title: Riboseq of raw264.7 with 12h LPS treatment, Rep2

description: with 12h LPS treatment

value: with 12h LPS treatment


title: Riboseq of raw264.7 with 12h LPS treatment, Rep1

status: Public on Sep 07 2025

type: SRA

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: WenYi west street

country: China

institute: Zhejiang University School of Medicine

description: with 12h LPS treatment

library_source: transcriptomic

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using STAR.
Assembly: GRCm39
Supplementary files format and content: rpkm files containing rpkm for each transcripts,which are seperated by Tab.
Library strategy: Ribo-seq

molecule: total RNA

organism: Mus musculus

growth_protocol: Raw264.7 were grown in DMEM medium containing 10% FBS at 37°C with 5% CO₂.

extract_protocol:
Cells were washed twice with cold PBS. 500 μl lysis buffer (8 mM HEPES, pH 7.4, 80 mM KCl, 4 mM MgCl2, 2% Triton x-100, and 200 μg/ml cycloheximide) was then added, and the cells were quickly scraped and collected into RNase-free tubes. The sample were centrifuged at 12,000 rpm for 12 minutes at 4°C, and the supernatant was sent to Novogene (China) for RNA-seq library construction. Approximately 100 μl of supernatant were treated with RNase I (Thermo Fisher Scientific) for 3 hours, followed by RNA extraction using TRIzol™ LS.
The extracted RNA was denatured at 65°C, 20 min and run on a 15% TBE-Urea gel. The band around 25-35 nt was excised and eluted overnight in RNA elution buffer (300 mM NaAc,1 mM EDTA) at 4°C. The RNA was precipitated with an equal volume of isopropanol. The RNA was treated by T4 Polynucleotide Kinase (NEB), and then polyadenylated using E. coli Poly(A) polymerase (NEB) for 37°C, 30min. The cDNA was generated using Template Switching RT Enzyme Mix from NEB (NEB) according to the manufacturer’s instructions. A portion of the resulting cDNA was amplified by PCR using Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific) with barcoded primers. The PCR products were run on a 8% TBE gel, and the band around 180 bp was excised and recovered using DNA PAGE Gel Extraction Kit ( Beyotime). The recovered DNA was sent to Novogene for sequencing.

treatment_protocol: When the RAW264.7 cells reach about 60% confluence as fully adherent cells, they are treated with 1 μg/mL of LPS for 0, 6, 12, and 24 hours.

tag: cell line

tag: cell type

value: monocyte-macrophage

tag: genotype

value: WT

tag: treatment


title: PreIVIG9

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description: 150 base pair

data_processing:
The cleaned sequence reads were aligned against the homo sapiens genome (Build version hg38), and the STAR aligner (v2.5.3a) was used to map reads to the genomic sequences.
Assembly: HG38
Supplementary files format and content: csv: gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Bulk blood RNA sequencing was conducted by the Australian Genome Research Facility (AGRF, Adelaide, Australia). This workflow includes RNA extraction from PAXgene™ blood RNA tubes, depletion of ribosomal RNA via hybrid capture
Illumina TruSeq Stranded Total RNA Library Preparation (input 200-1000 ng of Total RNA).stranded RNA samples are sequenced on the Illumina NovaSeq 6000 next generation sequencing platform (150 base pair paired end run) for a depth of 50 million paired end reads

treatment_protocol: venous blood samples were collected for testing in PAXgene™ blood RNA tubes (Qiagen, Hilden, Germany) and Acid Citric Dextrose tubes (BD)

tag: tissue

value: blood

tag: condition

value: PreIVIG


title: PreIVIG8

description: 150 base pair


title: Riboseq of raw264.7 with 6h LPS treatment, Rep2

description: with 6h LPS treatment

value: with 6h LPS treatment


title: C60

city: Norwich

first: Alice

last: Godden

state: Not applicable

address: School of Biological Sciences, University of East Anglia, Norwich Research Park

country: United Kingdom

institute: University of East Anglia

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

library_source: genomic

data_processing:
Standard QIIME2 pipeline was applied: https://docs.qiime2.org/2022.2/tutorials/overview/
Demultiplex, cutadapt, denoise, feature table, taxonomic assignment, differential abundance
Assembly: SILVA release 132: silva_132_99_16S.fna  , from https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip
Supplementary files format and content: OTU_matrix_2023.csv - differential abundance data
Supplementary files format and content: taxonomy_2023.csv -- the taxa associated to the OUT in the OUT_matrix_2023.csv file
Library strategy: 16S Amplicons V3-V4

molecule: genomic DNA

organism: Danio rerio

source_name: intestine

growth_protocol: standard zebrafish growth, supplemented with Gum Arabic food

extract_protocol:
genomic DNA was extracted from whole intestines of adult fish. This was done using a homogenizer and the FastDNA™ SPIN Kit for Soil kit from MP Biomedical.
IDT for Illumina-Nextera DNA Unique Dual Indexes

treatment_protocol: Organs were harvested from euthanized zebrafish and flash frozen in liquid nitrogen before storage at -80 C

value: intestine

tag: block

value: D

value: female

value: WT AB

value: 0% GA


title: T32

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: male

value: 6% GA


title: Riboseq of raw264.7 with 6h LPS treatment, Rep1

description: with 6h LPS treatment


title: Col-LUC_rep1

city: Nan Jing

first: La

middle: yu

last: mei

state: Jiang Su

address: XuanWu

institute: Nanjing Agricultural University

description:
Library name: SAMPLES1
14-day-old seeding

data_processing:
Raw sequencing data was first filtered by Trimmomatic low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed clean
Reads mapped to the exon regions of each gene by Hisat2 (v 2.1.0) and counted by featureCounts (v 1.6.3).
Genes differentially expressed between groups were identified using the DESeq2 (v 1.24.0). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge.
Assembly: TAIR10
Supplementary files format and content: Matrix table with count file for every sample

organism: Arabidopsis thaliana

source_name: seeding

growth_protocol: soil,16 hour light, 8 hour dark cycle

extract_protocol:
Total RNA was isolated from 14-day-old seeding with Plant Total RNA Isolation Kit (Vazyme, China) according to the manufacturer's instructions.2 μg total RNAs
RNA sequencing library prepared by using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the  standard Illumina protocols

value: seeding

value: Col-LUC

value: the whole plant


title: Col-LUC_rep2

description:
Library name: SAMPLES2
14-day-old seeding


title: Riboseq of raw264.7 with 24h LPS treatment, Rep2

description: with 24 LPS treatment

value: with 24 LPS treatment


title: PreIVIG7

description: 150 base pair


title: Riboseq of raw264.7 without LPS treatment, Rep2

description: without LPS treatment

value: without LPS treatment


title: T2

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: PreIVIG6

description: 150 base pair


title: C4-2

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: A


title: Riboseq of raw264.7 without LPS treatment, Rep1

description: without LPS treatment

value: monocyte-macrophage

value: WT


title: Riboseq of raw264.7 with 24h LPS treatment, Rep1

description: with 24 LPS treatment


title: PreIVIG5

description: 150 base pair

value: blood

value: PreIVIG


title: C32

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine


title: PreIVIG4

description: 150 base pair


title: SdrpoS_LBagar_3

city: Santa Cruz

first: Giordan

last: Kitts

state: CA

address: 1156 High St.

department: METX

country: USA

institute: UCSC

data_processing:
QC performed on reads with FastQC. FastQC output deemed trimming not required.
Transcript abundance against the reference transcriptome was determined using Salmon v1.5.2
Transcript abundance from Salmon was then imported into DESeq2 (1.32.0) for differential expression and downstream analyses
Assembly: NC_002505 and NC_002506, (using updated transcriptome deposited on genoscope from: https://doi.org/10.1186/s12864-018-4716-8)
Supplementary files format and content: CSV, normalized counts (DESeq2)

organism: Vibrio cholerae O1 biovar El Tor

source_name: bacterial culture

growth_protocol: Vibrio cholerae A1552 strains were spotted onto LB agar (0.5% yeast extract, 1% Tryptone, 1% NaCl, 1.5% Agar) and incubated for 48h at 30˚C. After incubation, spots were resuspended in TRIzol for RNA isolation

extract_protocol:
TRIzol-Chloroform total RNA extraction was performed as stated in manufacturers instructions (Invitrogen/Fisher), with the exception that when isopropanol was added, an equal volume of High Salt solution (0.8M Sodium Citrate, 1.2M NaCl) was also added to account for high levels of polysaccharide present. Samples were DNAase treated, and RiboZero Plus was used for rRNA depletion.
Illumina Stranded RNA library preparation (no modifcations from protocol)

tag: strain

value: bacterial culture

value: Smooth deltaVC0534 (SdeltarpoS)

value: 48hrs growth on LB agar


title: SdrpoS_LBagar_2


title: C15

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: female

value: WT AB

value: 0% GA


title: C19

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: B

value: male


title: T34

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: 6% GA


title: PreIVIG3

description: 150 base pair


title: Donor2, PBMC, Control, PLA

city: Chicago

first: Junjie

last: Xia

state: IL

address: 10th floor of KCBD, 900 E. 57th Street

department: Chemistry

institute: University of Chicago

description:
Library name: Sample6
10x Genomics

library_source: other

data_processing:
Sequencing reads were demultiplexed using Illumina bcl2fastq.
Cell Ranger (10x Genomics, v8.0.1) was used for alignment of mRNA reads to the GRCh38 human genome reference and for initial feature-barcoding count matrix generation.
The sequencing data of PLA were aligned with a custom Java program which is deposited at https://github.com/tay-lab/Prox-seq.
Assembly: GRCh38
Supplementary files format and content: Filtered cell-by-gene count matrices for mRNA (MTX/TSV format)
Supplementary files format and content: PLA count matrices (txt.gz format)
Supplementary files format and content: Integrated AnnData (.h5ad) and Seurat (.rds) objects

molecule: other

source_name: peripheral blood mononuclear cell

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were purchased from STEMCELL Technologies and maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin prior to processing.

extract_protocol:
Both mRNA and PLA product were extracted from intact single cells based on polyA-polydT capture
For mRNA, libraries were prepared following the manufacturer’s protocol for the 10x Genomics Chromium Single Cell 3′ v3.1 chemistry. For PLA product, library preparation was performed according to the GPS workflow, as described in the associated manuscript.

treatment_protocol: PBMC samples from Donor 1 and Donor 2 were thawed and rested overnight. For one sample from Donor 1, cells were stimulated with 1X Concanavalin A (ConA; Thermo Fisher Scientific) for 24 hours before proceeding to the GPS workflow.

