title: LF82 RpoB E1263A mutant 3

city: Bethesda

first: Melissa

last: Arroyo-Mendoza

address: 8 CENTER DR RM 2A11

department: LBG

institute: NIDDK

description:
Library name: SD107_3
SD107_3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with bbduk.sh tool from bbtools software (v37.62).
Trimmed reads were mapped to the Escherichia coli LF82 genome with STAR (v2.7.10a)
Quantification of fragments per gene was carried out with the featureCounts tool from Subread software (v2.0.1). Multimapper reads were counted as a fraction.
BigWig files were generated with bamCoverage tool from DeepTools (v3.5.1).
Genes with less than 20 reads per gene across samples were discarded
Differential expression analysis was carried out with the R package DESeq2 (v1.42.0)
Assembly: NC_011993.1
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: comma-separated values text file that includes based normalized gene expression across samples, RpoB E1263A mutant vs WT differential gene expression expressed as log2FoldChange and their corresponding p-value and p-adjusted value for each gene as estimated by DESeq2.

organism: Escherichia coli LF82

source_name: bacteria

growth_protocol: Isogenic E. coli LF82 and rpoB E1263A mutant were grown to a cell density of OD600 ~04-0.5 in LB broth at 37o C.

extract_protocol:
RNA was isolated using method II of (Hinton 1989).
Library for RNA-seq was prepared using a modified version of the methods published by  Alexander Shishkin et al. (doi:10.1038/nmeth.3313). rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions. cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications.  Illumina adaptors sequences based on TruSeq HT Sample Prep Kits were purchase from Integrated DNA Technologies and used in the ligation step.  TruSeq-1 and TruSeq-2 primer were used for PCR enrichment of adaptor ligated DNA.  Library size was verified with a Bioanalyzer using an Agilent High Sensitivity DNA kit.  The concentration of each library was determined using the KAPA Library Quantification Kit for Illumina platforms.  Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the MiSeq 2 x 250 bp Sequencing Kit (Illumina).

value: bacteria

value: LF82 RpoB E1263A mutant


title: LF82 RpoB E1263A mutant 2

status: Public on Dec 10 2025

type: SRA

state: MD

country: USA

description:
Library name: SD107_2
SD107_2

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: genotype


title: HumanLiver_S315

city: Singapore

first: Qing

last: Zhao

address: 28 Medical Dr

country: Singapore

institute: NUS

data_processing:
FastQC (v0.11.9) was used for quality control. STAR (v2.7.9a) was used for alignment to reference genome. RSEM (v1.3.1) was used for gene expression level estimation.
Assembly: GRCh38, Ensembl release 77
Supplementary files format and content: Tab-delimited text file includes TPM for each sample.

organism: Homo sapiens

source_name: Liver

extract_protocol:
RNA was extracted from liver biopsies using Trizol reagent.
The cDNA libraries were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit from Illumina (Yeasen) as per manufacturer’s instructions.

tag: tissue

value: Liver

tag: gender

value: Female

tag: age at_biopsy

tag: body mass_index

tag: diabetes

tag: steatosis grade

tag: fibrosis grade

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score

tag: diagnosis

value: MASL


title: WT cholinergic neurons, ZT16, biol rep 3

city: Chicago

first: Sharon

last: Tam

state: IL

address: 303 E Chicago Ave, Rm 13-270

institute: Northwestern University

description:
Library name: Sample 17
Column name in 'raw.counts.all.samples_timecourse.csv': ZT16_biol.rep.3

data_processing:
150bp paired-end sequencing was performed on a NovaSeq X Plus (Illumina) to a minimum depth of 30M reads.
Sequences were aligned to the mm10 transcriptome with STAR (v2.7.5) using the –quantMode Transcriptome and GeneCounts options.
Gene counts were obtained from mm10 annotations (Ensembl 98) using rsem-calculate-expression (v1.3.0).
Alternative splicing analysis was performed using rMATS (v4.0.2) to quantify reads across annotated splice junctions present in the mm10 assembly. Differentially spliced transcripts were defined as having an FDR-adjusted p-value < 0.05 and a minimum exon inclusion level difference > 10%.
Rhythmic mRNA expression and rhythmic splice frequency throughout the day were assessed by JTK_Cycle analysis, allowing for period lengths of 20, 24, or 28 hours to account for 4-hr sampling frequency. Rhythmicity was determined by an FDR-adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: .csv file includes raw counts for Input and Samples

molecule: polyA RNA

organism: Mus musculus

source_name: spinal cord cholinergic neurons

extract_protocol:
RNA was extracted using the Direct-zol RNA MicroPrep kit.
Libraries were constructed from 100 ng of RNA using the Illumina Stranded mRNA Prep kit according to the manufacturer's instructions.

value: spinal cord cholinergic neurons

value: wild-type


title: LF82 RpoB E1263A mutant 1

description:
Library name: SD107_1
SD107_1


title: HumanLiver_S314


title: WT cholinergic neurons, ZT12, biol rep 3

description:
Library name: Sample 16
Column name in 'raw.counts.all.samples_timecourse.csv': ZT12_biol.rep.3


title: Sham Endo 3mo (1)

first: Katia

last: Corano Scheri

address: 300 E. Superior St.

department: Ophthalmology, Feinberg School of Medicine

description: Library name: AF-6 (3mo)

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Data was demultiplexed and counted using Cell Range
Cell Ranger output was analyzed using Seurat version 4.3
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: Tab-delimited matrix files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Retina

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions.
Single cell suspensions were washed in PBS/2% BSA and checked for viability > 85%
Directional mRNA libraries were prepared using NEBNext Kits per the manufacturer’s instructions
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Retina

value: Endothelial cells

tag: treatment

value: Sham (control)


title: LF82_WT_3

description: Library name: LF82_WT_3

value: WT


title: LF82_WT_2

description: Library name: LF82_WT_2


title: STZ Endo 3mo (2)

description: Library name: AF-4 (3mo)

value: STZ (Diabetic)


title: Sham Retina 3mo (1)

description: Library name: AF-5 (3mo)

value: Retinal cells


title: HumanLiver_S312


title: HumanLiver_S313

value: MASH


title: WT cholinergic neurons, ZT4, biol rep 3

description:
Library name: Sample 14
Column name in 'raw.counts.all.samples_timecourse.csv': ZT4_biol.rep.3


title: WT cholinergic neurons, ZT8, biol rep 3

description:
Library name: Sample 15
Column name in 'raw.counts.all.samples_timecourse.csv': ZT8_biol.rep.3


title: STZ Retina 3mo (2)

description: Library name: AF-3 (3mo)


title: LF82_WT_1

description: Library name: LF82_WT_1


title: HumanLiver_S311


title: STZ Endo 3mo (1)

description: Library name: AF-2 (3mo)


title: WT cholinergic neurons, ZT0, biol rep 3

description:
Library name: Sample 13
Column name in 'raw.counts.all.samples_timecourse.csv': ZT0_biol.rep.3


title: RNASeq_AB5075_DrelA_SUP2_LIQ

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

description: Library name: 1055303

data_processing:
Between 15 x 10^6 and 20 x 10^6 paired-end sequence reads (2 x 100) were first mapped on the genome of A. baumannii AB5075 (CP008706.1) using Galaxy
The number of reads overlapping each genomic position was computed using Galaxy
A DESeq2 analysis was then peformed between the WT and DrelA, DrelA and DrelA_rpoB_R557C and between WT and DrelA_rpoB_R557C samples using Galaxy
Assembly: CP008706.1
Supplementary files format and content: The xlsx file "RNA-Seq_WT_DrelA_DrelA_SUP_MOT" reports (p)ppGpp-dependent regulon with Fold Change (FC) between WT, DrelA and DrelA_rpoB_R557C. The  different columns are organized as follows: column A: geneid1 (ABUW_RS gene identification number for the AB5075_UW strain); column B: gene name (predicted function of the corresponding gene); column C: geneid2 (ABUW gene identification number for the AB5075_UW strain);  column D: description (description of the predicted function of the corresponding gene); columns E-K: raw counts [raw counts for each replicate of WT, DrelA (relA) and DrelA_rpoB_R557C (supp)] ; columns L-R: normalized raw counts [normalized raw counts for each replicate of of WT, DrelA (relA) and DrelA_rpoB_R557C (supp)]; columns S-X: Comparison between DrelA and WT; columns T-AD: Comparison between DrelA and DrelA_rpoB_R557C; columns AE-AJ: Comparison between DrelA and DrelA_rpoB_R557C [baseMean (mean of normalized counts), log2FoldChange (base 2 log of fold change ), lfcSE (stanxard error), stat (Wald statistic), pvalue (Wald test p-value), padj (BH adjusted p-value)
Supplementary files format and content: The xlsx file "RNA-Seq_WT_DrelA_DrelA_SUP_LIQ" reports (p)ppGpp-dependent regulon with Fold Change (FC) between WT, DrelA and DrelA_rpoB_R557C. The  different columns are organized as follows: column A: geneid1 (ABUW_RS gene identification number for the AB5075_UW strain); column B: gene name (predicted function of the corresponding gene); column C: geneid2 (ABUW gene identification number for the AB5075_UW strain);  column D: description (description of the predicted function of the corresponding gene); columns E-K: raw counts [raw counts for each replicate of WT, DrelA (relA) and DrelA_rpoB_R557C (supp)] ; columns L-R: normalized raw counts [normalized raw counts for each replicate of of WT, DrelA (relA) and DrelA_rpoB_R557C (supp)]; columns S-X: Comparison between DrelA and WT; columns T-AD: Comparison between DrelA and DrelA_rpoB_R557C; columns AE-AJ: Comparison between DrelA and DrelA_rpoB_R557C [baseMean (mean of normalized counts), log2FoldChange (base 2 log of fold change ), lfcSE (stanxard error), stat (Wald statistic), pvalue (Wald test p-value), padj (BH adjusted p-value)

organism: Acinetobacter baumannii AB5075

source_name: Bacteria

growth_protocol: A. baumannii strains grown overnight at 37°C in complex medium (LB) to saturation were used to inoculate on LB low agar plates (MOT) and incubated 24h at 37°C or diluted in LB and grown until mid-exponential phase (OD600nm~0.5).

extract_protocol:
Total RNA was extracted with RNeasy® Protect Bacteria Kit from Qiagen and following manufacturer’s instructions.
RNA-Seq libraries were prepared at the Seqalis company (Belgium) using the RNASeq TTRNA library according to the manufacturer's instructions, after rRNA depletion and cDNA synthesis.

treatment_protocol: For samples from LB low agar plates, colonies were recovered from the plates and pooled before RNA extraction.

