte immune complexes


title: Donor2 slan+ non-classical monocyte LPS


title: SDPr35,preoperative SDT,baseline

description: Library name: SDPr35


title: BRCA_tumor_P06

description: Library name: P06


title: BRCA_tumor_P05

description: Library name: P05


title: Donor2 slan+ non-classical monocyte untreated


title: BRCA_tumor_P04

description: Library name: P04


title: Donor1 CD14+ classical monocyte LPS


title: SDPr34,preoperative SDT,baseline

description: Library name: SDPr34


title: 470140_Smooth_Glucose_R2

first: Traude

last: Beilharz

institute: Monash University

description: Library name: S2_Glu

source_name: Candida auris cells


title: SDPr33,preoperative SDT,baseline

description: Library name: SDPr33


title: BRCA_tumor_P03

description: Library name: P03


title: Donor1 CD14+ classical monocyte immune complexes


title: SDPr32,preoperative SDT,baseline

description: Library name: SDPr32


title: Positive Control (anti-H3K4me3) 24hrs-stimulation rep2

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

department: Genetics

institute: Yale University School of Medicine

description:
Library name: P_2
P.bw

data_processing:
FastQC (version: 0.12.1) was first used to examine the quality of the reads96. Then, reads of each sample (GTC_stimulated and SOCS-KO stimulated) were trimmed using Cutadapt (version: 5.0) and aligned to human genome GRCh38 (gencode v47) with Bowtie282,104. SAMtools (version: 1.21) was used to filter and sort the BAM files98. Duplicate reads were marked and removed using Picard. Then, we used BEDtools (version: v2.30.0) to filter out the reads overlapping with genomic regions curated in ENCODE blacklist99,100. Peak calling was conducted by MACS3 (version: 3.0.1)105 including all biological replicates for experimental group ad control group (IgG input control), followed by peak comparison between the samples using BEDtools100. Both peak annotation and motif analysis were done via HOMER (version: 5.1)106. For visualization, BAM files from GTC_stimulated and SOCS3-KO_stimulated were normalized by count per million (CPM) using bamCoverage (deepTools2, version: 3.5.5) and log2 fold change with respect to IgG control was calculated using bigwigCompare (deepTools2), followed by heatmap generation107. Normalized Bigwig files were then visualization on UCSC Genome Browser.
Assembly: GRCh38 (gencode v47)
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: CAR-T cells

extract_protocol:
CUT&RUN was performed on FACS-isolated CAR-T cells, including stimulated GTC and SOCS3-KO population, followed by the library prep using the EpiCypher CUTANA™ protocol. Briefly, 1 × 10⁶ CAR-T cells were washed with ice-cold PBS and resuspended in nuclei isolation buffer (100 mM HEPES-KOH pH 7.6, 100 mM KCl, 5 mM MgCl₂, 0.5% NP-40, supplemented with Roche Complete Protease Inhibitor).
EpiCypher CUTANA™ kit was used to construct the library. Briefly, 1 × 10⁶ CAR-T cells were washed with ice-cold PBS and resuspended in nuclei isolation buffer (100 mM HEPES-KOH pH 7.6, 100 mM KCl, 5 mM MgCl₂, 0.5% NP-40, supplemented with Roche Complete Protease Inhibitor). Cells were incubated on ice for 10 minutes to isolate nuclei. Isolated nuclei were washed twice with CUT&RUN wash buffer and incubated with activated concanavalin A (ConA) magnetic beads for 10 minutes at room temperature. The bead-bound nuclei were then incubated overnight at 4 °C in antibody buffer containing one of the following antibodies: anti-Nur77 (Cell Signaling), anti-H3K4me3 (positive control), or rabbit IgG (negative control). Following antibody binding, nuclei were washed with Cell Permeabilization Buffer and incubated with 2.5 μL of pAG-MNase for 10 minutes at room temperature. After two additional washes, targeted chromatin digestion was initiated by adding 1 μL of 100 mM CaCl₂ and incubating the samples on ice for 2 hours. The reaction was terminated by adding 33 μL of stop buffer, and 1 μL of Escherichia coli spike-in DNA was added to each sample as an internal control. DNA fragments were purified using spin-column-based DNA cleanup kits. Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina (Index Primer Sets 1 and 2). Library quality and fragment size distribution were assessed using an Agilent TapeStation. Libraries passing quality control were sequenced on an Illumina NovaSeq platform with 150-bp paired-end reads.

