title: MLP_2

description: Library name: MLP_2


title: PDAC tumor, PE300, 7 weeks, Sample_ID LA75_72

status: Public on Mar 10 2025

type: SRA

city: Stanford

first: Haiqing

last: Xu

state: CA

address: 327 Campus Drive

department: Biology

country: USA

institute: Stanford University

description: Library name: PDAC_tumor_PE300_7_weeks_Sample_ID_LA75_72

library_source: genomic

data_processing:
Paired-end reads were processed with regular expressions to identify the crRNA arrays and clonal barcodes. When identifying guide sequences, we strictly required a perfect match with the designed sequences.
For the same crRNA array, when we encountered low-frequency clonal barcodes within a 1-hamming distance of high-frequency clonal barcodes, we attributed them to sequencing or PCR errors. These low-frequency barcodes were merged with barcodes of higher frequencies
After extracting barcode and crRNA information, we converted the read counts associated with clonal tumors into absolute neoplastic cell numbers. This conversion was accomplished by normalizing the reads of the clonal tumor to the number of reads of the "spike-in" benchmark cell lines added to each sample prior to lung lysis and DNA extraction
Assembly: GRCm39
Supplementary files format and content: PDAC_Batch1.txt: This file contains processed Tuba-seq data for PDAC tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: OncogeneNegative_Batch1.txt: This file contains processed Tuba-seq data for oncogene-negative tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: SCLC_Batch1.txt: This file contains processed Tuba-seq data for SCLC tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: PDAC_Batch2.txt: This file contains processed Tuba-seq data for PDAC tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: OncogeneNegative_Batch2.txt: This file contains processed Tuba-seq data for oncogene-negative tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: SCLC_Batch2.txt: This file contains processed Tuba-seq data for SCLC tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Efficiency.txt: This file contains processed Tuba-seq data for tumors from the Cas12a efficiency experiment, sequenced using NovaSeq X Plus PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Triple_TSG_KO.txt: This file contains processed Tuba-seq data for tumors from the triple TSG knockout experiment, sequenced using NovaSeq X Plus PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: off_target_summary.csv: This file contains the indel sequencing results for three samples of oncogene-negative tumors. It includes the designed guide sequence, the chromosome, position, and sequence of predicted off-target sites (with lowercase letters indicating mismatches with the designed guide sequence), as well as the indel percentage.

molecule: genomic DNA

organism: Mus musculus

source_name: Pancreas

extract_protocol:
Bulk tumor-bearing tissues were homogenized in 6 mL of cell lysis buffer (Puregene, 158063, Qiagen) using a FastPrep-24 5G tissue homogenizer (116005500, MP Biomedicals) and digested overnight with proteinase K (AM2544, Life Technologies). Benchmark control cell lines containing unique barcodes (50,000 or 100,000 cells each) were added to each lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumor.
Q5 High-Fidelity 2x Master Mix (M0494X, New England Biolabs) was used to amplify the U6-BC-crRNA region from 32 μg of genomic DNA in a total reaction volume of 800 μL per sample using unique dual-indexed primers.

tag: tissue

value: Pancreas

tag: genotype


title: Neutrophil, PW_005_rep1

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

library_source: transcriptomic

data_processing:
The data pre-processing tool, fastp, was used to perform quality control and adapter trimming. Results were filtered by quality. The software program Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2) was used to map RNA sequencing reads prior to building the index using the human reference genome grch38. Indices were used to map sequential reads to the human genome. FeatureCounts were applied to generate a matrix of row counts of each of the genes in all the samples.
Assembly: human reference genome grch38
Supplementary files format and content: txt, counts

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: Blood was collected by venipuncture into an ethylenediaminetetraacetic acid (EDTA) vacutainer tube and centrifuged at 400XG to separate cells from platelet-rich plasma. After initial separation, plasma was centrifuged at 3000XG for 10 minutes at 4C to remove any remaining red blood cells or platelets prior to being frozen at -80C. Pelleted blood cells were resuspended in sterile phosphate buffered saline (PBS; Thermo Fisher Scientific, Waltham, MA) with 2.5 mM EDTA up to the original whole blood volume. Neutrophils were purified by negative selection from PBS-EDTA washed whole blood using the EasySep Direct Human Neutrophil Isolation kit (StemCell Technologies, Cambridge, MA) according to the manufacturer’s protocol. There was >99% neutrophil purity based on cytospin staining with Diff-Quik.