value: Bacteria

value: LB


title: HumanLiver_S310

value: Male


title: WT cholinergic neurons, ZT20, biol rep 2

description:
Library name: Sample 12
Column name in 'raw.counts.all.samples_timecourse.csv': ZT20_biol.rep.2


title: STZ Retina 3mo (1)

description: Library name: AF-1 (3mo)


title: RNASeq_AB5075_DrelA_SUP1_LIQ

description: Library name: 1055301


title: STZ Endo 1mo (3)

description: Library name: AF-12


title: HumanLiver_S309


title: WT cholinergic neurons, ZT16, biol rep 2

description:
Library name: Sample 11
Column name in 'raw.counts.all.samples_timecourse.csv': ZT16_biol.rep.2


title: HumanLiver_S308


title: STZ Endo 1mo (2)

description: Library name: AF-11


title: WT cholinergic neurons, ZT8, biol rep 2

description:
Library name: Sample 9
Column name in 'raw.counts.all.samples_timecourse.csv': ZT8_biol.rep.2


title: STZ Endo 1mo (1)

description: Library name: AF-10


title: HAECs, AdCEBPB, RNA-seq rep2

city: Hangzhou

first: Cong

last: Qiu

state: Zhejiang

address: No.866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human aortic endothelial cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Ambion, 15596026) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Human aortic endothelial cells

value: CEBPB overexpression


title: STZ Retina 1 mo (3)

description: Library name: AF-9


title: RNASeq_AB5075_WT2_LIQ

description: Library name: 1055287


title: HAECs, AdCEBPB, RNA-seq rep3


title: RNASeq_AB5075_DrelA1_LIQ

description: Library name: 1055291

value: DrelA


title: STZ Retina 1 mo (2)

description: Library name: AF-8


title: HAECs, AdCEBPB, RNA-seq rep1


title: WT cholinergic neurons, ZT12, biol rep 2

description:
Library name: Sample 10
Column name in 'raw.counts.all.samples_timecourse.csv': ZT12_biol.rep.2


title: RNASeq_AB5075_WT1_LIQ

description: Library name: 1055285


title: WT cholinergic neurons, ZT4, biol rep 2

description:
Library name: Sample 8
Column name in 'raw.counts.all.samples_timecourse.csv': ZT4_biol.rep.2


title: RNASeq_AB5075_DrelA_SUP2_MOT

description: Library name: 1185123

value: LB low agar plate


title: HumanLiver_S317

value: Liver

value: Female

value: MASL


title: HAECs, AdControl, RNA-seq rep3


title: RNASeq_AB5075_DrelA_SUP1_MOT

description: Library name: 1185121


title: STZ Retina 1 mo (1)

description: Library name: AF-7

value: Retina


title: HAECs, AdControl, RNA-seq rep2


title: WT cholinergic neurons, ZT16, biol rep 1

description:
Library name: Sample 5
Column name in 'raw.counts.all.samples_timecourse.csv': ZT16_biol.rep.1

value: spinal cord cholinergic neurons

value: wild-type


title: RNASeq_AB5075_DrelA2_MOT

description: Library name: 1185119


title: WT cholinergic neurons, ZT12, biol rep 1

description:
Library name: Sample 4
Column name in 'raw.counts.all.samples_timecourse.csv': ZT12_biol.rep.1


title: RNASeq_AB5075_DrelA2_LIQ

description: Library name: 1055293


title: RNASeq_AB5075_DrelA1_MOT

description: Library name: 1185117


title: Sham Endo 1mo (1)

description: Library name: AF-4

value: Endothelial cells

value: Sham (control)


title: Lung_spatial_CF1, scRNAseq

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  cellranger-6.0.1
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Lung Biopsy

extract_protocol:
Samples were cleaned with PBS washes and  40 μm filter. Single-cell suspensions were counted for viability assesment.
Library was performed according to the manufacter’s instructions(Chromium Next GEM Single Cell 3’ Reagent Kits v3.1, 10X Genomics).

tag: disease state

value: Cystic fibrosis (CF)

value: Lung Biopsy

tag: library type

value: Visium spatial


title: Sham Endo 1mo (2)

description: Library name: AF-5


title: HAECs, AdControl, RNA-seq rep1

value: WT


title: Lung_CF1_rep2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  cellranger-6.0.1
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: RNASeq_AB5075_WT1_MOT

description: Library name: 1185113

value: Bacteria


title: WT cholinergic neurons, ZT0, biol rep 2

description:
Library name: Sample 7
Column name in 'raw.counts.all.samples_timecourse.csv': ZT0_biol.rep.2


title: Lung_CF1_rep1, scRNAseq

description: 10x Genomics


title: WT cholinergic neurons, ZT4, biol rep 1

description:
Library name: Sample 2
Column name in 'raw.counts.all.samples_timecourse.csv': ZT4_biol.rep.1


title: BAL_CO3, scRNAseq

description: 10x Genomics

source_name: Bronchoalveolar Lavage

value: non-Cystic fibrosis control

value: Bronchoalveolar Lavage


title: Sham Retina 1mo (2)

description: Library name: AF-2

value: Retinal cells


title: RNASeq_AB5075_WT2_MOT

description: Library name: 1185115

value: LB low agar plate


title: CCL5_KO_A3

city: Beijing

first: Mingxuan

last: Zhou

state: China

address: No. 2 Nanwei Road, Tianqiao Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

description: Library name: KOA3

data_processing:
Fastp software was used to process raw reads in fastq format. Clean reads were obtained after low-quality reads were removed for subsequent data analysis. We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome. RSEM was used for gene qualification and FPKM values.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: left ventricle

growth_protocol: Mice were anesthetized following experimental treatment, and then the heart was punctured and flushed with 20 ml of saline to remove blood from systemic circulation.

extract_protocol:
Total RNA was extracted from CRC cells using the RNeasy kit (Beyotime, Shanghai, China, R0027) and subjected to reverse transcription using the SuperScript II reverse transcriptase. (TaKaRa, Japan, RR047) according to the manufacturer´s instructions.
The samples were tested by Nanodrop for RNA concentration, OD260/280, OD260/230, and Agilent 2100 for RNA fragment length. Then, mRNA was enriched using Oligo (dT) magnetic beads, and the enriched mRNA was interrupted and split into two pieces. After enrichment, the mRNA was broken into fragments and synthesized into one-stranded cDNA by adding six-base random primers, and then two-stranded cDNA was synthesized by adding buffer, dNTPs, and DNA polymerase I. The synthesized double-stranded cDNA was purified, end-repaired, A-added, spliced, and screened for fragment size by using AMPure XP beads. Finally, a cDNA library was constructed by polymerase chain reaction (PCR) amplification.

treatment_protocol: Mice were infused for 7 days with saline or a “pressor dose” of Ang II (1500 ng/kg/min) by osmotic mini-pumps (Alzet MODEL 1007D; DURECT, Cupertino, CA, USA) implanted subcutaneously.

value: left ventricle

value: ANG II infusion (1500 ng/kg/min) for 7 days

tag: batch

value: batch 1


title: WT cholinergic neurons, pooled input

description:
Library name: Input
Column name in 'raw.counts.all.samples_timecourse.csv': Input

tag: cell type


title: WT cholinergic neurons, ZT20, biol rep 1

description:
Library name: Sample 6
Column name in 'raw.counts.all.samples_timecourse.csv': ZT20_biol.rep.1

tag: genotype


title: CCL5_KO_A2

description: Library name: KOA2

tag: tissue


title: Quasi-Mesenchymal 5

city: Ithaca

first: Kimaya

middle: Milind

last: Bakhle

state: NY

address: 930 Campus Road VRT T7012

department: Department of Biomedical Sciences

institute: Cornell University

description: Library name: 147798-21

data_processing:
Reads were trimmed for low quality and adaptor sequences with fastp v0.21.0. Reads were mapped to the reference genome/transcriptome (Ensembl CanFam4) using STAR v2.7.0e. SARTools and DESeq2 v1.26.0 was used to generate normalized counts and statistical analysis of differential gene expression.
Assembly: CanFam4
Supplementary files format and content: Excel spreadsheet with normalized gene counts and differentially expressed genes.

organism: Canis lupus familiaris

source_name: Mammary carcinoma

extract_protocol:
RNA was extracted using the FormaPure XL RNA Reagent Kit (Beckmann Coulter #C36000). The Fast Select rRNA depletion kit (Qiagen) was used to rRNA.
UDI-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

value: Mammary carcinoma


title: Tracheal_CO2, scRNAseq

description: 10x Genomics

source_name: Tracheal Brush

value: Tracheal Brush


title: WT cholinergic neurons, ZT8, biol rep 1

description:
Library name: Sample 3
Column name in 'raw.counts.all.samples_timecourse.csv': ZT8_biol.rep.1

value: spinal cord cholinergic neurons

value: wild-type


title: Quasi-Mesenchymal 4

description: Library name: 012413-22


title: 004.Tumor.0871.RPL22 positive.immune high

type: protein

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

hyb_protocol: FFPE slides were prepared according to the GeoMx DSP slide preparation user manual (MAN-10087-04).

data_processing:
Raw data was downloaded directly from GeoMx DSP Analysis Suite and converted into txt files. Data QC was conducted using the standard parameters described in the GeoMx DSP data analysis user manual (MAN-10154-01). Minimum nuclei count was set to 20 nuclei and maximum nuclei count was set to 1600 nuclei. Filtering was performed at a minProbeRatio of 10% and ROIs were scaled to the geometric mean of nuclei in all ROIs. ROIs were normalized to the geometric mean of the housekeeping proteins GAPDH, Histone H3, and S6. Background correction was conducted using the geometric mean of signal to background ration of the negative targets Ms IgG1, Ms IgG2a, and Rb IgG.
QC and normalization were conducted online on GeoMx DSP Analysis Suite.
nCounter analysis system

label: fluorescent barcode

molecule: protein

source_name: FFPE endometrial tumor

extract_protocol: According to the GeoMx DSP slide preparation user manual (MAN-10087-04)

tag: rpl22 status

value: Positive

tag: immune status

value: Immune high


title: CCL5_KO_C3

description: Library name: KOC3

value: Saline infusion for 7 days


title: Sham Retina 1mo (3)

description: Library name: AF-3

value: Retina

value: Sham (control)


title: Tracheal_CO1, scRNAseq

description: 10x Genomics


title: Bronchial_CO2, scRNAseq

description: 10x Genomics

source_name: Bronchial Brush

value: Bronchial Brush


title: CCL5_KO_A1

description: Library name: KOA1


title: 004.Tumor.1675.RPL22 positive.immune high

scan_protocol: FFPE slides were prepared according to the GeoMx DSP slide preparation user manual (MAN-10087-04)


title: 005.Tumor.1675.RPL22 positive.immune high

label_protocol: FFPE slides were prepared according to the GeoMx DSP slide preparation user manual (MAN-10087-04)


title: 005.Tumor.0871.RPL22 positive.immune high


title: Sham Retina 1mo (1)

description: Library name: AF-1


title: WT cholinergic neurons, ZT0, biol rep 1

description:
Library name: Sample 1
Column name in 'raw.counts.all.samples_timecourse.csv': ZT0_biol.rep.1


title: Quasi-Mesenchymal 2

description: Library name: 222267-22


title: 003.Immune.1675.RPL22 positive.immune high


title: Quasi-Mesenchymal 1

description: Library name: 161422-22


title: CCL5_KO_C2

description: Library name: KOC2


title: BAL_CO1, scRNAseq

description: 10x Genomics

value: non-Cystic fibrosis control


title: CCL5_KO_C1

description: Library name: KOC1


title: 006.Tumor.0871.RPL22 positive.immune high


title: Heterogeneous 5

description: Library name: 149564-21


title: WT_A2

description: Library name: WTA2

value: WT


title: Tracheal_CF2, scRNAseq

description: 10x Genomics

value: Cystic fibrosis (CF)


title: Heterogeneous 4

description: Library name: 012538-22


title: WT_A1

description: Library name: WTA1


title: Heterogeneous 3

description: Library name: 035750-22


title: 006.Tumor.1675.RPL22 positive.immune high


title: Bronchial_CF2, scRNAseq

description: 10x Genomics


title: BAL_CO2, scRNAseq

description: 10x Genomics

value: Bronchoalveolar Lavage


title: WT_C3

description: Library name: WTC3

value: left ventricle


title: Quasi-Mesenchymal 3

description: Library name: 068555-24


title: WT_C2

description: Library name: WTC2


title: Bronchial_CO1, scRNAseq

description: 10x Genomics


title: Heterogeneous 1

description: Library name: 196608-22


title: 002.Immune.1272.RPL22 negative.immune low

value: Negative

value: Immune low


title: WT_A3

description: Library name: WTA3

value: ANG II infusion (1500 ng/kg/min) for 7 days

value: batch 1


title: WT_C1

description: Library name: WTC1


title: 002.Immune.0989.RPL22 positive.immune low


title: Epithelial 5

description: Library name: 011687-24

value: Mammary carcinoma


title: 003.Immune.0989.RPL22 positive.immune low


title: Epithelial 4

description: Library name: 062708-22


title: tp3_ATAC

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: scATACseq of organoid line