value: peripheral blood mononuclear cell

value: No treatment


title: GA6

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: A


title: IGF2BP1 overexpression 3

type: RNA

city: Beijing

first: Ai

last: Gao

address: Capital Medical University, 10 Xitoutiao, You An Men, Beijing 100069, P. R. China

institute: Capital Medical University

description: gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: biotin

source_name: gene expression of IGF2BP1 overexpressed mice after benzene exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mice were randomly divided into 4 groups (10 mice per group): (1) control group (AAV‐null), (2) control-AAV‐IGF2BP1 group, (3) benzene group (benzene + AAV‐null), and (4) benzene-AAV‐IGF2BP1 group. AAV‐null (2.5×1011viruses in 200 μL normal saline), or AAV‐ IGF2BP1 (2.5 ×1011 viruses in 200 μL normal saline) were injected through the tail vein using sterile disposable syringes. Two-week post injection, mice were exposed to 0 and 50 ppm benzene for 6 h/ day, 6 days/week and 9 weeks.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: The femur and tibia of mice were collected. The bone was cut off at both ends and bone marrow was flushed out with sterile phosphate buffered saline (PBS) using a syringe. Bone marrow cells were obtained by filtrating through a 70 μm cell strainer (SORFA, Beijing, China). After centrifugation at 1500 rpm for 5 min, cells were resuspended for counting.

value: bone marrow


title: PreIVIG1

description: 150 base pair


title: PreIVIG2

description: 150 base pair


title: SWT_LBagar_3

value: Smooth WT


title: T19

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: SWT_LBagar_2


title: Donor1, PBMC, Stimulated, PLA

description:
Library name: Sample5
10x Genomics

value: Concanavalin A, 24 hours


title: C38

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: Donor1, PBMC, Control, PLA

description:
Library name: Sample4
10x Genomics


title: SWT_LBagar_1


title: IGF2BP1 overexpression 1

description: gene expression data


title: PostIVIG8

description: 150 base pair

value: blood

value: PostIVIG


title: PostIVIG9

description: 150 base pair


title: RdrpoS_LBagar_3

growth_protocol: Vibrio cholerae A1552 Rugose variant strains were spotted onto LB agar (0.5% yeast extract, 1% Tryptone, 1% NaCl, 1.5% Agar) and incubated for 48h at 30˚C. After incubation, spots were resuspended in TRIzol for RNA isolation

value: bacterial culture

value: Rugose [delta]VC0534 ([delta]rpoS)


title: Donor2, PBMC, Control, RNA

description:
Library name: Sample3
10x Genomics

library_source: transcriptomic single cell


title: SdrpoS_LBagar_1

value: Smooth deltaVC0534 (SdeltarpoS)

value: 48hrs growth on LB agar


title: IGF2BP1 overexpression 2

description: gene expression data


title: Donor1, PBMC, Stimulated, RNA

description:
Library name: Sample2
10x Genomics


title: RdrpoS_LBagar_2


title: GA36

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine

value: C

value: WT AB


title: PostIVIG6

description: 150 base pair


title: Donor1, PBMC, Control, RNA

description:
Library name: Sample1
10x Genomics


title: C30

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: B

value: female

value: 0% GA


title: RdrpoS_LBagar_1


title: PostIVIG7

description: 150 base pair


title: brain myeloid cells of WT mice 3

city: Rehovot

first: Laura

last: Bellassen

address: 234 herzl

country: Israel

institute: Weizmann Institute of Science

description: Library name: WTEAE3

data_processing:
Raw reads were trimmed to remove poly-A/T stretches and Illumina adapters using cutadapt; reads shorter than 30 bp were discarded. Reads were mapped to 3' UTR regions (1000 bases) of the M. musculus genome (GRCm39) using STAR with End-to-End mapping and outFilterMismatchNoverLmax set to 0.05. Deduplication was performed using UMI information. Counts per gene were quantified with htseq-count (intersection-strict mode), using only uniquely mapped reads. Differential expression analysis was done with DESeq2, adjusting p-values using the Benjamini-Hochberg method.
Assembly: M. musculus GRCm39 (RefSeq)
Supplementary files format and content: Processed data files are tab-delimited text files (.tsv) containing gene-level UMI-corrected read counts for all samples. Optionally, differential expression results are provided as CSV files with log2 fold change, p-values, and adjusted p-values per gene.

source_name: brain

extract_protocol:
RNA was extracted from CD45+ CD11b+ sorted cells of the brain using Dynabeads mRNA Purification Kit.
RNA-seq libraries were prepared using a bulk adaptation of the MARS-Seq protocol. Briefly, 60 ng of input RNA from each sample was barcoded during reverse transcription and pooled. After Ampure XP bead cleanup, second-strand synthesis and linear amplification by T7 in vitro transcription were performed. The resulting RNA was fragmented and converted into sequencing-ready libraries by ligation of Illumina adapters, reverse transcription, and PCR. Libraries were quantified using Qubit and Tape Station.

treatment_protocol: EAE induction with MOG + PTX. Sacrifice at the peak of the disease at D15.

value: brain

value: brain myeloid cells

value: WT

value: EAE


title: RWT_LBagar_3

value: Rugose WT


title: T29

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: 6% GA


title: PostIVIG4

description: 150 base pair

value: blood

value: PostIVIG


title: brain myeloid cells of WT mice 2

description: Library name: WTEAE2


title: RWT_LBagar_2

value: bacterial culture


title: T5

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: PostIVIG5

description: 150 base pair


title: control 2

description: gene expression data

source_name: gene expression of control mice

value: bone marrow


title: benzene exposure 3

description: gene expression data

source_name: gene expression of benzene exposed mice

tag: agent

value: benzene


title: RWT_LBagar_1

value: 48hrs growth on LB agar


title: T30

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine

value: male


title: benzene exposure 1

description: gene expression data


title: brain myeloid cells of WT mice 1

description: Library name: WTEAE1


title: brain myeloid cells of WT mice 0

description: Library name: WTEAE0


title: control 3

description: gene expression data


title: benzene exposure 2

description: gene expression data


title: C46

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: C

value: WT AB


title: PostIVIG2

description: 150 base pair


title: T20

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: female


title: GA24

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: B


title: Control10

description: 150 base pair

value: Control


title: brain myeloid cells of KO of SLAMF5 mice 3

description: Library name: KOEAE3

value: brain

value: brain myeloid cells

value: KO of SLAMF5


title: PostIVIG1

description: 150 base pair


title: siB55a_repl3

city: Rome

first: Valentina

last: Cianfanelli

address: Viale Marconi 446

country: Italy

institute: University Roma TRE

description:
Library name: siB55a_new_repl_3
Transcriptome profile of Parkin-expressing HeLa cells transfected with a siRNA targeting B55a (siB55a),  biological rep 3

data_processing:
SOAPnuke (v1.5.2) for read filtering.
Assembly: HISAT2 (v2.0.4). Clean reads were aligned to the reference genome (hg19)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: HeLa cells

growth_protocol: HeLa cells were grown in high-glucose Glutamax Dulbecco Minimal Essential Medium (DMEM), supplemented with 10% Fetal Bovine Serum (FBS) and penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the NucleoSpin™ RNA Columns (Macherey-Nagel™, DE; cat# 740955), according to manufaturer's instructions. RNA integrity was verified by an Agilent 2100 Bioanalyzer. 1 microgr of RNA was used for the library construction.
Messenger RNA was enriched using oligo(dT) magnetic beads. A strand-specific RNA sequencing library was constructed following the BGI Standard mRNA-seq Library Prep protocol. Briefly, the enriched mRNA was fragmented and reverse-transcribed into first-strand cDNA using random hexamer primers. Second-strand cDNA was synthesized using dUTP instead of dTTP to achieve strand specificity. Double-stranded cDNA was purified, end-repaired, adenylated at the 3' ends, and ligated to BGI's proprietary duplex adapters. The adapter-ligated fragments were purified and size-selected (typically for insert sizes of ~200-300 bp). The libraries were then amplified via PCR, and the final products were purified. Library quality and concentration were assessed using a Bioanalyzer and qPCR. The amplified fragmented cDNA of 100 bp in size were sequenced in paired-end mode using the Genome Analyzer (Illumina) with a read length of 100 bp.

treatment_protocol: Cells were transfected with a siRNA targeting B55a /PPP2R2A or with an unspecific control siRNA, as a control, by using RNAi Max (Invitrogen), according to manifacturer's instructions. Parkin expression was induced by 16 hours Doxycyclin treatment.

value: HeLa cells

value: Cervical Adenocarcinoma

value: Doxycycline inducible for HA_Parkin expression

value: HeLa cells knocked-down for b55a/PPP2R2A and induced for HA-Parkin expression through Doxycycline


title: siB55a_repl2

description:
Library name: siB55a_new_repl_2
Transcriptome profile of Parkin-expressing HeLa cells transfected with a siRNA targeting B55a (siB55a),  biological rep 2


title: brain myeloid cells of KO of SLAMF5 mice 6

description: Library name: KOEAE6

value: EAE


title: control 1

description: gene expression data

value: bone marrow


title: GA1

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: A


title: Control9

description: 150 base pair

value: blood


title: C45

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine

value: 0% GA


title: brain myeloid cells of KO of SLAMF5 mice 1

description: Library name: KOEAE1


title: siB55a_repl1

description:
Library name: siB55a_new_repl_1
Transcriptome profile of Parkin-expressing HeLa cells transfected with a siRNA targeting B55a (siB55a),  biological rep 1


title: Control8

description: 150 base pair


title: siCTR_repl3

description:
Library name: siCtr_repl_3
Transcriptome profile of Parkin-expressing HeLa cells transfected with an unspecific siRNA (siCtrl),  biological rep 3

value: HeLa cells transiently transfected with an unpecific control oligo siRNA and induced for HA-Parkin expression through Doxycycline


title: brain myeloid cells of KO of SLAMF5 mice 2

description: Library name: KOEAE2


title: C33

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: C

value: male

value: WT AB


title: siCTR_repl2

description:
Library name: siCtr_repl_2
Transcriptome profile of Parkin-expressing HeLa cells transfected with an unspecific siRNA (siCtrl),  biological rep 2


title: PostIVIG3

description: 150 base pair

value: PostIVIG


title: C29

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: female


title: Control6

description: 150 base pair

value: Control


title: COH-MLCKtg 5

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
Library Quantification(qPCR) by using KAPA Library Quantification Kits
The library was loaded onto the instrument using MiSeq Sequencing Service 600cycle
Library strategy: 16s

source_name: Feces

extract_protocol:
Fecal pellets were collected aseptically and placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit  protocol
For the illumina library construction, 16S rRNA was amplified by using primer set  Forward Primer:5'- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3 and Reverse Primer:5'- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC-3'
Library Preparation: 16S Metagenomic Sequencing Library Preparation-Nextera XT DNA sample preparation

treatment_protocol: Untreated

tag: stain

value: MLCK-Tg

tag: time

value: Ten weeks old, Cohoused with B6 mice from six weeks old

value: Cohoused with B6 mice for four weeks


title: COH-MLCKtg 6


title: Control5

description: 150 base pair


title: GA46

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: COH-MLCKtg 4


title: Tumor tissue, Mll3 wild-type, scRNA-seq

first: Xinhua

last: Liu

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

description: Library name: scRNA-seq_Mll3WT

data_processing:
The raw data were preprocessed by using fastp. STAR and HTSeq was used for alignment and gene expression quantification in the RNA-seq analysis. For CUT&Tag, Bowtie2 was applied for the sequence alignment, deeptools for the computation and normalization of the enrichment signal. SEACR was used for the peak calling process.
Assembly: mm10
Supplementary files format and content: csv: Raw RNA-seq count for gene expression.
Supplementary files format and content: bigwig: Enrichment signal for CUT&Tag.

