title: CI_Day14

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using cellranger (6.1.2) mkfastq
Fastq files were aligned to Mus musculus mm10 reference using cellranger (6.1.2) count
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped cellranger count output directory (filtered_feature_bc_matrix).

source_name: brain

extract_protocol:
Tissue frozen with liquid nitrogen was placed between aluminum foil on dry ice and crashed with a hammer. Crushed tissue was placed in Lysis Buffer to extract nuclei and debris was removed using Debris Removal Solution. DAPI was added to the resulting nuclear suspension and DAPI-positive nuclei were sorted and collected using a BD FACS Aria III instrument.
Collected nuclei were washed with PBS containing 1% Bovine Serum Albumin (BSA) and resuspended at the appropriate concentration. Libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1(10x Genomics) according to the manufacturer's protocol.

value: brain

value: ischemic stroke


title: Breast cancer serum sample 124

status: Public on Feb 20 2026

type: RNA

city: Santander

first: Inés

last: Gómez-Acebo

state: CANTABRIA

address: Avda. Cardenal Herrera Oria S/N

country: Spain

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

data_processing: Cq values were determined using the second derivative method in Roche LightCycler software. Quality control included melting curve analysis, exclusion of reactions with more than one melting temperature, deviation from reference melting temperatures, and low amplification efficiency. Endogenous miRNAs let-7d-5p and let-7i-5p were used as internal reference controls. Expression data were normalized and subsequently log2-transformed for statistical analysis. Batch information is provided in the sample annotations.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: Not applicable. Quantification was performed using SYBR Green chemistry.

growth_protocol: Not applicable. Human serum samples collected from participants in the MCC-Spain study.

extract_protocol: Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN). Serum samples were thawed on ice and centrifuged at 3,000×g for 5 minutes at 4 °C. Buffer RPL containing carrier RNA and spike-in template mix was added, followed by Buffer RPP. RNA was eluted in 50 µL according to the manufacturer’s protocol.

treatment_protocol: Blood samples were collected prior to any oncological treatment (surgery, chemotherapy, or radiotherapy).

tag: tissue

value: Serum

value: case

value: Basal-like

tag: age


title: Mouse, beta cells, Chd3Db. Replicate 1

type: SRA

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

country: USA

institute: Indiana University

description: Library name: Chd3Db_1

library_source: transcriptomic

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10 UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: GRCm39
Supplementary files format and content: TPM all paired files included in 1 table

molecule: polyA RNA

organism: Mus musculus

source_name: Pancreatic beta cells

extract_protocol:
RNA was isolated from FACS-purified β cells using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher). The DNAse treated RNA was analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 7.5 were used for cDNA synthesis and library preparation.
cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). A dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. The average size of the library insert was approximately 300-400 bp

value: Pancreatic beta cells

tag: cell type

value: beta cell

tag: genotype


title: CI_Day3

library_source: transcriptomic single cell

tag: strain

tag: treatment


title: Breast cancer serum sample 122


title: ShamOpe

value: sham


title: Con_mock_1

city: Davis

first: Tina

last: Truong

state: California

address: One Shields Ave

institute: UC Davis

description:
Library name: Sample 4
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   Con_mock_1

data_processing:
R was used for limma-voom pipeline on R with multiple testing correction using Benjamini-Hochberg procedure.
Assembly: GRCh38.p13 human genome
Supplementary files format and content: Tab-delineated text file includes normalized counts for each sample.

growth_protocol: purchased from ATCC. THP-1 cells were cultured in RPMI media containing 10% fetal bovine serum (FBS), 10mM HEPES, 1mM sodium pyruvate, 4500 mg/L glucose, and 0.05 mM 2-mercaptoethanol.

extract_protocol:
Macrophages were lysed in Trizol and lysates were purified with silica spin columns (Purelink) per manufacturer instructions.
RNA was purified and barcoded 3'Tag-Seq libraries prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer by the UC Davis DNA Sequencing core.

treatment_protocol: Differentiated THP-1 cells were infected at MOI=10 for 6 h with lpqN Mtb in three independent experiments on different days.

tag: cell line

value: Macrophage

value: WT

value: Uninfected


title: Con_mock_2

description:
Library name: Sample 5
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   Con_mock_2


title: Breast cancer serum sample 123

value: Luminal A


title: Mouse, beta cells, Chd3-4Db. Replicate 1

description: Library name: Chd3-4Db_1

library_source: genomic

data_processing:
The pooled libraries were then denatured and neutralized before loading to NovaSeq 6000 sequencer at 300 pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 100 x 106 reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).
Assembly: GRCm39
Supplementary files format and content: TPM all paired files included in 1 table

molecule: genomic DNA

extract_protocol:
Tomato+ mature β-cells were collected for ATAC-Sequencing. Cells were first lysed to collect nuclei by incubating with 100 μL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 0.10% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA, 1 mM DTT, 40 U/uL RNase Inhibitor) for 3 minutes, centrifuging at 300 rcf for 5 minutes at 4°C, and discarding the supernatant. The resulting nuclei were then washed with 1 mL wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 1% BSA, 1 mM DTT, 40 U/μl RNase Inhibitor) and centrifuged at 200 rcf for 5 minutes at 4°C for 2-3 times. The final nuclei were used for tagmentation and library preparation
Nuclei were immediately suspended in 50 μL tagmentation reaction using 2xTD buffer (Illumina, FC-121-1030) and Nextera Tn5 Transposase enzyme (Illumina, FC-121-1030). Fragments greater than 600 bp were excluded in library preparation. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity


title: Con_TB_3

description:
Library name: Sample 3
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   Con_TB_3

value: Mtb infected


title: brain_6

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (v2.20.0.422)
Fastq files were aligned to Mus musculus mm10 reference using STAR aligner (2.7.9a)
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped STAR output directory (Solo.out).

source_name: Brain

extract_protocol:
Tissue was obtained from mouse brains by shaving with a razor blade. The resulting tissue was washed in PBS and dissociated into single cells using the Adult Brain Dissociation Kit.
RNA-seq library was constructed using a modified sciRNA-seq protocol. The target cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the xGen™ ssDNA & Low-Input DNA Prep (IDT). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

value: Brain


title: Breast cancer serum sample 125


title: Mouse, beta cells, Control. Replicate 4

description: Library name: Control_4

value: Control


title: Breast cancer serum sample 120


title: Mouse, beta cells, Chd3-4Db. Replicate 2

description: Library name: Chd3-4Db_2


title: Mouse, beta cells, Control. Replicate 3

description: Library name: Control_3


title: Con_TB_1

description:
Library name: Sample 1
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   Con_TB_1


title: Healthy


title: Con_TB_2

description:
Library name: Sample 2
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   Con_TB_2


title: Mouse, beta cells, Control. Replicate 2

description: Library name: Control_2


title: brain_5


title: ATAC_NSC29C_WT_siARID1A_72h

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

institute: National Cancer Center Research Institute

description: Library name: ATAC_NSC29C_WT_siARID1A_72h

data_processing:
Raw RNA-seq data were trimmed with fastp version 0.12.4 and mapped to the hg38 genome with HISAT2 version 2.2.1 (RRID: SCR_015530) (27). TPM values were calculated using Strand NGS ver 4.0 (TOMY).
Raw sequencing data from ATAC-seq were trimmed using fastp version 0.12.4 (RRID: SCR_016962) and mapped to the human reference genome (hg38) using Bowtie2 version 2.4.5 (RRID: SCR_016368), with parameters -k 1 --no-mixed --no-discordant -X 2000. Before all downstream analyses, duplicate reads were removed using the MarkDuplicates command in picard version 2.26.11 (RRID: SCR_006525) [http://broadinstitute.github.io/picard]. CPM values in the genome tracks were calculated from the ATAC-seq data.
Assembly: hg38
Supplementary files format and content: BigWig files for the ATAC-seq and RNA-seq data were generated using the bamCoverage command from deepTools version 3.5.1 (RRID: SCR_016366), with parameters --normalizeUsing CPM --binSize 10 --smoothLength 30.

source_name: diffuse gastric cancer

growth_protocol: RNA-seq: 5 × 10^5 cells were trypsinized, reseeded in 6-well plates for 24 h.

extract_protocol:
The cells were then washed with PBS, and RNA was isolated using the RNeasy Mini Kit (Qiagen)
Library preparation for RNA-seq samples was performed in the Rhelixa using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
ATAC-seq analysis was performed by DNAFORM. Cells (1 × 105) were lysed and the transposition reaction was performed with Tn5 Transposase (Illumina, FC121-1030) at 37°C for 30 min. The reaction liquid was purified using the MinElute PCR Purification Kit (Qiagen, 28004). Next, five cycles of PCR were conducted using custom Nextera PCR primers and NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB, M0543S). The number of additional PCR cycles was determined by qPCR of the partly amplified products. The PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), using double size selection (left ratio: 1.4×; right ratio: 0.5×), according to the manufacturer’s protocol.

treatment_protocol: ATAC-seq: ARID1A-proficient NSC-29C cells (5 × 105) were cultured in 6-well plates and transfected for 72 h with siRNAs (10 nM) for non-targeting or ARID1A using Lipofectamine RNAiMAX (Thermo Fisher Scientific; 13778150).

value: diffuse gastric cancer

value: Patient-derived Cells

value: siARID1A for 72 h


title: brain_4


title: Mouse, beta cells, Control. Replicate 1

description: Library name: Control_1


title: Breast cancer serum sample 117


title: brain_3


title: ATAC_NSC29C_WT_siNT_72h

description: Library name: ATAC_NSC29C_WT_siNT_72h

value: siNT for 72 h


title: Breast cancer serum sample 118

value: Serum


title: Breast cancer serum sample 121

value: case


title: Breast cancer serum sample 116


title: brain_2


title: brain_1


title: Breast cancer serum sample 119


title: DMEM_EV_FL3_unconditioned_medium_2

city: Saarbrücken

first: Shusruto

last: Rishik

state: Saarland

address: Informatik Campus E2.1

department: Zentrum für Bioinformatics

country: Germany

institute: Universität des Saarlandes

description:
Library name: DMEM_EV_FL3_unconditioned_medium_2
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL3_Medium_13

data_processing:
For miRNA miRmaster 2.0 pipeline was used to trim, collapse and quantify the single-end sequencing fastq files using miRNA set in miRBase 22.1 correspoinding to hg38. Counts were normalized using reads per million mapped miRNA.
Assembly: GRCh38
Supplementary files format and content: tab delimited file containing raw reads for each sample.

