title: M92-2,bhlh58-KO#6-2

description: Library name: Sample 8


title: CirculatingExTcirc_rep1

status: Public on Mar 23 2026

type: SRA

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: Library name: RNA_CirculatingExTcirc_rep1

library_source: transcriptomic

data_processing:
Raw ATAC-seq and RNA-seq reads were trimmed using Trim Galore (v0.6.7) to remove adapters and low-quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (NCBI build 38, mm10) using HISAT2 (v2.2.1).
Aligned reads were sorted and indexed with SAMtools (v1.15).
For ATAC-seq, peaks were called using MACS2 (v2.2.7.1) with FDR = 0.01, window size = 300, and gapsize = 300.
HOMER (v4.11) was used to generate tag directories and annotate peaks to the nearest promoter (annotatePeaks.pl).
HOMER (v4.11) was used to generate tag directories and annotate peaks to the nearest promoter (annotatePeaks.pl).
For RNA-seq, gene-level quantification was performed using StringTie (v3.0.1) with TPM and FPKM normalization.
Assembly: Mus musculus genome, NCBI build 38 (mm10).
Supplementary files format and content: Processed ATAC-seq data include normalized BigWig coverage tracks and peak BED files. Processed RNA-seq data include FPKM expression tables generated by StringTie. Raw sequencing data for both assays are provided as compressed FASTQ files (paired-end reads).

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Mice were maintained under specific pathogen-free conditions with a 12-hour light/dark cycle and were provided with food and water ad libitum.

extract_protocol:
At designated time points (day 49 or day 71 after transfer), circulating ex-TRM cells were isolated from peripheral blood, and tissue TRM and TCIRC cells were sorted from lungs using flow cytometry based on CD45.1/CD45.2, Ly5.1/Ly5.2, and CD69 expression. Sorted cells (3,000–50,000 per population) were pelleted and processed for nuclei isolation using lysis buffer prior to transposition (ATAC-seq) or RNA extraction (RNA-seq).
For ATAC-seq, nuclei were subjected to transposition using the Illumina Tn5 transposase (15027865, 15027866) in a 40 µL reaction for 30 min at 37 °C with shaking. Fragmented DNA was purified with a QIAGEN MinElute kit and PCR-amplified for 11–12 cycles. For RNA-seq, total RNA was extracted from sorted cells and converted into cDNA libraries using a strand-specific RNA-seq kit following the manufacturer’s instructions. All libraries were sequenced on an Illumina NextSeq 500/550 platform with 50-cycle paired-end reads.

treatment_protocol: Recipient C57BL/6 (Ly5.2) or BALB/c-nu/nu mice were sensitized intranasally with OVA to induce allergic airway inflammation. Effector Th2 cells derived from OT-II creER^T2 or DO11.10 TCR transgenic mice were transferred intravenously. Tamoxifen was administered intraperitoneally to induce Cre-mediated recombination, and OVA rechallenge was performed as indicated.

tag: tissue

value: Lung

tag: cell type

value: CD4+ Tcell

tag: age

value: 6-10 weeks old

tag: Sex

value: female

tag: host strain

value: Balb/c


title: time point 3, replicate 7 (treated)

city: Cleveland

first: Kristi

last: Lin-Rahardja

state: OH

address: 10900 Euclid Ave

department: Systems Biology & Bioinformatics

country: USA

institute: Case Western Reserve University

description:
Library name: VDC2_7
column names match library name

data_processing:
concatenate lanes for each sample/replicate (e.g. for WT1 R1, cat L001 and L002; repeat for WT1 R2)
align using STAR alignReads
count using srun featureCounts, saving each result as a .tsv
in R, compile all the separated .tsvs into one matrix
average the sequencing replicates (R1 and R2 per sample), then quantile normalize the counts by group (treated or control) using qsmooth package. Convert ENSEMBL IDs to gene symbols from org.Hs.eg.db
Assembly: using STAR aligner and Homo_sapiens_GRCh38.113
Supplementary files format and content: first column shows gene symbols (translated from ENSEMBL ID to SYMBOL via org.Hs.eg.db), remaining columns represent each sample.
Supplementary files format and content: Each value in the matrix represents the quantile-normalized count for that gene+sample

organism: Homo sapiens

source_name: bone

growth_protocol: allow growth to 80-90% confluency before treatment period (G1) and after treatment period (G2). Cells will be sampled for RNA extraction and drug screening after G2 is complete.

extract_protocol:
Qiagen Allprep kit used for all extraction
STAR aligner was used to align and count reads

treatment_protocol: Expose R1-7 to EC70 of VDC or EC for 5 days. Initial date of exposure counts as day 1. At day 5, drugged medium will be removed, cells will be washed with PBS, and drug-free medium will be replaced for G2.

value: bone

tag: cell line

value: Ewings sarcoma

tag: genotype

tag: treatment

value: VDC-EC

tag: time


title: TT-chem Seq, 1h RNAPIi, biol rep2

city: Munich

first: Julian

last: Stingele

address: Butenandtstraße 1

country: Germany

institute: LMU Munich

description:
Library name: TTchem_RNAPIi_1h_rep2
nascent RNA-Seq
bigwig files split by strand

library_source: other

data_processing:
The samples were demultiplexed using an in-house tool based on their dual barcodes.
A sequencing quality profile was generated using FastQC (version 0.11.9). If needed, sequences were trimmed using TrimGalore (version 0.6.5).
Reads were aligned to a combined genome from GCA_000001405.15_GRCh38_no_alt_analysis_set and Saccharomyces_cerevisiae.R64-1-1.dna.toplevel using STAR (version 2.7.7a/gcc-8.3.1) with settings –outFIlterMultimapNmax 20 and –outSAMmultNmax 1 to allow mapping of repetitive transcripts such as rRNA. .
Bam files were converted into stranded TagDirectories and spike-normalized University of California Santa Cruz (UCSC) genome tracks using Hypergeometric Optimization of Motif EnRichment tools (HOMER; version 4.8.2)
Example genome tracks were generated in Integrative Genomics Viewer (IGV; version 2.4.3). For all gene, tRNA and rRNA lists, read-density within coordinates were defined using the AnnotatePeaks.pl tool of HOMER and subsequently normalized to spike-in reads.
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set and Saccharomyces_cerevisiae.R64-1-1.dna.toplevel
Supplementary files format and content: bigwig files split by strand

molecule: other

growth_protocol: HAP1 cells were cultured in IMDM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin-Glutamine at 37°C and 5% CO2.

extract_protocol:
Cells were washed with PBS and lysed in TRIzol. 1.2µg spike-in RNA was added per 10 million cells, resulting in addition of ~1% spike RNA per condition. RNA was isolated by TRIzol–chloroform isolation and ethanol precipitation.
400 μg RNA (in a total volume of 116 μl) was fragmented by adding 4 μl 5 M NaOH and incubating on ice for 30 min, then stopped by addition of 80 μl of 1 M Tris pH 7 and cleaned up twice using the Micro Bio-Spin P-30 Gel Columns (Bio-Rad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4-SU residues was performed in a total volume of 250 μl, containing 10 mM Tris–HCl pH 7.4, 1 mM EDTA and 5 µg of MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at RT in the dark, followed by phenol–chloroform extraction and elution in 50ul water. 300 µg RNA (37.5 µl) was denatured by 10 min incubation at 65 °C and added to 100 μl μMACS Streptavidin MicroBeads (Milentyl, 130-074-101). RNA was incubated with beads for 15 min at RT and beads were applied to a μColumn in the magnetic field of a μMACS magnetic separator. The beads were washed three times with 55 °C pulldown wash buffer (100 mM Tris–HCl pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween-20). Biotinylated RNA was eluted twice by addition of 100 mM DTT and cleaned up using the RNeasy MinElute kit (Qiagen, 74204) using 1,050 μl ethanol (≥99%) per 200 μl reaction after addition of 700 μl of RLT buffer to precipitate RNA of less than 200 nucleotides. 50 to 1300 ng of the purified 4SU-labelled RNA was then used as input for in-house stranded RNA library prep, similar to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB #E7760) without rRNA depletion. The library was amplified with ten PCR cycles and quality-control checked on the TapeStation (Agilent) using the High Sensitivity DNA Kit before pooling.

treatment_protocol: Cells treated or not for 1h or 5h with 1uM RNAPI inhibitor  (BMH-21), 100uM RNAPII inhibitor (DRB) or 20uM RNAPIII inhibitor (ML-60218). During the last 30 minutes 1mM 4-SU was added.

value: near-haploid derivative of KBM-7

value: WT

value: 1h RNAPIi + 4-SU


title: TT-chem Seq, untreated, biol rep2

description:
Library name: TTchem_untreated_rep2
nascent RNA-Seq
bigwig files split by strand

value: untreated + 4-SU


title: TT-chem Seq, untreated, biol rep1

description:
Library name: TTchem_untreated_rep1
nascent RNA-Seq
bigwig files split by strand


title: TT-chem Seq, 5h RNAPIi, biol rep1

description:
Library name: TTchem_RNAPIi_5h_rep1
nascent RNA-Seq
bigwig files split by strand

value: 5h RNAPIi + 4-SU


title: TT-chem Seq, 5h RNAPIi, biol rep2

description:
Library name: TTchem_RNAPIi_5h_rep2
nascent RNA-Seq
bigwig files split by strand


title: time point 3, replicate 6 (treated)

description:
Library name: VDC2_6
column names match library name


title: TT-chem Seq, 1h RNAPIi, biol rep1

description:
Library name: TTchem_RNAPIi_1h_rep1
nascent RNA-Seq
bigwig files split by strand


title: TissueExTcirc_rep2

description: Library name: RNA_TissueExTcirc_rep2


title: TissueExTcirc_rep1

description: Library name: RNA_TissueExTcirc_rep1


title: TT-chem Seq, 5h RNAPIIi, biol rep2

description:
Library name: TTchem_RNAPIIi_5h_rep2
nascent RNA-Seq
bigwig files split by strand

value: 5h RNAPIIi + 4-SU


title: TissueExTRM_rep2

description: Library name: RNA_TissueExTRM_rep2


title: TT-chem Seq, 5h RNAPIIi, biol rep1

description:
Library name: TTchem_RNAPIIi_5h_rep1
nascent RNA-Seq
bigwig files split by strand


title: time point 3, replicate 4 (treated)

description:
Library name: VDC2_4
column names match library name


title: TT-chem Seq, 1h RNAPIIi, biol rep1

description:
Library name: TTchem_RNAPIIi_1h_rep1
nascent RNA-Seq
bigwig files split by strand

value: 1h RNAPIIi + 4-SU


title: TRM_rep2

description: Library name: ATAC_TRM_rep2

library_source: genomic

molecule: genomic DNA


title: TT-chem Seq, 5h RNAPIIIi, biol rep1

description:
Library name: TTchem_RNAPIIIi_5h_rep1
nascent RNA-Seq
bigwig files split by strand

value: 5h RNAPIIIi + 4-SU


title: TT-chem Seq, 5h RNAPIIIi, biol rep2

description:
Library name: TTchem_RNAPIIIi_5h_rep2
nascent RNA-Seq
bigwig files split by strand


title: time point 3, replicate 3 (treated)

description:
Library name: VDC2_3
column names match library name


title: time point 3, replicate 5 (treated)

description:
Library name: VDC2_5
column names match library name


title: TT-chem Seq, 1h RNAPIIIi, biol rep2

description:
Library name: TTchem_RNAPIIIi_1h_rep2
nascent RNA-Seq
bigwig files split by strand

value: 1h RNAPIIIi + 4-SU


title: TT-chem Seq, no 4SU, biol rep2

description:
Library name: TTchem_NON4SU_rep2
nascent RNA-Seq
bigwig files split by strand

value: no 4-SU


title: TRM_rep1

description: Library name: ATAC_TRM_rep1

value: Lung

value: CD4+ Tcell


title: EndogenousExTcirc_rep2_ATAC

description: Library name: ATAC_EndogenousExTcirc_rep2

value: 6-10 weeks old

value: female


title: time point 2, replicate 10 (control)