source_name: Tumor tissue

growth_protocol: The murine colorectal adenocarcinoma cell line CT26 was maintained in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% penicillin/streptomycin (P/S) (Gibco). Cells were cultured in a humidified incubator at 37°C with 5% CO2. The medium was changed every 2-3 days to ensure optimal growth conditions.

extract_protocol:
Total RNA was extracted from CT26 cells using TRIzol reagent (Invitrogen) according to the manufacturer's standard protocol. RNA integrity and concentration were measured by Agilent 2100 Bioanalyzer. Genomic DNA for CUT&Tag was extracted from CT26 cells/tissues using the DNeasy Blood & Tissue Kit. DNA concentration and purity were measured by NanoDrop spectrophotometry.
RNA-seq: Strand-specific RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer's instructions. The procedure includes RNA fragmentation, first and second strand cDNA synthesis, adapter ligation, and PCR enrichment. CUT&Tag: The CUT&Tag experiment was performed following the manufacturer’s protocol for the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (Cat. No. N259-YH01). Briefly, 1.2 × 10⁵ cells per sample were fixed with formaldehyde, permeabilized, and bound to NovoNGS® ConA Beads during a 10 minutes incubation at room temperature. The ConA bead-cell complexes were then incubated overnight with specific primary antibodies against histone modifications H3K27ac (abcam, ab4729) and H3K4me1 (CST, 5326S). After washing, samples were incubated for 2 hours at room temperature with a secondary antibody (Goat Anti-Rabbit IgG H&L, N269). Tagmentation was performed using the assembled transposome complex. DNA was purified using Tagment DNA Extract Beads and subsequently amplified via PCR. The final libraries were cleaned with NovoNGS® DNA Clean Beads. scRNA-seq: Tumor tissues were obtained from the COAD mouse models and cut into pieces that about 50 mg, which were then placed in 500 μL RNAlater (Thermo Fisher Scientific) in 1.5mL tubes followed by incubation overnight at 4℃. The C4 scRNA-seq kit (BGI, Tianjin, China) was applied for single cell RNA-sequencing libraries preparation. High-throughput sequencing was conducted in Romics (Shanghai, China).

value: Tumor tissue

value: Tissue

value: WT

tag: batch


title: Tumor tissue, Mll3 kncok-out, scRNA-seq

description: Library name: scRNA-seq_Mll3KO


title: GA16

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: A


title: COH-MLCKtg 3


title: Control4

description: 150 base pair

value: blood


title: Control3

description: 150 base pair


title: CT26 cell, Mll3 knock-out, H3K4me1 CUT&Tag

description: Library name: H3K4me1_Mll3KO

source_name: cell line

value: cell line


title: C26

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine

value: 0% GA


title: COH-MLCKtg 2


title: CT26 cell, Mll3 wild-type, H3K4me1 CUT&Tag

description: Library name: H3K4me1_Mll3WT


title: C4

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: Control2

description: 150 base pair


title: COH-MLCKtg 1


title: Control7

description: 150 base pair


title: GA41

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: C


title: COH-B6 6

value: Ten weeks old, Cohoused with Tg mice from six weeks old

value: Cohoused with MLCKtg mice  for four weeks


title: CT26 cell, Mll3 knock-out, H3K27ac CUT&Tag

description: Library name: H3K27ac_Mll3KO


title: Control1

description: 150 base pair


title: C64

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: D

value: male

value: WT AB


title: CT26 cell, Mll3 wild-type, H3K27ac CUT&Tag

description: Library name: H3K27ac_Mll3WT


title: COH-B6 5


title: CT26 cell, Mll3 knock-out, RNA-seq rep3

description: Library name: RNA-seq_Mll3KO_3


title: T27

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: female

value: 6% GA


title: siCTR_repl1

description:
Library name: siCtr_repl_1
Transcriptome profile of Parkin-expressing HeLa cells transfected with an unspecific siRNA (siCtrl),  biological rep 1

value: HeLa cells

value: Cervical Adenocarcinoma

value: Doxycycline inducible for HA_Parkin expression

value: HeLa cells transiently transfected with an unpecific control oligo siRNA and induced for HA-Parkin expression through Doxycycline


title: CT26 cell, Mll3 knock-out, RNA-seq rep2

description: Library name: RNA-seq_Mll3KO_2


title: C1

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: COH-B6 2


title: CT26 cell, Mll3 knock-out, RNA-seq rep1

description: Library name: RNA-seq_Mll3KO_1


title: C27

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: COH-B6 3


title: T3

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: CT26 cell, Mll3 wild-type, RNA-seq rep3

description: Library name: RNA-seq_Mll3WT_3

value: WT


title: COH-B6 1


title: Pat.#36's_FATHER

city: Nantes

first: Frédéric

last: Ebstein

address: IRS-UN - 8 quai Moncousu - BP 70721

department: L'unité de recherche de l'institut du thorax, Inserm UMR 1087

country: France

institute: French Institute of Health and Medical Research (Inserm)

hyb_protocol: One hundred nanograms total RNA was hybridized with the nCounter Autoimmune Profiling panel CodeSets for 16 hours at 65°C.

scan_protocol: Hybridized probes were immobilized on streptavidin-coated cartridges for digital counting by a nCounter™ Digital Analyzer.

data_processing: RCC files were analysed using nSolver 4.0. Normalization of RNA loading was performed using the geometric mean of a unique housekeeping gene.

label: NanoString CodSets

source_name: Stimulated T cells

label_protocol: Labelling was performed using gene-specific biotin-tagged molecular barcodes (CodeSets) designed and provided by the manufacturer.

growth_protocol: PBMC were cultured in U-bottom 96-well plates together with irradiated feeder cells using RPMI 1640 medium supplemented with 10% human AB serum.

extract_protocol: Total RNA was isolated from resting T cells using the kit from Analytic Jena AG following the manufacturer’s instructions.

treatment_protocol: PBMC were stimulated with 1 µg/µl L-PHA (Sigma) and 150 U/ml IL-2 (Miltenyi Biotec) for three weeks to expand naive T cells following the procedure of Fonteneau et al.

tag: gender

value: PSMC5 +/+ (wild-type)

tag: phenotype

value: Clinically healthy


title: Pat.#36

value: PSMC5 +/R325W

value: Neurodevelopmental disorder


title: Pat.#25

value: PSMC5 +/P320R


title: C5

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine


title: CT26 cell, Mll3 wild-type, RNA-seq rep2

description: Library name: RNA-seq_Mll3WT_2

value: cell line


title: CT26 cell, Mll3 wild-type, RNA-seq rep1

description: Library name: RNA-seq_Mll3WT_1


title: C6

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: 0% GA


title: SIN-MLCKtg 6

value: MLCK-Tg

value: Ten weeks old, conventionally raised

value: Untreated


title: P35, RhoP23H/+, standard cyclic 200 lux, retina

city: Indianapolis

first: Yoshikazu

last: Imanishi

state: Indiana

address: 1160 W Michigan Street

department: Department of Ophthalmology

institute: Indiana University School of Medicine

description:
Library name: Sample 5
Column name in FPKM: RhoP23H/+ mRNA quantity in 200 lux (FPKM)

data_processing:
Obtained sequence data, collections of 150 nt paired-end short reads, were mapped to the C57BL mouse genome reference sequence database (GRCm39) with HiSAT2.
Assembly: GRCm39
Supplementary files format and content: Excel files contains FPKM values for each sample.

source_name: Retina

growth_protocol: Wild-type, RhoQ344X/+, and RhoP23H/+ mice were reared from P0 to P35, the time point when the mice were sacrified. The mice were weaned from their parental cages at P21.

extract_protocol:
Retinas were collected and total RNA was extracted under corresponding light conditions using TRIzol™ Reagent.
RNA-seq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs) following the manufacturer's protocol.

treatment_protocol: Wild-type and RhoQ344X/+ mice were reared under either standard cyclic 200 lux light or dark conditions from P0 to P35, and RhoP23H/+ mice were reared under standard cyclic 200 lux light condition from P0 to P35.