treatment_protocol: Human CAR-T cells were infected with SOCS3-KO or GTC lentiviral vector and stimulated with cancer cells for 24hrs.

value: CAR-T cells

value: CAR-T 24hrs stimulation

tag: cut&run antibody


title: Donor1 slan+ non-classical monocyte LPS


title: Positive Control (anti-H3K4me3) 24hrs-stimulation rep3

description:
Library name: P_3
P.bw


title: SDPr30,preoperative SDT,baseline

description: Library name: SDPr30


title: Donor1 slan+ non-classical monocyte immune complexes


title: Donor1 CD14+ classical monocyte untreated


title: Positive Control (anti-H3K4me3) 24hrs-stimulation rep1

description:
Library name: P_1
P.bw


title: SDPr29,preoperative SDT,baseline

description: Library name: SDPr29


title: SDPr31,preoperative SDT,baseline

description: Library name: SDPr31


title: SOCS3-KO 24hrs-stimulation rep3

description:
Library name: S_S3
S_S.bw

value: SOCS3-KO 24hrs stimulation

value: anti-Nur77 (Cell Signaling Technology)


title: Donor1 slan+ non-classical monocyte untreated


title: SDPr28,preoperative SDT,baseline

description: Library name: SDPr28


title: SOCS3-KO 24hrs-stimulation rep2

description:
Library name: S_S2
S_S.bw


title: 06_wt_RNAi-dve1_3

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

description:
Library name: dve1_replicate3
Columns in ATAC_RNAi_dev1.tab: “seqnames”,"start",“end”,“width”, “strand”, “width”, “control_replicate1”, “control_replicate2”, “control_replicate3”, “dve1_replicate1” ,“dve1_replicate3”

data_processing:
Adaptors were trimmed using cutadapt  (https://github.com/marcelm/cutadapt)
reads were aligned to the ce10 genome assembly using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with alignment parameters set to --sensitive
Mapped reads were marked and removed using the MarkDuplicates function of pickard tools 2.20.0 (https://broadinstitute.github.io/picard/)
Paired end reads were converted to single end reads using bedtools 2.26 (https://github.com/arq5x/bedtools2) and reads were shifted + 4 bp and − 5 bp for positive and negative strand respectively to account for characteristics of the Tn5 enzyme.
Peaks were called using MACS2 with the following parameters: -g 93260000 --nomodel --shift -100 --extsize 200, or reads were counted 1.5kb upstream and 200 bp downstream of the TSS using the qcount function in the QuasR R package (v. 3.2)
Assembly: ce11 (WBcel235)
Supplementary files format and content: Tab-delimited file. First column contains chromosome identifier start, end position and width, following columns contain raw counts of reads overlapping each gene for each sample.

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: DNA was isolated from mixed embryos grown at 20°C after L1 synchronization in previous generation on RNAi bacteria expressing empty vector or dsRNA complementary to dve-1  in 3 independent biological replicates.

extract_protocol:
ATAC-seq was performed on 100000 sorted cells following the Omni-ATAC protocol (PMID: 28846090).
Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).

treatment_protocol: cells where isolated from embryos grown on RNAi bacteria expressing empty vector or dsRNA complementary to dve-1 for one generation in 3 independent biological replicates.