description:
Library name: EC1_10
column names match library name

value: bone

value: DMSO


title: time point 3, replicate 1 (treated)

description:
Library name: VDC2_1
column names match library name

value: Ewings sarcoma

value: VDC-EC


title: CirculatingExTRM_rep2_ATAC

description: Library name: ATAC_CirculatingExTRM_rep2

value: Balb/c


title: EndogenousExTcirc_rep1_ATAC

description: Library name: ATAC_EndogenousExTcirc_rep1


title: TT-chem Seq, 1h RNAPIIi, biol rep2

description:
Library name: TTchem_RNAPIIi_1h_rep2
nascent RNA-Seq
bigwig files split by strand

value: near-haploid derivative of KBM-7

value: WT


title: TT-chem Seq, no 4SU, biol rep1

description:
Library name: TTchem_NON4SU_rep1
nascent RNA-Seq
bigwig files split by strand


title: HAP1 cells, aza-C + GCN2i  treated, monosome, biol rep1

description:
Library name: HAP1_azaC_GCN2i_monosome_rep1
Sample in merged_conversion_statistics.csv: 2A_mono

data_processing:
Samples were demultiplexed using an in-house tool based on their dual barcodes and trimmed with cutadapt (version 5.0).
tRNA and rRNA sequences  were removed using bowtie2 (version 2.5.0). Remaining reads were aligned with STAR (version 2.7.10b) using the GRCh38 human reference genome and the associated gene annotations from Ensembl (GRCh18.p13).
Nucleotide conversion analysis was performed as previously described based on customized python scripts (Zhao et al, 2023). Reads containing nucleotide conversions were identified from BAM alignment files using a previously generated VCF file annotating HAP1 specific deviations from the hg38 annotation based on RNAseq data from three untreated samples (Zhao et al, 2023). If the site of conversion corresponded to a known SNP in the VCF file, these reads were ignored. The position of the remaining nucleotide conversions in the reads of standard ribosome footprints (30nt) were counted.
Assembly: GRCh38
Supplementary files format and content: csv file with nucleotide conversion statistics
Library strategy: Ribo-Seq

extract_protocol:
After treatment cells were washed with ice-cold PBS supplemented with 10 mM MgCl2 and 800 µM cycloheximide. Cells were scraped in 100 µL 5x lysis buffer (0,25 M HEPES (KOH) pH 7.5, 50 mM MgCl2, 1 M KCl, 5% (vol/vol) NP40, 1000 μM cycloheximide) on ice. Lysates were vortexed and clarified by centrifugation for 10 min at 20,000 xg and 4°C. For 120 ng RNA in the lysate, 100 U RNase I were added and incubated on ice for 5 min. Subsequently the lysates were loaded onto 10-50% sucrose density gradient (10 mM Tris pH 7.4, 10 mM MgCl2, 160 mM KCl) and centrifuged in an SW40Ti rotor (Beckman Coulter) at 202,408 x g for 165 minutes. Fractionation was performed using a BioComp Gradient Station and absorption profiles at 260 nm were recorded using a Triax Flow Cell FC-2. Monosome and disome fractions were collected. RNA extraction and size selection (25-35 nt for monosome footprints and 54-68 nt for disome footprints) was performed as decribed previsously (Wagner, Bohlen, Herrmannova et al., 2022).
rRNA depletion and library preparation were performed as decribed previsously (Wagner, Bohlen, Herrmannova et al., 2022).

treatment_protocol: Cells were pre-treated with 1 µM GCN2i for 1 h, followed by 2 h treatment with 20 µM aza-C and GCN2i and 2 h recovery with GCN2i.

value: 1h 1µM GCN2i, 2h 20µM aza-C + GCN2i, 2h GCN2i


title: HAP1 cells, aza-C + GCN2i  treated, disome, biol rep1

description:
Library name: HAP1_azaC_GCN2i_disome_rep1
Sample in merged_conversion_statistics.csv: 2A_di


title: time point 1, replicate 10 (control)

description:
Library name: VDC1_10
column names match library name


title: HAP1 cells, aza-C + GCN2i treated, disome, biol rep2

description:
Library name: HAP1_azaC_GCN2i_disome_rep2
Sample in merged_conversion_statistics.csv: 2B_di


title: CirculatingExTRM_rep1_ATAC

description: Library name: ATAC_CirculatingExTRM_rep1


title: AAVS1, 4h HF, biol rep3

description:
Library name: AAVS1_4h_HF_rep3
Column name in htseq-count: AAVS1_HF_3

data_processing:
The samples were demultiplexed using an in-house tool based on their dual barcodes.
Reads were aligned with STAR (version 2.7.10b) using the GRCh38 human reference genome and the associated gene annotations from Ensembl.
Reads per gene were counted using htseq-count (version 0.9.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts (htseq-count) for each sample.

molecule: polyA RNA

extract_protocol:
Cells were lysed in TRI reagent supplemented with 1% beta-mercaptoethanol. RNA was isolated from cell lysates using the Maxwell RSC 48 miRNA Tissue Kit AS1460 (Fa. Promega)  following manufacturer’s protocols.
Libraries were prepared using the CORALL mRNA-Seq V2 Kit (Fa. Lexogen) following manufacturer’s protocols.

treatment_protocol: Cells were treated or not with 5 uM azaC or 25 nM halofuginone (HF) for 4 hours.

value: 4h 25nM HF


title: GCN2 KO, 4h HF, biol rep3

description:
Library name: GCN2_KO_4h_HF_rep3
Column name in htseq-count: GCN2_KO_HF_3

value: GCN2 KO


title: time point 1, replicate 9 (control)

description:
Library name: VDC1_9
column names match library name


title: HAP1 cells, aza-C + GCN2i treated, monosome, biol rep2

description:
Library name: HAP1_azaC_GCN2i_monosome_rep2
Sample in merged_conversion_statistics.csv: 2B_mono


title: TissueExTRM_rep2_ATAC

description: Library name: ATAC_TissueExTRM_rep2


title: time point 2, replicate 8 (control)

description:
Library name: EC1_8
column names match library name


title: RNF25 KO, 4h HF, biol rep3

description:
Library name: RNF25_KO_4h_HF_rep3
Column name in htseq-count: RNF25_KO_HF_3

value: RNF25 KO


title: TT-chem Seq, 1h RNAPIIIi, biol rep1

description:
Library name: TTchem_RNAPIIIi_1h_rep1
nascent RNA-Seq
bigwig files split by strand

value: 1h RNAPIIIi + 4-SU


title: GCN2 KO, 4h azaC, biol rep3

description:
Library name: GCN2_KO_4h_azaC_rep3
Column name in htseq-count: GCN2_KO_aza-C_3

value: 4h 5uM azaC


title: ZNF598 KO, 4h azaC, biol rep3

description:
Library name: ZNF598_KO_4h_azaC_rep3
Column name in htseq-count: ZNF598_KO_aza-C_3

value: ZNF598 KO


title: time point 1, replicate 8 (control)

description:
Library name: VDC1_8
column names match library name


title: ATAC_OTII_CirculatingExTRM_rep2

description: Library name: OTII_ATAC_CirculatingExTRM_rep2

value: Lung

value: CD4+ Tcell


title: AAVS1, 4h azaC, biol rep3

description:
Library name: AAVS1_4h_azaC_rep3
Column name in htseq-count: AAVS1_aza-C_3


title: time point 1, replicate 7 (treated)

description:
Library name: VDC1_7
column names match library name


title: RNF25 GCN2 DKO, 4h azaC, biol rep3

description:
Library name: RNF25_GCN2_DKO_4h_azaC_rep3
Column name in htseq-count: RNF25_GCN2_DKO_aza-C_3

value: RNF25 GCN2 DKO


title: eS31 K113R, 4h azaC, biol rep3

description:
Library name: eS31_K113R_4h_azaC_rep3
Column name in htseq-count: eS31_K113R_KO_aza-C_3


title: RNF25 GCN2 DKO, untreated, biol rep3

description:
Library name: RNF25_GCN2_DKO_untreated_rep3
Column name in htseq-count: RNF25_GCN2_DKO_non_treated_3

value: untreated


title: TissueExTRM_rep1_ATAC

description: Library name: ATAC_TissueExTRM_rep1

value: 6-10 weeks old

value: female


title: ATAC_OTII_CirculatingExTRM_rep1

description: Library name: OTII_ATAC_CirculatingExTRM_rep1


title: time point 2, replicate 9 (control)

description:
Library name: EC1_9
column names match library name

value: bone

value: Ewings sarcoma

value: DMSO


title: time point 1, replicate 6 (treated)

description:
Library name: VDC1_6
column names match library name

value: VDC-EC


title: eS32_K223R, untreated, biol rep3

description:
Library name: eS32_K223R_untreated_rep3
Column name in htseq-count: eS31_K113R_KO_non_treated_3

value: near-haploid derivative of KBM-7


title: ZNF598 KO, untreated, biol rep3

description:
Library name: ZNF598_KO_untreated_rep3
Column name in htseq-count: ZNF598_KO_non_treated_3


title: time point 1, replicate 4 (treated)

description:
Library name: VDC1_4
column names match library name


title: GCN2 KO, untreated, biol rep3

description:
Library name: GCN2_KO_untreated_rep3
Column name in htseq-count: GCN2_KO_non_treated_3


title: RNF25 KO, 4h azaC, biol rep3

description:
Library name: RNF25_KO_4h_azaC_rep3
Column name in htseq-count: RNF25_KO_aza-C_3


title: ATAC_OTII_TissueExTcirc_rep1

description: Library name: OTII_ATAC_TissueExTcirc_rep1

value: Balb/c


title: AAVS1, untreated, biol rep3

description:
Library name: AAVS1_untreated_rep3
Column name in htseq-count: AAVS1_non_treated_3


title: RNF25 KO, untreated, biol rep3

description:
Library name: RNF25_KO_untreated_rep3
Column name in htseq-count: RNF25_KO_non_treated_3


title: time point 1, replicate 2 (treated)

description:
Library name: VDC1_2
column names match library name


title: RNF25 KO, 4h HF, biol rep2

description:
Library name: RNF25_KO_4h_HF_rep2
Column name in htseq-count: RNF25_KO_HF_2

value: 4h 25nM HF


title: GCN2 KO, 4h HF, biol rep2

description:
Library name: GCN2_KO_4h_HF_rep2
Column name in htseq-count: GCN2_KO_HF_2

value: GCN2 KO


title: AAVS1, 4h HF, biol rep2

description:
Library name: AAVS1_4h_HF_rep2
Column name in htseq-count: AAVS1_HF_2


title: ATAC_OTII_CirculatingExTcirc_rep1

description: Library name: OTII_ATAC_CirculatingExTcirc_rep1


title: ATAC_OTII_CirculatingExTcirc_rep2

description: Library name: OTII_ATAC_CirculatingExTcirc_rep2


title: time point 1, replicate 1 (treated)

description:
Library name: VDC1_1
column names match library name


title: ZNF598 KO, 4h azaC, biol rep2

description:
Library name: ZNF598_KO_4h_azaC_rep2
Column name in htseq-count: ZNF598_KO_aza-C_2


title: ATAC_OTII_TissueExTcirc_rep2

description: Library name: OTII_ATAC_TissueExTcirc_rep2


title: untreated parental CHLA-9 cell line

description:
Library name: WT1
column names match library name


title: RNF25 GCN2 DKO, 4h azaC, biol rep2

description:
Library name: RNF25_GCN2_DKO_4h_azaC_rep2
Column name in htseq-count: RNF25_GCN2_DKO_aza-C_2


title: TRAP1, 4h, 3 uM , Rep 3

city: Palo Alto

first: Steven

last: Corsello

state: California

address: 240 Pasteur Drive

department: Stanford School of Medicine

institute: Stanford University

description:
Library name: TRAP1_4h_3
Column name in processed files is library name

data_processing:
nf-core/rnaseq (3.18.0)
Salmon (1.10.3)
Assembly: hg38
Supplementary files format and content: Tab separated gene counts, columns are library names
Supplementary files format and content: Tab separated gene counts, length scaled, columns are library names
Supplementary files format and content: Tab separeted gene counts, scaled, columns are library names
Supplementary files format and content: Tab separated gene transcripts per million (TPM), columns are library names
Supplementary files format and content: Tab separated transcript counts, columns are library names
Supplementary files format and content: Tab separated transcript per million (TPM), columns are libarary names

growth_protocol: BxPC-3 cells were seeded in 6-well plates in RPMI 1640 with 10% FBS

extract_protocol:
Direct-zol RNA MicroPrep kit (Zymo Research)
Novogene

treatment_protocol: Treated with 3uM TRAP-1, TRAP-1-NegB, TRAP-1-NegP, JQ1, MS78, and DMSO for 2h and 4h timepoints.