value: Retina

value: Retinal cells

value: Standard cyclic 200 lux


title: SIN-MLCKtg 5


title: SIN-MLCKtg 4


title: Pat.#15's_FATHER

value: male


title: COH-B6 4

value: Ten weeks old, Cohoused with Tg mice from six weeks old

value: Cohoused with MLCKtg mice  for four weeks


title: C14

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: female

value: WT AB


title: Pat.#15

value: PSMC5 +/E250V


title: SIN-MLCKtg 3


title: Pat.#14

value: Neurodevelopmental disorder


title: P35, RhoQ344X/+, dark, retina

description:
Library name: Sample 4
Column name in FPKM: RhoQ344X/+ mRNA quantity in dark (FPKM)

value: Dark


title: P35, RhoQ344X/+, standard cyclic 200 lux, retina

description:
Library name: Sample 3
Column name in FPKM: RhoQ344X/+ mRNA quantity in 200 lux (FPKM)


title: Pat.#1


title: T18

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine

value: 6% GA


title: SIN-MLCKtg 2


title: P35, wild-type, dark, retina

description:
Library name: Sample 2
Column name in FPKM: Wild-type mRNA quantity in dark (FPKM)

value: Wild-type


title: HD_#2

value: PSMC5 +/+ (wild-type)

value: Clinically healthy


title: SIN-MLCKtg 1

value: MLCK-Tg

value: Ten weeks old, conventionally raised

value: Untreated


title: C12

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: 0% GA


title: C17

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: P35, wild-type, standard cyclic 200 lux, retina

description:
Library name: Sample 1
Column name in FPKM: Wild-type mRNA quantity in 200 lux (FPKM)

value: Retina

value: Retinal cells

value: Standard cyclic 200 lux


title: C18

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: male


title: Macrophages with LPS 6h, Actd 1h

description: Library name: LPS6h_ActD_1h

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using STAR.
Assembly: GRCm39
Supplementary files format and content: rpkm files containing rpkm for each transcripts,which are seperated by Tab

extract_protocol:
Cells were washed twice with cold PBS. 500 μl lysis buffer (8 mM HEPES, pH 7.4, 80 mM KCl, 4 mM MgCl2, 2% Triton x-100, and 200 μg/ml cycloheximide) was then added, and the cells were quickly scraped and collected into RNase-free tubes. The sample were centrifuged at 12,000 rpm for 12 minutes at 4°C, and the supernatant was sent to Novogene (China) for RNA-seq library construction. Approximately 100 μl of supernatant were treated with RNase I (Thermo Fisher Scientific) for 3 hours, followed by RNA extraction using TRIzol™ LS.
RNA samples were sent to Novogene for RNA-seq library construction

value: cell line


title: Pat.#14's_FATHER

value: Mild neurodevelopmental disorder


title: HD_#1


title: T12

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: female

value: WT AB


title: SIN-B6 6


title: Macrophages with LPS 6h, Actd 3h

description: Library name: LPS6h_ActD_3h


title: SIN-B6 5


title: C9

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: intestine


title: SIN-B6 4


title: SIN-B6 3


title: Macrophages without LPS treatment, Actd 3h

description: Library name: con_ActD_3h


title: T14

description:
OTU_matrix_2023.csv
taxonomy_2023.csv

value: 6% GA


title: Macrophages with LPS 6h, Actd 0h

description: Library name: LPS6h_ActD_0h


title: T10

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: SIN-B6 2


title: T11

description:
OTU_matrix_2023.csv
taxonomy_2023.csv


title: Macrophages without LPS treatment, Actd 1h

description: Library name: con_ActD_1h


title: SIN-B6 1


title: Macrophages without LPS treatment, Actd 0h

description: Library name: con_ActD_0h


title: RICOVER-60_761

status: Public on Sep 06 2025

city: Hannover

first: Robin

last: Kosch

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

hyb_protocol: Total RNA was hybridized to the codesets at 65°C overnight.

scan_protocol: standard protocol

data_processing: For processing of the reaction on nCounter PrepStation “high sensitivity” setting was used and gene expression data was then obtained on the nCounter™ Digital Analyzer at the “max resolution” setting (1155 FOV).

label: not provided

source_name: FFPEs from DLBCL

label_protocol: 200 ng RNA were used for digital GEP using the NanoString nCounter technology (NanoString Technologies, Seattle, WA).

extract_protocol: Nucleic acids were extracted with Qiagen AllPrep DNA/RNA FFPE Kit (Qiagen, Hil-den, Germany).

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort


title: MegaCHOEP_132

value: MegaCHOEP


title: RICOVER-60_773


title: RICOVER-60_618


title: RICOVER-60_574


title: RICOVER-60_570


title: RICOVER-60_522


title: RICOVER-60_694


title: Mus musculus liver_Infected+praziquantel_45Day_rep1

city: Hefei City

first: gong

last: li

state: Anhui Province

address: South First Ring Road

institute: Anhui Medical University

description: The gene expression in the livers of 45-day-old mice was studied. The experimental conditions were that the mice were infected with schistosomiasis and treated with praziquantel for 45 days before the study.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: liver, 45d,infection 45d+praziquantel, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The normal mice were divided into two groups. One group was not subjected to any treatment, while the other group was infected with schistosomes. The same feeding period of 0, 15, 24, and 45 days was observed, and then the mice were killed and their livers were collected and stored at -80 degrees.supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: liver

tag: age


title: RICOVER-60_508


title: RICOVER-60_496


title: RICOVER-60_497


title: RICOVER-60_397


title: Mus musculus liver_Infected_45Day_rep1

description: Gene expression in the livers of 45-day-old mice was processed under the condition of 45 days of schistosomiasis infection.

source_name: liver, 45d,infection 45d, replicate 1


title: Mus musculus liver_Control_45Day_rep2

description: Gene expression in the livers of 45-day-old mice was processed under the condition of zero days of schistosomiasis infection.

source_name: liver,45d,infection 0d, replicate 1


title: Mus musculus liver_Infected_24Day_rep1

description: Gene expression in the livers of 24-day-old mice was processed under the condition of 24 days of schistosomiasis infection.

source_name: liver, 24d,infection 24d, replicate 1


title: RICOVER-60_373


title: Mus musculus liver_Control_24Day_rep1

description: Gene expression in the livers of 24-day-old mice was processed under the condition of zero days of schistosomiasis infection.

source_name: liver, 24d,infection 0d, replicate 1


title: RICOVER-60_333


title: RICOVER-60_238


title: RICOVER-60_311


title: SMARTER_297

value: SMARTER


title: RICOVER-60_123


title: SMARTER_266


title: RICOVER-60_506


title: RICOVER-60_361


title: RICOVER-60_135


title: SMARTER_257


title: SMARTER_249


title: Mus musculus liver_Infected_15Day_rep1

description: Gene expression in the livers of 15-day-old mice was processed under the condition of 15 days of schistosomiasis infection.

source_name: liver, 15d,infection 15d, replicate 1


title: Mus musculus liver_Control_15Day_rep1

description: Gene expression in the livers of 15-day-old mice was processed under the condition of zero days of schistosomiasis infection.

source_name: liver, 15d,infection 0d, replicate 1


title: SMARTER_242


title: SMARTER_153


title: SMARTER_141


title: SMARTER_192


title: SMARTER_206


title: SMARTER_150


title: SMARTER_310


title: SMARTER_299


title: SMARTER_176


title: SMARTER_238


title: SMARTER_231


title: SMARTER_216


title: SMARTER_265


title: SMARTER_286


title: SMARTER_193


title: SMARTER_218


title: SMARTER_210


title: SMARTER_199


title: SMARTER_183


title: SMARTER_169


title: SMARTER_128


title: MegaCHOEP_447


title: MegaCHOEP_449


title: MegaCHOEP_446


title: RICOVER-noRTh_1468

value: RICOVER-noRTh


title: RICOVER-noRTh_1434


title: RICOVER-noRTh_1419


title: RICOVER-noRTh_1421


title: RICOVER-noRTh_1432


title: RICOVER-noRTh_1416


title: RICOVER-60_266


title: RICOVER-60_290


title: RICOVER-noRTh_1376


title: RICOVER-noRTh_1382


title: RICOVER-60_270


title: RICOVER-noRTh_1435


title: RICOVER-noRTh_1387


title: SMARTER_157


title: RICOVER-60_231


title: RICOVER-60_258


title: RICOVER-60_163


title: RICOVER-60_124


title: SMARTER_269


title: SMARTER_261


title: SMARTER_255


title: SMARTER_252


title: RICOVER-noRTh_1459


title: SMARTER_246


title: SMARTER_234


title: SMARTER_214


title: SMARTER_160


title: SMARTER_127


title: SMARTER_289


title: SMARTER_200


title: SMARTER_230


title: SMARTER_311


title: SMARTER_254


title: RICOVER-60_126


title: SMARTER_142


title: SMARTER_191


title: SMARTER_222


title: MegaCHOEP_394


title: RICOVER-noRTh_1343


title: RICOVER-noRTh_1378


title: RICOVER-noRTh_1363


title: RICOVER-noRTh_1384


title: RICOVER-noRTh_1496


title: RICOVER-noRTh_1354


title: MegaCHOEP_378


title: RICOVER-noRTh_1349


title: RICOVER-noRTh_1448


title: RICOVER-noRTh_1342


title: RICOVER-noRTh_1489


title: RICOVER-noRTh_1438


title: RICOVER-noRTh_1486


title: RICOVER-noRTh_1452


title: RICOVER-noRTh_1406


title: RICOVER-noRTh_1374


title: RICOVER-noRTh_1398


title: RICOVER-noRTh_1442


title: RICOVER-noRTh_1360


title: RICOVER-noRTh_1394


title: RICOVER-noRTh_1348


title: MegaCHOEP_448


title: RICOVER-noRTh_1361


title: RICOVER-noRTh_1372


title: RICOVER-noRTh_1443


title: RICOVER-noRTh_1368


title: RICOVER-noRTh_1344


title: RICOVER-noRTh_1427


title: RICOVER-noRTh_1475


title: RICOVER-noRTh_1400


title: RICOVER-noRTh_1388


title: RICOVER-noRTh_1391


title: RICOVER-noRTh_1492


title: RICOVER-noRTh_1478


title: P60 TfR1KO;KspCre Kidney 1

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

data_processing:
Illumina RTA was used to perform base calling, and CASAVA (version 1.8.2) was used for converting base call files (.BCL) to FASTQ format and for performing sequence adaptor trimming.
Reads were trimmed using TRIMMOMATIC (Bolger, 2014) with parameters LEADING:10, TRAILING:10, MINLEN:30.
Alignment was done against mouse mm9 genome using TOPHAT v2.0.11.
Raw reads per gene were counted using HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: tsv files with raw read count

source_name: Kidney

extract_protocol:
Total RNA was isolated using Ambion TRIzol Reagent (Life Technologies, Carlsbad, CA). RNA concentration and integrity for each sample were assessed on RNA 6000 Chips using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using Illumina TruSeq® RNA prep kits

value: kidney

value: post natal day 60

tag: diet

value: iron sufficient diet (220ppm iron)


title: P60 Control Kidney 2

value: wild type


title: P60 Control Kidney 3


title: RICOVER-noRTh_1488


title: RICOVER-noRTh_1487


title: RICOVER-noRTh_1437


title: P15 Iron Deficient Kidney 3

data_processing:
Illumina RTA was used to perform base calling, and CASAVA (version 1.8.2) was used for converting base call files (.BCL) to FASTQ format and for performing sequence adaptor trimming.
Reads were trimmed using TRIMMOMATIC (Bolger, 2014) with parameters LEADING:10, TRAILING:10, MINLEN:30.
Alignment was done against mouse mm9 genome using TOPHAT v2.0.11.
Raw reads per gene were counted using HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: tsv file with raw read count

treatment_protocol: 8-weeks-old female mice C57BL/6 (Charles River, USA) were divided into two groups, control and iron deficient. The iron deficient group was maintained on an iron deficient synthetic diet containing approximately 2-6ppm iron (TD.80396, Harlan,USA). The control group was provided with an iron sufficient diet containing 220ppm iron. Water was served ad libitum in plastic bottles. After one month the females were mated with C57BL/6 males. Females were fed their designated diets during the breeding period, throughout pregnancy, and after giving birth up to post-natal day 15.