value: embryo

value: wild type (N2)

value: RNAi dve-1


title: SOCS3-KO 24hrs-stimulation rep1

description:
Library name: S_S1
S_S.bw


title: SDPr27,preoperative SDT,baseline

description: Library name: SDPr27


title: 05_wt_RNAi-dve1_2

description:
Library name: dve1_replicate2
Columns in ATAC_RNAi_dev1.tab: “seqnames”,"start",“end”,“width”, “strand”, “width”, “control_replicate1”, “control_replicate2”, “control_replicate3”, “dve1_replicate1” ,“dve1_replicate3”


title: 04_wt_RNAi-dve1_1

description:
Library name: dve1_replicate1
Columns in ATAC_RNAi_dev1.tab: “seqnames”,"start",“end”,“width”, “strand”, “width”, “control_replicate1”, “control_replicate2”, “control_replicate3”, “dve1_replicate1” ,“dve1_replicate3”


title: SDPr26,preoperative SDT,baseline

description: Library name: SDPr26


title: 03_wt_RNAi-emptyVector_3

description:
Library name: control_replicate3
Columns in ATAC_RNAi_dev1.tab: “seqnames”,"start",“end”,“width”, “strand”, “width”, “control_replicate1”, “control_replicate2”, “control_replicate3”, “dve1_replicate1” ,“dve1_replicate3”

value: RNAi empty vector (L4440)


title: Negative Control (anti-IgG) 24 hrs-stimulation rep2

description:
Library name: N_2
N_2.bw

value: IgG control


title: SDPr25,preoperative SDT,baseline

description: Library name: SDPr25


title: Negative Control (anti-IgG) 24 hrs-stimulation rep3

description:
Library name: N_3
N_2.bw


title: Negative Control (anti-IgG) 24 hrs-stimulation rep1

description:
Library name: N_1
N_2.bw


title: PF+MBV repeat 4

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Library name: Sample 16

data_processing:
The raw sequencing data were filtered using Trimmomatic to remove low-quality reads and adapter sequences.
After preprocessing, the retained reads were aligned to the mouse reference genome (mm10) using the STAR aligner
Assembly: mm10
Supplementary files format and content: TAB for gene count

source_name: liver

extract_protocol:
Total RNA was extracted from liver tissue using RNA-STAT60 (Tel-Test, Ambion, Austin, TX) according to the manufacturer’s instructions. Briefly, samples were homogenized in RNA-STAT60, phase-separated with chloroform, and RNA was precipitated with isopropanol, washed with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA quantity and purity were assessed using a Nanodrop.
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.

value: liver

value: PF+MBV


title: GTC 24hrs-stimulation rep3

description:
Library name: G_S3
G_S.bw

value: GTC 24hrs stimulation


title: SDPr23,preoperative SDT,baseline

description: Library name: SDPr23

value: feces


title: 01_wt_RNAi-emptyVector_1

description:
Library name: control_replicate1
Columns in ATAC_RNAi_dev1.tab: “seqnames”,"start",“end”,“width”, “strand”, “width”, “control_replicate1”, “control_replicate2”, “control_replicate3”, “dve1_replicate1” ,“dve1_replicate3”


title: PF+MBV repeat 3

description: Library name: Sample 15


title: GTC 24hrs-stimulation rep2

description:
Library name: G_S2
G_S.bw


title: GTC 24hrs-stimulation rep1

description:
Library name: G_S1
G_S.bw


title: PF+MBV repeat 2

description: Library name: Sample 14


title: SCRNAseq_2

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: SCRNAseq_2
10x Genomics

library_source: transcriptomic single cell

data_processing:
10X
Other : CITE-seq
For the single cells, the demultiplexing, barcoded processing, gene counting  were made using the Cell Ranger software version 8.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A for the scRNA-seq and vdj_GRCh38_alts_ensembl-7.1.0 for sc V(D)J-seq.
Supplementary files format and content: barcodes, features and matrix files