value: pancreatic

value: WT


title: eS31 K113R, 4h azaC, biol rep2

description:
Library name: eS31_K113R_4h_azaC_rep2
Column name in htseq-count: eS31_K113R_KO_aza-C_2

value: 4h 5uM azaC


title: CD4TRM_rep2

description: Library name: Hirasawa_2ivnega

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed using Cell Ranger and aligned to mm10.
Gene–barcode matrices were generated based on UMI counts.
Low-quality cells were filtered.
Data were normalized and analyzed using Seurat (PCA, clustering, UMAP).
Differential expression and pathway analyses were performed.
Assembly: Mouse reference genome: NCBI38/mm10.
Supplementary files format and content: Raw sequencing data are provided as paired-end FASTQ files. Processed data include filtered gene-barcode expression matrices (h5), cell metadata tables containing cluster annotations and CD45(iv) status, and normalized expression matrices generated by Seurat.

growth_protocol: OVA-specific TCR-transgenic donor mice (DO11.10 or OT-II) and syngeneic recipient mice (BALB/c or C57BL/6 background) were maintained under specific pathogen-free conditions. Female mice aged 6–22 weeks were used for all experiments.

extract_protocol:
To distinguish tissue-resident from circulating leukocytes, mice were intravenously injected with PE-conjugated anti-CD45 antibody and sacrificed three minutes later. Lungs were perfused with cold PBS via the right ventricle and mechanically dissociated in digestion buffer containing collagenase type III and DNase I. Samples were incubated at 37°C for 30 minutes with agitation. Mononuclear cells were isolated by Percoll density centrifugation and filtered through a 70-μm cell strainer. CD4⁺ T cells were subsequently sorted and subjected to single-cell RNA sequencing.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v3.1 (10X Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end reads.

treatment_protocol: Naïve CD4⁺ T cells from OVA-specific TCR-transgenic mice were cultured under Th2-polarizing conditions in vitro in the presence of IL-2, IL-4, and anti–IFN-γ antibody for six days to generate effector Th2 cells. A total of 2 × 10⁷ effector Th2 cells were intravenously injected into recipient mice. Recipient mice were subsequently challenged intranasally with 100 μg ovalbumin to promote differentiation into memory CD4⁺ T cells and establishment of lung tissue-resident TRM cells.

value: Lung


title: time point 1, replicate 3 (treated)

description:
Library name: VDC1_3
column names match library name


title: TRAP1, 4h, 3 uM , Rep 2

description:
Library name: TRAP1_4h_2
Column name in processed files is library name


title: eS32_K223R, untreated, biol rep2

description:
Library name: eS32_K223R_untreated_rep2
Column name in htseq-count: eS31_K113R_KO_non_treated_2


title: CD4Tcric_rep1

description: Library name: Hirasawa_1ivposi


title: ZNF598 KO, untreated, biol rep2

description:
Library name: ZNF598_KO_untreated_rep2
Column name in htseq-count: ZNF598_KO_non_treated_2

value: ZNF598 KO


title: CD4Tcric_rep2

description: Library name: Hirasawa_2ivposi


title: AAVS1, 4h azaC, biol rep2

description:
Library name: AAVS1_4h_azaC_rep2
Column name in htseq-count: AAVS1_aza-C_2


title: GCN2 KO, untreated, biol rep2

description:
Library name: GCN2_KO_untreated_rep2
Column name in htseq-count: GCN2_KO_non_treated_2


title: TRAP1, 4h, 3 uM , Rep 1

description:
Library name: TRAP1_4h_1
Column name in processed files is library name


title: TRAP1, 2h, 3 uM , Rep 3

description:
Library name: TRAP1_2h_3
Column name in processed files is library name


title: RNF25 KO, untreated, biol rep2

description:
Library name: RNF25_KO_untreated_rep2
Column name in htseq-count: RNF25_KO_non_treated_2

value: RNF25 KO


title: RNF25 KO, 4h azaC, biol rep2

description:
Library name: RNF25_KO_4h_azaC_rep2
Column name in htseq-count: RNF25_KO_aza-C_2


title: RNF25 GCN2 DKO, untreated, biol rep2

description:
Library name: RNF25_GCN2_DKO_untreated_rep2
Column name in htseq-count: RNF25_GCN2_DKO_non_treated_2

value: RNF25 GCN2 DKO

value: untreated


title: AAVS1, untreated, biol rep2

description:
Library name: AAVS1_untreated_rep2
Column name in htseq-count: AAVS1_non_treated_2


title: CD4TRM_rep1

description: Library name: Hirasawa_1ivnega

value: female


title: TRAP1, 2h, 3 uM , Rep 2

description:
Library name: TRAP1_2h_2
Column name in processed files is library name


title: GCN2 KO, 4h azaC, biol rep2

description:
Library name: GCN2_KO_4h_azaC_rep2
Column name in htseq-count: GCN2_KO_aza-C_2


title: isolated living cells from  very aged mouse brain_8

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

description:
Library name: CA_20
10X Genomics Next GEM 3' Gene Expression v3

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software count pipeline v.9.0.1.
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
After euthanasia, mice were transcardially perfused with ice-cold PBS, and brains were immediately collected into ice-cold PBS. For the scRNA-seq experiment, brains were obtained from young and aged mice, with n = 5 per group. The brains were then washed in ice-cold PBS and cut into ~1 mm pieces. Single-cell suspensions for scRNA-seq were generated by adapting the authors’ brain flow-cytometry dissociation protocol. In the base protocol, the olfactory bulb, cerebellum, and brainstem were removed, and meningeal vessels were stripped by rolling the brain on Whatman paper. The tissue was finely chopped, and enzymatic digestion was performed using 50 μL collagenase, 2 μL elastase, 2 μL dispase I, and 3 μL hyaluronidase for 45 min at 37°C in a rotating incubator. Following digestion, the tissue was mechanically dissociated by pipetting with 10 mL and 5 mL pipettes, filtered through 100 μm and subsequently 30 μm nylon mesh, and centrifuged. For cleanup, Debris Removal Solution (Miltenyi Biotec) was used. In the flow-cytometry protocol, cells were resuspended in 3.1 mL PBS, 0.9 mL Debris Removal Solution was added, and the mixture was inverted five times to mix. The suspension was then slowly overlaid with 4 mL PBS and centrifuged at 3000 × g for 10 min. After centrifugation, the top buffer layer and the white myelin–debris interphase were removed, and the pelleted cells were washed in PBS and centrifuged again at 1000 × g for 10 min at 4°C. The scRNA-seq section confirms that digestion and purification using Debris Removal Solution were performed, although every enzyme quantity and centrifugation parameter was not explicitly restated; therefore, these values were inferred from the referenced flow-cytometry protocol that was adapted. After cleanup for scRNA-seq, the cell pellet was resuspended in PBS + 0.1% BSA and stained with SYTOX Green to identify live cells. The suspension was then subjected to low-pressure FACS using the WOLF Cell Sorter (NanoCellect) to remove debris and dead cells and to enrich for viable cells. Cells were maintained on ice pending sequencing. After sorting, cells were centrifuged at 2200 rpm for 10 min at 4°C and finally resuspended in 30–50 μL of 0.04% BSA, with the volume adjusted according to the number of recovered cells.
Following cell sorting, the recovered viable cells were processed using a droplet-based single-cell RNA sequencing workflow on the Chromium platform (10x Genomics). In this system, individual cells were partitioned into nanoliter-scale droplets together with barcoded gel beads to generate gel bead-in-emulsion (GEM) partitions. Within each GEM, cell lysis occurred and reverse transcription was carried out, allowing newly synthesized cDNA molecules to be labeled with both a unique molecular identifier (UMI) and a cell-specific barcode. This barcoding strategy enabled transcripts originating from individual cells to be distinguished during downstream analysis. After reverse transcription, the GEMs were broken and the pooled barcoded cDNA was recovered and purified. The resulting cDNA was then amplified through PCR to generate sufficient material for library preparation. Amplified cDNA products were subsequently processed through a series of enzymatic steps to generate sequencing-compatible fragments. During this stage, cDNA molecules were fragmented and end-repaired to produce fragments of an appropriate size distribution for sequencing. Fragmented DNA was then subjected to adaptor ligation so that sequencing adaptors required for Illumina sequencing platforms were incorporated. Following adaptor ligation, additional purification and size-selection steps were performed to remove small fragments, adaptor dimers, and other reaction by-products. The adaptor-ligated DNA fragments were then amplified through sample index PCR to introduce sample-specific index sequences and to produce the final sequencing-ready library. These index sequences enabled multiplexing of multiple samples within the same sequencing run while maintaining the ability to demultiplex reads during data processing. After library amplification, final cleanup and size-selection steps were performed to ensure a consistent fragment size distribution and to remove residual primers or adaptor fragments. Library quality and fragment size distribution were then assessed using capillary electrophoresis-based quality control. Libraries were quantified, pooled according to molar concentration, and prepared for sequencing.

value: brain

value: multiple

value: wild-type  p16- 3MR mouse

value: male

value: 21-32 months

tag: batch


title: isolated living cells from  very aged mouse brain_7

description:
Library name: CA_19
10X Genomics Next GEM 3' Gene Expression v3


title: isolated living cells from  very aged mouse brain_6

description:
Library name: CA_18
10X Genomics Next GEM 3' Gene Expression v3


title: RNF25 KO, 4h HF, biol rep1

description:
Library name: RNF25_KO_4h_HF_rep1
Column name in htseq-count: RNF25_KO_HF_1

value: near-haploid derivative of KBM-7


title: ZNF598 KO, 4h azaC, biol rep1

description:
Library name: ZNF598_KO_4h_azaC_rep1
Column name in htseq-count: ZNF598_KO_aza-C_1


title: eS31 K113R, 4h azaC, biol rep1

description:
Library name: eS31_K113R_4h_azaC_rep1
Column name in htseq-count: eS31_K113R_KO_aza-C_1


title: isolated living cells from  very aged mouse brain_4

description:
Library name: CA_16
10X Genomics Next GEM 3' Gene Expression v3


title: GCN2 KO, 4h HF, biol rep1

description:
Library name: GCN2_KO_4h_HF_rep1
Column name in htseq-count: GCN2_KO_HF_1

value: 4h 25nM HF


title: AAVS1, 4h HF, biol rep1

description:
Library name: AAVS1_4h_HF_rep1
Column name in htseq-count: AAVS1_HF_1


title: RNF25 GCN2 DKO, 4h azaC, biol rep1

description:
Library name: RNF25_GCN2_DKO_4h_azaC_rep1
Column name in htseq-count: RNF25_GCN2_DKO_aza-C_1


title: isolated living cells from  very aged mouse brain_5

description:
Library name: CA_17
10X Genomics Next GEM 3' Gene Expression v3


title: TRAP1, 2h, 3 uM , Rep 1

description:
Library name: TRAP1_2h_1
Column name in processed files is library name


title: RNF25 KO, 4h azaC, biol rep1

description:
Library name: RNF25_KO_4h_azaC_rep1
Column name in htseq-count: RNF25_KO_aza-C_1


title: TRAP-1-NegP, 4h, 3 uM , Rep 2

description:
Library name: TRAP-1-NegP_4h_2
Column name in processed files is library name