extract_protocol:
RNA was isolated from blood neutrophils using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara Bio, San Jose, CA). RNA was quantified using a NanoDrop Fluorospectrometer (Thermo Fisher). RNA was quality assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) in the Emory Integrated Genomics Core. cDNA was generated using the SMART-Seq® v4 Ultra® low Input RNA Kit (Takara Bio).
The final RNA-seq library was generated using the Nextera XT kit (Illumina, San Diego, CA).
RNA-seq libraries were sequenced on the Novaseq 6000 with a sequencing depth of 30M paired-end 100 base pair reads per sample.

treatment_protocol: Two million neutrophils were resuspended in Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher) without serum and cultured overnight at 37°C and 5% CO2 in a humidified incubator with 740 ng/ml low molecular weight lyoVec poly(I:C) (InvivoGen, San Diego, CA) resuspended in endotoxin-free water. After centrifugation at 400ΧG, neutrophil pellets were saved in RNAlater (Thermo Fisher) and frozen at -80°C.

value: blood

tag: cell line

value: primary human cell

tag: cell type

value: Neutrophil

tag: individual

value: Sensitized, male

tag: treatment

value: Baseline


title: MLP_1

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

description: Library name: MLP_1

data_processing:
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length. 4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length
Aligned to hg38 using BWA with default parameters
Duplicates removed using PICARD. All ENCODE hg38 blacklist regions removed, as well as reads from outside autosomes/sex chromosomes.
MACS2 used to call peaks
Bedtools used to compute maximum fold change over background from MACS2 data over catalogue of all called peaks.
Assembly: hg38
Supplementary files format and content: bed files of called narrowPeaks, and gzipped bedgraphs of fold enrichment over background computed with MACS2

source_name: primary

growth_protocol: Cells were freshly sorted from Cord Blood samples and resuspended in lysis buffer.

extract_protocol:
DNA purification following Buenrostro et al. 2013 protocol
Nextera DNA Sample Preparation kit (Illumina) following Buenrostro et al. 2013 protocol. 4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length. 4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

value: primary

value: MLP


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_11

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_11

source_name: Lung

value: Lung


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_74

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_74


title: Neutrophil, PW_004_rep2

value: Not sensitized, male


title: LMPP_3

description: Library name: LMPP_3

value: LMPP


title: Neutrophil, PW_004_rep1


title: LMPP_2

description: Library name: LMPP_2


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_19

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_19


title: Neutrophil, PW_003_rep2


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_23

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_23

value: KT


title: Neutrophil, PW_003_rep1


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_16

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_16


title: EproB

description: Library name: EproB

value: CLP


title: PreB_1

description: Library name: PreB_1

value: Pre-B


title: Neutrophil, PW_001_rep2

value: Sensitized, female


title: Neutrophil, PW_001_rep1


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_01

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_01


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_12

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_12


title: EarlyProB_4

description: Library name: EarlyProB_4


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_22

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_22


title: RNALM016_28

city: Warsaw

first: Pawel

middle: J.

last: Sikorski

address: Zwirki i Wigury 101

department: Faculty of Biology

country: Poland

institute: University of Warsaw

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
Optical duplicates were removed using MarkDuplicates tool from GATKpackage (version 4.1.2.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Reads that failed to map to the reference were extracted using Samtoolsand mapped to Silva meta-database of rRNA sequences(version 119) with Sortmerna(version 2.1b) using “–best 1” option.
Mapped reads were associated with transcripts from GRCh38 database(Ensembl, version 77) using HTSeq-count(version 0.9.1) with default parameters except –stranded set to “reverse”
Differentially expressed genes were selected using DESeq2 package(version 1.16.1)
Assembly: hg19
Supplementary files format and content: normalized abundance measurements - DESeq2 data

growth_protocol: DMEM supplemented with 10% FBS, GlutaMAX and penicillin/streptomycin

extract_protocol:
Total RNA extracted with RNeasy Kit (qiagen) followed phenol/chloroform extraction.
Twelve cycles of library amplification was applied. Size distribution of final libraries were validated using Agilent Bioanalyzer 2100 and High Sensitivity DNA kit (Agilent, USA). Final library concentration was determined by qPCR using Kapa Library Quantification kit (Roche, Switzerland).