source_name: tumor

extract_protocol:
FACS sorting for scRNAseq
Human TCR RNA Multiplex-Thrm-001 Kit (MiLaboratories)  for bulk TCR,

value: tumor

value: T cells


title: SDPr21,preoperative SDT,baseline

description: Library name: SDPr21


title: EtOH+MBV repeat 4

description: Library name: Sample 12

value: EtOH+MBV


title: SDPr20,preoperative SDT,baseline

description: Library name: SDPr20


title: tumor cell from control tumor, CR, replicate 1

city: Wuhan

first: Wenlong

last: Jia

address: 1095 Jiefang Avenue

institute: Tongji Hospital

description: Library name: CR

data_processing:
Raw sequencing reads were quality controlled. Reads from human LM3 samples were aligned to the Homo sapiens reference genome GRCh38/hg38, whereas reads from mouse tumor-cell samples were aligned to the Mus musculus reference genome GRCm38/mm10, using Bowtie2.
Genome-wide accessible chromatin regions were identified using MACS2. Peak files were generated separately for each biological sample.
Normalized chromatin-accessibility signal tracks were generated for genome-browser visualization. ATAC-seq accessibility profiles were visualized using Integrative Genomics Viewer.
Assembly: For human LM3 samples: Homo sapiens GRCh38/hg38  For mouse tumor-cell samples: Mus musculus GRCm38/mm10
Supplementary files format and content: Processed data include BED or narrowPeak files containing accessible chromatin regions identified for each sample and normalized bigWig signal files showing genome-wide ATAC-seq accessibility profiles. Differentially accessible region tables comparing high- versus low-glucose LM3 cells and control-diet versus caloric restriction–derived mouse tumor cells are also provided, where applicable.

source_name: liver tumor

growth_protocol: Human LM3 hepatocellular carcinoma cells were maintained in culture under standard conditions. For the in vivo arm, male C57BL/6J mice were housed under specific-pathogen-free conditions with controlled temperature, humidity, and a 12-hour light/dark cycle. GFP-labeled tumor cells were implanted into mice to establish tumor-bearing models. Mice were assigned to either a control diet or a caloric restriction (CR) diet.

extract_protocol:
For LM3 samples, cultured cells were collected, washed with ice-cold phosphate-buffered saline, and lysed in cold lysis buffer to release nuclei. For mouse tumor samples, sorted GFP-positive tumor cells were washed with ice-cold phosphate-buffered saline and lysed in cold lysis buffer to release nuclei. Approximately 50,000 cells were used for each sample. Nuclei were collected by centrifugation and subjected to Tn5 transposase-mediated tagmentation.
ATAC-seq libraries were constructed using a Tn5 transposase-based library preparation kit (Vazyme Biotech, TD711). Isolated nuclei were incubated with the transposition reaction mixture at 37°C for 30 minutes. Tagmented DNA was purified, PCR-amplified, and subjected to high-throughput sequencing on an Illumina platform.

treatment_protocol: For the in vitro arm, LM3 cells were cultured under plasma-level high-glucose or tumor-relevant low-glucose conditions before collection for bulk ATAC-seq. For the in vivo arm, tumor-bearing mice were maintained on a control diet or subjected to caloric restriction. At the designated experimental endpoint, tumors were collected and dissociated into single-cell suspensions. Live GFP-positive tumor cells were isolated by fluorescence-activated cell sorting and immediately processed for bulk ATAC-seq.