title: TRAP-1-NegP, 4h, 3 uM , Rep 1

description:
Library name: TRAP-1-NegP_4h_1
Column name in processed files is library name


title: AAVS1, 4h azaC, biol rep1

description:
Library name: AAVS1_4h_azaC_rep1
Column name in htseq-count: AAVS1_aza-C_1


title: eS31_K113R, untreated, biol rep1

description:
Library name: eS31_K113R_untreated_rep1
Column name in htseq-count: eS31_K113R_KO_non_treated_1


title: GCN2 KO, 4h azaC, biol rep1

description:
Library name: GCN2_KO_4h_azaC_rep1
Column name in htseq-count: GCN2_KO_aza-C_1

value: GCN2 KO


title: TRAP-1-NegP, 2h, 3 uM , Rep 3

description:
Library name: TRAP-1-NegP_2h_3
Column name in processed files is library name

value: pancreatic


title: isolated living cells from  very aged mouse brain_2

description:
Library name: CA_14
10X Genomics Next GEM 3' Gene Expression v3


title: ZNF598 KO, untreated, biol rep1

description:
Library name: ZNF598_KO_untreated_rep1
Column name in htseq-count: ZNF598_KO_non_treated_1


title: RNF25 GCN2 DKO, untreated, biol rep1

description:
Library name: RNF25_GCN2_DKO_untreated_rep1
Column name in htseq-count: RNF25_GCN2_DKO_non_treated_1


title: isolated living cells from  very aged mouse brain_1

description:
Library name: CA_13
10X Genomics Next GEM 3' Gene Expression v3


title: TRAP-1-NegP, 4h, 3 uM , Rep 3

description:
Library name: TRAP-1-NegP_4h_3
Column name in processed files is library name

value: WT


title: TRAP-1-NegP, 2h, 3 uM , Rep 2

description:
Library name: TRAP-1-NegP_2h_2
Column name in processed files is library name


title: AAVS1, untreated, biol rep1

description:
Library name: AAVS1_untreated_rep1
Column name in htseq-count: AAVS1_non_treated_1


title: TRAP-1-NegP, 2h, 3 uM , Rep 1

description:
Library name: TRAP-1-NegP_2h_1
Column name in processed files is library name


title: RNF25 KO, untreated, biol rep1

description:
Library name: RNF25_KO_untreated_rep1
Column name in htseq-count: RNF25_KO_non_treated_1


title: isolated living cells from  aged mouse brain_4

description:
Library name: CA_12
10X Genomics Next GEM 3' Gene Expression v3

value: 18-20 months


title: isolated living cells from  very aged mouse brain_3

description:
Library name: CA_15
10X Genomics Next GEM 3' Gene Expression v3


title: isolated living cells from  aged mouse brain_3

description:
Library name: CA_11
10X Genomics Next GEM 3' Gene Expression v3


title: GCN2 KO, untreated, biol rep1

description:
Library name: GCN2_KO_untreated_rep1
Column name in htseq-count: GCN2_KO_non_treated_1


title: PASMC+siGATA6 CM 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description:
Library name: siGATA6 3
Gene expression from HPASMCs treated with conditioned medium from HPAECs treated with siRNA targeting GATA6 (siGATA6).

data_processing:
FASTQ files were aligned to human genome build hg38 using STAR (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 112 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.32.0).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: hg38
Supplementary files format and content: counts.txt: 63103 x 6 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 63103 x 6 matrix of variance-stabilizing-transformed (VST) expression values

source_name: Human pulmonary artery smooth muscle cells (HPASMCs)

growth_protocol: Human pulmonary arterial endothelial cells (HPAECs) were purchased from Cell Applications (302-05a) and were cultured in complete endothelial cell growth medium MV2 (Promocell, C-22221) along with its supplements (Promocell, C-39221). HPASMCs were provided by the University of Pittsburgh Vascular Medicine Institute Cell Processing Core.  HPASMCs were maintained in complete LONZA growth media with SMGM-2 supplement, 100 U/mL penicillin, and 0.1 mg/mL streptomycin.  HPASMCs were grown to 80% confluency and growth arrested for 18 hours in the serum-free media supplemented with 0.1% BSA.

extract_protocol:
TRIzol (15596026, Fisher) was used to isolate RNA from HPAECs and mouse endothelial cells. RNA was isolated using the Zymo Quick-RNA Miniprep Kit (R1055, Zymo), following the manufacturer’s recommendations.
Libraries were prepared using the Illumina Stranded mRNA Prep kit according to the manufacturer's protocol.

treatment_protocol: Eighty percent confluent HPAECs were transfected with 10nM of siRNA GATA6 or control scrambled siRNA using Lipofectamine for 24 hours in endothelial cell growth medium MV2. The medium was changed to serum-free media with 0.1% BSA and is referred to as conditioned medium. This conditioned medium was collected after 24hrs. The HPASMCs were grown to 80% confluency, growth arrested for 18 hours in the serum-free media supplemented with 0.1% BSA, treated for 24 hours with medium conditioned by HPAECs transfected with siRNA scrambled or siRNA GATA6, and harvested for RNA analysis. The growth arrested HPASMCs were treated for 24 hours with medium conditioned by HPAECs transfected with siRNA scrambled or siRNA GATA6, and harvested for RNA analysis.

tag: sirna


title: PASMC+siGATA6 CM 2

description:
Library name: siGATA6 2
Gene expression from HPASMCs treated with conditioned medium from HPAECs treated with siRNA targeting GATA6 (siGATA6).

value: Human pulmonary artery smooth muscle cells (HPASMCs)


title: PASMC+siScr CM2

description:
Library name: siScr 2
Gene expression from HPASMCs treated with conditioned medium from HPAECs treated with scrambled control siRNA (siScr).

value: siScr


title: PASMC+siGATA6 CM1

description:
Library name: siGATA6 1
Gene expression from HPASMCs treated with conditioned medium from HPAECs treated with siRNA targeting GATA6 (siGATA6).


title: PASMC+siScr CM3

description:
Library name: siScr 3
Gene expression from HPASMCs treated with conditioned medium from HPAECs treated with scrambled control siRNA (siScr).


title: isolated living cells from  aged mouse brain_2

description:
Library name: CA_10
10X Genomics Next GEM 3' Gene Expression v3


title: isolated living cells from  aged mouse brain_1

description:
Library name: CA_9
10X Genomics Next GEM 3' Gene Expression v3


title: PASMC+siScr CM1

description:
Library name: siScr 1
Gene expression from HPASMCs treated with conditioned medium from HPAECs treated with scrambled control siRNA (siScr).


title: isolated living cells from middle aged mouse brain_4

description:
Library name: CA_8
10X Genomics Next GEM 3' Gene Expression v3

value: 10-17 months


title: MCF7 SALSa (119) 6 hours replicate b

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: Fermin Caballero 56, 3D

country: Spain

institute: CNIO

description: Library name: SALSa b

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
salmon was used for the pseudoaligment of raw reads
tximport was used to process salmon tpms
Assembly: GRCh38/hg38
Supplementary files format and content: Normalized counts and results tables from salmon and DESeq2, respectively, in a single MS Excel sheet.

growth_protocol: MCF7 cells were grown  at 37°C, 5% CO2, in high glucose DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS), 1% glutamine and 1% Penicillin/Streptomycin

extract_protocol:
RNA was purified by using absolutely RNA kit from Agilent.
Total RNA samples (300ng) were used as provided by the user. RNA Quality scores were 9.9 on average (range 9.0-10) when assayed on a PerkinElmer LabChip analyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: MCF7 cell were tretated with 10 µM of SALSa (119) for 6 hours.

value: SALSa (119)


title: TRAP-1-NegB, 2h, 3 uM , Rep 3

description:
Library name: TRAP-1-NegB_2h_3
Column name in processed files is library name


title: MCF7 SALSa (119) 6 hours replicate a

description: Library name: SALSa a


title: TRAP-1-NegB, 4h, 3 uM , Rep 3

description:
Library name: TRAP-1-NegB_4h_3
Column name in processed files is library name


title: TRAP-1-NegB, 4h, 3 uM , Rep 1

description:
Library name: TRAP-1-NegB_4h_1
Column name in processed files is library name


title: TRAP-1-NegB, 4h, 3 uM , Rep 2

description:
Library name: TRAP-1-NegB_4h_2
Column name in processed files is library name


title: MCF7 Mock 6 hours, replicate b

description: Library name: untreated b


title: TRAP-1-NegB, 2h, 3 uM , Rep 2

description:
Library name: TRAP-1-NegB_2h_2
Column name in processed files is library name


title: isolated living cells from middle aged mouse brain_3

description:
Library name: CA_7
10X Genomics Next GEM 3' Gene Expression v3


title: BTF3-auxin_ctrl_rep_1

city: Heidelberg

first: Manuel

last: Günnigmann

address: Im Neuenheimer Feld 282

institute: ZMBH

description: Library name: Sample17

data_processing:
Raw NextSeq550 sequencing files were converted with bcl2fastq2 conversion software (v2.20) to obtain single fastq files per indexed sample using following command: bcl2fastq -p16 -r4 -w4 --no-lane-splitting -R <path_to_input_folder> -o <path_to_output_folder>
3' adaptor sequences were trimmed with Cutadapt (v1.13). For samples 15-18, the following Cutadapt command was used: cutadapt --nextseq-trim=20 -q20 -m23 -j6 --discard-untrimmed -O6 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz ; Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (published in Bertolini et al. 2021). For samples 15-18 The following command was used: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 10.
For removal of rRNA contaminants, sequenced libraries were aligned to human rRNA sequences including: RNA45SN1 - RNA45SN5 (human 28S, 18S, 5.8S), RNA5S1 (human 5S), MTRNR2L10 (Mito 16S), MT-RNR1 (Mito 12S), MT-RNR2U1 (Mito 16S), 22 mito tRNAs, 631 nuclear human tRNAs. Mapping against rRNA contaminants was performed using Bowtie2 (v.2.3.5.1) with the following command: bowtie2 -p4 -t -x <path_to_folder_with_Bowtie-indexed_rRNA_contamination> -q <path_to_input_file>.fastq.gz' --un <path_to_output_file>.fastq -S /dev/null
Reads that did not align to rRNA were aligned to the human genome (GRCh38p10) using STAR (v2.7.1a) with the following command: STAR --runThreadN 24 --genomeDir <path_to_indexed_genome> --readFilesIn <path_to_input>.fastq --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix <path_to_output> --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
All reads aligning to the coding sequence (CDS) were assigned (a-, p-, e-site) via a custom Julia script (published in Bertolini et al. 2021). p-site assigned reads were used for all downstream analysis.This script accounts for soft-clipping via the '-c 1' option: the integer indicates the bases at the 5' end that often arise from untemplated addition by the reverse transcriptase during library preparation by using the following command: julia <path_to_script>/Script2.jl -c 1 -g <path_to_genome_annotation>.gff' -u -o <path_to_output> <path_to_input>.bam
Assembly: Human genome (GRCh38p10)
Supplementary files format and content: Processed data are stored in HDF5 files. Each HDF5 file contains one data set per gene. Each data set consists of a 2-row matrix, with the first row containing the 1-based position within the CDS, and the second row the number of detected P-site reads at this position. Additional information is stored in the data set attributes, including: gene and protein names, transcript isoform used for position assignment, length of the coding sequence, chromosome and strand location of the gene. In this study the p-side assignments stored in such HDF5 files were further analyzed using RiboSeqTools (available at: https://github.com/ilia-kats/RiboSeqTools)
Library strategy: Ribo-Seq

source_name: Embrionic Kidney

growth_protocol: HEK293-T cells (DSMZ Cat# ACC 635) were cultured in humidified 37°C with 5% CO2 using high glucose DMEM media containing GlutaMAX™ and pyruvate (Gibco) supplemented with 10% heat-inactivated FCS (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco). Cells were seeded on 10 cm dishes 48 hours prior to harvest to ensure an 70–80% confluency was reached at the time of collection.

extract_protocol:
RNA from ribosome fractions was extracted using hot acid phenol extraction as described in Günnigmann et al. 2023.
For samples 15-18, ribosome profiling libraries were prepared as described in Koubek et al. 2025 (Nucleic Acids Res).