library_source: genomic single cell

data_processing:
The raw files were processed using Cellranger-Arc. The gene expression summarised from the alignment files was further analysed using Seurat, version 4.3.0.1. The dimensionality reduction was performed using PCA (prcomp R package, version 4.3) and UMAP (uwot R package, version 0.2.1). Seurat was used to infer the Shared Nearest Neighbour graph; the clustering was performed using graph clustering approaches (Louvain, Louvain with multilevel refinement and SLM community detection methods).
The assessment of the stability of the cell partitions relied on ClustAssess (R package, version 0.3.1).
The expression profiles and resulting UMAP were used to infer the cell-fate. The pseudotime analysis, was performed using the monocle3 R package, version 1.3.1. The RNA velocity was inferred using velocity version 0.6 for building loom files. The scVelo python package, version 0.3.2, was used to calculate the splice ratio and to infer the velocity and the transition between cell states.
The raw files were processed using the Cellranger-Arc, version 2.0.0. To reduce the impact of the dataset imbalance (derived from number of cells and variable sequencing depth) on the interpretability of the chromatin openness, we applied a subsampling step on timepoints 1, 2 and 3 to match the fragment distribution observed in timepoint 0. The subsampled versions of the alignment and fragment files were used for identifying peaks using MACS3, version 3.0.1.
The default reference genome built from Cellranger-Arc was used to infer the association between identified peaks and regions. A peak is associated to a gene if >80% is overlapping with an annotated gene.
Using gene-associated peaks we inferred an expression matrix summarising the chromatin openness. To summarise variation in openness across samples, we merged peaks if either middle point falls inside the range of the other peak.
Assembly: GRCh38.p13
Supplementary files format and content: count matrix containing raw gene and peak expression (hdf5)

molecule: genomic DNA

source_name: liver

growth_protocol: Expansion media as described in Broutier et al, 2016

extract_protocol:
Isolation media as described in  Broutier et al, 2016
10x genomics protocol for nuclei isolation and library prep

treatment_protocol: Differentiation media as described in Broutier et al, 2016

value: liver

tag: cell line

value: organoid cell line

value: cholangiocytes

value: differentiation media as per protocol

tag: age

value: ealry passage organoids


title: BAL_CF1, scRNAseq

description: 10x Genomics


title: Thap2uM-rep3

city: Durham

first: Anant

last: Parekh

state: NORTH CAROLINA

address: 111 TW Alexander Drive

institute: NIH

description: Library name: Thap2uM-rep3

data_processing:
Reads were mapped to the rn7 reference genome via STAR v2.6 with default parameters.
Read counts per gene were calculated by featureCounts (Subread v1.5.0-p1) with parameter "-s2".
Signal tracks were generated by STAR v2.6 with parameters "--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM", then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: rn7
Supplementary files format and content: Counts per gene per sample in tab-delimited text format.
Supplementary files format and content: Normalized signal tracks in bigWig format.

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from RBL-2H3 cells using Qiagen RNeasy RNA mini prep kit with Qiagen on-column DNase digestion per the manufacturer’s instructions.
RNAseq librares were made using the Illumina Tru-seq Stranded mRNA library kit following the manufacturer's protcol.

value: 2 uM thapsigargin in 0.2 mM extracellular Ca2+


title: Thap2uM-rep2

description: Library name: Thap2uM-rep2


title: BAL_CF2, scRNAseq

description: 10x Genomics


title: 001.Immune.1272.RPL22 negative.immune low


title: tp2_ATAC

description: scATACseq of organoid line


title: Epithelial 3

description: Library name: 061352-23


title: Thap2uM-rep1

description: Library name: Thap2uM-rep1


title: Epithelial 2

description: Library name: 148359-23


title: 004.Tumor.0989.RPL22 positive.immune low

value: Positive


title: Tracheal_CF1, scRNAseq

description: 10x Genomics

value: Tracheal Brush


title: Heterogeneous 2

description: Library name: 255361-22


title: tp1_ATAC

description: scATACseq of organoid line


title: Epithelial 1

description: Library name: 137169-24


title: Bronchial_CF1, scRNAseq

description: 10x Genomics

value: Bronchial Brush


title: Patient 38_WT-FVPTC_6

type: RNA

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

country: Spain

institute: IDIBELL

description: Total RNA for all formalin-fixed paraffin-embedded (FFPE) tissues were extracted using the miRNeasy FFPE kit (QIAGEN).

hyb_protocol: Samples were denatured at 85°C for 5 min and then hybridized at 65°C for 16 h.

scan_protocol: Fluorescent reporter tags were scanned by an automated multi-channel epifluorescence scanner, generating the raw counts, using the MAX/FLEX Analysis System and software. Barcodes for each target molecule were counted across a maximum resolution of 555 fields of view (FOV).

data_processing:
miRNAs that did not match between codeset versions v3a and v3b were removed and only the endogenous miRNAs were kept.  Then, the miRNA data expression was adjusted using the trimmed mean of M values (TMM) method and the effective library size was calculated. miRNAs were considered detectable if they had expression levels of 10 counts per million (CPM) in more than 70 % of the samples in the discovery cohort, resulting in 540 detectable miRNAs. Subsequently, differential expression analysis was performed using the quasi-likelihood negative binomial generalized log-linear model (GLM) functions provided by the EdgeR package (4.10.16). The linear model was fitted using the batches of interest (experiment run#, version of the chip and sample source).
Normalized counts using the trimmed mean of M values (TMM) method

source_name: Malignant thyroid lesion, control

label_protocol: not applicable

extract_protocol: Total RNA for all fresh frozen tissue (FFT) were extracted using the mirVana miRNA isolation kit (ThermoFisher) and all formalin-fixed paraffin-embedded (FFPE) tissues were extracted using the miRNeasy FFPE kit (QIAGEN).

value: Thyroid

tag: histology

value: Follicular variant of papillary thyroid cancer (FVPTC)

tag: benign/malignant

value: Benign

tag: sample source

value: FFPE

tag: version of the chip

tag: experiment run #

tag: other sample title


title: tp0_ATAC

description: scATACseq of organoid line

tag: treatment


title: Thap20nM-rep2

description: Library name: Thap20nM-rep2

value: 20 nM thapsigargin in 2 mM extracellular Ca2+


title: 005.Tumor.0989.RPL22 positive.immune low

value: Immune low


title: 004.Tumor.1272.RPL22 negative.immune low

value: Negative


title: 005.Tumor.1272.RPL22 negative.immune low


title: Thap20nM-rep1

description: Library name: Thap20nM-rep1


title: Patient 37_DICER1-FVPTC_5

source_name: Malignant thyroid lesion, DICER1-mutated


title: tp3_RNA

description: scRNAseq of organoid line


title: 003.Immune.1272.RPL22 negative.immune low


title: 006.Tumor.0989.RPL22 positive.immune low


title: Patient 36_DICER1-FVPTC_4

value: Malignant


title: tp2_RNA

description: scRNAseq of organoid line

value: liver


title: IgE-rep3

description: Library name: IgE-rep3

value: IgE in 2 mM extracellular Ca2+


title: 006.Tumor.1272.RPL22 negative.immune low


title: IgE-rep2

description: Library name: IgE-rep2


title: tp1_RNA

description: scRNAseq of organoid line

value: organoid cell line

value: cholangiocytes


title: Patient 34_DGCR8-TFND_6

source_name: Benign thyroid lesion, DGCR8-mutated

value: Thyroid follicular nodular disease (TFND)

value: Sample 585


title: Thap20nM-rep3

description: Library name: Thap20nM-rep3


title: tp0_RNA

description: scRNAseq of organoid line

value: differentiation media as per protocol

value: ealry passage organoids


title: PID8027week45replicate8Primer,ADT

city: San Francisco

first: Julie

last: Frouard

state: California

address: 1650 Owens street

department: Virology

institute: Gladstone Institutes

library_source: other

data_processing:
Alignment of scRNAseq reads, collapsing of reads to unique molecular identifier (UMI) counts, and cell calling was performed using CellRanger 6.0.2 (10X Genomics).
Assembly: hg38  + consensus subtype B genome for HIV
Supplementary files format and content: CellRanger output files : features.tsv.gz, matrix.mtx.gz, barcodes.tsv.gz

source_name: blood

extract_protocol:
CD4+ T cells were purified by negative selection using the EasySep Human CD4 T cell enrichment kit (StemCell) followed by spiking back in of bulk PBMCs from the same donor at a ratio of 5:100 in order have non-CD4+ T cells
libraries construction according to 10X protocol "Chromium Single Cell 5’ Reagent Kits v2 (Dual Index) User Guide (10x Genomics CG000330, Rev A)".

value: blood

value: PBMC_T cells

value: ADT


title: 001.Immune.1292.RPL22 positive.immune low

value: Positive


title: Patient 33_WT-TFND_6

description: Total RNA for all fresh frozen tissue (FFT) were extracted using the mirVana miRNA isolation kit (ThermoFisher)

source_name: Benign thyroid lesion, control

value: Thyroid

value: Benign

value: FFT


title: PID8027week45replicate8Primer,GEX

value: GEX


title: 001.Immune.0561.RPL22 positive.immune low

value: Immune low


title: Patient 32_WT-TFND_5

value: Sample 18


title: control-rep2

description: Library name: control-rep2

value: control


title: 002.Immune.0561.RPL22 positive.immune low


title: PID8027week45replicate7Primer,ADT


title: PID8027week45replicate7Primer,GEX


title: control-rep1

description: Library name: control-rep1


title: Patient 31_WT-TFND_4

value: FFPE


title: 003.Immune.1292.RPL22 positive.immune low


title: 002.Immune.1292.RPL22 positive.immune low


title: Patient 27_WT-PDTC_2

value: Poorly differentiated thyroid cancer (PDTC)

value: Malignant


title: Uninfected_D14_6

city: Philadelphia

first: Theresa

middle: A

last: Freeman

state: PA

address: 1015 Walnut Street

department: Orthopedic Surgery Research

institute: Thomas Jefferson University

description: Library name: C_D14_Rat177

data_processing:
The data processing steps were done by Novogene and the methods detailed here are from their report and methods files.
Raw data was processed throuh fastp software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. Q20, Q30, and GC content the clean data were calculated. All downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from the genome website directly. Index for the reference genome was built using Hisat2 v.2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v.2.0.5. Hisat2 was selected since it can create a database of splice junctions based on the gene model annotation file.
featureCounts v1.5.0-p3 was used to count the reads numebrs mapped to each gene. FPKM of each gene was calculated based on the length of the gene and the reads count mapped to the gene. FPKM, expected number of Fragments per Kilobase of transcript sequence per Millions base pair sequenced considers the effect of sequencing depth and gene length for the reads count at the same time.
Assembly: ensembl_104_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: The Infection Manuscript 6h Processed Data contains the raw count numbers for the 6-hour samples prior to removing outliers and truncating the data for GSEA analysis. The outlier removal and data truncation thresholds are outlined in the Methods section of the manuscript. Infection Manuscript Pre-Revision Processed Data contains the raw count numbers for the pre-revision samples prior to removing outliers and truncating the data for GSEA analysis. The outlier removal and data truncation thresholds are outlined in the Methods section of the manuscript. Infection Manuscript Day 4 Processed Data contains the raw count numbers for the day 4 samples prior to removing outliers and truncating the data for GSEA analysis. The outlier removal and data truncation thresholds are outlined in the Methods section of the manuscript. Infection Manuscript Day 14 Processed data contains the raw count numbers for the day 14 samples prior to removing outliers and truncating the data for GSEA analysis. The outlier removal and data truncation thresholds are outlined in the Methods section of the manuscript.