source_name: Media Only

extract_protocol:
Total EV-RNA was isolated from 400 µl EV fraction with the highest particle concentration using miRNeasy Serum/Plasma Kit (Qiagen) according to the manufacturer’s instructions with modifications.
DNA libraries were prepared using the MGIEasy smallRNA Library Prep Kit (MGI Technologies) according to the manufacturer’s recommendations. In brief, 100 ng of RNA from conditioned or unconditioned medium EVs were used as input. Amplified PCR products were separated using 6 % TBE gel electrophoresis. Different barcoded samples were pooled in equal amount and circularized to generate single stranded DNA libraries (ssDNA). DNA nanoball (DNB) preparation and single-end sequencing (SE50) was carried out as a service at BGI (Shenzhen, China).

value: Media Only

tag: condition

value: unconditioned medium


title: MG91 HFpEF+SUC3

city: Beijing

first: Yumeng

last: Jia

state: Beijing

address: Youanmen street

country: China

institute: Capital Medical University

description:
Library name: Sample15
Column name in counts_anno.txt: MG91HFpEFSUC3

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 45 raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 40 clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2 FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. P value < 0.05 and foldchange < 0.58 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
After reads ressembled by StringTie2, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
Assembly: NCBI_GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv file include FPKM values for each Sample

source_name: Heart

growth_protocol: A two-hit HFpEF model was established using L-NAME in combination with a high-fat diet for 12 weeks

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: On the basis of the HFpEF model, mice were further treated with or without succinate

value: Heart

value: Myh6Cre Gpr91fl/fl

value: 2-Hit HFpEF model+succinate

tag: batch

value: HFpEF 12weeks


title: Breast cancer serum sample 115


title: Breast cancer serum sample 114


title: MG91 HFpEF+SUC2

description:
Library name: Sample14
Column name in counts_anno.txt: MG91HFpEFSUC2


title: AKOm6_P14_3

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
FASTQ files were extracted and sequencing adapters and low-quality reads were removed by Cutadapt (v.2.3)
Quality of the processed FASTQ files were checked by FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0)
EdgeR (v.3.26.1) was used to identify differentially expressed genes.
Assembly: Assembly: Esembl GRCm38.102
Supplementary files format and content: Supplementary files format and content: CSV, raw counts of sequencing reads on the gene level

source_name: Heart ventricle

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committees.

extract_protocol:
Total RNA from the embryonic heart ventricles was isolated using TRIzol (Invitrogen) from tissues using standard protocol. rRNA-depleted libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina) RNA-sequencing was processed by GENEWIZ using Illumina platform (paired-ended, 150bp read-length)
rRNA-depletion library

value: Heart ventricle

tag: developmental stage

tag: Sex

value: Female


title: DMEM_EV_FL3_unconditioned_medium_1

description:
Library name: DMEM_EV_FL3_unconditioned_medium_1
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL3_Medium_12


title: MG91 HFpEF+SUC4

description:
Library name: Sample16
Column name in counts_anno.txt: MG91HFpEFSUC4


title: AWT_P14_3


title: Caco2_EV_FL3_conditioned_medium_3

description:
Library name: Caco2_EV_FL3_conditioned_medium_3
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL3_3.MW_14

value: conditioned medium


title: MG91 HFpEF+SUC1

description:
Library name: Sample13
Column name in counts_anno.txt: MG91HFpEFSUC1


title: Breast cancer serum sample 113

value: Luminal B


title: Caco2_EV_FL3_conditioned_medium_2

description:
Library name: Caco2_EV_FL3_conditioned_medium_2
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL3_3.MW_13


title: AKOm6_P14_2


title: Caco2_EV_FL3_conditioned_medium_1

description:
Library name: Caco2_EV_FL3_conditioned_medium_1
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL3_3.MW_12


title: AWT_P14_2


title: Breast cancer serum sample 111

value: Luminal A


title: MG91 HFpEF2

description:
Library name: Sample10
Column name in counts_anno.txt: MG91HFpEF2

value: 2-Hit HFpEF model


title: DMEM_EV_FL2_unconditioned_medium_2

description:
Library name: DMEM_EV_FL2_unconditioned_medium_2
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL2_Medium_13


title: Breast cancer serum sample 112


title: MG91 HFpEF3

description:
Library name: Sample11
Column name in counts_anno.txt: MG91HFpEF3


title: Breast cancer serum sample 110

value: Basal-like


title: MG91 HFpEF1

description:
Library name: Sample9
Column name in counts_anno.txt: MG91HFpEF1


title: DMEM_EV_FL2_unconditioned_medium_1

description:
Library name: DMEM_EV_FL2_unconditioned_medium_1
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL2_Medium_12


title: AWT_P14_1


title: MG91 HFpEF4

description:
Library name: Sample12
Column name in counts_anno.txt: MG91HFpEF4


title: AKOm6_P14_1


title: Caco2_EV_FL2_conditioned_medium_3

description:
Library name: Caco2_EV_FL2_conditioned_medium_3
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL2_3.MW_14


title: Zmiz1HA ChIP N2a 2

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

data_processing:
Raw files were processed using illumina basespace ChIPseq pipeline.
Sequenced reads were aligned to the mm10 reference genome using illumina basespace ChIPseq app which use BWA (Burrows-Wheeler Aligner) alignment algorithm.
Peaks and motif were called using illumina basespace ChIPseq app which use MACS2 and HOMER algorithm.
Assembly: mm10
Supplementary files format and content: bam, csv for peaks

growth_protocol: Neuro-2a (ATCC, CCL-13) was cultured in DMEM high glucose supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C and 5% CO2.

extract_protocol: Zmiz1-HA was overexpressed in N2a cells and subsequently, ChIP DNA samples were obtained by using ChIP-IT Express Enzymatic Kit (Active Motif, 53009) and processed according to manufacturer specifications. Anti-HA-Tag Antibody (Cell Signaling, 3724) was used for immunoprecipitation. Pull down DNA quantity was measured using Qubit DNA HS kit (Thermo Fisher Scientific, Q32851). The sequencing library was prepared using TruSeq ChIP Library Preparation Kit (Illumina, IP-202–1012). Ten nanograms of starting material were used for library preparation. Library quality and quantity were assessed using Agilent DNA 1000 chip (Agilent 5067-1504) and Qubit DNA HS kit respectively. Libraries were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 (Illumina, 20046812) on a Nextseq1000/2000 system.

treatment_protocol: N2a were transfected with Zmiz1-HA plasmid using lipofectamine 3000.

value: mouse neuroblasts

tag: chip antibody

value: HA-Tag (cell signalling #3724)


title: Breast cancer serum sample 108

value: Serum


title: Breast cancer serum sample 109

value: case


title: G91 HFpEF+SUC3

description:
Library name: Sample7
Column name in counts_anno.txt: G91HFpEFSUC3


title: Zmiz1HA ChIP N2a 1


title: DMEM_EV_FL2_unconditioned_medium_3

description:
Library name: DMEM_EV_FL2_unconditioned_medium_3
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL2_Medium_14

value: Media Only


title: Caco2_EV_FL2_conditioned_medium_2

description:
Library name: Caco2_EV_FL2_conditioned_medium_2
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL2_3.MW_13


title: G91 HFpEF+SUC2

description:
Library name: Sample6
Column name in counts_anno.txt: G91HFpEFSUC2


title: G91 HFpEF+SUC4

description:
Library name: Sample8
Column name in counts_anno.txt: G91HFpEFSUC4


title: 2% input Zmiz1HA N2a 2


title: Breast cancer serum sample 106


title: Breast cancer serum sample 107


title: Caco2_EV_FL2_conditioned_medium_1

description:
Library name: Caco2_EV_FL2_conditioned_medium_1
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL2_3.MW_12


title: G91 HFpEF+SUC1

description:
Library name: Sample5
Column name in counts_anno.txt: G91HFpEFSUC1


title: 2% input Zmiz1HA N2a 1


title: G91 HFpEF4

description:
Library name: Sample4
Column name in counts_anno.txt: G91HFpEF4


title: P14 Zmiz1-KO neurons #3

data_processing:
Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Assembly: mm10
Supplementary files format and content: Comma separated spreadsheet file with raw counts for every gene for every sample.

source_name: Cortex

extract_protocol: RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 0.5 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).

treatment_protocol:
Zmiz1f/f as wildtype and Zmiz1f/f;Emx1Cre as Zmiz1-knockout P1 and P14 cortex were used to enrich cotical neurons.
Total RNA was extracted from Wildtype and Zmiz1KO P1 and P14 cortical enriched neurons using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732).

value: Cortex

value: Cortical neurons

value: Zmiz1 knockout


title: DMEM_EV_FL1_unconditioned_medium_3

description:
Library name: DMEM_EV_FL1_unconditioned_medium_3
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL1_Medium_14

value: unconditioned medium


title: G91 HFpEF3

description:
Library name: Sample3
Column name in counts_anno.txt: G91HFpEF3

value: Heart

value: HFpEF 12weeks


title: DMEM_EV_FL1_unconditioned_medium_2

description:
Library name: DMEM_EV_FL1_unconditioned_medium_2
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL1_Medium_13


title: Breast cancer serum sample 104


title: P14 Zmiz1-KO neurons #1


title: P14 Zmiz1-KO neurons #2


title: DMEM_EV_FL1_unconditioned_medium_1

description:
Library name: DMEM_EV_FL1_unconditioned_medium_1
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL1_Medium_12


title: P14 Wildtype neurons #3

value: Wildtype


title: G91 HFpEF1

description:
Library name: Sample1
Column name in counts_anno.txt: G91HFpEF1


title: Breast cancer serum sample 103


title: Caco2_EV_FL1_conditioned_medium_3

description:
Library name: Caco2_EV_FL1_conditioned_medium_3
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL1_3.MW_14

value: conditioned medium


title: Breast cancer serum sample 105


title: G91 HFpEF2

description:
Library name: Sample2
Column name in counts_anno.txt: G91HFpEF2


title: Caco2_EV_FL1_conditioned_medium_2

description:
Library name: Caco2_EV_FL1_conditioned_medium_2
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL1_3.MW_13


title: P14 Wildtype neurons #2


title: Breast cancer serum sample 101


title: Saline d14

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description:
Library name: Old Fgf10Cre Saline d14
10x Genomics

data_processing:
For demultiplexing and the subsequent FASTQ file generation we used Illumina’s bcl2fastq (2.19.0.316)
Sequencing reads were aligned to the mouse mm10 reference genome (refdata-gex-mm10-2020-A downloaded from 10xGenomics) using STAR solo (2.7.9a)
STAR was run in Velocyto mode in order to allow for downstream velocity analysis.
Droplet filtering was done using the EmptyDrops_CR parameter setting.
Resulting UMI count matrices were pre-processed for further analyses using Scanpy (1.9.6)
Assembly: Assembly: mm10
Supplementary files format and content: Normalized and integrated data including embeddings and clustering in H5AD format.