treatment_protocol: For samples 15-16; Cells were treated with 100 μg/mL indole-3-acetic acid sodium (Santa Cruz, sc-215171) for 9 hours prior to harvesting.

value: Embrionic Kidney

value: GS linker-miniIAA7-GFP11 sequence was inserted at residue 176 of endogenous BTF3 via CRISPR/Cas9-mediated homology-directed repair in cells stably expressing AtAFB4


title: isolated living cells from middle aged mouse brain_1

description:
Library name: CA_5
10X Genomics Next GEM 3' Gene Expression v3

value: brain


title: isolated living cells from middle aged mouse brain_2

description:
Library name: CA_6
10X Genomics Next GEM 3' Gene Expression v3

value: multiple


title: BTF3-auxin_9h_rep_2

description: Library name: Sample16

value: GS linker-miniIAA7-GFP11 sequence was inserted at residue 176 of endogenous BTF3 via CRISPR/Cas9-mediated homology-directed repair in cells stably expressing AtAFB3

value: Cells were treated with 100 μg/mL indole-3-acetic acid sodium (Santa Cruz  sc-215171) for 9 hours prior to harvesting


title: BTF3-auxin_9h_rep_1

description: Library name: Sample15

value: GS linker-miniIAA7-GFP11 sequence was inserted at residue 176 of endogenous BTF3 via CRISPR/Cas9-mediated homology-directed repair in cells stably expressing AtAFB2


title: TRAP-1-NegB, 2h, 3 uM , Rep 1

description:
Library name: TRAP-1-NegB_2h_1
Column name in processed files is library name


title: BTF3-auxin_ctrl_rep_2

description: Library name: Sample18

value: GS linker-miniIAA7-GFP11 sequence was inserted at residue 176 of endogenous BTF3 via CRISPR/Cas9-mediated homology-directed repair in cells stably expressing AtAFB5


title: Soluble_sample_for_SolubleRP_replicate2

description: Library name: Sample14

data_processing:
Raw NextSeq550 sequencing files were converted with bcl2fastq2 conversion software (v2.20) to obtain single fastq files per indexed sample using following command: bcl2fastq -p16 -r4 -w4 --no-lane-splitting -R <path_to_input_folder> -o <path_to_output_folder>
3' adaptor sequences were trimmed with Cutadapt (v1.13). For samples 5-14, the following Cutadapt command was used: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz ; For samples 1-4, the following Cutadapt command was used: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a TGGAATTCTCGGGTGCCAAGG -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz ; Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (published in Bertolini et al. 2021). For samples 5-10, the following command was used: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 2 ; For samples 11-14, the following command was used: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 5 ; For samples 1-4, the following command was used: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 4 --umi5 4
For removal of rRNA contaminants, sequenced libraries were aligned to human rRNA sequences including: RNA45SN1 - RNA45SN5 (human 28S, 18S, 5.8S), RNA5S1 (human 5S), MTRNR2L10 (Mito 16S), MT-RNR1 (Mito 12S), MT-RNR2U1 (Mito 16S), 22 mito tRNAs, 631 nuclear human tRNAs. Mapping against rRNA contaminants was performed using Bowtie2 (v.2.3.5.1) with the following command: bowtie2 -p4 -t -x <path_to_folder_with_Bowtie-indexed_rRNA_contamination> -q <path_to_input_file>.fastq.gz' --un <path_to_output_file>.fastq -S /dev/null
Reads that did not align to rRNA were aligned to the human genome (GRCh38p10) using STAR (v2.7.1a) with the following command: STAR --runThreadN 24 --genomeDir <path_to_indexed_genome> --readFilesIn <path_to_input>.fastq --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix <path_to_output> --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
All reads aligning to the coding sequence (CDS) were assigned (a-, p-, e-site) via a custom Julia script (published in Bertolini et al. 2021). p-site assigned reads were used for all downstream analysis.This script accounts for soft-clipping via the '-c 1' option: the integer indicates the bases at the 5' end that often arise from untemplated addition by the reverse transcriptase during library preparation by using the following command: julia <path_to_script>/Script2.jl -c 1 -g <path_to_genome_annotation>.gff' -u -o <path_to_output> <path_to_input>.bam
Assembly: Human genome (GRCh38p10)
Supplementary files format and content: Processed data are stored in HDF5 files. Each HDF5 file contains one data set per gene. Each data set consists of a 2-row matrix, with the first row containing the 1-based position within the CDS, and the second row the number of detected P-site reads at this position. Additional information is stored in the data set attributes, including: gene and protein names, transcript isoform used for position assignment, length of the coding sequence, chromosome and strand location of the gene. In this study the p-side assignments stored in such HDF5 files were further analyzed using RiboSeqTools (available at: https://github.com/ilia-kats/RiboSeqTools)
Library strategy: Ribo-Seq

growth_protocol: HEK293-T cells (DSMZ Cat# ACC 635) were cultured in humidified 37°C with 5% CO2 using high glucose DMEM media containing GlutaMAX™ and pyruvate (Gibco) supplemented with 10% heat-inactivated FCS (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco). Cells were seeded on 15 cm dishes 18–24 hours prior to harvest to ensure an 80–90% confluency was reached at the time of collection.

extract_protocol:
RNA from ribosome fractions was extracted using hot acid phenol extraction as described in Günnigmann et al. 2023.
For samples 5-14, ribosome profiling libraries were prepared as described in Günnigmann et al. 2023. For samples 1-4, ribosome profiling libraries were prepared using the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer).

value: wild-type


title: MS78, 4h, 3 uM , Rep 3

description:
Library name: MS78_4h_3
Column name in processed files is library name


title: isolated living cells from young mouse brain_4

description:
Library name: CA_4
10X Genomics Next GEM 3' Gene Expression v3

value: wild-type  p16- 3MR mouse

value: male

value: 4-6 months


title: MS78, 4h, 3 uM , Rep 2

description:
Library name: MS78_4h_2
Column name in processed files is library name

value: pancreatic

value: WT


title: Soluble_sample_for_SolubleRP_replicate1

description: Library name: Sample12


title: isolated living cells from young mouse brain_2

description:
Library name: CA_2
10X Genomics Next GEM 3' Gene Expression v3


title: Total_sample_for_SolubleRP_replicate2

description: Library name: Sample13


title: NACA_BTF3_SeRP_from_sucrose_cushion_TT_translatome_replicate2

description: Library name: Sample10


title: isolated living cells from young mouse brain_3

description:
Library name: CA_3
10X Genomics Next GEM 3' Gene Expression v3


title: Total_sample_for_SolubleRP_replicate1

description: Library name: Sample11


title: MS78, 4h, 3 uM , Rep 1

description:
Library name: MS78_4h_1
Column name in processed files is library name


title: isolated living cells from young mouse brain_1

description:
Library name: CA_1
10X Genomics Next GEM 3' Gene Expression v3


title: MCF7 Mock 6 hours, replicate a

description: Library name: untreated a


title: BTF3_SeRP_from_sucrose_cushion_IP_translatome_replicate2

description: Library name: Sample8


title: NACA_BTF3_SeRP_from_sucrose_cushion_TT_translatome_replicate1

description: Library name: Sample9


title: MS78, 2h, 3 uM , Rep 3

description:
Library name: MS78_2h_3
Column name in processed files is library name


title: BTF3_SeRP_from_sucrose_cushion_IP_translatome_replicate1

description: Library name: Sample7


title: JQ1, 4h, 3 uM , Rep 3

description:
Library name: JQ1_4h_3
Column name in processed files is library name


title: BTF3_SeRP_from_lysate_IP_translatome_replicate2

description: Library name: Sample2


title: BTF3_SeRP_from_lysate_TT_translatome_replicate1

description: Library name: Sample3


title: Primary Young mice tumors, wild type 1

city: Washington

first: Jiaxiang

last: Tao

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

description:
Library name: Sample 9
Tumors from yo mice, wild type

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Trimmed reads were mapped to the Mus musculus (mm10) reference genome, using the STAR aligner.
Gene expression quantification was calculated using RSEM algorithm. Data normalization and differential gene expression (DEG) analysis were performed using the DESeq2 package
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Using the Benjamini-Hochberg method for multiple testing adjustment, DEGs were identified as genes with a p-value < 0.05 and fold change of more than 50%. Overrepresentation enrichment analysis (ORA) was performed on DEGs and stratified by the direction of significant change, using ClusterProfiler R package
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample

source_name: tumor

growth_protocol: 6-8 week-old C57BL/6J wild-type mice (RAGE+/+) were purchased from Jackson Laboratory (Bar Harbor, ME, USA) and aged at Georgetown University. C57BL/6J RAGE-knockout mice (RAGE−/ −) were obtained, bred and genotyped. Power analysis for all animal experiments was performed using Statmate 2.0 (Graph Pad software). RAGE+/+ and RAGE-/- mice were aged to 3 and 21 months of age at Georgetown University for all experiments. For orthotopic experiments, 5 × 10⁵ Py8119, AT3 or E0771-LMB  cells were injected in 100 μl sterile PBS with 50% Matrigel into the fourth inguinal mammary fat pad of either wild-type ( RAGE +/+) or RAGE knockout (RAGE -/-) young or aged mice. Primary tumor growth was measured with calipers every three to five days, and tumor volume was calculated using the formula: V = length x width2 x 0.5. All major animal experiments were repeated (pilot with wild-type mice and then larger experiment with wild-type and RAGE knockout).

extract_protocol:
RNA extraction and paired-end RNA sequencing were performed by Novogene. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample

value: tumor

value: primary

value: breast tumor


title: BTF3_SeRP_from_lysate_TT_translatome_replicate2

description: Library name: Sample4

value: Embrionic Kidney


title: Primary Young mice tumors, RAGE KO 2

description:
Library name: Sample 8
Tumors from yo mice, RAGE KO

value: RAGE KO


title: Primary Young mice tumors, wild type 2

description:
Library name: Sample 10
Tumors from yo mice, wild type


title: BTF3_SeRP_from_lysate_IP_translatome_replicate1

description: Library name: Sample1


title: JQ1, 4h, 3 uM , Rep 1

description:
Library name: JQ1_4h_1
Column name in processed files is library name


title: MS78, 2h, 3 uM , Rep 1

description:
Library name: MS78_2h_1
Column name in processed files is library name


title: LIP3

city: Seoul

first: Yun-Sil

last: Lee

address: 1 Gwanak-ro, Gwanak-gu, Bldg 86/Rm 405

department: Department of Molecular Genetics

country: South Korea

institute: Seoul National University

description:
Library name: Sample6
10X Genomics

data_processing:
Sample demultiplexing, alignment to the reference genome, and generation of gene–cell count matrices were performed using the 10x Genomics Cell Ranger pipeline (v9.0.1). Downstream analyses were conducted using Seurat (v5.3.0), including quality control filtering, data normalization, dimensionality reduction, clustering, and cell-type annotation.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Palatal gingiva

growth_protocol: 8 weeks old male C57BL/6 mice were used for the periodontitis-induced ligature experiment.

extract_protocol:
Palatal gingival tissues were collected after cardiac puncture. The gingiva tissue was minced and enzymatically dissociated using sequential trypsin–EDTA, followed by Dispase and Collagenase IV digestion. After enzyme digestion, the cells were filtered through a 40-µm strainer, and washed in PBS containing BSA. Cells were counted, resuspended at the appropriate concentration, and kept on ice prior to 10x Genomics library preparation.
Single-cell suspensions were loaded onto a Chromium Controller (10x Genomics), and libraries were prepared according to the manufacturer’s protocol for the Chromium GEM-X Single Cell 3′ v4 Gene Expression kit, targeting 15,000 cells per sample. Libraries were pooled and sequenced on a NextSeq 2000 system (Illumina) using the read configuration recommended by 10x Genomics.

treatment_protocol: To induce periodontitis, mice were injected intraperitoneally with ketamine (100mg/kg) and xylazine (10mg/kg) and 5-0 black silk (Covidien) was placed bilaterally on the cervical region of the maxillary second molar.