source_name: Biceps Femoris

extract_protocol:
The muscle tissue was homogenized by resuspending crushed muscle in TRIzol reagent at 1 ml of reagent per 0.1 g of muscle. Then the tissue was dissociated by using M tubes and a gentleMACS tissue dissociator. The RNA was extracted using the Macherey-Nagel NucleoSpin RNA Midi Kit after chloroform phase separation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Biceps Femoris

value: Uninfected

tag: time point


title: 001.Immune.0989.RPL22 positive.immune low


title: PID8027week0replicate6Primer,ADT

tag: library type


title: Uninfected_D14_5

description: Library name: C_D14_Rat133


title: IgE-rep1

description: Library name: IgE-rep1

value: IgE in 2 mM extracellular Ca2+


title: Patient 26_WT-PDTC_1


title: Patient 35_DICER1-TFND_4

source_name: Benign thyroid lesion, DICER1-mutated

value: Thyroid follicular nodular disease (TFND)


title: Patient 25_WT-FVPTC_5

value: Follicular variant of papillary thyroid cancer (FVPTC)


title: Uninfected_D14_4

description: Library name: C_D14_Rat65


title: PID8027week0replicate6Primer,GEX

value: blood

value: PBMC_T cells


title: control-rep3

description: Library name: control-rep3


title: 003.Tumor.0561.RPL22 positive.immune low

value: Positive


title: 004.Tumor.1292.RPL22 positive.immune low


title: PID8027week0replicate5Primer,ADT

value: ADT


title: Uninfected_D14_2

description: Library name: C_D14_Rat41


title: 005.Tumor.0561.RPL22 positive.immune low


title: Patient 23_WT-FVPTC_3

value: Thyroid

value: FFT


title: 005.Tumor.1292.RPL22 positive.immune low

value: Immune low


title: Patient 20_WT-FTC_1

value: Follicular thyroid cancer (FTC)


title: Uninfected_D14_1

description: Library name: C_D14_Rat21


title: PID8027week45replicate4NOTHING,ADT


title: Patient 19_DICER1-TFND_3

value: Benign

value: Sample 21


title: PID8027week45replicate4NOTHING,GEX

value: GEX


title: 006.Immune.0561.RPL22 positive.immune low


title: Uninfected_D4_6

description: Library name: C_D4_Rat195


title: PID8027week45replicate3NOTHING,ADT


title: 004.Tumor.0561.RPL22 positive.immune low


title: Patient 18_DICER1-TFND_2

value: Follicular thyroid adenoma (FTA)

value: Sample 8


title: Uninfected_D4_5

description: Library name: C_D4_Rat193

value: Biceps Femoris

value: Uninfected


title: PID8027week45replicate3NOTHING,GEX


title: Patient 17_DICER1-TFND_1

value: Thyroid follicular nodular disease (TFND)

value: FFPE


title: Uninfected_D4_4

description: Library name: C_D4_Rat126


title: 001.Immune.2045.RPL22 negative.immune low

value: Negative


title: PID8027week0replicate2NOTHING,ADT

value: blood

value: PBMC_T cells


title: Patient 16_DICER1-PDTC_2

value: Poorly differentiated thyroid cancer (PDTC)

value: Malignant

value: Sample 584


title: Uninfected_D4_3

description: Library name: C_D4_Rat64


title: 001.Tumor.0398.RPL22 negative.immune low

value: Immune low


title: Patient 24_WT-FVPTC_4

value: Thyroid

value: Follicular variant of papillary thyroid cancer (FVPTC)

value: FFT


title: PID8027week0replicate2NOTHING,GEX

value: GEX


title: PID8027week0replicate5Primer,GEX


title: 002.Tumor.0398.RPL22 negative.immune low


title: 002.Immune.2045.RPL22 negative.immune low


title: Uninfected_D4_2

description: Library name: C_D4_Rat35


title: Patient 14_DICER1-FVPTC_3

value: Sample 17


title: Uninfected_D4_1

description: Library name: C_D4_Rat17


title: PID8027week0replicate1NOTHING,GEX


title: PID8027week0replicate1NOTHING,ADT

value: ADT


title: 003.Immune.2045.RPL22 negative.immune low


title: 006.Tumor.1292.RPL22 positive.immune low

value: Positive


title: Uninfected_prerevision_5

description: Library name: C_D0M_111_MU

value: Biceps Femoris

value: Uninfected

value: prerevision


title: Uninfected_prerevision_4

description: Library name: C_D0M_109_MU


title: PID1052week0replicate6Primer,ADT


title: Patient 13_DICER1-FVPTC_2

value: FFPE


title: Uninfected_prerevision_3

description: Library name: C_D0M_108_MU


title: 004.Immune.2045.RPL22 negative.immune low

value: Negative


title: Patient 11_DICER1-FTC_3

value: Follicular thyroid cancer (FTC)


title: 005.Immune.2045.RPL22 negative.immune low


title: Patient 10_DICER1-FTC_2

value: Minimally invasive follicular thyroid cancer (MIFTC)

value: Sample 25


title: PID1052week0replicate6Primer,GEX

value: blood

value: PBMC_T cells


title: PID1052week0replicate5Primer,ADT


title: Patient 15_DICER1-PDTC_1

value: Thyroid

value: Poorly differentiated thyroid cancer (PDTC)

value: Malignant


title: Uninfected_prerevision_2

description: Library name: C_D0M_107_MU


title: 006.Tumor.2045.RPL22 negative.immune low

value: Immune low


title: Patient 9_DICER1-FTC_1

value: Encapsulated angioinvasive follicular thyroid cancer (EAIFTC)

value: FFT

value: Sample 14


title: PID1052week0replicate4Primer,ADT

value: ADT


title: PID1052week0replicate5Primer,GEX

value: GEX


title: Uninfected_D14_3

description: Library name: C_D14_Rat47

value: Biceps Femoris

value: Uninfected


title: Infected_D14_6

description: Library name: B_D14_Rat93

value: Infected


title: Patient 1_DGCR8-FTC_1

source_name: Malignant thyroid lesion, DGCR8-mutated

value: FFPE

value: Sample 543


title: Uninfected_prerevision_1

description: Library name: C_D0M_104_MU

value: prerevision


title: 007.Tumor.2045.RPL22 negative.immune low

value: Negative


title: PID1052week0replicate4Primer,GEX

value: blood

value: PBMC_T cells


title: Infected_D14_5

description: Library name: B_D14_Rat90


title: 003.Tumor.0398.RPL22 negative.immune low


title: Patient 12_DICER1-FVPTC_1

value: Thyroid

value: Follicular variant of papillary thyroid cancer (FVPTC)


title: PID1052week0replicate3Primer,ADT


title: 009.Immune.2045.RPL22 negative.immune low

value: Immune low


title: 008.Tumor.2045.RPL22 negative.immune low


title: Infected_D14_4

description: Library name: B_D14_Rat74


title: female Tg(TauP301L-dsRed) zebrafish, replicate 2

city: Esch-Sur-Alzette

first: Mohamed

last: Soudy

address: 2 Avenue de l'Universite

department: Luxembourg Centre for Systems Biomedicine (LCSB)

country: Luxembourg

institute: University of Luxembourg

description:
Library name: TauFemale2
10X Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v7.1.0 (10X Genomics) with alignment to the zebrafish genome (GRCz11/danRer11). Initial quality metrics included total reads per cell, median genes per cell, median UMI counts per cell, and mitochondrial gene expression percentages across samples.
Stringent quality control filters were applied using Seurat v5.1.0 to retain high-quality nuclei with >200 and <7000 detected genes (threshold determined after manual outlier checking using QC metric violin plots, following the Seurat tutorial on satijalab.org), and <5% mitochondrial gene expression. Genes expressed in fewer than 3 nuclei were excluded from downstream analyses.
Assembly: zebrafish genome (danRer11, Genome Reference Consortium)
Supplementary files format and content: filtered feature barcoded matrices, raw gene expression matrices

organism: Danio rerio

source_name: Brain

extract_protocol:
Nuclei from brain tissue were extracted using Minute single nucleus isolation kit for neuronal tissues/cells (cat # BN-020) from Invent Biotechnologies according to the provided protocol.
Libraries were constructed according to the manufacturers protocol (Chromium GEM-X Single Cell 3' Kit v4).

treatment_protocol: Wild-type AB and Tg(TauP301L-dsRed) zebrafish were maintained under standard conditions at 28.5 ± 0.5°C with a 14h light/10h dark cycle. Adult fish (6 months old) were housed at 4-6 fish per liter in 3.5L tanks with controlled water parameters (pH 7.5, conductivity 700-900 μS/cm). Fish were euthanized using buffered tricaine methanesulfonate (MS-222; 250 mg/L) for 15 minutes, and brains were dissected under stereomicroscopic guidance using sterilized tools, immediately flash-frozen in liquid nitrogen, and stored at -80°C until processing.

value: Brain

value: brain nuclei

value: Tau

tag: batch


title: female Tg(TauP301L-dsRed) zebrafish, replicate 1

description:
Library name: TauFemale1
10X Genomics

tag: cell type


title: 001.Immune.1808.RPL22 positive.immune low

value: Positive


title: PID1052week0replicate3Primer,GEX

value: GEX


title: Infected_D14_3

description: Library name: B_D14_Rat72

value: Biceps Femoris


title: Infected_D14_2

description: Library name: B_D14_Rat70


title: PID1052week0replicate2NOTHING,ADT

value: ADT


title: male Tg(TauP301L-dsRed) zebrafish, replicate 1

description:
Library name: TauMale1
10X Genomics

tag: genotype


title: 002.Immune.1808.RPL22 positive.immune low


title: male Tg(TauP301L-dsRed) zebrafish, replicate 2

description:
Library name: TauMale2
10X Genomics

tag: tissue


title: 001.Immune.2201.RPL22 negative.immune low

tag: rpl22 status


title: Infected_D14_1

description: Library name: B_D14_Rat15

value: Infected


title: PID1052week0replicate2NOTHING,GEX


title: male control (AB) zebrafish, replicate 2

description:
Library name: ABMale2
10X Genomics

value: AB

value: Wild-type AB


title: 002.Immune.2201.RPL22 negative.immune low

tag: immune status


title: PID1052week0replicate1NOTHING,ADT


title: male control (AB) zebrafish, replicate 1

description:
Library name: ABMale1
10X Genomics


title: Infected_D4_6

description: Library name: B_D4_Rat78


title: PID1052week0replicate1NOTHING,GEX


title: Infected_D4_5

description: Library name: B_D4_Rat33


title: Infected_D4_4

description: Library name: B_D4_Rat31


title: PID8026week0replicate8Primer,ADT


title: female control (AB) zebrafish, replicate 2

description:
Library name: ABFemale2
10X Genomics


title: female control (AB) zebrafish, replicate 1

description:
Library name: ABFemale1
10X Genomics


title: Infected_D4_3

description: Library name: B_D4_Rat27


title: 003.Immune.2201.RPL22 negative.immune low


title: STZ 3mo

description: Library name: STZ_S2

source_name: Retina

value: Retina

value: STZ (Diabetic)


title: PID8026week0replicate8Primer,GEX

value: blood


title: 004.Tumor.1808.RPL22 positive.immune low


title: 004.Tumor.2201.RPL22 negative.immune low

value: Negative


title: PID8026week0replicate7Primer,GEX

value: PBMC_T cells


title: Sham 3mo

description: Library name: W_S1

value: Sham (control)


title: Infected_D4_2

description: Library name: B_D4_Rat25


title: PID8026week0replicate7Primer,ADT


title: Infected_D4_1

description: Library name: B_D4_Rat19


title: PID8026week0replicate6Primer,ADT


title: Infected_prerevision_5

description: Library name: B_D0M_191_MU

value: prerevision


title: 005.Tumor.1808.RPL22 positive.immune low

value: Immune low


title: CX3CR1-, BSA-FA, ex-vivo, d8 p.i., rep2

city: La Jolla

first: Katelynn

middle: Rose

last: Kazane

state: CA

address: 9500 Gilman Drive, #0329

department: Biological Sciences

institute: University of California San Diego

description:
Library name: Ex-vivo_FA-CX3CR1neg_2
Column name in processed files: FA-CX3CR1neg_2.count

data_processing:
Raw sequencing data were aligned to mouse genome mm10 (Genome Reference Consortium GRCm38) by using Spliced Transcripts Alignment to a Reference (STAR) aligner106 with the following parameters: “--outFilterType BySJout -- outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 -- alignIntronMax 1000000 --alignMatesGapMax 1000000”.
Assembly: mm10
Supplementary files format and content: csv files were generated with DEseq2 and include normalized counts for each sample.