source_name: lung

extract_protocol:
Library preparation was carried out using the Chromium Next GEM Single-Cell 3ʹ Reagent Kit v3.1 (10x Genomics) according to manufacturer’s instructions.
scRNA-Seq

value: lung

value: Lipofibroblasts / AF1

value: Fgf10Cre-ERT2; tdTomatoflox

value: Tamoxifen injections (three i.p.) 2 weeks before saline administation. Lungs were harvested at day 14


title: Bleo d14

description:
Library name: Old Fgf10Cre Bleomycin d14
10x Genomics

value: Tamoxifen injections (three i.p.) 2 weeks before bleomycin administration.Lungs were harvested at day 14 post bleomycin.


title: P14 Wildtype neurons #1


title: Breast cancer serum sample 100

value: Luminal A


title: Breast cancer serum sample 99

value: Serum

value: Basal-like


title: Breast cancer serum sample 102

value: case


title: PBS 48h Z5

description:
Library name: V350159056_L04_104
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_104

data_processing:
Snakepipes v2.7.3
Sequence reads were processed using Snakepipes where STAR was used to map to GRCh38 using default options.
FeatureCount from subreads was used to quantify mRNA counts with the parameters (-C -Q 10 --primary)
Assembly: GRCh38
Supplementary files format and content: tsv file contains raw read counts for each sample

growth_protocol: Human colon adenocarcinoma cells, Caco-2 (ATCC HTB-37), were maintained in DMEM (Thermo Fisher Scientific) supplemented with 10 % (v/v) FCS (Thermo Fisher Scientific) and 1 % (v/v) non-essential amino acids (Thermo Fisher Scientific) at 37 °C and 5 % CO2. Medium was exchanged every 2-3 days, and the cells were split once a week. All experiments were performed during passage 19 ± 5.

extract_protocol:
Total RNA was isolated from the Caco-2 cells using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
DNA libraries were prepared with the high-throughput MGISP-960 sample preparation system using the MGIEasy rRNA Depletion Kit (MGI Technologies) and MGIEasy RNA Library Prep Set (MGI Technologies) according to the manufacturer’s recommendations. After PCR, different barcoded samples were pooled in equal amount and circularized to generate single stranded DNA libraries (ssDNA). DNA nanoball (DNB) were generated by rolling circle amplification. Paired-end sequencing (PE100) was performed using DNBSEQ-G400RS High-throughput Sequencing Reagent Set (MGI Technologies) on the DNBSEQ-G400 instrument.

treatment_protocol: See description for samples

tag: incubation time

tag: bacterial strain

value: not applicable

value: incubation with PBS


title: P1 Zmiz1-KO neurons #3

value: Cortex

value: Cortical neurons

value: Zmiz1 knockout


title: Breast cancer serum sample 98


title: PBS 48h Z4

description:
Library name: V350158887_L04_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_102


title: P1 Zmiz1-KO neurons #2


title: Caco2_EV_FL1_conditioned_medium_1

description:
Library name: Caco2_EV_FL1_conditioned_medium_1
Column name in raw_counts_Caco2_miRNA.tsv: Caco2_FL1_3.MW_12


title: Bleo d60

description:
Library name: Old Fgf10Cre Bleomycin d60
10x Genomics

value: Tamoxifen injections (three i.p.) 2 weeks before bleomycin administration.Lungs were harvested at day 60 post bleomycin.


title: Bleo d30

description:
Library name: Old Fgf10Cre Bleomycin d30
10x Genomics

value: Tamoxifen injections (three i.p.) 2 weeks before bleomycin administration. Lungs were harvested at day 30 post bleomycin.


title: Breast cancer serum sample 97


title: P1 Zmiz1-KO neurons #1


title: Breast cancer serum sample 96


title: WT-whole heart-2 replicates

city: Houston

first: Tamer

last: Mohamed

state: TX

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

description: Library name: MHM_70143

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The error rate for each base can be transformed by the Phred score as in equation 1. "e" represents sequencing error rate, "Qphred" represents base quality values of Illumina platforms (equation 1: Qphred = -10log10(e)).
GC content distribution detects potential AT/GC separation, which affects subsequent gene expression quantification. In view of random fragmentation and biological law of G/C-A/T content, G and C, A and T should be respectively equal, and the content should be stable throughout the entire sequencing process for non-stranded library(Parkhomchuk et al., 2009) (If the library is strand-specific, AT separation or GC separation may occur). A large variation of sequencing error in the first 6-7 bases is allowed considering the use of random primer in library construction, in which it is normal that the first few bases have certain preference in existing high-throughput sequencing technology.
The sequencing reads/raw reads often contain low quality reads or reads with adapters, which will affect the quality of downstream analysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads.
Assembly: Alignments were made with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons.
Supplementary files format and content: .csv file for filtered features was created.
Library strategy: Spatial Transcriptomics

source_name: Whole heart tissue slices

extract_protocol:
The pups’ hearts were extracted at P1, sliced, fixed in 4% PFA and embedded in Parrafin
Using 5 µm tissue sections on Visium HD Gene Expression slides (10X genomics), libraries were formed with Spatial Gene Expression Reagent Kits for FFPE tissues. These sections, after H&E staining, were imaged at 40X on a Leica Aperio ImageScope and processed for Visium libraries with CytAssist, targeting a slide size of 6.5 x 6.5 mm. Capture Areas were arrayed with a continuous lawn of oligonucleotides organized into millions of 2 x 2 µm barcoded squares without gaps. After checking the quality control, cDNA libraries were sequenced on the Illumina NovaSeq 6000, aiming for >275 million read pairs for capture areas covered fully by tissue

value: Whole heart tissue slices

value: wild-type


title: PBS 48h Z3

description:
Library name: V350158887_L02_46
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_46


title: P1 Wildtype neurons #2

value: Wildtype


title: PBS 48h Z2

description:
Library name: V350158887_L01_97
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_97


title: PBS 24h Z5

description:
Library name: V350158887_L03_48
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_48


title: Breast cancer serum sample 95


title: Kitl_cKO

city: TianJin

first: Liu

last: Chang

address: Weijin Road

institute: Nankai University

description:
Library name: cKO
Test the TRANSCRIPTOM changes after Kitl conditional deficiency

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Gonad were manually picked up using mouth pipette at E14.5 and washed three times in 0.04% BSA/PBS. And dissociated with 0.25% trypsin-ETDA (GIBCO, 25200072) at 37 °C for 30 min in the shaker. Dissociated cells were spun down and wash with 0.04% BSA/PBS for three times and resuspended in the same buffer.Dissociated cells were loaded into the Chromium Single Cell B Chip (10X Genomics, PN-120262) and processed in the Chromium single cell controller (10X Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
The library was generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) according to the manufacturer’s manual. The libraries were pooled and sequenced using llumina NovaSeq X.


title: Kitl_WT

description:
Library name: WT
Test the TRANSCRIPTOM changes after Kitl conditional deficiency


title: P1 Wildtype neurons #1


title: Breast cancer serum sample 94

value: Luminal B


title: PBS 24h Z4

description:
Library name: V350158887_L03_43
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_43


title: Breast cancer serum sample 93


title: Zmiz1-KO #4

description: Raw counts

extract_protocol:
RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 0.5 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).
RNA sequencing using Illumina NextSeq 2000 system.

treatment_protocol:
Zmiz1f/f as wildtype and Zmiz1f/f;Emx1Cre as Zmiz1-knockout E15.5 embryos were used to isolate progenitors cells.
Total RNA was extracted from Wildtype and Zmiz1KO E15.5 progenitors using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732).

value: Cortical progenitors


title: PBS 24h Z3

description:
Library name: V350158887_L01_47
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_47


title: PCBP1_Input_heart_1

description: input-RNA

data_processing:
3’-adapters were trimmed from reads using Cutadapt (v2.7), and reads shorter than 18 bp were removed. Reads were then mapped to a database of human and mouse repetitive elements and rRNA sequences compiled from Dfam and Genbank. All non-repeat mapped reads were mapped to the mouse genome (mm10) using STAR (v2.6.0c). PCR duplicates were removed using umi_tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions. Peaks were identified within eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper), using parameters consistent with the Encyclopedia of DNA Element (ENCODE) standards.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: heart ventricle

extract_protocol:
eCLIP studies were performed according to the published single-end seCLIP protocol with the following modifications. Approximately 80 mg of frozen embryonic mouse heart tissue was cryogrinded and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation. The equivalence of 75 μg of RNA was lysed using 1 mL of eCLIP lysis mix and subjected to two rounds of sonication for 4 minutes with 30 seconds ON/OFF at 75% amplitude. A pre-validated PCBP1 antibody (Abcam cat# ab168377) was then pre-coupled to Anti-Rabbit IgG Dynabeads (ThermoFisher), added to lysate, and incubated overnight at 4°C. Before immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers. IP and input samples were cut from the membrane at the relative band size of 40kDa to 75kDa above that band size.
The eCLIP cDNA adapter contains a sequence of 10 random nucleotides at the 5’ end. This random sequence serves as a unique molecular identifier (UMI) after sequencing primers are ligated to the 3’ end of cDNA molecules.UMIs were pruned from read sequences using umi_tools (v0.5.1)
RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described.

value: heart ventricle

value: Wild-type

value: Input


title: P1 Wildtype neurons #3


title: PCBP1_Input_heart_2

description: input-RNA


title: PBS 24h Z2

description:
Library name: V350158887_L01_3
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_3


title: Zmiz1-KO #3

description: Raw counts


title: Zmiz1-KO #2

description: Raw counts


title: Breast cancer serum sample 92

extract_protocol: Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN). Serum samples were thawed on ice and centrifuged at 3,000×g for 5 minutes at 4 °C. Buffer RPL containing carrier RNA and spike-in template mix was added, followed by Buffer RPP. RNA was eluted in 50 µL according to the manufacturer’s protocol.