treatment_protocol: 35 ng per 100 ul of cell culture, 5 h

value: epithelial cell

value: dsRNA treated

tag: dsrna modification

value: NAD

tag: replicate


title: EarlyProB_3

description: Library name: EarlyProB_3


title: RNALM016_27


title: EarlyProB_2

description: Library name: EarlyProB_2


title: RNALM016_26


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_13

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_13


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_14

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_14


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_20

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_20


title: PDAC tumor, PE300, 6 weeks, Sample_ID LA75_71

description: Library name: PDAC_tumor_PE300_6_weeks_Sample_ID_LA75_71

value: Pancreas


title: B5_5

description: Library name: B5_5


title: RNALM016_25


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_15

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_15


title: RNALM016_24

value: OH


title: 4E_K27me3_Palb_rep3

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
CUT&Tag and CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed and reads trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to either the mm10 version of Mus musculus genome or the hg38 version of the human genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates
Assembly: hg38
Supplementary files format and content: BigWig files were created based on coverage at 100 bp windows genome-wide, which was calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads). 2800000000 was a number chosen arbitrarily.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag in SU-DIPG-IV cells: Nuclei were prepared from SU-DIPG-IV cells, and up to 5x105 cells were used per individual CUT&Tag reaction using CUT&Tag V3 (https://www.protocols.io/view/cut-amp-tag-direct-for-whole-cells-with-cutac-x54v9mkmzg3e/v3). pAG-Tn5 was purchased from Epicypher (Durham, North Carolina), and H3K27me3 antibody was purchased from Cell Signalling Technologies (#9733). Rabbit Isotype IgG control (ab172730) was purchased from Abcam. Antibodies were used at 1:100 dilution. Sequencing was performed on an Illumina NextSeq 500 using a P1/100 cycle kit with 50bp paired-end reads, targeting 10 million reads per sample. CUT&Tag in HEK293: Genome-wide H3K27me3 domain changes were profiled using the CUT&Tag protocol adapted from EpiCypher. Cells were harvested via 0.25% trypsin-EDTA solution and counted using 0.4% trypan blue stain and Countess automated cell counter. A single-cell suspension was prepared by washing cells with cold 1x PBS and resuspending 1.0 x 106 cells in 1 mL cold nuclear extraction buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton x-100, 20% glycerol, & 0.5 mM spermidine), then incubated on ice for 10 minutes to isolate nuclei. Biomag Plus Concanavalin A beads were activated with two washes of cold bead activation buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, & 1 mM MnCl22). After activation, beads were added to aliquots of 0.1 x 106 isolated nuclei and incubated at room temperature for 10 minutes. Nuclei:bead samples were resuspended in 50 µL cold Antibody150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, & protease inhibitors) followed by the addition of 0.5 µg of anti-H3K27me3 (#9733S, Cell Signaling Technology). To facilitate primary antibody binding, samples were incubated on nutator at room temperature for 1 hour. Samples were resuspended in 50 µL Digitonin150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors) followed by the addition of 0.5 µg CUTANA anti-rabbit secondary antibody (#13-1047, EpiCypher). Samples were then incubated on nutator at room temperature for 1 hour to facilitate binding, followed by two washes with 200 µL cold Digitonin300 buffer (20 mM HEPES-KOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors). The tagmentation reaction was performed by resuspending samples in 50 µL cold Tagmentation buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, & protease inhibitors) and incubating at 37°C in thermocycler for 1 hour. Samples were washed with 50 µL TAPS buffer (10 mM TAPS pH 8.5 & 0.2 mM EDTA) then resuspended in 5 µL SDS Release buffer (10 mM TAPS pH 8.5 & 0.1% SDS) to quench the tagmentation reaction and release adaptor-tagged DNA fragments into solution. After incubating samples at 58°C in thermocycler for 1 hour, 15 µL SDS Quench buffer (0.67% Triton x-100), 2 µL i5 universal primer (EpiCypher), 2 µL i7 barcoded primer (EpiCypher), 0.005 ng Escherichia coli spike-in DNA (made in-house), and 25 µL NEBNExt High Fidelity 2x PCR Master Mix were added to each sample for library construction with the following PCR protocol: 5 minutes at 58°C, 5 minutes at 72°C, 45 seconds at 98°C, 14 cycles of 15 seconds at 98°C and 10 seconds at 60°C, with a final extension for 1 minute at 72°C. Libraries were checked for quality using the Qubit dsDNA HS Assay kit and TapeStation High Sensitivity DNA assay kit and then sequencing was performed using Novaseq 6000 (Novogene) to generate 150 bp paired-end reads.
Library were constructed by tagmentation followed by PCR as described in the extract protocol.