source_name: splenocytes

extract_protocol:
RNA was harvested using the RNeasy mini kit (Qiagen) following manufacturers instructions. 50,000-75,000 cells were used per sample.
RNAseq library was generated using a TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturers instructions.

value: splenocytes

tag: cell line

value: CD8+ T cells

value: BSA-palmitate incubation (200 uM - 8hrs)


title: 005.Tumor.2201.RPL22 negative.immune low


title: 006.Tumor.1808.RPL22 positive.immune low

value: Positive


title: PID8026week0replicate6Primer,GEX

value: GEX


title: 003.Immune.1808.RPL22 positive.immune low


title: Infected_prerevision_4

description: Library name: B_D0M_114_MU

value: Biceps Femoris


title: PID8026week0replicate5Primer,ADT

value: ADT


title: Infected_prerevision_3

description: Library name: B_D0M_113_MU

value: Infected


title: CX3CR1+, BSA-FA, ex-vivo, d8 p.i., rep3

description:
Library name: Ex-vivo_FA-CX3CR1pos_3
Column name in processed files: FA-CX3CR1pos_3.count


title: 006.Tumor.2201.RPL22 negative.immune low


title: PID8026week0replicate5Primer,GEX


title: 001.Immune.2244.RPL22 positive.immune high

value: Immune high


title: Infected_prerevision_2

description: Library name: B_D0M_112_MU


title: CX3CR1+, BSA-FA, ex-vivo, d8 p.i., rep2

description:
Library name: Ex-vivo_FA-CX3CR1pos_2
Column name in processed files: FA-CX3CR1pos_2.count


title: PID8026week24replicate4Primer,ADT


title: Infected_prerevision_1

description: Library name: B_D0M_105_MU


title: 001.Tumor.0949.RPL22 positive.immune high


title: CX3CR1+, BSA-FA, ex-vivo, d8 p.i., rep1

description:
Library name: Ex-vivo_FA-CX3CR1pos_1
Column name in processed files: FA-CX3CR1pos_1.count


title: Infected_6h_6

description: Library name: B_6h_Rat190


title: CX3CR1-, BSA-FA, ex-vivo, d8 p.i., rep3

description:
Library name: Ex-vivo_FA-CX3CR1neg_3
Column name in processed files: FA-CX3CR1neg_3.count


title: 002.Immune.2244.RPL22 positive.immune high


title: CX3CR1-, BSA only, ex-vivo, d8 p.i., rep3

description:
Library name: Ex-vivo_Untr-CX3CR1neg_3
Column name in processed files: Un-CX3CR1neg_3.count

value: BSA incubation (200 uM - 8hrs)


title: PID8026week24replicate4Primer,GEX


title: 002.Tumor.0949.RPL22 positive.immune high


title: PID8026week24replicate3Primer,ADT


title: 003.Immune.2244.RPL22 positive.immune high


title: Infected_6h_5

description: Library name: B_6h_Rat189


title: PID8026week24replicate3Primer,GEX


title: CX3CR1-, BSA only, ex-vivo, d8 p.i., rep1

description:
Library name: Ex-vivo_Untr-CX3CR1neg_1
Column name in processed files: Un-CX3CR1neg_1.count


title: CX3CR1-, BSA only, ex-vivo, d8 p.i., rep2

description:
Library name: Ex-vivo_Untr-CX3CR1neg_2
Column name in processed files: Un-CX3CR1neg_2.count


title: Infected_6h_4

description: Library name: B_6h_Rat185


title: CX3CR1-, BSA-FA, ex-vivo, d8 p.i., rep1

description:
Library name: Ex-vivo_FA-CX3CR1neg_1
Column name in processed files: FA-CX3CR1neg_1.count


title: PID8026week24replicate2Primer,ADT


title: Infected_6h_3

description: Library name: B_6h_Rat184


title: PID8026week24replicate2Primer,GEX


title: Infected_6h_2

description: Library name: B_6h_Rat125


title: 004.Immune.2244.RPL22 positive.immune high


title: CX3CR1+, BSA only, ex-vivo, d8 p.i., rep2

description:
Library name: Ex-vivo_Untr-CX3CR1pos_2
Column name in processed files: Un-CX3CR1pos_2.count


title: CX3CR1+, BSA only, ex-vivo, d8 p.i., rep3

description:
Library name: Ex-vivo_Untr-CX3CR1pos_3
Column name in processed files: Un-CX3CR1pos_3.count


title: PID8026week24replicate1Primer,ADT


title: 005.Immune.2244.RPL22 positive.immune high


title: Infected_6h_1

description: Library name: B_6h_Rat122


title: CX3CR1+, BSA only, ex-vivo, d8 p.i., rep1

description:
Library name: Ex-vivo_Untr-CX3CR1pos_1
Column name in processed files: Un-CX3CR1pos_1.count


title: PID8026week24replicate1Primer,GEX


title: PGC, ody, 36 hpf,2

city: Münster

first: Katsiaryna

last: Tarbashevich

state: NRW

address: Von-Esmarch-Str. 56

department: Institute of Cell Biology

country: Germany

institute: University Münster

description: Library name: 11_OD36-2_S11

data_processing:
The Next-generation sequencing was performed on an Illumina NextSeq 550 machine using 2x 75 bp paired-end reads. To quantify transcripts from raw fastq files Salmon mapping-based mode (Patro et al., 2017) was used.
Assembly: Transcript information from Ensembl (Cunningham et al., 2019) release 97 for Danio_rerio GRCz11 was utilized.
Supplementary files format and content: Excel file, normalized read counts

source_name: primordial germ cell

extract_protocol:
Total RNA was extracted using the PicoPure RNA extraction kit (Arcturus)
mRNA was extracted from the total RNA using NEXTflex Poly(A) Beads (Hiss Diagnostics) following the manufacturer’s instructions. 14 μl of the mRNA elute was transferred to a fresh 1.5 ml tube (Eppendorf). Next, cDNA was synthesized using the NEXTflex Rapid directional qRNA-Seq kit (Hiss Diagnostics)

value: primordial germ cell

value: odysseus (ody) mutant


title: TexTERM, FA-treated, in-vivo, d21 p.i., rep3

description:
Library name: In-vivo_FA-Term_3
Column name in processed files: FA-term_4.count

value: TexTERM

value: palmitic/lauric acid injection (i.p.)


title: PGC, ody, 36 hpf,1

description: Library name: 2_OD36-1_S2


title: 006.Immune.2244.RPL22 positive.immune high


title: TexTERM, FA-treated, in-vivo, d21 p.i., rep2

description:
Library name: In-vivo_FA-Term_2
Column name in processed files: FA-term_3.count


title: PID145week0replicate2Primer,ADT

value: blood

value: PBMC_T cells


title: 007.Tumor.2244.RPL22 positive.immune high


title: 008.Tumor.2244.RPL22 positive.immune high


title: PID145week0replicate2Primer,GEX


title: PGC, ody, 24 hpf,2

description: Library name: 10_OD24-2_S10


title: 009.Tumor.2244.RPL22 positive.immune high


title: TexTERM, FA-treated, in-vivo, d21 p.i., rep1

description:
Library name: In-vivo_FA-Term_1
Column name in processed files: FA-term_2.count


title: PGC, ody, 24 hpf,1

description: Library name: 1_OD24-1_S1


title: PID145week0replicate1Primer,GEX


title: TexINT, FA-treated, in-vivo, d21 p.i., rep3

description:
Library name: In-vivo_FA-Int_3
Column name in processed files: FA-int_4.count

value: TexINT


title: 001.Immune.1364.RPL22 positive.immune high


title: PGC, WT, 36 hpf,2

description: Library name: 14_WT36-3_S14

value: wild-type


title: 003.Tumor.0949.RPL22 positive.immune high


title: PID145week0replicate1Primer,ADT


title: 001.Immune.1884.RPL22 negative.immune low

value: Negative

value: Immune low


title: R08A - RNA-Seq human colorectal adenoma

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Sequencing reads were quality controlled and preprocessed using fastp.
Sequencing reads were aligned to the human Gencode v36 transcriptome using Salmon v1.4.0 in default settings.
Read count tables were preprocessed with tximport v1.18.0 R package and significantly differentially expressed genes were identified using DESeq2 v1.30.0 using a paired Wald test analysis adjusted for the sample cohort and adenoma subtype
A gene was considered differentially expressed (DE) if associated with a median level greater than 1 Transcript Per Million (TPM) in data of adenoma or adjacent mucosa samples, with a Benjamini-Hochberg (BH) adjusted p-value lower than 0.05 in analysis, and with an absolute log2 fold change greater than 1
Assembly: hg38
Supplementary files format and content: TPM normalized gene expression levels

source_name: human colorectal adenoma

extract_protocol:
RNA was isolated by Rneasy mini kit (Qiagen) with RNase-Free DNase Set (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Library was prepared by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) following manufacturer's protocols. Ribosomal RNAs (rRNAs) were removed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat, New England Biolabs, USA).

treatment_protocol: Samples were stored in RNA later.

value: human colorectal adenoma

tag: Sex

value: Male

tag: adenoma type

value: Tubular

tag: age of_sampling

tag: adenoma grade

value: Low

tag: localization

value: colon

value: DNase treatment


title: 002.Immune.1364.RPL22 positive.immune high

value: Positive

value: Immune high


title: R08N - RNA-Seq human colorectal healthy mucosa

source_name: human colorectal healthy mucosa

value: human colorectal healthy mucosa


title: PGC, WT, 24 hpf,2

description: Library name: 13_WT24-3_S13

value: primordial germ cell


title: PGC, WT, 36 hpf,1

description: Library name: 9_WT36-2_S9


title: 003.Immune.1364.RPL22 positive.immune high

source_name: FFPE endometrial tumor


title: TexSTEM, FA-treated, in-vivo, d21 p.i., rep3

description:
Library name: In-vivo_FA-Stem_3
Column name in processed files: FA-stem_4.count

value: splenocytes

value: CD8+ T cells

value: TexSTEM

value: palmitic/lauric acid injection (i.p.)


title: R07A - RNA-Seq human colorectal adenoma

value: Sessile serrated


title: TexINT, FA-treated, in-vivo, d21 p.i., rep1

description:
Library name: In-vivo_FA-Int_1
Column name in processed files: FA-int_2.count

value: TexINT


title: TexSTEM, FA-treated, in-vivo, d21 p.i., rep2

description:
Library name: In-vivo_FA-Stem_2
Column name in processed files: FA-stem_3.count


title: PGC, WT, 24 hpf,1

description: Library name: 8_WT24-2_S8

value: wild-type


title: R07N - RNA-Seq human colorectal healthy mucosa


title: PGC, WT, 14 hpf,2

description: Library name: 3_WT14-2_S3


title: TexSTEM, FA-treated, in-vivo, d21 p.i., rep1

description:
Library name: In-vivo_FA-Stem_1
Column name in processed files: FA-stem_2.count


title: R06A - RNA-Seq human colorectal adenoma

value: human colorectal adenoma


title: PGC, WT, 14 hpf,1

description: Library name: 12_WT14-1_S12


title: TexTERM, untreated, in-vivo, d21 p.i., rep3

description:
Library name: In-vivo_Untr-Term_3
Column name in processed files: Un-term_4.count

value: TexTERM

value: PBS injection (i.p.)