value: Serum

value: Luminal A


title: Breast cancer serum sample 91

value: case


title: Breast cancer serum sample 90

value: Basal-like


title: PCBP1_eCLIP_heart_2

description: eCLIP-RNA

value: eCLIP


title: Breast cancer serum sample 89


title: PBS 10h Z4

description:
Library name: V350158887_L04_43
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_43

value: not applicable

value: incubation with PBS


title: PBS 10h Z3

description:
Library name: V350159056_L02_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_98


title: Tumor, Nano-273 treated, scRNAseq

city: Ann Arbor

first: Chengyi

last: Li

state: Michigan

address: B520, 1600 Huron Pkwy

institute: University of Michigan

data_processing:
Pooled libraries were subjected to 150 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate demultiplexed Fastq files, and a CellRanger Pipeline (10x Genomics) was used to align reads and generate count matrices.
Assembly: mm10
Supplementary files format and content: Table-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor samples were harvested and dissociated into single-cell suspensions 9 days after the final dosage. Dead cells were excluded using a dead cell removal kit (Miltenyi Biotec). The single-cell suspensions were then stained with TotalSeq™-C Mouse antibody. These suspensions were subjected to final cell counting on a Countess II Automated Cell Counter (Thermo Fisher) and diluted to a concentration of 700-1000 nuclei/µL.
We constructed 3′ single-nucleus libraries using the 10x Genomics Chromium Controller and followed the manufacturer's protocol for 3′ V3.1 chemistry with NextGEM Chip G reagents (10x Genomics). The final library quality was assessed using a TapeStation 4200 (Agilent), and the libraries were quantified by Kapa qPCR (Roche)

value: Tumor

value: Tumor and immune cells

value: WT


title: PBS 10h Z5

description:
Library name: V350158887_L03_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_102


title: Wildtype #4

description: Raw counts

value: Cortex


title: PCBP1_eCLIP_heart_1

description: eCLIP-RNA


title: Zmiz1-KO #1

description: Raw counts

value: Zmiz1 knockout


title: PBS 10h Z2

description:
Library name: V350159056_L01_42
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_42


title: Tumor,IPI-549 treated, scRNAseq


title: Breast cancer serum sample 87

data_processing: Cq values were determined using the second derivative method in Roche LightCycler software. Quality control included melting curve analysis, exclusion of reactions with more than one melting temperature, deviation from reference melting temperatures, and low amplification efficiency. Endogenous miRNAs let-7d-5p and let-7i-5p were used as internal reference controls. Expression data were normalized and subsequently log2-transformed for statistical analysis. Batch information is provided in the sample annotations.


title: Breast cancer serum sample 86


title: Wildtype #2

description: Raw counts

value: Wildtype


title: Tumor, SH-273 treated, scRNAseq


title: Tumor, MSA-2 treated, scRNAseq


title: Tumor, Control, scRNAseq

value: Control


title: Breast cancer serum sample 88


title: Wildtype #3

description: Raw counts

value: Cortical progenitors


title: Breast cancer serum sample 85


title: Pm OMV RNA 24h Z3

description:
Library name: V350158887_L01_101
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_101

value: P. mirabilis DSM 4479

value: transfection with 2 ng BEV-RNA


title: Breast cancer serum sample 84

value: Serum


title: Pm OMV RNA 24h Z5

description:
Library name: V350158887_L04_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_98


title: Pm OMV RNA 24h Z2

description:
Library name: V350159056_L01_48
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_48


title: Breast cancer serum sample 83


title: Wildtype #1

description: Raw counts


title: DATG_rep2

city: Redwood City

first: Jin

last: Chen

address: 2800 Bridge Parkway

institute: Altos Labs

description: 10X Genomics

data_processing:
Base calls were simultaneously demultiplexed based on i5 and i7 barcodes and converted to fastq format using BCL Covert v4.0.3 from Illumina.
Teratoma sequencing reads were mapped to a joint human and mouse reference genome (GRCh38 and GRCm38 2024-A available from 10X Genomics) using cellranger v8.0.1 with default settings.
Assembly: GRCh38, v108
Supplementary files format and content: Cellranger output

source_name: H1 ESC

extract_protocol:
The teratoma samples were dissociated to single nuclei suspension using the SingulatorTM 200 system from S2 Genomics.
Single nuclei preparation was performed in accordance with 10x Genomics Single Cell 3’ Gene Expression v3.1 Dual Index protocol (10x Genomics #1000120, 1000268, 1000215), with a target of 10,000 nuclei per reaction.

value: H1 ESC

value: Human Embryonic Stem Cells


title: DATG_rep1

description: 10X Genomics


title: Pm OMV RNA 24h Z4

description:
Library name: V350159056_L04_44
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_44


title: KO_rep2

description: 10X Genomics


title: Pm OMV RNA 10h Z4

description:
Library name: V350158887_L04_41
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_41


title: fl125

city: Napoli

first: Maria

middle: Angela

last: Da Stefano

address: Via S. Pansini, 5

country: Italy

institute: University of Naples "Federico II"

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with htseq-count 0.9.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Skeletal muscle stem cells

extract_protocol:
RNA extraction was performed with RNeasy Mini Kit (QIAGEN).
NEGEDIA DIgital RNAseq research sequencing service (NEGEDIA srl)

value: Skeletal muscle stem cells

value: Tamoxifene


title: Breast cancer serum sample 82


title: fl128


title: KO_rep1

description: 10X Genomics


title: WT_rep2

description: 10X Genomics


title: c130

value: Pax7nGFP/+;Pax7+/+;Dio2Fl/Fl (control)


title: c129


title: Pm OMV RNA 10h Z3

description:
Library name: V350159056_L02_3
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_3


title: Breast cancer serum sample 80


title: Breast cancer serum sample 81


title: Pm OMV RNA 10h Z5

description:
Library name: V350158887_L02_48
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_48


title: Pm OMV RNA 10h Z2

description:
Library name: V350159056_L01_103
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_103


title: fl126


title: c124


title: E. coli BW25113 ΔacrB cells, DMSO treated, biolrep1 collected with Rb1_10xDZD

city: San Francisco

first: Jordan

middle: I

last: Kleinman

institute: UCSF

description:
Library name: Rb1_DMSO-d
Ribosome protected footprints; columns labeled with Rb1_DMSO or DMSO
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
DZD-10_codonStalls.csv

library_source: other

data_processing:
Preprocessing: Raw, demultiplexed reads from next-generation sequencing were trimmed to exclude 3’ linkers (CTGTAGGCACCATCAAT) using cutadapt version 4.4. Reads with fewer than 15 or greater than 45 nt were excluded from downstream analysis. Sequences of tRNA, rRNA, and tmRNA were copied from the parent strain genome (CP009273.1) to a new fasta file along with ladder (SC-15 and SC-45) and illumina (P5, P7_iXX) primer sequences. This collated file was used to exclude the described sequences from downstream analysis via Bowtie alignment with a maximum of 2 errors per alignment. Remaining sequences were then Bowtie aligned to the full parent strain E. coli BW25113 genome with a maximum allowable error of 2 nt and a maximum of one alignment location within the genome. Bowtie output files were converted to Wig format by aligning reads to their 3’ ends, trimming to remove end mismatches and filtering to exclude resulting reads less than 15 nt long. FastQC was performed at each stage to verify quality.
Metagene analysis: P-site assignment and periodicity analysis were performed essentially as described previously (Mangano et al. 2022). Periodicity was measured by averaging reads at every third position within coding sequences (CDS) transcriptome-wide, excluding the first 18 nt of each CDS, and comparing between each of the three nt positions. Low-expression and coverage genes (average reads/position ≤ 0.5 and < 20% nonzero reads) were excluded from this analysis. Genes were further filtered to exclude CDS < 100 nt long for the following metagene analyses. Reads were analyzed around the start and stop codons of open reading frames, and the P-site was assigned at -15 nt from the 3’ end of measured reads. Read distribution analysis across ORFs was performed as described previously(Diamond et al. 2025). Nucleotide positions within genes were divided by full gene length and reads were assigned to the resulting fractional position (rounded to two decimal places). Reads were averaged across all ORFs under analysis and plotted.
Gene-level analysis: P-site aligned reads with an offset of -15 nt were used for all analyses, and gene-level analyses were performed essentially as described previously(Mangano et al. 2022). Gene RPKM (reads per kilobase per million) scores were calculated by summing reads over the full ORF for and normalizing to gene length and total sequencing depth of the sample. Ribosome profiling RPKM scores were further normalized to RNA-seq RPKM scores, resulting in a measure of translation efficiency (TE) which was used for correlation analysis. Where indicated, TE for each gene was averaged across two replicates for each experimental condition. Statistical significance of differences in TE for each condition compared to DMSO control was calculated using independent t-tests for each gene with Benjamini-Hochberg FDR correction. Data was filtered to exclude ORFs < 18 nt, with <20% nonzero reads, and ≤ 0.5 average reads/position, and genes not present in both conditions being analyzed after application of these filters were eliminated from analysis.
Codon-level analysis: Codon analyses were performed following the same filters as the gene-level analyses. Further filters were applied to exclude the terminal 2-10 codons of each CDS and codons with fewer than 5 reads total. Codons not appearing in both conditions being analyzed were removed from consideration. Codon reads were normalized to total gene reads to produce pause scores for each codon, and pause scores were averaged across replicates. Average pause scores were sorted on the basis of log2 fold change compared to DMSO. pLOGO analysis was performed using the top 1000 stalling codons as foreground and all remaining codons as background, selecting an 11 amino acid window with the P-site codon peak at position 10 (-9:+1). For transcriptome-wide heat maps, codon RPM (reads per million) was calculated by normalizing codon reads to total sequencing depth. These codon RPM scores were applied at each amino acid in an 11mer window (-9:+1) around the peak, and individual amino acid frequency was calculated at each position by averaging RPM scores across all codons and replicates. Heat maps were plotted as the log2 fold change in averaged RPM scores compared to DMSO control. Pairwise heatmaps were produced to evaluate the frequency of amino acid pairs at the -2:-1 positions. For each potential amino acid pairing, codon RPM scores were averaged across all codons and replicates, and the log2 fold change in averaged pairwise RPM was calculated compared to the DMSO control.
data processing was performed by custom script
Assembly: CP009273.1
Supplementary files format and content: gene_profiling_table... csv files include gene RPKM for each sample and use RNAseq (Rn) samples for TE calculation. Log fold change between treated and DMSO samples is also shown.
Supplementary files format and content: ...codonStalls.csv files include codon cpm, RPKM, and pausescore for each sample. Log fold change between treated and DMSO samples is also shown.
Library strategy: Ribo-Seq

molecule: other

organism: Escherichia coli

source_name: BW25113 delta-acrB

growth_protocol: Individual colonies of E. coli BW25113 ΔacrB were grown overnight at 200 rpm & 37°C in MOPS EZ Rich media (Teknova M2105). Cultures were diluted 1:200 and grown to OD600 ~ 0.3-0.5.