value: 10 uM Palbociclib for 72 hours


title: LMPP_1

description: Library name: LMPP_1


title: B5_4

description: Library name: B5_4


title: RNALM016_23

value: ppp


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_18

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_18


title: EarlyProB_5

description: Library name: EarlyProB_5


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_06

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_06


title: RNALM016_22

value: mock


title: 4E_K27me3_Palb_rep2


title: B5_3

description: Library name: B5_3

value: primary


title: B5_2

description: Library name: B5_2


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_05

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_05


title: 4E_K27me3_Palb_rep1


title: RNALM016_20


title: RNALM016_21


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_21

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_21


title: B5_1

description: Library name: B5_1


title: EarlyProB_1

description: Library name: EarlyProB_1


title: B4_4

description: Library name: B4_4


title: 4E_K27me3_DMSO_rep3


title: 4E_K27me3_DMSO_rep1


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_07

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_07


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_04

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_04


title: RNALM016_19


title: 4E_K27me3_DMSO_rep2


title: Hpgds KO TAMs replicate 3

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49 box 912

department: Center for Cancer Biology

country: Belgium

institute: VIB - KULeuven

data_processing:
Reads were aligned to the mus musculus reference genome GRCm39 using STAR (v2.7.10b) with default parameters.
Aligned reads were quantified using featureCounts (v2.0.1) in R (v4.3.3) with options -t gene and -s 2.
Subsequent analyses were performed using DESeq2 package (v1.42.0).
Gene Set Enrichment Analysis (GSEA) was conducted with clusterProfiler (v4.10.0) and org.Mm.eg.db (v3.18.0) and visualized using DOSE (v3.28.1) and enrichplot (v1.22.0).
Assembly: mm39; GRCm39
Supplementary files format and content: csv file of matrix containing all samples with raw counts (not normalized by library size)

source_name: tumor-associated macrophages

extract_protocol:
Total RNA was isolated from in vivo sorted Hpgds KO and Ctrl TAMs (Viable, CD45+, CD11b+, F4/80+ cells) using the RNeasy Minikit (Qiagen) following the manufacturer's protocol and resuspended in RNase-free water.
Frozen samples were shipped to Novogene where the Plant and Animal Eukaryotic Strand Specific mRNA (WOBI) service was performed and sequenced paired-end (150bp) on a Novaseq X Plus instrument.

value: tumor-associated macrophages

tag: strain

value: Hpgds l/l x Cd64:Cre Tg/W

tag: condition

value: Hpgds KO


title: B4_2

description: Library name: B4_2


title: Hpgds KO TAMs replicate 2


title: B4_3

description: Library name: B4_3


title: RNALM016_17


title: RNALM016_18


title: B3_5

description: Library name: B3_5


title: Hpgds KO TAMs replicate 1


title: ChIPbis_AtT_ERPax7_Tam24h

city: Montréal

first: Juliette

middle: Emilie

last: Harris

state: Québec

address: 110 avenue des Pins O

institute: IRCM

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools 3.5
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: counts per million