value: post natal day 15

value: iron-deficient diet (2-6ppm iron)


title: P60 Control Kidney 1


title: P15 Iron Deficient Kidney 2


title: P15 Control Kidney 3


title: P15 Iron Deficient Kidney 1


title: RICOVER-noRTh_1403


title: RICOVER-noRTh_1390


title: P60 TfR1KO;KspCre Kidney 2


title: P60 TfR1KO;KspCre Kidney 3


title: RICOVER-noRTh_1425


title: RICOVER-noRTh_1364


title: RICOVER-noRTh_1358


title: P13 TfR1KO;Six2Cre Kidney 3

data_processing:
Illumina RTA was used to perform base calling, and CASAVA (version 1.8.2) was used for converting base call files (.BCL) to FASTQ format and for performing sequence adaptor trimming.
Reads were trimmed using TRIMMOMATIC (Bolger, 2014) with parameters LEADING:10, TRAILING:10, MINLEN:30.
Alignment was done against mouse mm9 genome using TOPHAT v2.0.11.
Raw reads per gene were counted using HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: tsv files with raw read count.

value: post natal day 13


title: RICOVER-noRTh_1380


title: P13 TfR1KO;Six2Cre Kidney 2


title: P13 TfR1KO;Six2Cre Kidney 1


title: P13 Control Kidney 3


title: MegaCHOEP_436


title: MegaCHOEP_439


title: RICOVER-noRTh_1454


title: MegaCHOEP_429


title: MegaCHOEP_414


title: MegaCHOEP_434


title: P13 Control Kidney 2


title: P13 Control Kidney 1


title: FSTL1_2

city: Guangzhou

first: Yao

last: Lei

address: 107 Yan Jiang West Road

department: Department of Cardiology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Library name: sample5
FSTL1_2_FPKM

data_processing:
Reads were filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region,  For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: GRCh38
Supplementary files format and content: FPKM

source_name: Vascular smooth muscle cells

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.And the amplified flowcell was sequenced single end on the Illumina Novaseq X plus platform (Tsingke Beijing, China)

value: Vascular smooth muscle cells

value: Wild type

value: PBS


title: FSTL1_3

description:
Library name: sample6
FSTL1_3_FPKM


title: P15 Control Kidney 2


title: FSTL1_1

description:
Library name: sample4
FSTL1_1_FPKM


title: MegaCHOEP_396


title: MegaCHOEP_392


title: MegaCHOEP_389


title: P15 Control Kidney 1


title: MegaCHOEP_377


title: CTL2

description:
Library name: sample2
CTL2_FPKM

value: recombinant FSTL1


title: MegaCHOEP_375

value: FFPEs from DLBCL


title: MegaCHOEP_372

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²


title: MInT_D-70-8


title: MegaCHOEP_386

value: MegaCHOEP


title: CTL1

description:
Library name: sample1
CTL1_FPKM


title: A549 cells, ChIP-seq_anti-HDAC1_Control

first: Deng

last: Pan

address: Tsinghua University Medical Science Building

department: School of Basic Medical Sciences

institute: Tsinghua University

description: Library name: Sample3

data_processing:
Raw sequencing reads were first trimmed to remove adapters and low-quality bases using Trim Galore (v0.6.7) with default parameters.
Sequencing reads were aligned to the human genome (GRCh38, hg38) using bowtie2 (version 2.4.5).
Peaks were called using MACS2 (v2.2.7.1) .
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Lung

extract_protocol:
3 × 10⁷ cells were cross-linked using 1% formaldehyde and quenched with 0.125 M glycine. Lysates were prepared in buffer (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 0.1% SDS, 140 mM NaCl, 0.1% sodium deoxycholate, and 1% Triton X-100), sonicated on ice, and precleared.
Chromatin-immunoprecipitated (ChIP) DNA was purified after elution and reverse cross-linking, followed by library preparation using the Universal Pro DNA Library Prep Kit for Illumina (Vazyme ND608)

value: Lung

tag: cell line

value: lung cancer

value: WT


title: MInT_D-70-3


title: A549 cells, ChIP-seq_anti-flag(ZNF296)

description: Library name: Sample2

tag: cell type

value: ZNF296 overexpression


title: A549 cells, ATAC-seq,ZNF296OE-rep3

description: Library name: Sample6

data_processing:
Raw sequencing reads were first trimmed to remove adapters and low-quality bases using Trim Galore (v0.6.7) with default parameters.
Sequencing reads were aligned to the human genome (GRCh38, hg38) using bowtie2 (version 2.4.5) with default parameters.
Peaks were called using MACS2 (v2.2.7.1) with the significance cut-off q value <= 0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
A total of 5× 104 cells were harvested, washed twice with ice-cold PBS, and lysed using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme TD711) to release nuclei. The nuclei were pelleted by centrifugation at 500 × g for 10 minutes at 4°C and used for downstream ATAC-seq library preparation.
ATAC-seq sequencing libraries were prepared using theTruePrep Index Kit V2 for Illumina (Vazyme, #TD202) following the manufacturer's protocol.

tag: genotype


title: A549 cells, ChIP-seq_anti-HDAC1_ZNF296

description: Library name: Sample4


title: MInT_D-70-25

tag: treatment


title: MInT_D-70-22

tag: tissue


title: A549 cells, ATAC-seq,ZNF296OE-rep2

description: Library name: Sample5


title: A549 cells, ATAC-seq,ZNF296OE-rep1

description: Library name: Sample4


title: A549 cells, ChIP-seq_anti-IgG

description: Library name: Sample1


title: MInT_D-70-12


title: MInT_D-70-18


title: MInT_D-70-1


title: MInT_D-58-16


title: CTL3

description:
Library name: sample3
CTL3_FPKM


title: A549 cells, ATAC-seq,Control-rep3

description: Library name: Sample3


title: A549 cells, ATAC-seq,Control-rep2

description: Library name: Sample2


title: A549 cells, ATAC-seq,Control-rep1

description: Library name: Sample1


title: A549 cells, ZNF296OE-rep3

description: Library name: Sample6

data_processing:
Raw RNA-Seq reads were quality-checked using Fastp to remove low-quality bases and adapter contamination.
RNA-seq reads were aligned to either the mm9 or GRCh38 genome using HISAT2 (version 2.2.1) with default parameters, and unmapped reads were removed.
Gene-level counts were calculated using featureCounts (version 2.0.6) based on uniquely mapped reads
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total mRNA from A549, MDA-MB-453, and 4T1 cells was extracted using TRIzol (Invitrogen, Cat# 15596026)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer's protocol.


title: MInT_D-355-11


title: MInT_D-268-11


title: MInT_D-337-5


title: MInT_D-43-9


title: A549 cells, ZNF296OE-rep2

description: Library name: Sample5


title: A549 cells, ZNF296OE-rep1

description: Library name: Sample4


title: A549 cells, Control-rep3

description: Library name: Sample3


title: A549 cells, Control-rep2

description: Library name: Sample2


title: A549 cells, Control-rep1

description: Library name: Sample1


title: MInT_D-268-10


title: MInT_D-24-2


title: MInT_D-24-5


title: MInT_D-268-1


title: MInT_D-24-1


title: NT3Kcr_nontargeting siRNA anti-Kcr ChIP-seq 4

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Library preparation and sequencing was by NOVOGENE, novaseq 150bp Paired End, Trimming was with Trim Galore version: 0.6.5  Cutadapt version: 2.3, Quality Phred score cutoff: 20, Reads were mapped using Bowtie2
Genome_build: Homo sapiens GRCh38
Read alignment was with SEQMONK v:1.47.2, GRCh_v97, Import options - Remove duplicates from start and end,                    min mapping quality 20,                    primary alignments only,                    Paired end,                    Distance cutoff 1000bp
MACS peaks were selected and quantified within SEQMONK v1.47.2 MACS peaks   P-value cutoff 1 x E-5  Fragment size 300  Input store used; InputKcr_L001_R1_val_1_GRCh38_bowtie2    Read count quantitation   All reads  correct for total read count  Largest datastore  Log transform count    All probe count 49916    All probe converted to annotation probe report.   -annotate with overlapping genes  -included unannotated probes  -included data for currently visible stores
Supplementary_files_format_and_content:  ChIP-seq_Annotated_Probe_Report_for_DAXX_and_crotonylation_study.txt (annotated_probe_report text file txt)

growth_protocol: HCT116 cells were grown in in DMEM media containing glucose and pyruvate, 10 % FBS, 2 mM L-glutamine, 100 units/ml penicillin and 100 µg/ml streptomycin

extract_protocol:
Cells where trypsinized and fixed in 1 % formaldehyde for 10 minutes. After quenching with 0.125 M glycine, cells were washed with PBS and processed for ChIP using the anti-Kcr atibody from PTM PTM-501
libraries were constructed by NOVOGENE
ChIP-seq ibraries were sequenced on a NovaSeq PE150 platform

treatment_protocol: HCT116 cells were treated with either 25 nM Non-targeting siRNA or 35 nM DAXX siRNA and either with or without 10 mM crotonic acid for 48 h.