extract_protocol:
Cells were mechanically lysed on Qiagen TissueLyser II with 650 µL frozen lysis buffer [20 mM Tris pH 8.0, 10 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 0.4% TritonX-100, 0.1% NP-40, 100 U/mL RNase-free DNase I (Roche 04716728001), 10 U/mL SUPERase-In RNase Inhibitor (Invitrogen AM2696), antibiotic 10x MIC]. Canisters were pre-chilled in LN2, and lysis was performed over 5 cycles of 3 min at 15 Hz. Pulverized lysate was thawed and clarified by centrifugation at 20,000 xg for 10 min at 4°C. 12.5 AU clarified lysate (~0.5 mg RNA) was digested for 1 hr at 25°C and 1400 rpm with 750 U MNase (Roche 10107921001), and the reaction was quenched with 5 mM EGTA and placed on ice. Clarified lysate was also aliquoted for RNA-seq. Digested samples were then applied to a 10-50% sucrose gradient (20 mM Tris pH 8.0, 10 mM MgCl2, 100 mM NH4Cl, 2 mM DTT, 10 U/mL SUPERase-In) and centrifuged at 201,000 xg for 2.5 hr at 4°C. Polysome profiles were obtained using the BioComp Fractionator, and monosome-containing fractions were collected and pooled. Combined monosome samples were purified by hot phenol extraction and 20 µg of sample was resolved by 15% TBE Urea gel (Novex EC6885BOX). Ribosome-protected mRNA fragments 15-45 nt in length (guided by primers SC-15 & SC-45) were excised and eluted from gel (RNA Elution buffer: 300mM NaOAc pH 5.5, 1mM EDTA pH 8.0) for library preparation as described below.
Total size-selected mRNA was dephosphorylated using 10 U T4 polynucleotide kinase (NEB M0201L) at 37°C for 1 h. Dephosphorylated RNA was ligated to 0.4 µL of 50 µM Universal miRNA cloning linker (NEB S1315S) using 200 U of T4 RNA ligase 2 truncated KQ (NEB M0373L) for 3 h at 37°C. Ligated products of appropriate size range (32-62 nt) were isolated from 15% TBE Urea gel (Novex EC6885BOX) and eluted with RNA Elution buffer. RNA was converted to cDNA by reverse transcription with 200 U SuperScript IV RT (ThermoFisher 180900510) and 1.25 µL of 10 µM primer Ni-Ni-9. RT products were resolved on 10% TBE Urea gel (Novex EC6875BOX) and the appropriate size bands (111-141 nt) were eluted out (DNA Elution buffer: 10 mM Tris pH 8.0, 300 mM NaCl, 1 mM EDTA pH 8.0). Circularization of cDNA was performed using 100 U CircLigase ssDNA ligase (Epicentre CL4115K) at 60°C for 1 h. Ribosomal RNA was removed from ribosome profiling samples by incubating with biotinylated primers b-rRNA-1 through b-rRNA-5 and pulling down with MyOne Streptavidin C1 Dynabeads (Invitrogen 65001) to remove corresponding cDNA. Remaining cDNA was PCR amplified with primer P5 and barcoded P7_index primers to add on NGS handles for 5-9 cycles. Amplified DNA (154-184 bp) was then purified from 10% TBE gel (Novex EC6275BOX) and eluted in DNA elution buffer. NGS-amplified products were evaluated on Agilent Tapestation.

treatment_protocol: Oxazolidinones, dissolved in DMSO at 50x final concentration, were added to log-phase culture at a final concentration of 10x MIC (20 μg/mL TZD, 80 μg/mL DZD). Equal amounts of DMSO were added to the ‘no drug’ control cultures (2% DMSO final concentration). Cultures were shaken for 2.5 min, then filtered through a 0.2 µM nitrocellulose membrane (Whatman 7182-009), and the filtrate was rapidly flash-frozen.

value: BW25113 delta-acrB

value: acrB knockout

value: 2% DMSO


title: Pm OMV LPS RNA 24h Z4

description:
Library name: V350158887_L03_47
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_47

value: P. mirabilis

value: transfection with 1ng/µl LPS


title: E. coli BW25113 ΔacrB cells, DMSO treated, biolrep2 collected with Rb1_10xDZD

description:
Library name: Rb2_DMSO-d
Ribosome protected footprints; columns labeled with Rb2_DMSO or DMSO
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
DZD-10_codonStalls.csv


title: E. coli BW25113 ΔacrB cells, DMSO treated, biolrep2 collected with Rb2_10xTZD

description:
Library name: Rb2_DMSO-t
Ribosome protected footprints; columns labeled with Rb2_DMSO or DMSO
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
TZD-10_codonStalls.csv


title: Pm OMV LPS RNA 24h Z5

description:
Library name: V350158887_L02_42
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_42


title: Breast cancer serum sample 78


title: Hepatic myeloid cells, naive, PBS treatment

city: Edinburgh

first: Stephen

last: Jenkins

address: 47, Little France Crescent

department: Centre For Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description: 10x Genomics

data_processing:
The demultiplexing of the raw data was performed using CellRanger software (10x – version 2.0.2; cellranger mkfastq which wraps Illumina’s bcl2fastq). The reads obtained from the demultiplexing were used as the input for ‘cellranger count’ (CellRanger software), which aligns the reads to the mouse reference genome (mm10) using STAR and collapses to unique molecular identifier (UMI) counts.
The aggregation of the samples was performed using ‘cellranger aggr’ (CellRanger software). The samples have a mean number of reads per cell of 103,629 to 154,446 and a median number of genes per cell of 1,658 to 2,610 dependent on sample.
Preprocessing of the data was done by the scater R package (v1.6.3) according to workflow proposed by the Marioni lab 85. Outlier cells were first identified based on 3 metrics (library size, number of expressed genes and mitochondrial proportion) and cells were removed when they were 3 median absolute deviations distant from the median value of each metric across all cells.
As second filtering, a principal component analysis plot was generated using the runPCA function of the scater R package (default parameters). Outlier cells in this principal component analysis plot were identified using the R package mvoutlier.
Assembly: Mouse reference genome mm10
Supplementary files format and content: Tab-separated value files and matrix files

extract_protocol: Cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 and the Chromium Single Cell A Chip Kit  per the manufacturer’s protocol. Single cells were sorted into PBS plus 0.1% BSA . Of these Tim4+ Kupffer cells were either limited to or enriched to 20% of the total to ensure coverage of all hepatic myeloid cells in all conditions. 20,000 cells were then added to each lane of the 10X chip. The cells were partitioned into Gel Beads in Emulsion in the Chromium instrument, in which cell lysis and bar-coded reverse tran- scription of RNA occurred, followed by amplification, fragmentation and 5′ adaptor and sample index attachment.

treatment_protocol: Mice were injected intraperitoneally with CCl4 or left naïve. 24 hrs later mice were given intravascular injection of IL-4c or PBS control. 48hrs later mice were sacrificed and live single CD45+CD19-CD3-CD31-NK1.1- liver leukocytes were FACS sorted and process through the chromium Single Cell Platform.

value: Male

tag: injury status

value: naive

value: PBS


title: Hepatic myeloid cells, naive, IL-4 treatment

description: 10x Genomics

source_name: live single CD45+CD19-CD3-CD31-NK1.1- liver leukocytes


title: Breast cancer serum sample 77

value: Control


title: Pm OMV LPS RNA 24h Z3

description:
Library name: V350158887_L01_103
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_103


title: Breast cancer serum sample 79


title: E. coli BW25113 ΔacrB cells, DMSO treated, biolrep1 collected with Rb1_10xTZD

description:
Library name: Rb1_DMSO-t
Ribosome protected footprints; columns labeled with Rb1_DMSO or DMSO
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
TZD-10_codonStalls.csv


title: Breast cancer serum sample 76


title: Hepatic myeloid cells, CCl4 injury, PBS treatment

description: 10x Genomics

value: live single CD45+CD19-CD3-CD31-NK1.1- liver leukocytes


title: E. coli BW25113 ΔacrB cells, delpazolid treated, biolrep2

description:
Library name: Rb2_10xDZD
Ribosome protected footprints; columns labeled with Rb2_10xDZD or DZD-10
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
DZD-10_codonStalls.csv

value: 80 μg/mL delpazolid


title: Breast cancer serum sample 75

value: Serum


title: Hepatic myeloid cells, CCl4 injury, IL-4 treatment

description: 10x Genomics


title: E. coli BW25113 ΔacrB cells, delpazolid treated, biolrep1

description:
Library name: Rb1_10xDZD
Ribosome protected footprints; columns labeled with Rb1_10xDZD or DZD-10
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
DZD-10_codonStalls.csv


title: Pm OMV LPS RNA 10h Z4

description:
Library name: V350159056_L04_41
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_41


title: Pm OMV LPS RNA 24h Z2

description:
Library name: V350159056_L01_100
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_100


title: NT NC, rep3

city: Shanghai

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: lymph node

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: lymph node

tag: group

value: NT NC


title: Breast cancer serum sample 74

city: Santander

first: Inés

last: Gómez-Acebo

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

source_name: Serum


title: E. coli BW25113 ΔacrB cells, tedizolid treated, biolrep2

description:
Library name: Rb2_10xTZD
Ribosome protected footprints; columns labeled with Rb2_10xTZD or TZD-10
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
TZD-10_codonStalls.csv

value: 20 μg/mL tedizolid


title: Breast cancer serum sample 73


title: NT NC, rep1


title: Pm OMV RNA LPS 10h Z3

description:
Library name: V350158887_L01_1
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_1


title: Pm OMV LPS RNA 10h Z5

description:
Library name: V350158887_L02_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_98


title: Breast cancer serum sample 72


title: Pm OMV RNA LPS 10h Z2

description:
Library name: V350159056_L01_44
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_44


title: E. coli BW25113 ΔacrB cells, DMSO treated, biol rep2 collected with Rn1_10xDZD

description:
Library name: Rn2_DMSO-d
mRNA; columns labeled with Rn1_DMSO, used for TE normalization of Rb2_DMSO and DMSO columns
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF06.csv