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept and six to twelve independent ChIPs were pooled. Bisulfite conversion was done with EZ DNA Methylation-Lightning (Zymo Research).
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Corticotrope

value: Tam 24h


title: B4_1

description: Library name: B4_1


title: RNALM016_16


title: cd3

city: Bethesda

first: Joana

middle: A

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

description: Library name: Sample 6

library_source: other

data_processing:
Sequencing was performed on NextSeq 500 using SR75. Reads were trimmed using cutadapt (v 4.7). Trimmed reads were mapped to either miRNA or hairpin customized genomes using STAR aligner, with sequences retrieved from miRBase (2.7.11b). Read alignments were counted using Subread featureCounts (v 2.0.3) where features were retrieved from miRBase.
Assembly: custom genome with mature miRNA sequences retrieved from miRBase
Supplementary files format and content: txt with count data

molecule: other

source_name: Placenta

extract_protocol:
RNA was isolated from E18.5 Ago2+/+ and Ago2D598A/D598A placentas using TRIzol reagent (Thermo Fisher Scientific #15596018) and treated with TURBO DNA-free kit (Thermo Fisher Scientific #AM1907)
NEBNext® Multiplex Small RNA Library Prep Set for Illumina

value: Placenta

tag: developmental stage


title: B3_3

description: Library name: B3_3


title: B3_2

description: Library name: B3_2


title: wt3

description: Library name: Sample 3


title: Control TAMs replicate 1

value: Hpgds l/l x Cd64:Cre W/W

value: Control


title: RNALM016_12

value: epithelial cell


title: cd2

description: Library name: Sample 5


title: RNALM016_15

value: dsRNA treated


title: B3_4

description: Library name: B3_4


title: RNALM016_14

value: NAD


title: cd1

description: Library name: Sample 4


title: WT_D7

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

description: Infected Pex5^flox/flox mice

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Count v8.0.1
Assembly: Mouse (GRCm39) 2024-A
Supplementary files format and content: matrix files

extract_protocol:
Right lobes of the lungs were collected and cut into small pieces and digested with 180 U/ml Collagenase Type 2 (Worthington Biochemical) for 30 min at 37 °C, followed by disruption using gentleMACS tissue dissociator (Miltenyi). Single cell suspension was obtained after red blood cell lysis, filtration through 70 μm mesh, and washed with flow cytometry buffer. Single cell suspension was centrifuged and re-suspended in flow cytometry buffer
For library preparation, we utilized the Chromium Single Cell 3′ Reagent Kit from 10x Genomics, strictly adhering to the manufacturer's guidelines

treatment_protocol: Cd11c-cre Pex5^flox/flox or Pex5^flox/flox mice were either uninfected (day 0) or infected with 2000 PFU of SARS-CoV-2 MA30 virus. Lung cells were harvested on day 0 and day 7 post infection. For each time point, cells from three individual mice per genotype were pooled and subjected to single-cell RNA sequencing (scRNA-seq) analysis

value: Lung

value: tissue


title: Control TAMs replicate 2


title: B2_3

description: Library name: B2_3


title: ChIPbis_AtT_ERPax7_Tam48h_rep1

value: Tam 48h


title: RNALM016_10

value: OH


title: P12KO-6

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: mm10
Supplementary files format and content: TSV text file containing FPKM for all samples and genes

source_name: Bone marrow (B/L femur and tibia)

growth_protocol: Cells were not grown in media, they were directly processed for RNA extraction after isolation from animals.

extract_protocol:
Total RNA was extracted using column separation by the Qiagen Rneasy Micro Kit. RNA which met RIN >8.5 (Agilent Bioanalyzer) was used for library prep.
Ribosomal RNA was depleted (NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat, New England Biolabs, USA), and this rRNA-depleted RNA was used as input for the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England BioLabs, USA) in which libraries were tagged with unique adapter-indexes. Final libraries were validated on the Fragment Analyzer, quantified via qPCR, and pooled at equimolar ratios.
Pooled libraries were diluted, denatured, and loaded onto the Illumina NovaSeq X sequencing system, following the Illumina User Guide for a paired-end run.

treatment_protocol: No treatment was performed on cells.