value: Non-targeting siRNA 25 nM

tag: chip antibody

value: anti-Kcr


title: DENSER_119

value: DENSER


title: NT_CR3Kcr_nontargeting siRNA Crotonate anti-Kcr ChIP-seq 2

value: Non-targeting siRNA 25 nM, Crotonic acid 10 mM


title: NT2Kcr_nontargeting siRNA anti-Kcr ChIP-seq 3


title: DENSER_122


title: DENSER_118


title: NT1BKcr_nontargeting siRNA anti-Kcr ChIP-seq 2


title: MInT_D-107-1


title: MInT_D-113-16


title: MInT_D-113-3


title: NT1AKcr_nontargeting siRNA anti-Kcr ChIP-seq 1


title: INPUTKcr_anti-Kcr ChIP-seq INPUT

description: InputKcr

source_name: INPUTKcr_anti-Kcr ChIP-seq INPUT

value: DAXX siRNA 35 nM


title: NT_CR2Kcr_nontargeting siRNA Crotonate anti-Kcr ChIP-seq 1


title: DAXX_CR3Kcr_DAXX siRNA Crotonate anti-Kcr ChIP-seq 2

value: DAXX siRNA 35 nM, Crotonic acid 10 mM


title: DENSER_116


title: DAXX_CR2Kcr_DAXX siRNA Crotonate anti-Kcr ChIP-seq 1


title: DAXX3Kcr_DAXX siRNA anti-Kcr ChIP-seq 4

source_name: DAXX3Kcr_DAXX siRNA anti-Kcr ChIP-seq


title: DENSER_114


title: DAXX2Kcr_DAXX siRNA anti-Kcr ChIP-seq 3

source_name: DAXX2Kcr_DAXX siRNA anti-Kcr ChIP-seq


title: DENSER_104


title: DENSER_106


title: DAXX1BKcr_DAXX siRNA anti-Kcr ChIP-seq 2

source_name: DAXX1BKcr_DAXX siRNA anti-Kcr ChIP-seq


title: DENSER_101


title: DENSER_100


title: NTi_CR_4_RNAseq-nontargeting siRNA_crotonate_4

data_processing:
Reads were generated by NOVOGENE, NovaSeq, 150bp paired-end, Trimming was with Trim Galore version: 0.6.2 (Cutadapt version: 2.3), Quality Phred score cutoff: 20, reads were mappd using HISAT2 v2.2.1
Genome_build: Homo sapiens GRCh38
Read analysis was with SEQMONK v:1.47.2  Homo sapiens GRCh_v97 assembly       Import options - Do not remove duplicate reads,                    min mapping quality 20,                    primary alignments only,                   treat as RNA-seq data,                    Paired endQuantitate pipelines  -RNA-seq quantitation pipeline    mRNA,   Non-strand specific,   merge transcript isoforms,   Log transform
RNA-seq Annotated Probe Report for DAXX study                                                                All probe count 38148    All probe converted to annotated probe report  -annotate with overlapping genes  -included unannotated probes  -included data for currently visible stores
Supplementary_files_format_and_content:  RNA-seq_Annotated_Probe_Report_for_DAXX_and_crotonylation_study.txt (MACS_annotated_probe_report text file txt)

extract_protocol:
1.3 million cells per sample were used for total RNA extraction with Monarch® Total RNA Miniprep Kit (NEB, cat. T2010S). RNA was quantified using Qubit™ RNA HS Assay kit (Invitrogen, cat. Q32852) on a Qubit™ 3.0 fluorimeter and analysed for RNA integrity on Agilent Bioanalyzer using Agilent RNA 6000 Pico kit (Agilent Technologies, cat. 5067-1513).
mRNA-seq libraries were constructed by NOVOGENE
mRNA-seq ibraries were sequenced on a NovaSeq PE150 platform

treatment_protocol: HCT116 cells were treated with either 25 nM Non-targeting siRNA (NTi) or 35 nM DAXX siRNA (DAXXi) and either with or without 10 mM crotonic acid for 48 h.


title: NTi_CR_3_RNAseq-nontargeting siRNA_crotonate_3


title: DENSER_91


title: DAXX1AKcr_DAXX siRNA anti-Kcr ChIP-seq 1

source_name: DAXX1AKcr_DAXX siRNA anti-Kcr ChIP-seq


title: DENSER_96


title: NTi_CR_1_RNAseq-nontargeting siRNA_crotonate_1


title: DENSER_84


title: NTi_CR_2_RNAseq-nontargeting siRNA_crotonate_2


title: NTi_2_RNAseq_nontargeting siRNA_2

source_name: NTi_2_RNAseq_nontargeting siRNA


title: DENSER_79

source_name: FFPEs from DLBCL


title: DENSER_63


title: DENSER_69


title: NTi_1_RNAseq_nontargeting siRNA_1

source_name: NTi_1_RNAseq_nontargeting siRNA


title: DENSER_74


title: DENSER_70


title: DAXXi_CR_4_RNAseq_DAXX siRNA_crotonate_4

source_name: DAXXi_CR_4_RNAseq_DAXX siRNA_crotonate


title: DAXXi_CR_3_RNAseq_DAXX siRNA_crotonate_3

source_name: DAXXi_CR_3_RNAseq_DAXX siRNA_crotonate


title: DAXXi_CR_2_RNAseq_DAXX siRNA_crotonate_2

source_name: DAXXi_CR_2_RNAseq_DAXX siRNA_crotonate


title: DENSER_68


title: DENSER_62


title: DENSER_61


title: DAXXi_CR_1_RNAseq_DAXX siRNA_crotonate_1

source_name: DAXXi_CR_1_RNAseq_DAXX siRNA_crotonate


title: DENSER_57


title: DAXXi_4_RNAseq_DAXX siRNA_4

source_name: DAXXi_4_RNAseq_DAXX siRNA


title: DENSER_56


title: DENSER_54


title: DENSER_90


title: DENSER_47


title: NTi_4_RNAseq_nontargeting siRNA_4

source_name: NTi_4_RNAseq_nontargeting siRNA


title: DAXXi_2_RNAseq_DAXX siRNA_2

source_name: DAXXi_2_RNAseq_DAXX siRNA


title: NTi_3_RNAseq_nontargeting siRNA_3

source_name: NTi_3_RNAseq_nontargeting siRNA


title: DENSER_38


title: WT-Sham_6

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Library name: WT-Sham_6

data_processing:
RNA libraries were sequenced using a NovaSeq 6000 system and the NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run) with an average of 3 * 10^7 reads per sample (Illumina, San Diego, CA, USA). Quality reports were generated for each FASTQ file using the FASTQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc). Raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using fastq-mcf (https://expressionanalysis.github.io/ea-utils/). Reads shorter than 15 bp were removed from FASTQ files. Next, trimmed reads were aligned to the murine reference genome using the open-source short-read aligner STAR with settings according to the log file.
Illumina RTA v3.1.5 was used for basecalling and Illumina bcl2fastq2 was used for fastq file generation
Feature Count /Read Summarization performed by Rsubread_2.16.1
Assembly: GRCm39 (ENSMBL GRCm39 release 109)
Supplementary files format and content: txt files containing feature counts

source_name: Heart

growth_protocol: Animals were housed with a 14 h light / 10 h dark cycle with free access to food and water.

extract_protocol:
Total RNA from the infarct border zone was isolated using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany).
The RNA sequencing library was generated from 500 ng of total RNA using the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs, Frankfurt, Germany) with the NEBNext® Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions.

treatment_protocol: Mice with Stra6 germline deletion, Vitamin A deficiency (VAD) induced by Lrat germline deletion and feeding with vitamin A-deficient diet, and the combination of both were subjected to myocardial infarction (MI) or Sham surgery. Mice were sacrificed 3-days post-surgery and mRNA was extracted from the infarct border zone.

value: Heart

value: Sham


title: DAXXi_1_RNAseq_DAXX siRNA_1

source_name: DAXXi_1_RNAseq_DAXX siRNA


title: WT-Sham_4

description: Library name: WT-Sham_4


title: WT-Sham_5

description: Library name: WT-Sham_5


title: Whole blood, VC-9002-97_PETCT1

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

institute: WEHI

description:
PCM131
batch2_fc_counts.txt

data_processing:
Forward and reverse reads were then aligned to the reference genome index using the Rsubread align function.
Gene counts were quantified using the BAM files generated from this step, featureCounts (v2.0.3).
Assembly: GRCh38 DNA primary assembly
Supplementary files format and content: .txt formatted gene count matrix

source_name: Whole blood

extract_protocol:
RNA was extracted from thawed Tempus tubes using PerfectPure™ Blood RNA Kit (5 PRIME) or Norgen Preserved Blood RNA kits (for Tempus Tubes), including DNAse treatment.
1000 ng of the isolated total RNA was globin reduced, where indicated, using the Human Globinclear Kit and 200 ng of RNA was used to make cDNA libraries for sequencing using the MGIeasy RNA Library Prep with PE100 chemistry.

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Male

tag: hiv status

value: HIV+

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Globin Depleted


title: Whole blood, VC-9002-92_PETCT1

description:
PCM132
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status


title: Whole blood, VC-9002-93_PETCT1

description:
PCM130
batch2_fc_counts.txt

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus


title: DENSER_33

value: FFPEs from DLBCL

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort


title: WT-Sham_2

description: Library name: WT-Sham_2

tag: genotype


title: DENSER_34


title: DAXXi_3_RNAseq_DAXX siRNA_3

source_name: DAXXi_3_RNAseq_DAXX siRNA

tag: cell line


title: DENSER_27


title: DENSER_29


title: WT-Sham_1

description: Library name: WT-Sham_1


title: DENSER_32


title: DENSER_19


title: Whole blood, VC-9002-89_PETCT1

description:
PCM129
batch2_fc_counts.txt

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: WT-MI_9

description: Library name: WT-MI_9

tag: tissue

value: MI


title: DENSER_21


title: DENSER_16


title: DENSER_14


title: WT-MI_8

description: Library name: WT-MI_8

value: WT


title: Whole blood, VC-9002-86_PETCT1

description:
PCM128
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold


title: DENSER_13

tag: treatment

tag: cohort


title: Whole blood, VC-9002-82_PETCT1

description:
PCM127
batch2_fc_counts.txt

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: DENSER_37

tag: tissue


title: DENSER_17


title: DENSER_6


title: DENSER_12


title: WT-MI_13

description: Library name: WT-MI_13

tag: genotype


title: Whole blood, VC-9002-42_PETCT1

description:
PCM126
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

tag: tb history

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: DENSER_2

tag: treatment

tag: cohort


title: WT-MI_12

description: Library name: WT-MI_12


title: WT-MI_11

description: Library name: WT-MI_11


title: MegaCHOEP_346

value: MegaCHOEP


title: Whole blood, VC-9001-93_PETCT1

description:
PCM125
batch2_fc_counts.txt

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: Whole blood, VC-9001-34_PETCT1

description:
PCM124
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: Whole blood, VC-9001-27_PETCT1