data_processing:
Preprocessing: Raw, demultiplexed reads from next-generation sequencing were trimmed to exclude 3’ linkers (CTGTAGGCACCATCAAT) using cutadapt version 4.4. Reads with fewer than 15 or greater than 45 nt were excluded from downstream analysis. Sequences of tRNA, rRNA, and tmRNA were copied from the parent strain genome (CP009273.1) to a new fasta file along with ladder (SC-15 and SC-45) and illumina (P5, P7_iXX) primer sequences. This collated file was used to exclude the described sequences from downstream analysis via Bowtie alignment with a maximum of 2 errors per alignment. Remaining sequences were then Bowtie aligned to the full parent strain E. coli BW25113 genome with a maximum allowable error of 2 nt and a maximum of one alignment location within the genome. Bowtie output files were converted to Wig format by aligning reads to their 3’ ends, trimming to remove end mismatches and filtering to exclude resulting reads less than 15 nt long. FastQC was performed at each stage to verify quality.
Metagene analysis: P-site assignment and periodicity analysis were performed essentially as described previously (Mangano et al. 2022). Periodicity was measured by averaging reads at every third position within coding sequences (CDS) transcriptome-wide, excluding the first 18 nt of each CDS, and comparing between each of the three nt positions. Low-expression and coverage genes (average reads/position ≤ 0.5 and < 20% nonzero reads) were excluded from this analysis. Genes were further filtered to exclude CDS < 100 nt long for the following metagene analyses. Reads were analyzed around the start and stop codons of open reading frames, and the P-site was assigned at -15 nt from the 3’ end of measured reads. Read distribution analysis across ORFs was performed as described previously(Diamond et al. 2025). Nucleotide positions within genes were divided by full gene length and reads were assigned to the resulting fractional position (rounded to two decimal places). Reads were averaged across all ORFs under analysis and plotted.
Gene-level analysis: P-site aligned reads with an offset of -15 nt were used for all analyses, and gene-level analyses were performed essentially as described previously(Mangano et al. 2022). Gene RPKM (reads per kilobase per million) scores were calculated by summing reads over the full ORF for and normalizing to gene length and total sequencing depth of the sample. Ribosome profiling RPKM scores were further normalized to RNA-seq RPKM scores, resulting in a measure of translation efficiency (TE) which was used for correlation analysis. Where indicated, TE for each gene was averaged across two replicates for each experimental condition. Statistical significance of differences in TE for each condition compared to DMSO control was calculated using independent t-tests for each gene with Benjamini-Hochberg FDR correction. Data was filtered to exclude ORFs < 18 nt, with <20% nonzero reads, and ≤ 0.5 average reads/position, and genes not present in both conditions being analyzed after application of these filters were eliminated from analysis.
data processing was performed by custom script
Assembly: CP009273.1
Supplementary files format and content: gene_profiling_table... csv files include RPKM for each sample and use samples for TE calculation with RiboSeq (Rb) samples

extract_protocol:
Cells were mechanically lysed on Qiagen TissueLyser II with 650 µL frozen lysis buffer [20 mM Tris pH 8.0, 10 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 0.4% TritonX-100, 0.1% NP-40, 100 U/mL RNase-free DNase I (Roche 04716728001), 10 U/mL SUPERase-In RNase Inhibitor (Invitrogen AM2696), antibiotic 10x MIC]. Canisters were pre-chilled in LN2, and lysis was performed over 5 cycles of 3 min at 15 Hz. Pulverized lysate was thawed and clarified by centrifugation at 20,000 xg for 10 min at 4°C, then aliquoted and flash frozen. 12.5 AU clarified lysate aliquots were thawed and hot-phenol extracted. Small RNA and tRNA were removed from the total RNA via MegaClear Transcription Clean-Up kit (Invitrogen, AM1908), and rRNA was depleted using MicrobExpress Bacterial mRNA Enrichment kit (Ambion, AM1905). Remaining mRNA was fragmented using RNA Fragmentation Reagents (Ambion, AM8740) under stringent conditions (95°C 1 min 45 sec). Fragments 20-100 nt in length were selected and purified from 20 µg sample on 15% TBE Urea gel (Novex EC6885BOX) with RNA Elution buffer (300mM NaOAc pH 5.5, 1mM EDTA pH 8.0).
Total size-selected mRNA was dephosphorylated using 10 U T4 polynucleotide kinase (NEB M0201L) at 37°C for 1 h. Dephosphorylated RNA was ligated to 0.4 µL of 50 µM Universal miRNA cloning linker (NEB S1315S) using 200 U of T4 RNA ligase 2 truncated KQ (NEB M0373L) for 3 h at 37°C. Ligated products of appropriate size range (32-62 nt) were isolated from 15% TBE Urea gel (Novex EC6885BOX) and eluted with RNA Elution buffer. RNA was converted to cDNA by reverse transcription with 200 U SuperScript IV RT (ThermoFisher 180900510) and 1.25 µL of 10 µM primer Ni-Ni-9. RT products were resolved on 10% TBE Urea gel (Novex EC6875BOX) and the appropriate size bands (111-141 nt) were eluted out (DNA Elution buffer: 10 mM Tris pH 8.0, 300 mM NaCl, 1 mM EDTA pH 8.0). Circularization of cDNA was performed using 100 U CircLigase ssDNA ligase (Epicentre CL4115K) at 60°C for 1 h. Ribosomal RNA was removed from ribosome profiling samples by incubating with biotinylated primers b-rRNA-1 through b-rRNA-5 and pulling down with MyOne Streptavidin C1 Dynabeads (Invitrogen 65001) to remove corresponding cDNA. Remaining cDNA was PCR amplified with primer P5 and barcoded P7_index primers to add on NGS handles for 5-9 cycles. Amplified DNA (154-184 bp) was then purified from 10% TBE gel (Novex EC6275BOX) and eluted in DNA elution buffer. NGS-amplified products were evaluated on Agilent Tapestation.


title: E. coli BW25113 ΔacrB cells, tedizolid treated, biolrep1

description:
Library name: Rb1_10xTZD
Ribosome protected footprints; columns labeled with Rb1_10xTZD or TZD-10
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
TZD-10_codonStalls.csv


title: Breast cancer serum sample 71


title: T NC, rep2

value: T NC


title: NT NC, rep2


title: Breast cancer serum sample 70

value: case

value: Basal-like


title: T NC, rep1


title: E. coli BW25113 ΔacrB cells, DMSO treated, biol rep2 collected with Rn2_10xTZD

description:
Library name: Rn2_DMSO-t
mRNA; columns labeled with Rn1_DMSO, used for TE normalization of Rb2_DMSO and DMSO columns
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF05.csv

value: BW25113 delta-acrB

value: acrB knockout


title: Pm OMV LPS 24h Z4

description:
Library name: V350158887_L04_44
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_44

value: P. mirabilis

value: incubation with 0.2 ng/µl LPS


title: Pm OMV LPS 24h Z3

description:
Library name: V350158887_L01_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_102


title: E. coli BW25113 ΔacrB cells, DMSO treated, biol rep1 collected with Rn1_10xTZD

description:
Library name: Rn1_DMSO-t
mRNA; columns labeled with Rn1_DMSO, used for TE normalization of Rb1_DMSO and DMSO columns
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF05.csv

value: 2% DMSO


title: NT NDE, rep3

value: NT NDE


title: Breast cancer serum sample 68


title: T NC, rep3


title: E. coli BW25113 ΔacrB cells, DMSO treated, biol rep1 collected with Rn1_10xDZD

description:
Library name: Rn1_DMSO-d
mRNA; columns labeled with Rn1_DMSO, used for TE normalization of Rb1_DMSO and DMSO columns
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF06.csv


title: Breast cancer serum sample 69


title: Pm OMV LPS 24h Z5

description:
Library name: V350158887_L03_104
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_104


title: E. coli BW25113 ΔacrB cells, delpazolid treated, biol rep2

description:
Library name: Rn2_10xDZD
mRNA; columns labeled with Rn2_10xDZD, used for TE normalization of Rb2_10xDZD and DZD-10 columns
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF06.csv


title: Pm OMV LPS 10h Z5

description:
Library name: V350158887_L02_97
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_97


title: Pm OMV LPS 24h Z2

description:
Library name: V350158887_L01_48
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_48


title: Breast cancer serum sample 67


title: Breast cancer serum sample 66


title: NT NDE, rep2


title: E. coli BW25113 ΔacrB cells, delpazolid treated, biol rep1

description:
Library name: Rn1_10xDZD
mRNA; columns labeled with Rn1_10xDZD, used for TE normalization of Rb1_10xDZD and DZD-10 columns
gene_profiling_table_filt-by-DZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF06.csv


title: NT NDE, rep1


title: Pm OMV LPS 10h Z4

description:
Library name: V350158887_L03_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_98


title: T NDE, rep3

value: T NDE


title: E. coli BW25113 ΔacrB cells, tedizolid treated, biol rep2

description:
Library name: Rn2_10xTZD
mRNA; columns labeled with Rn2_10xTZD, used for TE normalization of Rb2_10xTZD and TZD-10 columns
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF05.csv


title: Breast cancer serum sample 64


title: Pm OMV LPS 10h Z3

description:
Library name: V350159056_L01_97
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_97


title: E. coli BW25113 ΔacrB cells, tedizolid treated, biol rep1

description:
Library name: Rn1_10xTZD
mRNA; columns labeled with Rn1_10xTZD, used for TE normalization of Rb1_10xTZD and TZD-10 columns
gene_profiling_table_filt-by-TZD-10_3pr_offset_-15.csv
gene_profiling_master_table_3pr_offset_-15_JKDF05.csv


title: Breast cancer serum sample 65


title: scRNA-seq of Dermacentor andersoni unfed adult female salivary glands

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

description:
Library name: Dand_UN_SG
10x Genomics

data_processing:
The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Raw sequencing data were aligned to the D. andersoni (GCF_023375885.1) reference genome and quantified using Cell Ranger tool (v7.0.1). Low-quality cells (4,405 cells) were excluded using a threshold of three median absolute deviations (MAD) from the median of the overall cell population for both unique molecular identifier (UMI) or feature counts and mitochondrial content. Putative doublets were identified and removed using scDblFinder R package (v 1.18.0), yielding 14,400 high-quality cells for downstream analyses. Cell clustering was performed following routine steps provided in the Seurat (v4.3) pipeline. Counts were natural log (log1p)-transformed, followed by scaling and dimensionality reduction (1:10), with visualization using PCA and UMAP. Cells were clustered using the shared nearest-neighbor approach based on the Louvain algorithm (resolution = 0.15), and the results were projected onto UMAP. Differential gene expression analysis (min.pct = 0.25, logfc.threshold = 0.25, q < 0.05) across cell clusters were conducted using the Wilcoxon rank-sum test via the ‘FindMarkers’ and ‘FindAllMarkers’ functions, respectively. "
Assembly: Dermacentor andersoni reference genome (GCF_023375885.1)

organism: Dermacentor andersoni

source_name: salivary glands

extract_protocol:
Dermacentor andersoni adult ticks were collected in May 2023 from vegetation near Lake Como, Montana, USA. Ticks were sampled using the flagging method, where a white flannel cloth was swept over low-lying vegetation and bushes. After collection, ticks were transported to the laboratory and maintained in an environmental incubator at 21°C and 85% relative humidity, with a 12h/12h light/dark cycle. Ticks were removed from incubator and salivary glands were dissected. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization.
The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the library was sequenced by the Illumina NovaSeq 6000 System.