title: 003.Immune.1884.RPL22 negative.immune low

value: Negative

value: Immune low


title: 004.Tumor.1364.RPL22 positive.immune high


title: 004.Tumor.1884.RPL22 negative.immune low


title: R06N - RNA-Seq human colorectal healthy mucosa

value: Male

value: colon

value: DNase treatment


title: Patient_2_Day_7

city: New Haven

first: Jonathan

middle: Howard

last: DeLong

state: CT

address: 300 George St Ste 353

department: Neurology

institute: Yale University

description:
Library name: Sample 3
10X Genomics

data_processing:
Reads were aligned using CellRanger v7.1.0, using the human reference transcriptome GRCh38-2020-A.
Assembly: Human GRCh38-2020-A
Supplementary files format and content: Feature Barcode Market Exchange Matrices (MEX) produced by CellRanger v7.1.0

source_name: Blood

extract_protocol:
PBMC were isolated and cryopreserved. PBMC were thawed in batches, with all timepoints for a given patient thawed and analyzed at once. Five total batches: Patient 2, Patients 3 & 4, Patient 5, Patient 6, Patients 7 & 8. Cells were then stained with fluorescently-labeled antibodies specific for canonical cell lineage markers, fixable Live/Dead stain, and in some cases hashing antibodies. Live cells were isolated via FACS Aria before analysis by 10X.
Library construction was performed according to manufacturer's protocol using 10X genomics single cell 3' v3 chemistry.

treatment_protocol: Patients were treated with BAF312 or placebo control

value: Blood

value: PBMC

value: mRNA


title: R05A - RNA-Seq human colorectal adenoma

value: Female

value: Tubular

value: Low


title: 005.Tumor.1884.RPL22 negative.immune low


title: Patient_2_Day_2

description:
Library name: Sample 2
10X Genomics


title: 005.Tumor.1364.RPL22 positive.immune high

value: Positive

value: Immune high


title: R05N - RNA-Seq human colorectal healthy mucosa

value: human colorectal healthy mucosa


title: TexTERM, untreated, in-vivo, d21 p.i., rep1

description:
Library name: In-vivo_Untr-Term_1
Column name in processed files: Un-term_2.count

value: splenocytes

value: CD8+ T cells


title: 006.Tumor.1364.RPL22 positive.immune high


title: TexINT, untreated, in-vivo, d21 p.i., rep3

description:
Library name: In-vivo_Untr-Int_3
Column name in processed files: Un-int_4.count

value: TexINT

value: PBS injection (i.p.)


title: Patient_2_Day_1

description:
Library name: Sample 1
10X Genomics


title: Syn

city: Seoul

first: Eun-Jin

last: Bae

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

description:
Library name: Syn
scRNAseq data of aSyn treated sample

data_processing:
Single cell transcriptome was processed using cell ranger.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes feature for each Sample

extract_protocol:
RNA was harvested using RNeasy mini Kit.
RNA libraries for RNA-seq were prepared using 10X Genomics Next GEM-X 3’ technology following manufacturer's protocols.

value: Brain

value: Oligodendrocyte

value: WT

value: aSyn


title: R04N - RNA-Seq human colorectal healthy mucosa

value: rectum

value: DNase treatment


title: TexINT, untreated, in-vivo, d21 p.i., rep1

description:
Library name: In-vivo_Untr-Int_1
Column name in processed files: Un-int_2.count


title: LacZ

description:
Library name: LZ
scRNAseq data of LacZ treated sample

value: LacZ


title: 001.immune.0458.RPL22 positive.immune high


title: 006.Tumor.1884.RPL22 negative.immune low

value: Negative

value: Immune low


title: R03N - RNA-Seq human colorectal healthy mucosa

value: Male

value: colon


title: TexSTEM, untreated, in-vivo, d21 p.i., rep3

description:
Library name: In-vivo_Untr-Stem_3
Column name in processed files: Un-stem_4.count

value: TexSTEM


title: Thi_14

description:
Library name: Thi_14
RNA-seq

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous adipose tissues

extract_protocol:
RNA was extracted with Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen #74804)
Library prepration and sequencing was performed by GENEWIZ

value: subcutaneous adipose tissues

value: F

tag: depot

value: Thi

tag: age

tag: bmi


title: TexTERM, untreated, in-vivo, d21 p.i., rep2

description:
Library name: In-vivo_Untr-Term_2
Column name in processed files: Un-term_3.count

value: splenocytes

value: CD8+ T cells

value: TexTERM

tag: treatment


title: Abd_14

description:
Library name: Abd_14
RNA-seq

value: Abd


title: TexSTEM, untreated, in-vivo, d21 p.i., rep2

description:
Library name: In-vivo_Untr-Stem_2
Column name in processed files: Un-stem_3.count

value: PBS injection (i.p.)


title: R02A - RNA-Seq human colorectal adenoma

value: human colorectal adenoma

value: Female

value: Tubular

value: Low


title: Glu_13

description:
Library name: Glu_13
RNA-seq

value: M

value: Glu


title: TexSTEM, untreated, in-vivo, d21 p.i., rep1

description:
Library name: In-vivo_Untr-Stem_1
Column name in processed files: Un-stem_2.count


title: 002.Immune.0458.RPL22 positive.immune high

value: Positive

value: Immune high


title: 001.Immune.0636.RPL22 positive.immune low

value: Immune low


title: Abd_13

description:
Library name: Abd_13
RNA-seq

value: subcutaneous adipose tissues


title: 002.Immune.0636.RPL22 positive.immune low


title: R04A - RNA-Seq human colorectal adenoma

value: rectum

value: DNase treatment


title: KOPSO_3

city: Xinjiang Uygur Autonomous Region

first: Huiqin

last: Wang

address: No. 91 Tianchi Road, Tianshan District, Urumqi, Xinjiang Uygur Autonomous Region

institute: People's Hospital of Xinjiang Uygur Autonomous Region

description: Library name: Sample 9

data_processing:
The raw unique molecular identifier (UMI) count matrix was converted into a Seurat object by the Seurat package (v4.3.0). Cells with UMI counts (<1,000), detected genes (<500), or percentage of mitochondrial genes (≥15%) were then filtered out.Doublets and genes expressed in fewer than 5 cells were also excluded. After removing low-quality cells, the data was log-normalized using the NormalizeData function and the top 2,000 highly variable genes were selected for downstream analysis. Data integration was accomplished through the Harmony algorithm and scaling was conducted using the ScaleData function. Principal component analysis (PCA) was executed using the RunPCA function, and the top 30 principal components were selected for dimensionality reduction and subsequent clustering. The main cell clusters were identified using the FindClusters function (res=0.4), and then visualized with UMAP plots. Marker genes for each cluster were detected using the FindMarkers function, and celltypes were annotated meticulously using ScType tool.
Assembly: GRCm39
Supplementary files format and content: UMI count matrix of each sample

source_name: skin

extract_protocol:
Freshly collected skin tissues were rinsed with ice-cold PBS and minced into small pieces on ice using sterile scissors. The tissues were then dissociated using a BD tissue dissociation kit, and the resulting cell suspension was filtered through a 70-μm cell strainer. Cell viability was assessed by trypan blue staining, and the concentration of live cells was adjusted to the desired range. Finally, the cells were loaded onto BD Rhapsody Cartridge Kits to facilitate the formation of single-cell magnetic beads within the microwells according to manufacturer instructions.
BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification Kit was used to construct single-cell libraries.

value: skin

value: imiquimod applied after S100a4 knockout


title: R02N - RNA-Seq human colorectal healthy mucosa

value: human colorectal healthy mucosa

value: colon


title: TexINT, untreated, in-vivo, d21 p.i., rep2

description:
Library name: In-vivo_Untr-Int_2
Column name in processed files: Un-int_3.count

value: splenocytes

value: CD8+ T cells

value: TexINT

value: PBS injection (i.p.)


title: R01A - RNA-Seq human colorectal adenoma

value: human colorectal adenoma

value: Female

value: Tubular

value: High


title: Glu_12

description:
Library name: Glu_12
RNA-seq

value: M

value: Glu


title: 003.Immune.0636.RPL22 positive.immune low

value: Positive

value: Immune low


title: KOPSO_2

description: Library name: Sample 8


title: R03A - RNA-Seq human colorectal adenoma

value: Male

value: Traditional serrated

value: DNase treatment


title: R01N - RNA-Seq human colorectal healthy mucosa

value: human colorectal healthy mucosa


title: Abd_12

description:
Library name: Abd_12
RNA-seq

value: subcutaneous adipose tissues

value: Abd


title: KOPSO_1

description: Library name: Sample 7

value: skin

value: imiquimod applied after S100a4 knockout


title: 20230727_154229_016_2023-SNP-1005

type: genomic

city: Shanghai, China

first: Yang

last: Lily

address: No.1239, Siping Road, Yangpu District, Shanghai

institute: Tongji University

description:
20230727_154229_016_2023-SNP-1005.cychp
Hybridized to CytoScan750K Array

hyb_protocol: As per manufacturer (Affymetrix),prepare Hybridization Master Mix and add Hybridization Master Mix to the samples.Place the plate onto the pre-heated thermal cycler and run the CytoScan Hyb protocol.Using a P200 pipette, remove 200 µL of the first sample and immediately inject it into an array.Allow the arrays to rotate at 50°C, 60 rpm for 16 to 18 hours.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip® System 3000Dx v.2

data_processing:
Using ChAS v4.4 for data analysis,Reference Model File Creation is done with fixed parameters in the Reference Creation workflow.Beginning with the raw signal data in the CEL file, the Single Sample CytoScan  Workflow implements a series of steps that perform probe set summarization,  normalization, removal of variation caused by known properties and residual variation, and completing with calling genotypes, copy number segments and LOH segments.For CytoScan arrays, markers are individually assigned a copy number call by a Hidden Markov model (HMM). The sample specific inputs to the HMM are the Weighted Log2 Ratios generated by the Signal Restoration module.
Processed data.txt: The weighted Log2 Ratios are centered on copy number (CN) = 2. In theory, when Log2 Ratio = 0 then CN = 2, when Log2 Ratio = -1 the CN = 1, etc. In truth, microarrays, or any hybridization-based technology, exhibit Log2 Ratio compression due to many factors, so the Log2 Ratios never exhibit the amplitude expected by the math. The following table shows theoretical and actual Log2 Ratios for different Copy Number States.Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: biotin

source_name: Peripheral Blood

label_protocol: As per manufacturer (Affymetrix),prepare labeling Master Mix and add Labeling Master Mix to pre-chilled strip tubes on cooling block on ice.Place the labeling plate in thermal cycler and run CytoScan Label protocol.