value: liver tumor

value: Tumor cells

value: Caloric restriction


title: SCTCR_1

description:
Library name: SCTCR_1
10x Genomics


title: SDPr24,preoperative SDT,baseline

description: Library name: SDPr24


title: tumor cellr, High glucose, replicate 1

description: Library name: High

data_processing:
Raw sequencing reads were subjected to quality control and adapter trimming. Clean reads were aligned to the Homo sapiens reference genome GRCh38/hg38 using Bowtie2.
Duplicate or low-quality reads were removed, and genome-wide MYC-enriched regions were identified using a peak-calling algorithm. Peak files were generated separately for each biological sample.
Normalized MYC occupancy signal tracks were generated for genome-browser visualization. Genome-wide signal profiles and MYC-binding regions were visualized using Integrative Genomics Viewer.
Comparative analyses were performed to identify changes in MYC chromatin occupancy among high-glucose, low-glucose, and low-glucose plus MYC-overexpression conditions, with particular attention to the promoter and transcription start site regions of SLC1A5.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: Processed data include BED or narrowPeak files containing MYC-enriched chromatin regions identified for each sample and normalized bigWig files showing genome-wide MYC occupancy profiles. Differential binding tables comparing the indicated glucose and MYC-expression conditions are also provided, where applicable.
Library strategy: CUT&Tag

growth_protocol: Human hepatocellular carcinoma cells were maintained under standard culture conditions at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Cells were collected and incubated with concanavalin A–coated magnetic beads. Cell membranes were permeabilized, and bead-bound cells were incubated with an anti-MYC primary antibody overnight at 4°C, followed by incubation with a secondary antibody. After washing, the cells were incubated with a protein A–Tn5 transposase fusion complex for antibody-guided chromatin tagmentation.
CUT&Tag libraries were constructed using the Hyperactive Universal CUT&Tag Assay Kit (Vazyme Biotech, TD904) according to the manufacturer’s protocol. Tagmented DNA was purified and PCR-amplified to generate sequencing libraries. Libraries were subjected to paired-end high-throughput sequencing on the SURFSeq 5000 platform.

treatment_protocol: Cells were cultured under plasma-level high-glucose, tumor-relevant low-glucose, or tumor-relevant low-glucose conditions with MYC overexpression before CUT&Tag profiling. CUT&Tag was performed using an antibody against MYC to assess glucose- and MYC-dependent changes in chromatin occupancy.

value: MHCC97H cultured in high glucose, MYC bindding


title: SDPr19,preoperative SDT,baseline

description: Library name: SDPr19


title: tumor cell from control tumor, Con, replicate 1

description: Library name: Con

value: Control


title: HTO_1

description:
Library name: HTO_1
10x Genomics

data_processing:
10X
Other : CITE-seq
For the single cells, the demultiplexing, barcoded processing, gene counting  were made using the Cell Ranger software version 8.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A for the scRNA-seq and vdj_GRCh38_alts_ensembl-7.1.0 for sc V(D)J-seq.
Supplementary files format and content: barcodes, features and matrix files
Library strategy: CITE-seq


title: HTO_2

description:
Library name: HTO_2
10x Genomics


title: EtOH+MBV repeat 3

description: Library name: Sample 11


title: SDPr18,preoperative SDT,baseline

description: Library name: SDPr18


title: SCRNAseq_1

description:
Library name: SCRNAseq_1
10x Genomics


title: EtOH+MBV repeat 2

description: Library name: Sample 10


title: SDPr17,preoperative SDT,baseline

description: Library name: SDPr17


title: Tyrphostin 6

city: Hanover

first: Hannah

last: VanBenschoten

state: NH

address: 15 Thayer Dr

department: Thayer School of Engineering

institute: Dartmouth College

description:
Library name: Tyrp_6
Column name in ProcessedData.csv: Tyrp_6

data_processing:
Sequence reads were aligned to GRCm38.97 using STAR Aligner
Read count extraction was performed using ht-seq
Assembly: GRCm38.97
Supplementary files format and content: ProcessedData.csv file includes raw counts for all samples

source_name: eIVFG follicle

extract_protocol:
RNA was extracted using RNA-SPRI beads with 10 µL of cell lysate
RNA libraries for RNA-seq were constructed using Smart-Seq2 protocol