value: salivary glands


title: T NDE, rep1


title: Pm OMV LPS 10h Z2

description:
Library name: V350159056_L02_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_102


title: Pm OMV 24h Z5

description:
Library name: V350158887_L03_3
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_3

value: P. mirabilis DSM 4479

value: incubation with 6.0x10^9 BEVs


title: Breast cancer serum sample 62

address: Avda. Cardenal Herrera Oria S/N

value: Serum


title: RNA-seq sample 3: midgut from a morphologically confirmed wild-caught Tabanus nipponicus (biological replicate 3)

city: Obihiro

first: Noboru

last: Inoue

state: Hokkaido

address: 11 Nishi 2-sen, Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

description:
Library name: Sample 3
Tni.4_Tni.4
Assembled unigene file：All_locP_CpT10_covnr_longest.fasta

data_processing:
CLC Genomics Workbench 26.
Sequence reads were trimmed for adapter sequences and low-quality bases using CLC Genomics Workbench with a quality threshold of 0.05.
Read count extraction and normalization were performed using CLC Genomic Workbench.
Assembly: De novo transcriptome assembly was performed using CLC Genomics Workbench.
Supplementary files format and content: FASTA file containing de novo assembled unigenes from the midgut transcriptome of Tabanus nipponicus.
Supplementary files format and content: Excel file containing the gene expression FPKM values and the annotations of de novo assembled unigenes from the midgut transcriptome of Tabanus nipponicus.

organism: Tabanus nipponicus

source_name: midgut

growth_protocol: Not applicable.

extract_protocol:
RNA was harvested using TRIZOL reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kits (Roche) following manufacturer’s protocols.

treatment_protocol: Under sterile conditions, quickly dissect 3 adult female horse flies, collect the midgut, and put each of them in a separate sample.

value: midgut

value: WT

value: This is one of three RNA-seq samples, each derived from the midgut of a single, morphologically identified wild-caught horse fly (Tabanus nipponicus).


title: T NDE, rep2

value: lymph node


title: LY2 siCtrl, rep 3

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

description: Library name: LY2_siCtrl_n3

data_processing:
Raw sequencing reads were pre-filtered using BGI internal software SOAPnuke to remove adaptors, reads containing more than 0.1 % unknown bases (N) and low quality reads. Clean reads were mapped to the GRCh38 human reference genome using Bowtie2 and gene expression levels were estimated with RSEM.
Genes differentially expressed between LY2 siCDK12 and LY2 siCtrl were determined using DESeq2. An adjusted P value of P < 0.05 was used for comparative analysis. Genes with log2FC < 0 were downregulated in siCDK12, and genes with log2FC > 0 were considered upregulated.
Pathway enrichment analysis was performed with Enrichr and MSigDB Hallmark 2020 database identified significant pathways (Adjusted P < 0.05).
Assembly: GRCh38
Supplementary files format and content: Excel file contains FPKM values for each sample.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (74106, Qiagen).
Library preparation for RNA sequencing were performed by BGI (Hong Kong) as per standard company protocol.

treatment_protocol: Cells seeded in a 6-well plate were transfected with 30 nmol/L of ON-TARGETplus SMARTpool siRNA targeting CDK12 (siCDK12), or with a non-targeting pool (siCtrl) using Lipofectamine™ 2000 reagent (Invitrogen) according to manufacturer's instructions. Cells were harvested 48 hours post-transfection.

tag: disease state

value: breast cancer

value: siCtrl


title: LY2 siCtrl, rep 2

description: Library name: LY2_siCtrl_n2


title: Breast cancer serum sample 63

tag: tissue

value: case

value: Basal-like


title: Breast cancer serum sample 61

value: Luminal A

tag: age


title: Pm OMV 24h Z4

city: Saarbrücken

first: Shusruto

last: Rishik

institute: Universität des Saarlandes

description:
Library name: V350158887_L02_41
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_41


title: LY2 siCtrl, rep 1

description: Library name: LY2_siCtrl_n1


title: RNA-seq sample 2: midgut from a morphologically confirmed wild-caught Tabanus nipponicus (biological replicate 2)

description:
Library name: Sample 2
Tni.2_Tni.2
Assembled unigene file：All_locP_CpT10_covnr_longest.fasta


title: RNA-seq sample 1: midgut from a morphologically confirmed wild-caught Tabanus nipponicus (biological replicate 1)

description:
Library name: Sample 1
Tni.1_Tni.1
Assembled unigene file：All_locP_CpT10_covnr_longest.fasta


title: QMU-SF-s012: SORT-seq scRNA-seq, human heart Treg/T cells

city: London

first: Federica

last: Marelli-Berg

address: Mile End Road

institute: Queen Mary University of London

description: Library name: QMU-SF-s012

data_processing:
Reads mapped to GRCh38 (Ensembl release 98) using STARsolo v2.7.10b; STARsolo default cell calling plus ≥500 UMI/cell filter; non_poisson-corrected filtered UMI gene-count matrices generated; exploratory analysis in Seurat. Raw FASTQ files not deposited in unrestricted access due to privacy concerns.
Assembly: GRCh38 (Ensembl release 98)
Supplementary files format and content: Filtered gene-by-cell UMI count matrices per plate are provided in Matrix Market format (matrix.mtx) with corresponding barcodes.tsv and features.tsv. Barcode sequences can be mapped to 384-well positions using the supplementary files barcode_info.csv and position_of_cells_on_plate.tsv, enabling assignment of each cell (well) to subject/condition according to the plate layout.

source_name: heart

extract_protocol:
Purified Treg cells were obtained from four individuals per group. Based on FACS analysis, Aqua−CD3+CD4+CD25+CD127− Treg cells were sorted into 384-well plates (Single Cell Discoveries, Utrecht, The Netherlands) using a BD FACSAria Fusion (BD Biosciences). Plates were centrifuged at 1500 rpm, stored at −80°C, and shipped to Single Cell Discoveries (Utrecht, The Netherlands) for processing
SORT-seq library preparation

value: heart

tag: cell type

value: Tregs

value: mixed (disease+control)


title: Breast cancer serum sample 60


title: Pm OMV 24h Z2

address: Informatik Campus E2.1

description:
Library name: V350159056_L01_47
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_47

extract_protocol:
Total RNA was isolated from the Caco-2 cells using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
DNA libraries were prepared with the high-throughput MGISP-960 sample preparation system using the MGIEasy rRNA Depletion Kit (MGI Technologies) and MGIEasy RNA Library Prep Set (MGI Technologies) according to the manufacturer’s recommendations. After PCR, different barcoded samples were pooled in equal amount and circularized to generate single stranded DNA libraries (ssDNA). DNA nanoball (DNB) were generated by rolling circle amplification. Paired-end sequencing (PE100) was performed using DNBSEQ-G400RS High-throughput Sequencing Reagent Set (MGI Technologies) on the DNBSEQ-G400 instrument.


title: LY2 siCDK12, rep 3

description: Library name: LY2_siCDK12_n3


title: Pm OMV 24h Z3

description:
Library name: V350158887_L01_41
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_41


title: Pm OMV 10h Z5

description:
Library name: V350158887_L02_47
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_47


title: Breast cancer serum sample 59


title: Breast cancer serum sample 58


title: QMU-SF-s011: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s011


title: LY2 siCDK12, rep 2

description: Library name: LY2_siCDK12_n2


title: LY2 siCDK12, rep 1

description: Library name: LY2_siCDK12_n1


title: QMU-SF-s009: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s009


title: Pm OMV 10h Z4

description:
Library name: V350159056_L04_100
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_100


title: QMU-SF-s010: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s010


title: LY2 cells, siCtrl (INPUT), rep 3

description: Library name: siCtrl_INPUT_n3

data_processing:
Adapter sequences and low-quality sequences were filtered using BGI software SOAPnuke. Clean data was further analyzed with the help of the nf-core ChIP-seq framework.
Briefly, quality control metrics for each sample were assessed using FastQC and 50 bp single-end sequencing reads were mapped to the GRCh38 human reference genome using bwa-mem.
Binding peaks were detected using MACS2 in narrowPeak mode, with a minimum FDR (q-value) cutoff of 0.05.
Differential binding affinity analysis was conducted using the DiffBind R Bioconductor package. Differentially bound sites (DBS) between siCDK12 knockdown and siRNA control were determined using the dba.analyze function with the default DESeq2 method. Candidate binding sites with a FDR < 0.05 were considered significant. Distance from the nearest UCSC hg38 gene for each significantly differentially bound peak was annotated using the ChIPpeakAnno R Bioconductor package.
Assembly: GRCh38
Supplementary files format and content: narrowPeak (except for Input samples)

growth_protocol: LY2 cells were seeded at 9 × 104 cells per well in 2mL complete media in 6-well plates.

extract_protocol:
DNA/protein complexes were cross-linked with 1 % formaldehyde for 10 minutes and quenched with 1 mol/L glycine. Cells were washed with PBS, harvested in PBS supplemented with protease inhibitors and centrifuged at 3000 g for 10 minutes at 4°C. Cell pellets were lysed, and chromatin was extracted as described in Schmidt et al. 2009. Chromatin samples were sonicated using Bioruptor Pico (Diagenode), resulting in an average chromatin fragment size of 200 bp. Triton X-100 was added to sonicated lysates (1 % final concentration) and subjected to centrifugation at 20,000 g for 10 minutes at 4°C.
Library preparation and DNA sequencing (10 ng minimum DNA) were performed by BGI (Hong Kong) as per standard company protocol.