value: Palatal gingiva

value: LIP


title: Primary Young mice tumors, RAGE KO 1

description:
Library name: Sample 7
Tumors from yo mice, RAGE KO


title: MS78, 2h, 3 uM , Rep 2

description:
Library name: MS78_2h_2
Column name in processed files is library name


title: LIP2

description:
Library name: Sample5
10X Genomics


title: Primary Aged mice tumors, wild type 3

description:
Library name: Sample 6
Tumors from old mice, wild type


title: NACA_SeRP_from_sucrose_cushion_IP_translatome_replicate1

description: Library name: Sample5


title: NACA_SeRP_from_sucrose_cushion_IP_translatome_replicate2

description: Library name: Sample6


title: Ctrl2

description:
Library name: Sample2
10X Genomics

value: Ctrl


title: JQ1, 4h, 3 uM , Rep 2

description:
Library name: JQ1_4h_2
Column name in processed files is library name


title: JQ1, 2h, 3 uM , Rep 3

description:
Library name: JQ1_2h_3
Column name in processed files is library name


title: Primary Aged mice tumors, wild type 2

description:
Library name: Sample 5
Tumors from old mice, wild type


title: Ctrl3

description:
Library name: Sample3
10X Genomics


title: Ctrl1

description:
Library name: Sample1
10X Genomics


title: JQ1, 2h, 3 uM , Rep 2

description:
Library name: JQ1_2h_2
Column name in processed files is library name


title: Primary Aged mice tumors, wild type 1

description:
Library name: Sample 4
Tumors from old mice, wild type


title: JQ1, 2h, 3 uM , Rep 1

description:
Library name: JQ1_2h_1
Column name in processed files is library name


title: Primary Aged mice tumors, RAGE KO 3

description:
Library name: Sample 3
Tumors from old mice, RAGE KO


title: DMSO, 4h, Rep 3

description:
Library name: DMSO_4h_3
Column name in processed files is library name

value: DMSO


title: WDA-cells, biopsy samples, Resolution control/DMSO, Resolution RAR agonist

type: RNA

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

description: Mouse 5k Panel

hyb_protocol: Xenium Prime 5K Mouse Pan Tissue and Pathways Assay Kit was used according to manufacturer's instructions

scan_protocol: Spatial transcriptomics was performed using fully automated Xenium Analyzer instrument.

data_processing:
Xenium Onboard Analysis v4.0.1
cell_id for treatment groups: cells_stats.csv
file description: WDA-cells of the biopsy samples, Resolution control/DMSO - 4 weeks resolution control treated, Resolution RAR agonist - 4 weeks resolution treated with AM580

label: Xenium probe set

source_name: liver

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Five-micron tissue sections were cut from FFPE tissue blocks using a microtome and adhered to Xenium slides (10x Genomics).

treatment_protocol: Mice were fed western diet with 20% alcohol in drinking water for 16 weeks. At the end of the feeding a small liver biopsy was collected and mice were placed on chow diet with plain water for 4 weeks. During this time mice were treated with AM580 (5 mg/kg) or vehicle control (DMSO) twice weekly.

value: liver

tag: tissue preservation method

value: FFPE

value: western diet, alcohol and DMSO or RAR agonist


title: LIP1

description:
Library name: Sample4
10X Genomics


title: 3-week Vehicle-Treated Replicate 3 Kidney

city: Ithaca

first: Paula

last: Cohen

address: 618 Tower Rd

institute: Cornell University

description: Library name: JQ3WTC3K

data_processing:
fastp (v0.20.1)
Salmon (v1.10.0) in quasi-mapping mode
Assembly: Mouse mm10
Supplementary files format and content: quant.sf Salmon output

source_name: Kidney

extract_protocol:
Total RNA was extracted from frozen liver and kidney samples using TRIzol Reagent (Thermo Fisher Scientific, 15596018) following the TREx RNA Extraction Protocol v1.8 (Cornell University Transcription Regulation and Expression Facility). After tissue homogenization, chloroform was added to promote phase separation of RNA from DNA and protein, and the aqueous phase was transferred to Phaselock Gel tubes (VWR 01847‐802) for clean extraction. The RNA was precipitated with isopropanol (molecular biology grade), using GlycoBlue (Thermo AM9515) to enhance recovery. Pellets were washed twice with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA concentration was quantified using a NanoPhotometer N50 (Implen) and RNA integrity assessed with an Agilent 2100 Bioanalyzer. Libraries were generated using the NEBNext UltraExpress RNA Library Prep Kit (NEB #E3330), incorporating poly(A) enrichment to select mRNA. Sequencing was performed across one lane of an Illumina NextSeq 2000 using single-end 75 bp reads, targeting ~20-25 million reads per sample. Each experimental group included 3 Treatment samples, 3 Recovery samples, and 4 Control samples per organ (3 Control from the treatment timepoint, 1 from the recovery timepoint).
NEBNext UltraExpress RNA Library Prep Kit (NEB #E3330)

treatment_protocol: JQ1 (50 mg/kg daily, 3 weeks, intraperitoneal) or vehicle control

value: Kidney

value: 10 weeks

tag: strain

value: Vehicle


title: Primary Aged mice tumors, RAGE KO 2

description:
Library name: Sample 2
Tumors from old mice, RAGE KO


title: 3-week Vehicle-Treated Replicate 3 Liver

description: Library name: JQ3WTC3L

source_name: Liver

value: Liver

value: male


title: Lactobacillus delbrueckii subsp. bulgaricus cells,CT

city: qingdao

first: Liang

last: Liu

country: China

institute: Ocean University of China

description: Library name: Sample1

data_processing:
After obtaining sequencing data, the raw data is subjected to data quality control and splitting. We used the official M20 Genomics software VITAseer to perform quality control and splitting on the raw data, obtaining effective Barcode+UMI+cDNA. By using STARsolo to compare cDNA to the reference genome, high-quality quality control results such as cell count, gene count, and genome comparison information can be obtained for sample data.
Assembly: Lactobacillus delbrueckii subsp. bulgaricus

source_name: bacterial cell

extract_protocol:
The L. bulgaricus solution cultured at 37 degrees Celsius for 13 hours in normal MRS medium was used as the control group, and after 13 hours, 0.64mg/ml rifampicin was added and treated for 3 hours to form the experimental group.
Using M20 Genomics VITA series MscRNA seq, prepare a single-cell suspension and immobilize the cells, then add random primers into the single cells. Afterwards, reverse transcription was performed using random primers as the amplification starting point to obtain random RNA segments. Finally, Gel Beads with sequence labels, pre mixed samples and reagents, and oil were loaded into their respective injection channels for cell labeling to obtain a library of single-cell cell markers for microorganisms. Finally, cDNA amplification was performed on the single-cell library to obtain Illumina based library for sequencing.（n=1）

value: bacterial cell


title: Lactobacillus delbrueckii subsp. bulgaricus cells,RFP

description: Library name: Sample2

value: MRS,37degree,13h,then 0.64mg/ml rifampicin  3h


title: Primary Aged mice tumors, RAGE KO 1

description:
Library name: Sample 1
Tumors from old mice, RAGE KO

value: tumor

value: primary

value: breast tumor


title: DMSO, 4h, Rep 2

description:
Library name: DMSO_4h_2
Column name in processed files is library name

value: pancreatic

value: WT


title: 3-week Vehicle-Treated Replicate 2 Liver

description: Library name: JQ3WTC2L


title: 3-week Vehicle-Treated Replicate 1 Liver

description: Library name: JQ3WTC1L


title: DMSO, 4h, Rep 1

description:
Library name: DMSO_4h_1
Column name in processed files is library name


title: mRNAKss3, Treated, biol rep3

city: Chascomús

first: Andrés

middle: Mariano

last: Alonso

state: Buenos Aires

address: Av. Intendente Marino Km 8.2

country: Argentina

institute: INTECH

description:
Library name: Sample 6
Column name in gene_counts.csv: MRNAKss_3

data_processing:
Reads were demultiplexed using Illumina bcl2fastq2 v2.20 with default settings
Quality control of reads for each Illumina library was performed using the FASTQC tool (https://github.com/s-andrews/FastQC)
Adapter trimming and filtering of low-quality reads were carried out using the TrimmGalore software (https://github.com/FelixKrueger/TrimGalore).
Reads were then aligned to the reference genome of T. foetus strain K (ASM183968v1) using the HISAT2 v2.2.1; alignaments were sorted by samtools v1.21 (hisat2 -p 20 --dta -x .. -1 .. -2 .. 2> aln_summary_KSS3.txt| samtools sort -O BAM -@ 20 -o ..)
Transcript quantification was performed following the StringTie protocol (v2.1.7; 10.1038/nprot.2016.095). An alternative step for  the raw count matrix generation was implemented (python prepDE.py -g -i sample_lst.txt)
Assembly: T. foetus strain K (ASM183968v1)
Supplementary files format and content: Output file include gene raw counts in csv format

organism: Tritrichomonas foetus

source_name: K strain

growth_protocol: T. foetus K strain was cultured in Diamond’s  Trypticase-yeast extract-maltose (TYM) medium supplemented with 10% horse serum and 10 U/ml penicillin/10 μg/ml streptomycin (Invitrogen) at pH 6.4. Parasites were grown at 37°C and passed daily.

extract_protocol:
Total RNA from T. foetus parasites (strain K) was extracted using the RNAspin Mini RNA Isolation Kit (GE Healthcare Life Sciences). Three independent RNA samples were obtained from parasites incubated for 48 hours in serum-free culture medium (Treated). As a control, RNA was extracted from parasites cultured under standard conditions with serum suplementation (Untreated). To eliminate genomic DNA contamination, all RNA samples were treated with DNase I (Invitrogen) before Amplification
RNA libraries for RNA-seq were prepared by al Quick Biology Inc. using TruSeq RNA Sample Prep Kit (Illumina).

treatment_protocol: Nutrient deprivation: Parasites (1x106 parasites/ml) were incubated in TYM culture media without maltose and serum supplementation for 48 hrs.

value: K strain

value: under nutrient restriction conditions for 48 hours


title: 3-week Vehicle-Treated Replicate 2 Kidney

description: Library name: JQ3WTC2K


title: DKO_BM

city: Cambridge

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: Library name: DKO_BM

data_processing:
Reads mapped using 10X Cellranger v6.0.1
Assembly: mm10
Supplementary files format and content: .h5 raw counts from cellranger

source_name: bone marrow

extract_protocol: Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) following manufacturer’s protocols

value: bone marrow

value: Female

value: Lin-cKit+

value: KJAJ10.1k_Adh5(tm1a):c/c Adh5 (tm1d):untested Fancd2:hom Vav1 iCre:pos


title: DMSO, 2h, Rep 3

description:
Library name: DMSO_2h_3
Column name in processed files is library name

value: DMSO


title: mRNAKss2, Treated, biol rep2

description:
Library name: Sample 5
Column name in gene_counts.csv: MRNAKss_2


title: 3-week Vehicle-Treated Replicate 1 Kidney

description: Library name: JQ3WTC1K

value: Kidney

value: 10 weeks

value: Vehicle


title: Fancd2_BM

description: Library name: Fancd2_BM

value: KJAJ10.1f_Adh5(tm1a):c/c Adh5 (tm1d):untested Fancd2:hom Vav1 iCre:neg


title: 3-week Treatment Replicate 3 Liver

description: Library name: JQ3WT3L

value: Liver

value: male


title: Adh5_BM

description: Library name: Adh5_BM

value: KJAJ10.1i_Adh5(tm1a):c/c Adh5 (tm1d):untested Fancd2:WT Vav1 iCre:pos


title: mRNAKss1, Treated, biol rep1

description:
Library name: Sample 4
Column name in gene_counts.csv: MRNAKss_1


title: WT_BM

description: Library name: WT_BM

value: KJAJ10.1e_Adh5(tm1a):c/c Adh5 (tm1d):untested Fancd2:WT Vav1 iCre:neg


title: DMSO, 2h, Rep 1

description:
Library name: DMSO_2h_1
Column name in processed files is library name