treatment_protocol: Triplicate antral eIVFG follicles per sample were treated with 10 µM Tyrphostin-AG1478 in DMSO and hCG for 4 hours

value: eIVFG follicle


title: Tyrphostin 5

description:
Library name: Tyrp_5
Column name in ProcessedData.csv: Tyrp_5


title: PTEC, vehicle control, replicate 3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Library name: Sample9

data_processing:
FASTQ files were aligned to the Gencode GRCh38 v45 genome using HiSat2 and coordinate sorted using samtools
Counts/gene were summarized using the Bioconductor Rsubread package, using the gencode v45 GTF file
Assembly: Gencode GRCh38 v45
Supplementary files format and content: Text file with genes in rows and samples in columns

source_name: Primary PTEC cell culture

growth_protocol: The 3D platform used in these experiments was developed by Nortis Inc, specifically carried out with triple channel MPS devices (Triplex ™; Nortis Inc) and  prepared according to previous procedures (Imaoka et al., 2020; Weber et al., 2016). Briefly, the devices were filled with 6 mg/mL rat tail collagen type 1 (Ibidi, Madison, WI) at 4°C, and left at room temperature overnight to allow the extracellular matrix to solidify. Mandrels of the platforms were removed and PTEC media perfused through the hollow channels overnight at 1 µL/min. Channels were coated with mouse collagen IV at 0.1 mg/mL (Corning, NY) to facilitate PTEC adhesion, followed by injection of 2.5 µL of a PTEC suspension (PTM16) at 20 x 106 cells/mL. Cells were left to adhere to channels for 3-4 hours in 5% CO2 incubator and devices were subsequently perfused at 1 µL/min for several days before experiment treatment. Kidney MPS that exhibited functional channels and appropriate cell density were used for treatment. All chip related experiments used donor PTM16.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891).
Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA).

treatment_protocol: MPS were treated with vehicle (0.1% DMSO; n=3), 100 nM of C12 BAC (n=3) and 100 nM C14 BAC (n=3) for 1 week. Chip effluents were collected every 24 hours to evaluate quantitation of BACs and metabolites.

value: Primary PTEC cell culture

value: PTEC

value: vehicle control


title: EtOH+MBV repeat 1

description: Library name: Sample 9


title: SDPr16,preoperative SDT,baseline

description: Library name: SDPr16

data_processing:
Relative abundance: Top 20 taxa of each sample at each taxonomic ranks (Phylum, Class, Order, Family, Genus, Species) were selected to plot the distribution histogram of relative abundance in Perl through SVG function. Alpha and Beta Diversity: For analyzing community diversity, richness, and evenness, alpha diversity was calculated using Shannon and Simpson indices in QIIME2. Beta diversity was performed with Principal Coordinates Analysis (PCoA) and Adonis analysis. Community difference analysis: T-test, and linear discriminant analysis effect size (LEfSe) were conducted to characterize community structure differentiation. Function Prediction: PICRUSt2 (V2.3.0) was applied to predict metagenomic functions based on marker genes. Canonical correspondence analysis (CCA) were used to explore interspecies symbiosis and environmental impacts on community structure, reflecting correlations between environmental factors and genus/species abundance.
Continuous variables were expressed as mean with standard deviation and compared using the Student’s T test. Categorical data, on the other hand, were represented as frequencies and percentages, and comparisons were made using the Pearson χ2 test or the Fisher exact test, depending on suitability. A two-sided p value less than 0.05 was considered statistically significant. All data analyses were conducted using the R software package (version 4.0).
Assembly: 16S rRNA gene reference database(Silva 138.1)
Supplementary files format and content: Processed data are ASV feature count matrix (tab-delimited TSV format). Rows represent individual ASVs, columns correspond to sample IDs, and values denote raw sequencing read counts of each ASV across all fecal samples. Taxonomic classification results assigned against SILVA 138.1 database are also provided in the feature table.
Library strategy: 16S rRNA-seq