extract_protocol: Genomic DNA was extracted from Amniotic Fluid or peripheral blood samples using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Adult

value: Peripheral Blood


title: 20240111_143420_020_2024-SNP-0028

description:
20240111_143420_020_2024-SNP-0028.cychp
Hybridized to CytoScan750K Array

source_name: Amniotic Fluid

value: Fetus

value: Amniotic Fluid


title: Abd_11

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Abd_11
RNA-seq


title: PSO_2

description: Library name: Sample 5

value: imiquimod applied


title: Liver tissue CDAA Rat4

city: Vancouver

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

description: Library name: Sample 8

data_processing:
Sequencing was performed on the HiSeq2500 platform in high-throughput mode, with 3-4 rats sequenced per lane, generating 1x50 bp reads. Sequencing reads were quality-trimmed, removing Illumina TruSeq adapter sequences. FastQC and FastX tools were used for quality control of the data before and after trimming. Tophat2 was applied to align the trimmed reads to the rat rn6 reference genome. Differential expression analysis was carried out using Bioconductor package DESeq2. This data was uploaded to the Galaxy web platform, and usegalaxy.org was used to generate the volcano plot. Statistically significant changes in gene expression were defined as differentially expressed genes (DEGs).
Bioconductor packages Cufflinks, DESeq2, and EdgeR were used for differential expression analysis
Assembly: rn6
Supplementary files format and content: Excel file Rat_stefanska_rat_allGenes_cdaaVScdaaPTS

source_name: Liver

growth_protocol: Compound incorporated into the diet

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Liver

tag: strain

value: Fischer 344 (F344)

value: 1 year old

value: male

value: wilde type

value: Choline-deficient amino acid defined (CDAA) to trigger hepatocellular carcinoma.


title: 005.Tumor.0636.RPL22 positive.immune low

value: Positive

value: Immune low


title: Thi_10

description:
Library name: Thi_10
RNA-seq

value: subcutaneous adipose tissues

value: F

value: Thi


title: 005.Tumor.0458.RPL22 positive.immune high

value: Immune high


title: PSO_1

description: Library name: Sample 4

value: skin


title: Liver tissue CDAA Rat3

description: Library name: Sample 7


title: 003.Immune.0458.RPL22 positive.immune high


title: Abd_10

description:
Library name: Abd_10
RNA-seq

value: Abd


title: 006.Tumor.0458.RPL22 positive.immune high


title: sham_2

description: Library name: Sample 2

value: sham operation group coated with Vaseline


title: 006.Tumor.0636.RPL22 positive.immune low


title: sham_3

description: Library name: Sample 3


title: Glu_10

description:
Library name: Glu_10
RNA-seq

value: Glu


title: Thi_9

description:
Library name: Thi_9
RNA-seq


title: Liver tissue CDAA Rat1

description: Library name: Sample 5


title: 004.Tumor.0458.RPL22 positive.immune high


title: sham_1

description: Library name: Sample 1


title: Thi_11

description:
Library name: Thi_11
RNA-seq

value: M


title: Liver tissue CDAA Rat2

description: Library name: Sample 6

value: Liver


title: pituitary, ND_2

city: changchun

first: Haixiang

last: Guo

address: Xi’an Road 5333#, Changchun

institute: Jilin University

description:
Library name: ND_2
10× Genomics

data_processing:
Raw sequencing data were aligned to the genome, background cells were filtered, and single-cell gene expression matrices were generated using CellRanger analysis software. Based on information such as barcodes and unique molecular identifiers (UMIs), the expression levels of genes detected in each cell were calculated using algorithms, and the above data were optimized using Seurat software. Data normalization and identification of highly variable genes were performed using NormalizeData and FindVariableFeatures functions in the Seurat package. After cell clustering, t-SNE and UMAP algorithms were used to visualize the cell clustering results. Subsequently, the expression of marker genes in each cell cluster was identified using the FindAllMarkers function in the Seurat package.
Assembly: Mus musculus  Ensembl v105
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pituitary

extract_protocol:
Pituitary single-cell RNA sequencing (scRNA-seq) was performed with three mouse pituitary tissues per group collected as one sample. The pituitaries were placed in tissue preservation solution (130-100-008, Miltenyi, Germany) and sent to LC Bio Technology Co., Ltd. (Hangzhou, China) for sequencing and analysis. Briefly, the collected pituitaries were minced and incubated with pre-prepared enzyme solution (130-107-677, Miltenyi, Germany) at 37℃ for 1 h. Cell counting was conducted using a Countess™ II Automated Cell Counter (ThermoFisher, USA). Cell viability was determined by trypan blue staining, and the viability rate of viable cells was above 90% in all samples.
Single-cell 3’ cDNA libraries were generated using the 10× Genomics platform (USA) according to the manufacturer's protocol. RNA sequencing was then performed on the Illumina NovaseqTM 6000 platform (LC Bio Technology, Hangzhou, China).

value: pituitary

value: gonadotroph

value: normal diet (ND)


title: TexINT, FA-treated, in-vivo, d21 p.i., rep2

description:
Library name: In-vivo_FA-Int_2
Column name in processed files: FA-int_3.count

value: splenocytes

value: CD8+ T cells

value: TexINT

value: palmitic/lauric acid injection (i.p.)


title: 001.Immune.0871.RPL22 positive.immune high

city: Chapel Hill

last: Gladden

address: 160 N. Medical Drive

institute: The University of North Carolina at Chapel Hill

data_processing:
Raw data was downloaded directly from GeoMx DSP Analysis Suite and converted into txt files. Data QC was conducted using the standard parameters described in the GeoMx DSP data analysis user manual (MAN-10154-01). Minimum nuclei count was set to 20 nuclei and maximum nuclei count was set to 1600 nuclei. Filtering was performed at a minProbeRatio of 10% and ROIs were scaled to the geometric mean of nuclei in all ROIs. ROIs were normalized to the geometric mean of the housekeeping proteins GAPDH, Histone H3, and S6. Background correction was conducted using the geometric mean of signal to background ration of the negative targets Ms IgG1, Ms IgG2a, and Rb IgG.
QC and normalization were conducted online on GeoMx DSP Analysis Suite.
nCounter analysis system

extract_protocol: According to the GeoMx DSP slide preparation user manual (MAN-10087-04)

value: Positive


title: PSO_3

description: Library name: Sample 6

value: imiquimod applied


title: 004.Tumor.0636.RPL22 positive.immune low

value: Immune low


title: Liver tissue CDAA+PTS Rat3

description: Library name: Sample 3

value: Fischer 344 (F344)

value: 1 year old

value: male

value: wilde type

value: Choline-deficient amino acid defined (CDAA) diet supplemented with pterostilbene (PTS) at 1.34g/kg of diet.


title: 002.Immune.0871.RPL22 positive.immune high

value: Immune high


title: Glu_8

description:
Library name: Glu_8
RNA-seq

value: subcutaneous adipose tissues

value: M

value: Glu


title: pituitary, ND_1

description:
Library name: ND_1
10× Genomics

value: pituitary

value: gonadotroph

value: normal diet (ND)


title: pituitary, HFD_2

description:
Library name: HFD_2
10× Genomics

value: high-fat diet (HFD) feeding


title: Liver tissue CDAA+PTS Rat2

description: Library name: Sample 2

value: Liver


title: pituitary, HFD_1

description:
Library name: HFD_1
10× Genomics


title: Liver tissue CDAA+PTS Rat1

description: Library name: Sample 1


title: Thi_7

description:
Library name: Thi_7
RNA-seq

value: F

value: Thi


title: Abd_9

description:
Library name: Abd_9
RNA-seq

value: Abd


title: Liver tissue CDAA+PTS Rat4

description: Library name: Sample 4

value: Fischer 344 (F344)


title: Primary T cells, HIV-1 A77V infection, donor 3, 96 h, replicate 1

city: Rochester

first: Eric

middle: John

last: Wagner

address: 575 Elmwood Avenue

department: Biochemistry and Biophysics

institute: University of Rochester Medical Center

description:
Library name: 28
28_R1.DeDup.sorted
Samples_20_24_28_vs_17_21_25_APA_BBstats.txt

data_processing:
Fastp was used to remove the Illumina adapters (using -a option), trim low-quality bases in the start of the read (using -f 4) and to discard reads that are shorter than forty bases (using -l 40).
The quality trimmed reads were then aligned to the reference genome (GRCh38, version 33 downloaded from GENCODE portal), using bowtie2 version 2.3.5.1 in single end mode. Umitools were used to discard de-duplicated reads
Assembly: GRCh38, version 33
Supplementary files format and content: PolyA-miner was then run to generate counts for each polyA site in all the samples which are provided in the processed data files.

source_name: Peripheral blood T lymphocytes

growth_protocol: A549 and HEK293T cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 29.2 mg/ml L-glutamine, and 5 μg/ml plasmocin at 37°C with 5% CO₂. Primary human T cells were isolated from peripheral blood mononuclear cells from healthy donors and cultured in RPMI-1640 medium containing 10% FBS, 4 μg/ml PHA-L, and 20 IU/ml IL-2.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacturer’s protocol. Following phase separation with chloroform, RNA was precipitated with isopropanol, washed with 75% ethanol, and dissolved in RNase-free water.
First, 2 µg total RNA was mixed with 1 µl of 100 µM 3’ Illumina_4N_21T_VN primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNTTTTTTTTTTTTTTTTTTTTTVN-3’), 2 µl of 5 mM AzNTP (Baseclick, #BCT–25 to −28)/dNTP mixture, at a ratio of 1 to 5, and the total volume was raised to 13 µL by the addition of H2O. The mixture was heated at 65°C/5 min and snap-cooled on ice for 3 min. Reverse transcription was performed using SuperScript III (ThermoFisher, #18080093). In brief, 7 µl master mix containing 4 µl 5× Superscript First Strand buffer, 1 µl of 0.1 M DTT, 1 µl RNaseOUT (ThermoFisher, #10777019), and 1 µl SuperScript III were mixed with the RNA sample. Heating was performed in a thermocycler sequentially as follows: 25°C/10 min, 50°C/40 min, and 75°C/15 min, followed by RNase H (ThermoFisher, #AM2293) treatment using 1U per reaction for 37°C/30 min and then 80°C/10 min. The resulting cDNA was purified using Sera-Mag Speedbeads (Cytiva, #65152105050250). Speedbeads working solution was made by washing 1 ml bead slurry twice in 1×TE buffer and then resuspending beads in 50 ml of 1×TE buffer containing 9 g PEG-8000, 1 M NaCl, and 0.05% Tween-20. Speedbeads, 1.8× reaction volume, was mixed with cDNA followed by a 5 min incubation at room temperature. The beads were then pelleted using a magnetic bead collector, and the supernatant was discarded. Two washes with 80% ethanol were performed while the beads were pelleted on the magnet. The beads were then dried, and the cDNA was eluted by resuspending the beads in 22 µl of 50 mM HEPES pH 7.2 for 2 min at room temperature. Then, 20 µl cDNA was mixed with 11 µl Click Mix (2.5 M NaCl, 30% EtOH in H2O) and 4 µl of 5 µM UMI-click-adapter (5’-Hexynyl-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’, HPLC purified). To activate the reaction, 4 µl of 50 mM vitamin C and 1 µl of Click Catalyst (4 mM CuSO4 in H2O and 20 mM THPTA [Baseclick, #BCMI-006] in H2O) were pre-mixed before being added into the cDNA solution for 60 min incubation at room temperature in the dark. Clicked cDNA was then purified in the same manner as post-RT purification but eluted in 22 µl of 10 mM Tris pH7.4. Half of the eluted cDNA was subjected to PCR amplification with indexing primers i5 (5’-AATGATACGGCGACCACCGAGATCTACAC[Index]ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’) and i7 (5’-CAAGCAGAAGACGGCATACGAGAT[Index]GTGACTGGAGTTCAGACGTGTGCTCTTCCGAT*C-3’). Both primers have a phosphorothioate bond added at the 3’ end (denoted as *) to increase stability. The PCR reaction was conducted in a 50 µl volume, including 25 µl 2× OneTaq Master Mix (NEB, #M0482), 2 µl each of 5 µM i5 and i7, and cDNA in H2O. A total of 13 amplification cycles were conducted on 2 µg input RNA. The program was run at 94°C/4 min; 53°C/30 sec; 68°C/10 min; 15× [94°C/30 sec, 53°C/30 sec; 68°C/2 min]; 68°C/5 min; hold at 4°C. The library was then purified and size-selected with Speedbeads. In brief, 45 µl beads (0.9× volume of PCR reaction) were mixed with the reaction to remove larger fragments. Supernatant was collected and mixed with 10 µl beads (0.2× volume of PCR reaction) to remove smaller fragments and primer dimers. Two washes with 100% ethanol were then performed while the beads were on the magnet. Beads were dried before being resuspended in 12 µl of 10 mM Tris pH7.4. The library was then collected and subjected to quality control on Agilent 2200 TapeStation and analysis by Illumina NovaSeq 6000 at the Genomics Research Center at the University of Rochester.