value: pancreatic


title: mRNAK3, Untreated, biol rep3

description:
Library name: Sample 3
Column name in gene_counts.csv: MRNAK_3

value: incubated in standard culture media


title: 3-week Treatment Replicate 3 Kidney

description: Library name: JQ3WT3K


title: mRNAK2, Untreated, biol rep2

description:
Library name: Sample 2
Column name in gene_counts.csv: MRNAK_2

value: K strain


title: 3-week Treatment Replicate 2 Liver

description: Library name: JQ3WT2L


title: mRNAK1, Untreated, biol rep1

description:
Library name: Sample 1
Column name in gene_counts.csv: MRNAK_1


title: DKO_spleen

description: Library name: DKO_spleen

source_name: spleen

value: spleen

value: Male

value: #10760_Adh5(tm1a):c/c Adh5 (tm1d):untested Fancd2:hom Vav1 iCre:pos


title: VEEV_neuro_106_DPI_batch2

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

description:
Library name: Sample 6
10X Genomics

data_processing:
The raw sequencing reads were trimmed and aligned to the mouse reference genome (mm10) using Cell Ranger (10x genomics, v.8.0.1) and quantified using ‘Cell Ranger count’. The resulting count matrix was further processed using the R package Seurat (v.5.1.0) for quality control and downstream analysis. The following filtering steps were applied to remove low-quality nucleus, nuclei with the number of expressed genes (denoted as nFeature_RNA) over 200 and cellular mitochondrial genes detected < 10% were retained. Based on the 2,000 most variable genes, the normalized scRNA-seq count matrix was used for subsequent PCA analysis. The first 20 PCs were used for uniform manifold approximation and projection (UMAP) and the shared nearest neighbor (SNN) computation.  The harmony package (v1.2.1) was adopted to remove batch effects among samples.
Assembly: mouse reference genome (mm10)
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Hippocampus

extract_protocol:
From the right hemisphere, the hippocampus was dissected and placed into 10x genomics fixation buffer solution (Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit #1000414, 10x Genomics, Pleasanton, CA). N=5 pooled hippocampus was minced in a petri dish until they could be pipetted through a wide bore pipette tip and weighed to achieve 30mg total fixed tissue. After fixation, the pieces were spun down and washed with PBS following 10X sample fixation protocol and stored at 4°C and shipped to Medgenome, Foster City, CA. At Medgenome, Fixed and quenched tissues were dissociated for 10 minutes at 37°C using an Miltenyi Octo Dissociator (Mitenyi Biotec, Gladbach, Germany #130-096), dissociated tissue were filtered through a 30 um filter to remove debris and undissociated tissue pieces, and centrifuged at 850 rcf for 5 minutes. The cell pellet was resuspended in chilled quenching buffer. Cells were stained with ethidium homodimer-1 and counted using countess II FL. The cell concentration was determined based on the reactive fluorescent protein positive concentration.
For custom probe spike in, single cell gene expression flex probe configuration with sequences (Table 4) ordered from Integrated DNA Technologies (Integrated DNA Technologies, Coralville, IA). Each probe represents 25 bp sequences homologous to the target transcript (VEEV genome identified from NCBI GenBank: L01443.1). One – two million cells were hybridized with a modified probe hybridization mix containing mouse WTA probes BC001 and custom probes, each probe at 40 nM for 16-24 h at 42°C. Each Left-hand probe (LHS) contained a linker region 5’-CCTTGGCACCCGAGAATTCCA-target_LHS-3’ and right hand probe /5Phos/-target_RHS-ACGCGGTTAGCACGTANNACTTTAGGCGGTCCTAGCAA-3’. Following probe hybridization, gel beads in emulsions were generated for 6000 cells targeted recovery using 10x genomics chromium fixed RNA profiling reagent kit (10X Genomics, Pleasanton, CA, #1000414). The libraries were generated and sequenced in NovaSeq X for 120M paired reads.

treatment_protocol: Mice were euthanized via CO2 asphyxiation and secondarily euthanized via cardiac exsanguination. Mice were perfused with 10mL heparin (2000 units/kg) or 1% EDTA in phosphate buffered saline (PBS) via the apex of the heart into the left ventricle followed by 50mL of PBS. Brains were dissected and left hemisphere was placed into 10% formalin.

value: Hippocampus

tag: mouse strain

value: 27-29 weeks old

tag: infection

value: VEEV TC-83


title: HM_4_2_CG

city: Gangnam-gu

first: Hong-Hee

last: Won

address: 81, Irwon-ro

institute: SungKyunKwan University

description:
Library name: HM_4_2_CG
column name in salmon.merged.gene_counts.tsv: HM_4_2_CG

data_processing:
nf-core/rnaseq v.3.17.0
read alignment using STAR v.2.7.11b, after filtering out alternate loci (ALT), human leukocyte antigen (HLA), and decoy sequence (Decoy) contigs
Isoform expressions of known Ensembl transcripts were quantified using Salmon (v.1.10.3) with GENCODE release 47
QC and generating read counts were performed by the nf-core/rnaseq pipeline with RSeQC, Preseq, Qualimap, dupRadar, DESeq2, Kranken2, and MultiQC
Assembly: GRCh38
Supplementary files format and content: tab-delimited
Supplementary files format and content: files including

source_name: skin

growth_protocol: Three types of primary human skin cells were used. Normal Human Epidermal Keratinocytes (Cat. no. PCS-200-010, ATCC, VA, USA) were cultured in Keratinocyte Growth Medium (Lonza, KGMTM Gold, Cat. no. 00192060, BS, Switzerland) supplemented with 10% fetal bovine serum (Gibco, Waltham, MA, USA), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). Human Epidermal Melanocytes, neonatal, Light Pigmented (HEMn-LP, Cat. no. C0025C, ThermoFisher Scientific, Waltham, MA, USA) were cultured in Cascade BiologicsTM medium 254 supplemented with Human Melanocyte Growth Supplement (Gibco, S0025). Human Dermal Fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (Sol Bio Pharm, Gyeonggi-do, Korea) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). Cells were maintained in a humidified incubator at 37 °C with 5% CO2. For the assay, Normal Human Epidermal Keratinocytes and HEMn-LP were seeded at 2 × 105 cells/well, and Human Dermal Fibroblasts at 1 × 105 cells/well in 6-well plates. The cells were maintained for 10 h in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Thermo Fisher Scientific), QIAzol® Lysis Reagent (Qiagen, Germany), and RNeasy® Mini Kit (Qiagen). A library was independently prepared using 0.5 μg of total RNA for each sample.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, San Diego, CA, USA) following the instructions in the Illumina TruSeq Stranded Total RNA Reference Guide.

treatment_protocol: Chlorogenic acid (Arshine Pharmaceutical Co., Ltd., Changsha, China) and taurine (Qianjiang Yongan Pharmaceutical, Co., Ltd., Qianjiang, China) were treated either individually or in combination at appropriate concentrations, followed by incubation for 24 h under the same conditions. After 24 h, the culture medium was removed, and 1mL of RNAlater (Cat no. AM7020, ThermoFisher Scientific) was added to each well to preserve RNA integrity. The plates were then immediately stored at -80 °C in a deep freezer for high-quality RNA preparation.

value: skin

value: human skin cell line

value: melanocytes

value: chlorogenic acid


title: Adh5_spleen

description: Library name: Adh5_spleen

value: Female

value: #10777_Adh5(tm1a):c/c Adh5 (tm1d):untested Fancd2:WT Vav1 iCre:pos


title: 3-week Treatment Replicate 2 Kidney

description: Library name: JQ3WT2K

value: Kidney

value: 10 weeks

value: male


title: 3-week Treatment Replicate 1 Kidney

description: Library name: JQ3WT1K


title: HM_3_3_Tau

description:
Library name: HM_3_3_Tau
column name in salmon.merged.gene_counts.tsv: HM_3_3_Tau

value: taurine


title: No_Vav_iCre_spleen

description: Library name: No_Vav_iCre_spleen

value: #10105_Adh5(tm1a):WT Adh5 (tm1d):untested Fancd2:het Vav1 iCre:neg


title: Fancd2_spleen

description: Library name: Fancd2_spleen

value: spleen

value: #10762_Adh5(tm1a):WT Adh5 (tm1d):untested Fancd2:hom Vav1 iCre:pos


title: HM_3_2_Tau

description:
Library name: HM_3_2_Tau
column name in salmon.merged.gene_counts.tsv: HM_3_2_Tau


title: 3-week Treatment Replicate 1 Liver

description: Library name: JQ3WT1L

value: Liver


title: HM_4_3_CG

description:
Library name: HM_4_3_CG
column name in salmon.merged.gene_counts.tsv: HM_4_3_CG


title: HM_3_1_Tau

description:
Library name: HM_3_1_Tau
column name in salmon.merged.gene_counts.tsv: HM_3_1_Tau


title: VEEV_106_DPI

description:
Library name: Sample 4
10X Genomics

value: Hippocampus

value: Male


title: VEEV_neuro_106_DPI

description:
Library name: Sample 5
10X Genomics

value: 27-29 weeks old

value: VEEV TC-83


title: 3-week Vehicle-Recovery Replicate 1 Liver

description: Library name: JQ3WRCL

value: 16 weeks

value: Vehicle


title: WT_spleen

description: Library name: WT_spleen

value: #10779_Adh5(tm1a):WT Adh5 (tm1d):untested Fancd2:WT Vav1 iCre:pos


title: HM_4_1_CG

description:
Library name: HM_4_1_CG
column name in salmon.merged.gene_counts.tsv: HM_4_1_CG

value: skin

value: human skin cell line

value: melanocytes

value: chlorogenic acid


title: 3-week Vehicle-Recovery Replicate 1 Kidney

description: Library name: JQ3WRCK

value: Kidney

value: male


title: HM_2_3_CGA

description:
Library name: HM_2_3_CGA
column name in salmon.merged.gene_counts.tsv: HM_2_3_CGA

value: chlorogenic acid and taurine


title: scRNA-seq_3-week Untreated Replicate 2

description:
Library name: UC2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation was made using the Cell Ranger software v3.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes-archive)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files after cellRanger

source_name: Testis

extract_protocol:
One testis was collected for single cell RNA sequencing (n = 3 mice). Testes were detunicated and minced on ice and transferred to a 50 mL tube containing 40 ml of collagenase IV (1 mg/mL, Sigma-Aldrich, C4-BIOC) and DNase I (7 mg/mL, Sigma Aldrich DN25) in Dulbecco's Modified Eagle Medium (DMEM, Gibco, 11-965-092). Tissue was incubated in a 37 °C incubator for 15 minutes. Tubule fragments were then centrifuged at 60 x g for 10 minutes, the supernatant discarded, washed with 15 mL Dulbecco's Phosphate Buffered Saline (dPBS, Sigma-Aldrich, D8537), and centrifuged again at 60 x g for 10 minutes. The fragments were then incubated in 10 mL 0.05% trypsin-EDTA (Invitrogen, 25200056) solution in 37 °C incubator for 12 minutes. Trypsin was quenched with 10% v/v fetal bovine serum (FBS, Thermo Fisher Scientific, A5256701), cells were passed through a 40 µm filter, spun down at 300 x g for 5 minutes, and resuspended in 1mL 0.04% bovine serum albumin (BSA, Sigma-Aldrich, A4737) in 1X dPBS.
Library was performed according to the manufacturer's instructions (single cell 3' v3.1 protocol 10x genomics). Briefly, testicular cells were resuspended in the master mix and loaded together with partitioning oil andn gel beads into the chip to generate a gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which containes an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane Dynabeads, amplified by PCR and the apropiated size fragments were selected with SPRIselect reagent for subseqeunt library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Testis