source_name: feces


title: Tyrphostin 4

description:
Library name: Tyrp_4
Column name in ProcessedData.csv: Tyrp_4


title: PTEC, vehicle control, replicate 2

description: Library name: Sample8


title: SDPr15,preoperative SDT,baseline

description: Library name: SDPr15


title: EtOH repeat 4

description: Library name: Sample 8

value: EtOH


title: Tyrphostin 3

description:
Library name: Tyrp_3
Column name in ProcessedData.csv: Tyrp_3


title: PTEC, vehicle control, replicate 1

description: Library name: Sample7


title: EtOH repeat 3

description: Library name: Sample 7

value: liver


title: SDPr14,preoperative SDT,baseline

description: Library name: SDPr14


title: Tyrphostin 2

description:
Library name: Tyrp_2
Column name in ProcessedData.csv: Tyrp_2


title: PTEC, 100nM C14 BAC, replicate 3

description: Library name: Sample6

value: 100nM C14 BAC


title: EtOH repeat 2

description: Library name: Sample 6


title: Tyrphostin 1

description:
Library name: Tyrp_1
Column name in ProcessedData.csv: Tyrp_1


title: PTEC, 100nM C14 BAC, replicate 2

description: Library name: Sample5


title: EtOH repeat 1

description: Library name: Sample 5


title: SDPr13,preoperative SDT,baseline

description: Library name: SDPr13


title: SDPr12,preoperative SDT,baseline

description: Library name: SDPr12


title: Control 11

description:
Library name: Ctrl6_2
Column name in ProcessedData.csv: Ctrl6_2


title: PTEC, 100nM C14 BAC, replicate 1

description: Library name: Sample4


title: PF repeat 4

description: Library name: Sample 4

value: PF


title: SDPr11,preoperative SDT,baseline

description: Library name: SDPr11

value: feces


title: Control 10

description:
Library name: Ctrl6_1
Column name in ProcessedData.csv: Ctrl6_1


title: PTEC, 100nM C12 BAC, replicate 3

description: Library name: Sample3

value: 100nM C12 BAC


title: PF repeat 3

description: Library name: Sample 3


title: SDPr10,preoperative SDT,baseline

description: Library name: SDPr10


title: Control 9

description:
Library name: Ctrl5_1
Column name in ProcessedData.csv: Ctrl5_1


title: PTEC, 100nM C12 BAC, replicate 2

description: Library name: Sample2


title: PF repeat 2

description: Library name: Sample 2


title: SDPr09,preoperative SDT,baseline

description: Library name: SDPr09


title: PTEC, 100nM C12 BAC, replicate 1

description: Library name: Sample1


title: Control 8

description:
Library name: Ctrl4_2
Column name in ProcessedData.csv: Ctrl4_2


title: 02_wt_RNAi-emptyVector_2

description:
Library name: control_replicate2
Columns in ATAC_RNAi_dev1.tab: “seqnames”,"start",“end”,“width”, “strand”, “width”, “control_replicate1”, “control_replicate2”, “control_replicate3”, “dve1_replicate1” ,“dve1_replicate3”

value: embryo

value: wild type (N2)

value: RNAi empty vector (L4440)


title: PF repeat 1

description: Library name: Sample 1


title: DNA from Wilms Tumor 11

city: Caserta

first: Abu

last: Saadat

state: Caserta

address: Via Vivaldi, 43

department: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies

country: Italy

institute: Università degli Studi della Campania Luigi Vanvitelli

description: DNA from Wilms Tumor

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing:
R library minfi and ChAMP
processed value definition: Normalized Beta value

source_name: Kidney

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard phenol-chloroform-isoamyl alchohol protocol

value: Kidney

tag: Sex

value: Female

tag: tissue type

value: Wilms tumor


title: Control 7

description:
Library name: Ctrl4_1
Column name in ProcessedData.csv: Ctrl4_1

value: Control