description:
PCM123
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: MegaCHOEP_88

tag: treatment

tag: cohort


title: MegaCHOEP_93


title: Whole blood, VC-9002-83_PETCT1

description:
PCM122
batch2_fc_counts.txt

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: VAD-Sham_34

description: Library name: VAD-Sham_34

tag: tissue

tag: genotype

value: Lrat-/-

value: Sham and vitamin A-deficient diet


title: VAD-Sham_33

description: Library name: VAD-Sham_33


title: MegaCHOEP_42


title: MegaCHOEP_77


title: MegaCHOEP_52


title: Whole blood, VC-9002-79_PETCT1

description:
PCM121
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

tag: tb history

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: Whole blood, VC-9002-67_PETCT1

description:
PCM120
batch2_fc_counts.txt

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: RICOVER-60_1287

tag: tissue

tag: treatment

tag: cohort


title: RICOVER-60_1289


title: VAD-Sham_32

description: Library name: VAD-Sham_32

tag: genotype


title: RICOVER-60_1248


title: RICOVER-60_1247


title: VAD-Sham_31

description: Library name: VAD-Sham_31


title: VAD-Sham_30

description: Library name: VAD-Sham_30


title: RICOVER-60_1175


title: RICOVER-60_1148


title: RICOVER-60_1058


title: RICOVER-60_1081


title: WT-MI_10

description: Library name: WT-MI_10


title: Whole blood, VC-9002-65_PETCT1

description:
PCM119
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: Whole blood, VC-9002-51_PETCT1

description:
PCM118
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: VAD-Sham_29

description: Library name: VAD-Sham_29

tag: tissue

tag: genotype

tag: treatment


title: RICOVER-60_1013

tag: cohort


title: RICOVER-60_978


title: RICOVER-60_973


title: VAD-MI_41

description: Library name: VAD-MI_41

value: MI and vitamin A-deficient diet


title: RICOVER-60_928


title: VAD-MI_40

description: Library name: VAD-MI_40


title: Whole blood, VC-9002-16_PETCT1

description:
PCM116
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: qft-plus

tag: petct definition

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Whole blood, VC-9002-03_PETCT1

description:
PCM115
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: RICOVER-60_904

tag: tissue

tag: treatment

tag: cohort


title: RICOVER-60_866


title: VAD-MI_39

description: Library name: VAD-MI_39

tag: genotype


title: VAD-MI_38

description: Library name: VAD-MI_38


title: RICOVER-60_822


title: RICOVER-60_873


title: Whole blood, VC-9001-54_PETCT1

description:
PCM114
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: qft-plus

tag: petct definition

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: Whole blood, VC-9001-49_PETCT1

description:
PCM113
batch2_fc_counts.txt

tag: hiv status

tag: tb history

value: No

tag: disease status

value: prevalent

tag: symtoms at_tb_diagnosis

value: Asymptom

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: RICOVER-60_704

tag: tissue

tag: treatment

tag: cohort


title: VAD-MI_36

description: Library name: VAD-MI_36

value: Heart

tag: genotype


title: Whole blood, VC-9001-46_PETCT1

description:
PCM112
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Male

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: RICOVER-60_712


title: RICOVER-60_665


title: RICOVER-60_632


title: RICOVER-60_948


title: VAD-MI_35

description: Library name: VAD-MI_35


title: RICOVER-60_583


title: Whole blood, VC-9002-33_PETCT1

description:
PCM117
batch2_fc_counts.txt

tag: hiv status

value: HIV+

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: Globin Depleted


title: Whole blood, VC-9001-45_PETCT1

description:
PCM111
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Whole blood, VC-9001-44_PETCT1

description:
PCM110
batch2_fc_counts.txt

tag: initial age

tag: Sex

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive


title: Stra6_KOxVAD-Sham_46

description: Library name: Stra6_KOxVAD-Sham_46

tag: genotype

value: Stra6-/- Lrat-/-

tag: treatment


title: Whole blood, VC-9001-20_PETCT1

description:
PCM109
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: other hot_lung

tag: other cold_lung


title: RICOVER-60_910

tag: tissue

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort


title: RICOVER-60_408


title: RICOVER-60_384


title: RICOVER-60_355


title: Stra6_KOxVAD-Sham_45

description: Library name: Stra6_KOxVAD-Sham_45


title: RICOVER-60_336


title: Whole blood, VC-9001-10_PETCT1

description:
PCM108
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: RICOVER-60_701

tag: treatment


title: RICOVER-60_320


title: RICOVER-60_216


title: Stra6_KOxVAD-Sham_44

description: Library name: Stra6_KOxVAD-Sham_44

tag: genotype


title: Stra6_KOxVAD-Sham_43

description: Library name: Stra6_KOxVAD-Sham_43


title: Whole blood, VC-9001-02_PETCT1

description:
PCM107
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive


title: Whole blood, VC 9001-15_PETCT1

description:
PCM106
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: qft-gold

tag: other hot_lung

tag: other cold_lung


title: RICOVER-60_150

tag: treatment

tag: cohort


title: Stra6_KOxVAD-Sham_42

description: Library name: Stra6_KOxVAD-Sham_42

tag: genotype


title: Stra6_KOxVAD-Sham_47

description: Library name: Stra6_KOxVAD-Sham_47


title: RICOVER-60_111


title: RICOVER-60_469


title: Whole blood, VC-0054-37_PETCT1

description:
PCM105
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: RICOVER-60_102

tag: tissue


title: Stra6_KOxVAD-MI_53

description: Library name: Stra6_KOxVAD-MI_53


title: RICOVER-60_623


title: RICOVER-60_597


title: RICOVER-60_120


title: RICOVER-60_99


title: RICOVER-60_101


title: Whole blood, VC-0050-63_PETCT1

description:
PCM103
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: months to_diagnosis_from_baseline

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive


title: Stra6_KOxVAD-MI_51

description: Library name: Stra6_KOxVAD-MI_51

tag: genotype

tag: treatment


title: Stra6_KOxVAD-MI_52

description: Library name: Stra6_KOxVAD-MI_52


title: MegaCHOEP_302

tag: cohort

value: MegaCHOEP


title: MegaCHOEP_231


title: Whole blood, VC-0050-62_PETCT1

description:
PCM102
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: qft-gold

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: Stra6_KOxVAD-MI_50

description: Library name: Stra6_KOxVAD-MI_50

tag: tissue


title: MegaCHOEP_195


title: MegaCHOEP_327


title: Whole blood, PET0-037_M6

description:
PCM101
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: months to_diagnosis_from_baseline

tag: qft-plus

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Stra6_KOxVAD-MI_49

description: Library name: Stra6_KOxVAD-MI_49

tag: genotype

tag: treatment


title: MegaCHOEP_313

tag: cohort


title: MegaCHOEP_308


title: Whole blood, VC-0050-65_PETCT1

description:
PCM104
batch2_fc_counts.txt

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: qft-gold

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: Stra6_KOxVAD-MI_48

description: Library name: Stra6_KOxVAD-MI_48

tag: tissue


title: MegaCHOEP_297


title: Whole blood, KY-0049-01_PETCT2

description:
PCM072
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: HIV-

value: no TB

tag: months to_diagnosis_from_baseline

tag: qft-plus

value: Negative

value: Normal lung

tag: other cold_lung

tag: no lesion

value: Yes

tag: hot lymph_nodes

value: No change


title: Stra6-KO-Sham_20

description: Library name: Stra6-KO-Sham_20

tag: genotype

tag: treatment

value: Sham


title: MegaCHOEP_260

tag: cohort


title: MegaCHOEP_246


title: MegaCHOEP_243


title: MegaCHOEP_238


title: Stra6-KO-Sham_19

description: Library name: Stra6-KO-Sham_19


title: Whole blood, KY-0037-02_PETCT1

description:
PCM069
batch2_fc_counts.txt

tag: hiv status

tag: tb history

value: No

tag: disease status

tag: symtoms at_tb_diagnosis

tag: qft-gold

tag: petct definition

value: Other cold lung lesion

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Not globin depleted


title: MegaCHOEP_233

tag: tissue


title: Stra6-KO-Sham_18

description: Library name: Stra6-KO-Sham_18

value: Heart


title: MegaCHOEP_229


title: Whole blood, KY-0081-02_TB_endpoint

description:
PCM068
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

value: endpoint - 24Aug2020

tag: initial age

tag: Sex

value: Male

value: Incident

value: Symptomatic

tag: months to_diagnosis_from_baseline

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: MegaCHOEP_225

value: FFPEs from DLBCL

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: MegaCHOEP


title: Stra6-KO-Sham_17

description: Library name: Stra6-KO-Sham_17

tag: genotype


title: Whole blood, KY-0087-04_PETCT2

description:
PCM066
batch2_fc_counts.txt

value: Female

tag: hiv status

value: HIV-

tag: tb history

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: qft-gold

value: Negative

tag: qft-plus

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: MegaCHOEP_214

tag: tissue


title: MegaCHOEP_200


title: MegaCHOEP_194


title: BAL, KY-0073-04_BAL1

description:
PCM065
batch2_fc_counts.txt

source_name: BAL

value: BAL

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: months to_diagnosis_from_baseline

value: Positive

tag: petct definition

value: No PETCT

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: MegaCHOEP_192

tag: treatment

tag: cohort


title: Whole blood, PET0-005_M0

description:
PCM082
batch2_fc_counts.txt

tag: hiv status

value: HIV+

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: qft-gold

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Globin Depleted


title: Whole blood, KY-0037-02_PETCT2

description:
PCM070
batch2_fc_counts.txt

tag: tissue

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

value: No

tag: qft-plus

value: Other cold lung lesion

tag: other cold_lung

value: Yes

tag: no lesion

tag: hot lymph_nodes

value: No change

value: Not globin depleted


title: Stra6-KO-Sham_15

description: Library name: Stra6-KO-Sham_15

value: Heart

tag: genotype

tag: treatment

value: Sham


title: Stra6-KO-MI_28

description: Library name: Stra6-KO-MI_28

value: MI


title: Whole blood, KY-0119-08_TB_end

description:
PCM064
batch2_fc_counts.txt

tag: Sex

value: Female

tag: hiv status

value: HIV-

tag: tb history

value: DN/A detected not treated

tag: months to_diagnosis_from_baseline

tag: petct definition

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: MegaCHOEP_54

tag: tissue

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: MegaCHOEP


title: Whole blood, KY-0119-08_PETCT2

description:
PCM063
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: disease status