value: 15 weeks


title: 3-week Recovery Replicate 3 Liver

description: Library name: JQ3WR3L

value: Liver


title: MOCK_106_DPI

description:
Library name: Sample 3
10X Genomics

value: Hippocampus

value: MOCK


title: scRNA-seq_3-week Untreated Replicate 3

description:
Library name: UC3
10x Genomics


title: MOCK_7_DPI

description:
Library name: Sample 1
10X Genomics

value: 13-15 weeks old

value: Male


title: VEEV_7_DPI

description:
Library name: Sample 2
10X Genomics

value: VEEV TC-83


title: 3-week Recovery Replicate 3 Kidney

description: Library name: JQ3WR3K

value: 16 weeks


title: 3-week Recovery Replicate 2 Liver

description: Library name: JQ3WR2L


title: DMSO, 2h, Rep 2

description:
Library name: DMSO_2h_2
Column name in processed files is library name

data_processing:
nf-core/rnaseq (3.18.0)
Salmon (1.10.3)
Assembly: hg38
Supplementary files format and content: Tab separated gene counts, columns are library names
Supplementary files format and content: Tab separated gene counts, length scaled, columns are library names
Supplementary files format and content: Tab separeted gene counts, scaled, columns are library names
Supplementary files format and content: Tab separated gene transcripts per million (TPM), columns are library names
Supplementary files format and content: Tab separated transcript counts, columns are library names
Supplementary files format and content: Tab separated transcript per million (TPM), columns are libarary names

extract_protocol:
Direct-zol RNA MicroPrep kit (Zymo Research)
Novogene

value: pancreatic

value: WT

value: DMSO


title: RNA-seq fetal sheep liver GD144_6

city: Sendai

first: Hideyuki

last: Ikeda

state: Miyagi

address: 1-1 Seiryo-machi

department: Pediatrics

institute: Tohoku university hospital

description:
Library name: GD144_liver_6
VENT23098

data_processing:
Raw sequencing reads were processed and aligned to the Ovis aries reference genome (ARS-UI_Ramb_v3.0) using DRAGEN RNA pipeline (v3.8.4).
Gene-level expression quantification was performed using quant.genes.sf output files generated by the DRAGEN pipeline.
Read counts were aggregated into a count matrix (NumReads_time.txt) for downstream analysis.
Differential expression analysis and downstream statistical analyses were performed in R using standard bioinformatics workflows.
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: Processed data are provided as a tab-delimited matrix of gene-level read counts (NumReads_time.txt), where rows correspond to genes and columns correspond to samples.

organism: Ovis aries

extract_protocol:
Total RNA was extracted from fetal liver tissues using a standard RNA extraction method. RNA quality and integrity were assessed prior to library preparation.
Total RNA was extracted from fetal liver tissues and sequencing libraries were prepared using a standard RNA-seq library preparation protocol. Paired-end libraries were generated following poly(A) selection.

tag: gestational stage


title: 3-week Recovery Replicate 2 Kidney

description: Library name: JQ3WR2K


title: HM_1_2_Ctrl

description:
Library name: HM_1_2_Ctrl
column name in salmon.merged.gene_counts.tsv: HM_1_2_Ctrl

value: skin

value: human skin cell line

value: melanocytes

value: untreated


title: scRNA-seq_3-week Untreated Replicate 1

description:
Library name: UC1
10x Genomics

value: male


title: RNA-seq fetal sheep liver GD144_5

description:
Library name: GD144_liver_5
VENT23097


title: scRNA-seq_3-week Vehicle-Recovery Replicate 2

description:
Library name: JQ3WRC2
10x Genomics

value: Testis

value: Vehicle


title: RNA-seq fetal sheep liver GD144_4

description:
Library name: GD144_liver_4
VENT23096

value: Liver


title: scRNA-seq_3-week Vehicle-Recovery Replicate 1

description:
Library name: JQ3WRC1
10x Genomics


title: HM_1_3_Ctrl

description:
Library name: HM_1_3_Ctrl
column name in salmon.merged.gene_counts.tsv: HM_1_3_Ctrl


title: scRNA-seq_3-week Vehicle-Recovery Replicate 3

description:
Library name: JQ3WRC3
10x Genomics


title: 3-week Recovery Replicate 1 Liver

description: Library name: JQ3WR1L


title: HM_1_1_Ctrl

description:
Library name: HM_1_1_Ctrl
column name in salmon.merged.gene_counts.tsv: HM_1_1_Ctrl


title: HM_2_1_CGA

description:
Library name: HM_2_1_CGA
column name in salmon.merged.gene_counts.tsv: HM_2_1_CGA

value: chlorogenic acid and taurine


title: HM_2_2_CGA

description:
Library name: HM_2_2_CGA
column name in salmon.merged.gene_counts.tsv: HM_2_2_CGA


title: RNA-seq fetal sheep liver GD144_3

description:
Library name: GD144_liver_3
VENT23094


title: NHEK_4_2_CG

description:
Library name: NHEK_4_2_CG
column name in salmon.merged.gene_counts.tsv: NHEK_4_2_CG

value: epidermal keratinocytes

value: chlorogenic acid


title: scRNA-seq_3-week Recovery Replicate 3

description:
Library name: JQ3WR3
10x Genomics


title: scRNA-seq_3-week Recovery Replicate 2

description:
Library name: JQ3WR2
10x Genomics


title: 3-week Recovery Replicate 1 Kidney

description: Library name: JQ3WR1K

value: Kidney


title: NHEK_4_3_CG

description:
Library name: NHEK_4_3_CG
column name in salmon.merged.gene_counts.tsv: NHEK_4_3_CG


title: NHEK_3_3_Tau

description:
Library name: NHEK_3_3_Tau
column name in salmon.merged.gene_counts.tsv: NHEK_3_3_Tau

value: taurine


title: RNA-seq fetal sheep liver GD144_2

description:
Library name: GD144_liver_2
VENT23092


title: scRNA-seq_3-week Vehicle-Treated Replicate 2

description:
Library name: JQ3WTC2
10x Genomics

value: 10 weeks


title: scRNA-seq_3-week Recovery Replicate 1

description:
Library name: JQ3WR1
10x Genomics

value: 16 weeks


title: E_mu-Myc lymphoma from the Hematogenous  model of dissemination 4

city: Bellinzona

first: Santiago

last: Gonzalez

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

description: Library name: Sample 12

data_processing:
We used FastQC v0.11.9  to assess the quality of raw reads.
Adapters sequences were trimmed using Trimmomatic v0.39.
Reads were subsequently aligned to the mouse genome using HISAT2 v2.1.0.
We then used HTSeq-count v2.0.2 to generate the table of counts.
Assembly: GENCODE vM30 (GRCm39)
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Lymph node

extract_protocol:
After dissection, lymph nodes were disrupted into single cell suspension using sterile nuclease free tools. Following Eu-myc lymphoma sorting in sterile condition, Total RNA was extracted using the Direct‐zol RNA Miniprep kit (R2051, Zymo Research, Irvine, CA, USA). RNA quality and concentration were assessed using the Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).
NEBNext Ultraexpress RNA Library Prep Kit for Illumina (E3330S - New England BioLabs Inc.) was used with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The pre-pool sequencing was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

value: Lymph node

value: E_mu-Myc lymphoma

value: B cell


title: NHEK_3_1_Tau

description:
Library name: NHEK_3_1_Tau
column name in salmon.merged.gene_counts.tsv: NHEK_3_1_Tau

value: skin

value: human skin cell line


title: RNA-seq fetal sheep liver GD124_2

description:
Library name: GD124_liver_2
SAL8D23038


title: scRNA-seq_3-week Treatment Replicate 3

description:
Library name: JQ3WT3
10x Genomics


title: RNA-seq fetal sheep liver GD124_5

description:
Library name: GD124_liver_5
SAL8D23065


title: NHEK_4_1_CG

description:
Library name: NHEK_4_1_CG
column name in salmon.merged.gene_counts.tsv: NHEK_4_1_CG


title: E_mu-Myc lymphoma from the Hematogenous  model of dissemination 2

description: Library name: Sample 10


title: scRNA-seq_3-week Vehicle-Treated Replicate 3

description:
Library name: JQ3WTC3
10x Genomics


title: E_mu-Myc lymphoma from the Lymphatic model of dissemination 2

description: Library name: Sample 6


title: RNA-seq fetal sheep liver GD124_4

description:
Library name: GD124_liver_4
SAL8D23049


title: scRNA-seq_3-week Treatment Replicate 1

description:
Library name: JQ3WT1
10x Genomics


title: RNA-seq fetal sheep liver GD144_1

description:
Library name: GD144_liver_1
VENT23091


title: NHEK_3_2_Tau

description:
Library name: NHEK_3_2_Tau
column name in salmon.merged.gene_counts.tsv: NHEK_3_2_Tau


title: E_mu-Myc lymphoma from the Hematogenous  model of dissemination 3

description: Library name: Sample 11


title: E_mu-Myc lymphoma from the Hematogenous  model of dissemination 1

description: Library name: Sample 9


title: NHEK_2_3_CGA

description:
Library name: NHEK_2_3_CGA
column name in salmon.merged.gene_counts.tsv: NHEK_2_3_CGA


title: RNA-seq fetal sheep liver GD124_3

description:
Library name: GD124_liver_3
SAL8D23040


title: E_mu-Myc lymphoma from the Lymphatic model of dissemination 4

description: Library name: Sample 8


title: scRNA-seq_3-week Vehicle-Treated Replicate 1

description:
Library name: JQ3WTC1
10x Genomics


title: E_mu-Myc lymphoma from the Lymphatic model of dissemination 3

description: Library name: Sample 7


title: NHEK_2_1_CGA

description:
Library name: NHEK_2_1_CGA
column name in salmon.merged.gene_counts.tsv: NHEK_2_1_CGA


title: scRNA-seq_3-week Treatment Replicate 2

description:
Library name: JQ3WT2
10x Genomics


title: RNA-seq fetal sheep liver GD100_4

description:
Library name: GD100_liver_4
APC18024


title: NHEK_2_2_CGA

description:
Library name: NHEK_2_2_CGA
column name in salmon.merged.gene_counts.tsv: NHEK_2_2_CGA


title: E_mu-Myc lymphoma from the Lymphatic model of dissemination1

description: Library name: Sample 5


title: RNA-seq fetal sheep liver GD100_3

description:
Library name: GD100_liver_3
APC18023


title: RNA-seq fetal sheep liver GD124_1

description:
Library name: GD124_liver_1
SAL8D23037


title: PP_MBC_Tneg_612

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: PP_MBC_Tneg_612

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2
bigWig files were normalized to reads per million and generated using GenomicRanges and the bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

source_name: Peyer's Patch

extract_protocol:
Tissue were harvested and cells of each immune population were sorted into tdTomato positive and negative fractions representing early life origin B cells or non-early life origin B cells, respectively.
Cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: To time-stamp early life origin B cells, Tamoxifen was dissolved in peanut oil at 10 mg/ml and either administered to Mb1Cre-ERT2;R26fl-STOP-tdTomato mice orally (≤ 10-day-old) or injected intraperitoneally (≥10-day-old).

value: Peyer's Patch

tag: time stamp

value: Tneg

value: Memory B cell

tag: sorting markers

value: CD19+, IgD–, CD38+

tag: mouse id


title: NHEK_1_2_Ctrl

description:
Library name: NHEK_1_2_Ctrl
column name in salmon.merged.gene_counts.tsv: NHEK_1_2_Ctrl

tag: tissue

tag: cell type

value: untreated


title: E_mu-Myc lymphoma from cell culture 4

description: Library name: Sample 4


title: PP_MBC_Tpos_612

description: Library name: PP_MBC_Tpos_612

value: Tpos


title: RNA-seq fetal sheep liver GD100_2

description:
Library name: GD100_liver_2
APC18019

value: Liver


title: NHEK_1_3_Ctrl

description:
Library name: NHEK_1_3_Ctrl
column name in salmon.merged.gene_counts.tsv: NHEK_1_3_Ctrl

value: epidermal keratinocytes


title: RNA-seq fetal sheep liver GD100_1

description:
Library name: GD100_liver_1
APC18018


title: NHEK_1_1_Ctrl

description:
Library name: NHEK_1_1_Ctrl
column name in salmon.merged.gene_counts.tsv: NHEK_1_1_Ctrl