value: Bone marrow (B/L femur and tibia)

value: Neutrophils

value: Myeloid-KLF2 knockout


title: Control TAMs replicate 4

value: tumor-associated macrophages


title: RNALM016_9

value: ppp


title: RNALM016_11


title: wt1

description: Library name: Sample 1


title: P12KO-7


title: RNALM016_8

value: mock


title: RNALM016_13


title: B2_1

description: Library name: B2_1

value: primary


title: B1_3

description: Library name: B1_3


title: KO_D7

description: Infected Cd11c-cre Pex5^flox/flox


title: B2_2

description: Library name: B2_2


title: P12KO-5


title: KO_D0

description: Uninfected Cd11c-cre Pex5^flox/flox


title: B3_1

description: Library name: B3_1


title: wt2

description: Library name: Sample 2

value: Placenta


title: RNALM016_7


title: B1_1

description: Library name: B1_1


title: Low-IMF pectoral tissues F0010

city: Nanchang

first: mengyun

last: zou

address: No. 602, Nanlian Road, Qingyunpu District

country: China

institute: Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural

description: Library name: F0010

data_processing:
The sequences of inferior quality, along with the adaptor sequences, were eliminated from the raw dataset utilizing the Sequence CLEAN software to produce clean data (Fastq files). Following quality control checks with fastaQC (version 0.11.7), the sequences were aligned to the Anser_cygnoides.gigadb_v1.genome.fa assembly using Hisat2. The analysis of differentially expressed genes (DEGs) was conducted via DESeq2, adhering to the established criteria of |log2 FC| > 1.0 and a false discovery rate (FDR) of < 0.05.
Assembly: Anser_cygnoides.gigadb_v1.genome.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPkMvalues for each Sample

organism: Anser cygnoides

source_name: pectoral tissues

extract_protocol:
Total RNA was extracted from breast muscle tissues employing the TRIzol reagent (Invitrogen).(1) NanoDrop 2000 spectrophotometer: detection of RNA purity and concentration; (2) Agient2100/LabChip GX detection: accurate detection of RNA integrity.
(1) Enrichment of eukaryotic mRNA with magnetic beads with Oligo (dT); (2) mRNA was randomly interrupted by Fragmentation Buffer. (3) Using mRNA as template, the first cDNA chain and two strands were synthesized, and the cDNA was purified; (4) The purified double-stranded cDNA was then end-repaired, A-tail was added and sequencing joints were connected, and AMPure XP beads were used for fragment size selection; (5) cDNA library was obtained by PCR enrichment

value: pectoral tissues


title: Low-IMF pectoral tissues F0016

description: Library name: F0016


title: B1_2

description: Library name: B1_2


title: P12KO-4


title: RNALM016_5


title: RNALM016_6


title: Low-IMF pectoral tissues F0011

description: Library name: F0011


title: P12KO-2


title: WT_D0

description: Uninfected Pex5^flox/flox mice


title: PEX5-KO-Poly(I:C)-3

data_processing:
12 samples were sequenced on DNBSEQ PE100 platform, averagely generating about 4.41G Gb bases per sample. The average mapping ratio with reference genome is 98.00%, the average mapping ratio with gene is 90.49%; 15368 genes were identified.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: FPKM values for each Sample

source_name: lung

growth_protocol: AMs were obtained from bronchoalveolar lavage of mice and purified by adherence for 2 h in complete medium (RPMI-1640, 10% FBS, 1% Pen/Strep/glutamate) at 37 ̊C and 5% CO2. The non-adherent cells were washed off with warm PBS. The remaining adherent cells were cultured in complete medium supplemented with 10 ng/ml recombinant murine granulocyte macrophage CSF (GM-CSF).

extract_protocol:
Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit, and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: WT or Pex5-deficient AMs were treated with or without Poly(I:C) for 24 hours. Then, the cells were harvested for RNA-seq.