tag: symtoms at_tb_diagnosis

value: no TB

tag: qft-gold

value: Positive

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Mixed


title: MegaCHOEP_38

tag: treatment


title: Whole blood, KY-0119-08_PETCT1

description:
PCM062
batch2_fc_counts.txt

value: Whole blood

tag: Sex

tag: hiv status

tag: tb history

value: No

tag: months to_diagnosis_from_baseline

tag: qft-plus

value: Subclinical TB

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: MegaCHOEP_24

tag: tissue

tag: cohort


title: Stra6-KO-MI_26

description: Library name: Stra6-KO-MI_26

tag: genotype


title: Whole blood, KY-0119-05_PETCT2

description:
PCM061
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: disease status

value: NTM

tag: symtoms at_tb_diagnosis

tag: petct definition

value: Subclinical TB-inactive

value: Yes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: Minimal worsening

tag: globin status


title: RICOVER-60_1283

tag: treatment


title: Stra6-KO-Sham_16

description: Library name: Stra6-KO-Sham_16

value: Heart

value: Sham


title: RICOVER-60_1235


title: RICOVER-60_1269


title: Stra6-KO-MI_23

description: Library name: Stra6-KO-MI_23

value: MI


title: MegaCHOEP_83


title: RICOVER-60_1164


title: RICOVER-60_1128


title: RICOVER-60_1018


title: Whole blood, KY-0119-05_PETCT1

description:
PCM060
batch2_fc_counts.txt

tag: Sex

value: Female

tag: hiv status

value: HIV-

tag: tb history

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Not globin depleted


title: Whole blood, KY-0107-01_PETCT2

description:
PCM059
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

value: Other cold lung lesion

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: Improvement


title: Stra6-KO-MI_27

description: Library name: Stra6-KO-MI_27

tag: genotype

tag: treatment


title: MegaCHOEP_59

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: MegaCHOEP


title: Whole blood, KY-0107-01_PETCT1

description:
PCM058
batch2_fc_counts.txt

value: Whole blood

tag: Sex

tag: hiv status

tag: tb history

value: No

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

value: Positive

tag: petct definition

value: Other hot lung lesion

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: PBS-1

description:
Library name: sample7
PBS-1_tpm

data_processing:
Reads were filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: mm10
Supplementary files format and content: TPM

source_name: Aorta

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.

tag: tissue

value: Aorta

value: ApoE-/-

value: Ang II-infused mice treated with PBS


title: Whole blood, KY-0106-04_PETCT2

description:
PCM057
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

value: Male

value: Yes

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

value: Subclinical TB

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Mixed


title: RICOVER-60_977

tag: treatment

tag: cohort


title: RICOVER-60_750


title: PB2-2

description:
Library name: sample5
PB2-2_tpm

tag: genotype


title: RICOVER-60_706


title: Whole blood, KY-0106-04_PETCT1

description:
PCM056
batch2_fc_counts.txt

tag: Sex

tag: hiv status

value: HIV-

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: petct definition

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: Not globin depleted


title: RICOVER-60_911

tag: tissue

value: FFPEs from DLBCL


title: Stra6-KO-MI_25

description: Library name: Stra6-KO-MI_25

value: Heart

value: MI


title: RICOVER-60_1190

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²


title: CL316-4

description:
Library name: sample4
CL316-4_tpm

value: Ang II-infused mice treated with CL316,243


title: RICOVER-60_369


title: SMARTER_312

value: SMARTER


title: RICOVER-60_1060


title: RICOVER-60_996


title: CL316-3

description:
Library name: sample3
CL316-3_tpm


title: Whole blood, KY-0100-01_PETCT2

description:
PCM055
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

value: Female

value: No

value: no TB

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Negative

tag: qft-plus

value: Normal lung

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: No change

tag: globin status


title: Whole blood, KY-0100-01_PETCT1

description:
PCM054
batch2_fc_counts.txt

tag: Sex

tag: hiv status

tag: tb history

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Yes


title: PB2-3

description:
Library name: sample6
PB2-3_tpm

value: Aorta

tag: genotype

value: ApoE-/-

tag: treatment

value: Ang II-infused mice treated with PBS


title: SMARTER_290

tag: tissue

value: FFPEs from DLBCL

tag: cohort


title: SMARTER_284


title: SMARTER_287


title: Whole blood, KY-0098-02_PETCT2

description:
PCM053
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

value: HIV-

tag: disease status

tag: symtoms at_tb_diagnosis

tag: petct definition

value: Other cold lung lesion

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: Not globin depleted


title: CL316-1

description:
Library name: sample1
CL316-1_tpm

value: Ang II-infused mice treated with CL316,243


title: mouse liver cells

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

description:
Library name: SamplePooled
10X Genomics

data_processing:
deultiplexing, bocoded processing, gene counting and aggregation were performed with Cell Ranger v2.1.1
Assembly: mm10 and HAV HM175
Supplementary files format and content: tab separated value files and matrix files

source_name: liver

extract_protocol:
Intrahepatic CD45⁺ leukocytes and hepatocytes were isolated from the livers of two uninfected and two infected Alb Cre Ifnar1 Floxed mice (day 2 p.i.) following a previously described protocol (PMID: 33111119). Mice were euthanized using the isoflurane drop method. The inferior vena cava was cannulated, and the liver was sequentially perfused with 0.5M EDTA and collagenase solutions (Liberase, Sigma-Aldrich) using a peristaltic pump. The liver was then harvested, and viable hepatocytes and leukocytes were separated by density-based centrifugation with Percoll. Cells were filtered through a 70 µm strainer and collected into separate tubes for staining and sorting. Leukocytes were stained with APC anti-mouse CD45.2 (BioLegend). Dead cells were identified using SYTOX™ Blue Dead Cell Stain (ThermoFisher, #S34857) and Annexin-V (BioLegend, #640918). Each sample was tagged with TotalSeq-B anti-mouse hashtag antibodies 1-4 (BioLegend, #155831, #155833, #155835, #155837) to allow individual mouse identification. Leukocytes were sorted as CD45⁺ live cells, while hepatocytes were sorted as live cells using via a Sony SH800Z cell sorter. The final yield was approximately 4,000 CD45⁺ leukocytes and 1,000 hepatocytes per mouse. Post-sort single cell viability, assessed using propidium iodide/acridine orange staining on a Luna-FX7 cell counter, was around 85% for leukocytes and 56% for hepatocytes. All eight sorted samples (four leukocyte and four hepatocyte samples) were pooled into a single cell suspension, maintaining an 80:20 ratio of immune cells to hepatocytes.
library construction was performed according to the manufacturer's instruction (Chromium Next GEM Single Cell 3’ v3.1 kit, 10XGenomics)

value: liver

value: Ifnar1-/- (Alb cre)


title: SMARTER_271

source_name: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

value: SMARTER


title: Whole blood, KY-0097-02_PETCT2

description:
PCM051
batch2_fc_counts.txt

value: Whole blood

tag: Sex

value: Female

tag: hiv status

tag: tb history

value: no TB

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

value: Subclinical TB

value: No

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: Mixed

tag: globin status


title: Hek293T,NSP14-2,Day 4

city: Hangzhou

first: Wei

last: Xie

address: No. 866 Yuhangtang Road, West Lake District

institute: Zhejiang University

description:
Library name: sample 20
treatment
total-2_count.txt
NSP14-2-3

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed usingCLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

source_name: embryonic kidney

growth_protocol: HEK293t cells were maintained in DMEM suppiemented with 10% fetal bovine serum (FBS) and antibiodics in humidied atmosphere with 5% CO2 at 37℃.

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

treatment_protocol: The recombinant pLVX-EF1α-HA-NSP14-IRES-EGFP-Puro plasmid was transiently transfected into HEK293t mammalian cells when the cell density reached 60%.

tag: tissue

value: embryonic kidney

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: genotype

value: WT

tag: treatment

value: TRANSFECTION


title: SMARTER_264

value: FFPEs from DLBCL

tag: cohort


title: Hek293T,NSP14-2,Day 3

description:
Library name: sample 19
treatment
total-2_count.txt
NSP14-2-2


title: EMT6_KO_2

city: Xiamen

last: Su

state: Fujian

address: No. 4221 Xiang'an South Road

institute: Xiamen university

description: Library name: EMT6_KO_2

data_processing:
Reads cleaning: pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:0.1)
Alignment: clean reads were processed to pseudo-align to mouse transcriptome GRCm38 using Hisat2 (v2.2.1)
Quantification: transcriptional level expression was aggregated to gene level expression using HTSeq (v0.6.1)
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05
Assembly: mm 10
Supplementary files format and content: CSV files include FPKM values for samples

growth_protocol: 4T1 and EMT6 cell culture in DMEM supplentment with 10%FBS and 0.1%PS at 37°C in a humidified incubator (95% air, 5% CO2)

extract_protocol:
Total RNA were extract using HiPure Unviersal RNA Mini Kit (Magen, R4130)
The cDNA libraries were constructed using VAHTS mRNA Capture Beads (N401, Vazyme)+VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina（NR605, Vazyme）following the guidelines of the manufacturers

value: KO

tag: batch


title: Whole blood, KY-0093-01_PETCT2

description:
PCM050
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

value: Male

value: HIV-

tag: disease status

tag: symtoms at_tb_diagnosis

tag: petct definition

tag: subclinical tb

value: Yes

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: Worsening

value: Not globin depleted


title: Whole blood, KY-0093-01_PETCT1

description:
PCM049
batch2_fc_counts.txt

tag: tissue

value: Whole blood

tag: Sex

tag: hiv status

tag: tb history

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

value: Other cold lung lesion

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: SMARTER_233

data_processing: For processing of the reaction on nCounter PrepStation “high sensitivity” setting was used and gene expression data was then obtained on the nCounter™ Digital Analyzer at the “max resolution” setting (1155 FOV).

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: Hek293T,NSP14-2,Day 2

description:
Library name: sample 18
treatment
total-2_count.txt
NSP14-2-1

tag: cell line

tag: cell type

tag: genotype


title: SMARTER_244


title: Whole blood, KY-TBCO-10_W24

description:
PCM048
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

value: Female

value: No

tag: disease status

value: Active TB

tag: symtoms at_tb_diagnosis

value: Symptomatic

value: Positive

tag: petct definition

value: No PETCT

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion


title: EMT6_Control_3

description: Library name: EMT6_WT_3

value: WT

tag: batch


title: EMT6_KO_1

description: Library name: EMT6_KO_1

value: KO