treatment_protocol: Cells were serum depleted for 24 h in 4-OHT-free media, and were transfected with siCDK12 or siCtrl. After 48 h of transfection, media was removed, and cells were treated with 1 µmol/L β-estradiol for 1 h in 4-OHT-free media.


title: Breast cancer serum sample 57


title: Breast cancer serum sample 56


title: QMU-SF-s008: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s008


title: Pm OMV 10h Z3

description:
Library name: V350159056_L02_2
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_2

data_processing:
Snakepipes v2.7.3
Sequence reads were processed using Snakepipes where STAR was used to map to GRCh38 using default options.
FeatureCount from subreads was used to quantify mRNA counts with the parameters (-C -Q 10 --primary)
Assembly: GRCh38
Supplementary files format and content: tsv file contains raw read counts for each sample


title: Pm OMV 10h Z2

description:
Library name: V350159056_L02_101
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_101


title: QMU-SF-s006: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s006


title: QMU-SF-s007: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s007


title: Lc MV RNA 48h Z5

description:
Library name: V350158887_L04_45
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_45

value: L. casei DSM 20011

value: transfection with 100 ng BEV-RNA


title: LY2 cells, siCtrl (ER IP), rep 3

description: Library name: siCtrl_ER_n3

value: ER


title: Breast cancer serum sample 53


title: LY2 cells, siCtrl (INPUT), rep 2

description: Library name: siCtrl_INPUT_n2


title: Lc MV RNA 48h Z4

description:
Library name: V350158887_L02_103
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_103


title: Lc MV RNA 48h Z3

description:
Library name: V350159056_L04_46
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_46


title: QMU-SF-s005: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s005


title: Breast cancer serum sample 54

value: Luminal B


title: QMU-SF-s004: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s004


title: LY2 cells, siCDK12 (ER IP), rep 4

description: Library name: siCDK12_ER_n4


title: Lc MV RNA 48h Z2

description:
Library name: V350159056_L02_43
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_43


title: LY2 cells, siCDK12 (INPUT), rep 4

description: Library name: siCDK12_INPUT_n4


title: Breast cancer serum sample 55

value: Serum


title: Breast cancer serum sample 52


title: Lc MV RNA 24h Z5

description:
Library name: V350159056_L04_2
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_2


title: Breast cancer serum sample 51

value: Control


title: LY2 cells, siCtrl (ER IP), rep 2

description: Library name: siCtrl_ER_n2


title: Breast cancer serum sample 50


title: LY2 cells, siCDK12 (INPUT), rep 3

description: Library name: siCDK12_INPUT_n3


title: QMU-SF-s003: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s003


title: Lc MV RNA 24h Z3

description:
Library name: V350159056_L02_99
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_99


title: QMU-SF-s002: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s002


title: LY2 cells, siCDK12 (ER IP), rep 3

description: Library name: siCDK12_ER_n3


title: QMU-SF-s001: SORT-seq scRNA-seq, human heart Treg/T cells

description: Library name: QMU-SF-s001


title: Lc MV RNA 24h Z2

description:
Library name: V350159056_L01_46
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_46


title: human.PDAC.CAF.3.uM.TEADi.3

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

description: Library name: SAM24526234

data_processing:
Quality check and trimming of raw reads were performed using fastp 0.23.4 with the parameters: --disable_quality_filtering -l 12 --disable_adapter_trimming --trim_poly_x.
Single-end (SE) trimmed reads were aligned to the human genome GRCh38 and a feature count matrix was generated using HTSeqGenie 4.4.6.
The expression profiles were filtered to drop low-expressed genes using edgeR::filterByExpr and then normalized using limma-voom.
Differential expression analysis was performed by fitting a linear model to the data using lmFit from limma. To identify DE calls, we used a logFC threshold of |0.58| to test the significance of fold change (limma::treat()). To report significant DE genes, we used logFC and FDR thresholds of |0.58| and 0.05, respectively.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing the gene-level feature count matrix (raw counts) generated by HTSeqGenie for all samples.
Supplementary files format and content: Tab-delimited text file containing the CPM (Counts Per Million) normalized expression matrix for all samples.

source_name: PDAC CAF CAF08

growth_protocol: Commercially available human lung adenocarcinoma cancer-associated fibroblasts (CAF07-AD, Vitro Biopharma) and pancreatic adenocarcinoma cancer-associated fibroblasts (CAF08, Vitro Biopharma) were obtained from Vitro Biopharma. Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) High Glucose supplemented with 10% tetracycline-negative heat-inactivated fetal bovine serum and 1X GlutaMAX. Low-passage CAFs were seeded in 6-well tissue culture plates at 300,000 cells per well and grown to approximately 70% confluence.

extract_protocol:
After 48 hours of treatment, cells were harvested using 1X Gibco TrypLE (Thermo Fisher Scientific) and centrifuged at 5000 rpm for 5 minutes to collect cell pellets. Total RNA was isolated using the QIAGEN RNeasy Plus Mini Kit (QIAGEN) following the manufacturer’s instructions. RNA quality was assessed using High Sensitivity RNA ScreenTape on TapeStation 4200 (Agilent Technologies) and quantified using the Quant-iT RiboGreen RNA Kit (Thermo Fisher Scientific) on a Victor X2 Multilabel Microplate Reader.
Sequencing libraries were generated using the Illumina Stranded mRNA kit (Illumina) with an input of 100-1000 nanograms of total RNA. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific). The average library size was determined using D5000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq X Plus (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: Cells were treated with the TEAD inhibitor GNE-7883 at final concentrations of 1 µM or 3 µM. Control conditions were treated with DMSO to match the DMSO content of the drug-treated samples. Treatments were conducted for 48 hours.

value: PDAC CAF CAF08

value: Cancer associated fibroblasts

value: TEADi 3uM


title: Breast cancer serum sample 49


title: human.PDAC.CAF.3.uM.TEADi.2

description: Library name: SAM24526233


title: Ef MV RNA 24h Z3

description:
Library name: V350158887_L01_44
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_44

value: E. faecalis DSM 20478

value: transfection with 5 ng BEV-RNA


title: Ef MV RNA 24h Z4

description:
Library name: V350158887_L03_99
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_99


title: Breast cancer serum sample 47


title: SW620_INVIVO_PARENT_CON_6H_C

city: Sutton

first: Konstantinos

last: Mitsopoulos

state: London

address: 15 Cotswold Road

department: Cancer Therapeutics Unit

institute: The Institute of Cancer Research

description: Replicate 3 of 3

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
# 1. Initialisation
library(limma)
# 2. Read in tab-delimited targets file
sw620_in_vivo_targets <- readTargets(sw620_in_vivo_sample_annotation.txt)
# 3. Use LIMMA's read.maimages function to load data into an RGList object
sw620_in_vivo_RG <- read.maimages(sw620_in_vivo_targets, source=agilent)
# 4. Subtract the background (optional, but recommended)
sw620_in_vivo_RG.b <- backgroundCorrect(sw620_in_vivo_RG, method=normexp, offset=50)
# 5. Normalize within and between the arrays - remove controls
sw620_in_vivo_MA.p <- normalizeWithinArrays(sw620_in_vivo_RG.b, method=loess)
sw620_in_vivo_MA.pAq <- normalizeBetweenArrays(sw620_in_vivo_MA.p, method=Aquantile)
sw620_in_vivo_MA2.pAq <- sw620_in_vivo_MA.pAq[sw620_in_vivo_MA.pAq$genes$ControlType==0,]
# 6. Use the avereps function to average replicate spots
sw620_in_vivo_MA2.ave <- avereps(sw620_in_vivo_MA2.pAq, ID=sw620_in_vivo_MA2.pAq$genes$ProbeName)
# 7. Whole spot contrasts (to use for deriving average expression):
write.table(sw620_in_vivo_MA2.ave$A, file = sw620_in_vivo_MA2_ave_A_expression_matrix.txt, sep=\t)
# 8. Within spot contrasts (to use for log2FC calculations)
write.table(sw620_in_vivo_MA2.ave$M, file = sw620_in_vivo_MA2_ave_M_expression_matrix.txt, sep=\t)

label_protocol: Cy5 (red): human reference standard (Stratagene), Cy3 (green): experimental samples

extract_protocol: standard protocol

value: in vitro

tag: cell line background

value: colorectal cell line

tag: clone

value: PARENT

tag: compound

source_name: human reference standard

value: reference


title: Breast cancer serum sample 46


title: Breast cancer serum sample 45


title: SW620_INVIVO_PARENT_CON_6H_B

description: Replicate 2 of 3


title: human.PDAC.CAF.3.uM.TEADi.1

description: Library name: SAM24526232

tag: cell line

tag: treatment


title: Lc MV RNA 10h Z5

description:
Library name: V350159056_L04_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_102


title: human.PDAC.CAF.1.uM.TEADi.3

description: Library name: SAM24526231

value: TEADi 1uM


title: Breast cancer serum sample 44


title: Ef MV RNA 24h Z2

description:
Library name: V350159056_L02_47
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_47


title: Breast cancer serum sample 48


title: SW620_INVIVO_PARENT_CON_6H_A

description: Replicate 1 of 3

tag: condition


title: human.PDAC.CAF.1.uM.TEADi.2

description: Library name: SAM24526230


title: human.PDAC.CAF.1.uM.TEADi.1

description: Library name: SAM24526229


title: SW620_INVIVO_PARENT_CCT2431726_6H_B

description: Replicate 2 of 3


title: Breast cancer serum sample 42


title: Lc MV RNA 10h Z4

description:
Library name: V350159056_L04_99
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_99


title: Breast cancer serum sample 43


title: SW620_INVIVO_PARENT_CCT2431726_6H_C

description: Replicate 3 of 3


title: SW620_INVIVO_PARENT_CCT2431726_6H_A

description: Replicate 1 of 3


title: Lc MV RNA 10h Z3

description:
Library name: V350159056_L01_1
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_1


title: human.PDAC.CAF.DMSO.3

description: Library name: SAM24526228

value: DMSO


title: human.PDAC.CAF.DMSO.2

description: Library name: SAM24526227


title: SW620_INVIVO_CDK19_CL2_CON_6H_C

description: Replicate 3 of 3

value: CDK19 KO, clone2


title: Breast cancer serum sample 41

value: case

value: Luminal A