treatment_protocol: Cells were infected with HIV-1 WT, HIV-1 N74D, or HIV-1 A77V viral particles, or mock treated, for the indicated time points. Infection was performed at the desired MOI and incubated for 40–48 h for A549 cells or 96 h for primary T cells. CPSF6 knockout A549 clones were generated using CRISPR-Cas9 RNP electroporation followed by clonal selection via limiting dilution.

value: Peripheral blood T lymphocytes

value: primary T cells

value: HIV-1 A77V infection, 96 h


title: EGME75_40

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description: Library name: Library_40

data_processing:
Libraries were sequenced in single-end configuration on the IonProton sequencer.
Initial quality control was performed using FASTQC (Andrews, 2010). Two samples with extremely low read counts were identified as outliers and excluded from downstream analysis.
Small RNA expression levels were then profiled using sRNAbench (Aparicio-Puerta et al., 2022) in genome mode. Reads were mapped against the rat genome (Rnor_6_0) and compared to miRBase Release 22.1 (Kozomara et al., 2019). Default sRNAbench parametersl were applied: the bowtie seed alignment, seed length 20, minimum read count 2, minimum read length 15, allowed 1 mismatch, and 10 multiple mappings. After expression profiling, multi-map adjusted read counts for small RNAs (miRNAs, tRNAs, ncRNAs, cDNA) from sRNAbench ".grouped" files were parsed using a custom Python script.
Differential expression of small RNAs across dosage groups was determined using DESeq2 (Love et al., 2014) with default filtering.
Assembly: Rnor_6_0
Supplementary files format and content: mature_sense_counts.csv: miRNA read counts
Supplementary files format and content: Rnor_6_0_RNAcentral_sense_counts.csv: piRNA read counts
Supplementary files format and content: Rnor_6_0_genomic_tRNA_sense_counts.csv: tRNA read counts
Supplementary files format and content: Rnor_6_0_ncRNA_sense_counts.csv: other small noncoding RNA read counts

source_name: spermatozoa

growth_protocol: Spermatozoa obtained from the cauda epididymis of 11-12 week-old male Fischer rats.

extract_protocol:
Total RNA was extracted using the ThermoFisher miRvana kit per manufacturer's instructions, including Dnase treatment, as described in our publication.
10 ng RNA from each sample was used to construct the library using the Ion total RNA seq kit v2 (ThermoFisher)

treatment_protocol: Daily oral gavage with 0, 50, 60, or 75 mg/kg/d EGME for 5 days, followed by 5 weeks of no exposure.

value: spermatozoa

value: wild-type

value: 75 mg/kg/d EGME

tag: batch


title: No treatment

city: Suita

first: Sikun

last: Meng

state: Osaka

address: Yamadaoka 2-2

country: Japan

institute: the Universiy of Osaka

description: Library name: Sample 3

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger (v7.1.0, 10x Genomics).
Reads were aligned to the mouse reference genome (mm10) with STAR through the Cell Ranger pipeline.
Gene–cell expression count matrices were generated in the standard 10x Genomics format.
Assembly: mm10
Supplementary files format and content: Processed data include Cell Ranger output in the form of gene–cell count matrices. Files are provided in Matrix Market exchange format (matrix.mtx.gz) with accompanying barcode (barcodes.tsv.gz) and gene annotation (features.tsv.gz) files.

source_name: tumor tissue

extract_protocol:
Tumor tissues were harvested from three syngeneic colorectal tumor models. Approximately 10–15 mg of tissue per sample was minced in 2 mL of DMEM containing 10% FBS, ulinastatin (2 μg/mL), and sivelestat (2 μg/mL) on ice. Subsequently, 8 mL of digestion buffer (DMEM supplemented with Collagenase D and DNase) was added, and the mixture was incubated at 37 °C in a water bath with gentle shaking (100 rpm) for 1 hour. Following enzymatic digestion, the suspension was filtered through a 40 μm cell strainer, centrifuged at 380 × g for 5 minutes at 4 °C, and the pellet was resuspended in 1 mL of pre-warmed ACK lysis buffer for 3 minutes at 37 °C. After red blood cell lysis, 9 mL of HBSS was added, followed by a second centrifugation step. The resulting cell pellet was resuspended in 0.05% BSA/PBS and adjusted to a final concentration of 1000 cells/μL in 50 μL for downstream single-cell RNA sequencing.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 5′ Gene Expression kit according to the manufacturer’s protocol.

value: tumor tissue

value: MC38; NIH/3T3-FAP

value: C57BL/6 wild-type

value: No treatment


title: Abd_7

description:
Library name: Abd_7
RNA-seq

value: subcutaneous adipose tissues


title: Glu_7

description:
Library name: Glu_7
RNA-seq

value: Glu


title: Primary T cells, HIV-1 WT infection, donor 3, 96 h, replicate 1

description:
Library name: 26
26_R1.DeDup.sorted
Samples_18_22_26_vs_17_21_25_APA_BBstats.txt

tag: cell type

value: HIV-1 WT infection, 96 h


title: EGME75_39

description: Library name: Library_39

tag: genotype


title: Relapse 2

description: Library name: Sample 2

tag: tissue

value: FAP-CAR mRNA-LNP + 5-FU + anti-PD1 + anti-CTLA4


title: EGME75_32

description: Library name: Library_32


title: Primary T cells, HIV-1 N74D infection, donor 3, 96 h, replicate 1

description:
Library name: 27
27_R1.DeDup.sorted
Samples_19_23_27_vs_17_21_25_APA_BBstats.txt

value: HIV-1 N74D infection, 96 h


title: Relapse 1

description: Library name: Sample 1


title: Thi_6

description:
Library name: Thi_6
RNA-seq

value: F

value: Thi


title: Primary T cells, mock infected, donor 3, 96 h, replicate 1

description:
Library name: 25
25_R1.DeDup.sorted
Samples_18_22_26_vs_17_21_25_APA_BBstats.txt

value: Peripheral blood T lymphocytes

value: mock infected, 96 h


title: EGME75_31

description: Library name: Library_31


title: Abd_6

description:
Library name: Abd_6
RNA-seq

value: Abd


title: 001.Immune.1675.RPL22 positive.immune high

first: Andrew

tag: rpl22 status

value: Positive

value: Immune high


title: 8-week old C57BL/6J mouse lung Ly6G⁻Ly6C⁻CX3CR1⁺CD11b⁺SIGLEC-F⁻CD16.2^hi non-classical monocytes rep2 - GEX

city: Bethesda

first: Beatriz

last: León

state: Maryland

address: Building 10, Room 11N240A, 10 Center Drive

department: NIAID

institute: NIH

description:
Library name: C57BL-6J_mouse_lung_papain_treated_nonClassical_monocytes_rep2_GEX
10x Genomics

data_processing:
Single-cell gene expression FASTQ files were processed through the OpenOmics/cell-seek pipeline v3.0.2 leveraging 10x Genomics Cell Ranger v9.0.0 with transcriptome reference GRCm39-2024-A. Seurat QC filtering was performed using Seurat v5.2.1 in R v4.4.0 to remove low count cells and potential doublets using manual filtering thresholds.  The Ly6G⁺ MΦ sample was filtered to cells containing a minimum of 700 and maximum of 8,500 RNA features.  The non-classical monocyte samples filtered to cells containing a minimum of 1,200 and maximum of 7,500 RNA features.  All samples were required to have a mitochondrial percentage less than 5%.  Log-normalized count matrices were merged, and dimensionality reduction conducted using 30 principal components. Integration was performed using the R package Harmony v1.2.3, followed by clustering at a resolution of 0.2.  Following closer inspection of the clusters the Seurat object was subset to clusters 0-2 and 5-7.  Layers were split on sample prior to re-running the Seurat workflow with dimensionality reduction using 30 principal components.  Integration was performed using joint PCA followed by clustering at a resolution of 0.2. Cluster 2 was further clustered using a resolution of 0.1.
Assembly: GRCm39-2024-A
Supplementary files format and content: 10x Genomics Cell Ranger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Seurat Processed File: seuratv5.rds

source_name: Lung

extract_protocol:
Eight-week-old C57BL/6J mice (Mus musculus) were treated intranasally with 10 µg of the cysteine protease papain in a 100 µL volume. After 24 hours, lungs were processed into a single-cell suspension, and two distinct cell populations were isolated by fluorescence-activated cell sorting (FACS): Ly6G⁺Ly6C⁺CX3CR1⁺CD11b^hi SIGLEC-F⁻ macrophages (Ly6G⁺ MΦ) and Ly6G⁻Ly6C⁻CX3CR1⁺CD11b⁺SIGLEC-F⁻CD16.2^hi non-classical monocytes. The sorted cells were subjected to scRNA-seq to characterize their transcriptional profiles.
Cell suspension and 10x barcoded gel beads were loaded into the 10x Chromium™ Single Cell Chip G (PN 1000120) to capture single cells in nanoliter-scale oil droplets using the 10x Genomics Chromium X Controller with Chromium Next GEM Single Cell 3’ v3.1 reagents (PN-1000268). The single-cell gene expression libraries were constructed following the 10x Genomics 3’ Next GEM 3.1 kit instructions. The libraries were then sequenced on an Illumina NovaSeq 6000, targeting 20,000 reads per cell.

value: Lung

value: C57BL/6J mouse lung papain treated non-classical monocytes

value: 8-weeks old

tag: library type

value: GEX


title: Abd_8

description:
Library name: Abd_8
RNA-seq

value: M


title: Primary T cells, HIV-1 A77V infection, donor 2, 96 h, replicate 1

description:
Library name: 24
24_R1.DeDup.sorted
Samples_20_24_28_vs_17_21_25_APA_BBstats.txt

value: primary T cells

value: HIV-1 A77V infection, 96 h


title: EGME75_24

description: Library name: Library_24

value: spermatozoa

value: wild-type

value: 75 mg/kg/d EGME


title: Thi_5

description:
Library name: Thi_5
RNA-seq

value: subcutaneous adipose tissues

value: F


title: 002.Immune.1675.RPL22 positive.immune high

tag: immune status


title: Primary T cells, HIV-1 N74D infection, donor 2, 96 h, replicate 1

description:
Library name: 23
23_R1.DeDup.sorted
Samples_19_23_27_vs_17_21_25_APA_BBstats.txt

value: Peripheral blood T lymphocytes

value: HIV-1 N74D infection, 96 h


title: 8-week old C57BL/6J mouse lung Ly6G⁻Ly6C⁻CX3CR1⁺CD11b⁺SIGLEC-F⁻CD16.2^hi non-classical monocytes rep1 - GEX

description:
Library name: C57BL-6J_mouse_lung_papain_treated_nonClassical_monocytes_rep1_GEX
10x Genomics


title: Glu_5

description:
Library name: Glu_5
RNA-seq

tag: Sex

value: Glu


title: 8-week old C57BL/6J mouse lung Ly6G⁺Ly6C⁺CX3CR1⁺CD11b^hi SIGLEC-F⁻ macrophages - GEX

description:
Library name: C57BL-6J_mouse_lung_papain_treated_Ly6g_positive_macrophages_GEX
10x Genomics

value: C57BL/6J mouse lung papain treated Ly6g+ macrophages


title: 003.Immune.0871.RPL22 positive.immune high

value: Positive

value: Immune high