value: lung

value: Alveolar macrophages


title: Low-IMF pectoral tissues F006

description: Library name: F006


title: High-IMF pectoral tissues M0035

description: Library name: M035


title: Low-IMF pectoral tissues F009

description: Library name: F009


title: PEX5-KO-Poly(I:C)-2


title: RNALM016_2

value: epithelial cell

value: dsRNA treated


title: WT-Poly(I:C)-3

value: WT


title: RNALM016_3


title: WT-Poly(I:C)-2


title: P12Cre-7

value: Lyz2 Cre


title: Low-IMF pectoral tissues F001

description: Library name: F001


title: RNALM016_4


title: P12Cre-6


title: PEX5-KO-Poly(I:C)-1


title: P12KO-1


title: WT-Poly(I:C)-1


title: P12Cre-3


title: High-IMF pectoral tissues M0027

description: Library name: M027


title: P12Cre-4


title: Low-IMF pectoral tissues F0013

description: Library name: F0013


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 175h, replicate 1

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

description:
Library name: Salt_t4_A
Salt_t4_A

data_processing:
Basecalls were performed using RTA v 1.18.66.3
Read trimming/filtering was performed using trimmomatic v0.39 with parameters PE  SLIDINGWINDOW:4:15 MINLEN:25
Sequenced reads were mapped to CP110836 using bowtie2 v2.3.2 with parameters -X 600
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g locus_tag -s 2
Read count normalization and data analysis were performed using DESeq2
Assembly: CP110836.1
Supplementary files format and content: tab-delimited matrix table with raw read counts for every gene and every sample
Supplementary files format and content: tab-delimited matrix table with normalized read counts derived via DESeq2 for each gene

organism: Streptomyces sp. Je 1-4 4N24

source_name: liquid culture

growth_protocol: early exponential phase (17 h), mid-exponential phase after glucose and mannitol depletion (33 h), stationary phase after galactose and mannose exhaustion (75 h), and late phase (175 h)

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 instrument using 75 bases read length (Illumina).

treatment_protocol: The medium for the second preculture as well as for the main cultivation was made in two different setups. In the first, the medium was prepared using deionized water and contained per liter: 0.4 g MgCl₂·6H₂O, 0.0265 g CaCl₂·2H₂O, 7 g (NH₄)₂SO₄, 20 g MOPS buffer (pH 7.0), 0.5 g K₂HPO₄, and 40 mL of vitamin solution. The vitamin solution contained, per liter, 10 mg biotin, 4 mg thiamine-HCl, 40 mg inositol, 8 mg pantothenic acid, and 4 mg pyridoxine-HCl. In the second setup, deionized water was replaced with artificial seawater (Fang et al., 2015), which had the following composition per liter: 27.13 g NaCl, 1.17 g CaCl₂, 3.38 g MgSO₄, 2.5 g MgCl₂, 0.74 g KCl, and 0.21 g NaHCO₃. The rest of the medium composition remained unchanged. For growth, the medium was supplemented with a sugar mixture of 2 g/L each of glucose, xylose, galactose, mannose, mannitol, and arabinose.

value: liquid culture

tag: time

value: artificial sea water


title: High-IMF pectoral tissues M0011

description: Library name: M011


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 175h, replicate 2

description:
Library name: Salt_t4_B
Salt_t4_B


title: PEX5-KO-Mock-3

value: Mock


title: P12KO-3

value: Bone marrow (B/L femur and tibia)

value: Neutrophils


title: High-IMF pectoral tissues M006

description: Library name: M006


title: PEX5-KO-Mock-2


title: P12Cre-2


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 175h, replicate 3

description:
Library name: Salt_t4_C
Salt_t4_C


title: RNALM016_1


title: P12Cre-5


title: TA33

type: RNA

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing: none provided

extract_protocol: Liver samples containing tumors were snap frozen, preserved in optimal cutting temperature and kept at −80 °C until sectioning. Samples were sectioned at −20 °C on a cryostat 10-µm thick and placed on a MERSCOPE slide. Samples were processed and acquired according to MEROSCOPE protocol.

value: liver


title: High-IMF pectoral tissues M001

description: Library name: M001


title: TA33.Combo


title: P12Cre-1


title: WT-Mock-3


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 75h, replicate 3

description:
Library name: Salt_t3_C
Salt_t3_C


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 33h, replicate 3

description:
Library name: Salt_t2_C
Salt_t2_C


title: P4KO-7

value: Myeloid-KLF2 knockout


title: P4KO-5


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 33h, replicate 2

description:
Library name: Salt_t2_B
Salt_t2_B


title: PEX5-KO-Mock-1


title: MMP3 Low affinity sub-population rep 4

city: Be'er Sheva

first: Dor

middle: Shlomo

last: Gozlan

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gurion University

description: Library name: MMP3_L_4

data_processing:
The analysis was performed in Python, version 2.7.5.  The number of reads of each variant from each library was counted following the alignment of the DNA sequences and their amino acid translations to the sequence of N-TIMP2WT.
Assembly: N-terminal domain of the tissue inhibitor of metalloproteinase 2 (N-TIMP2)  reference sequence: CSCSPVHPQQAFCNADVVIRAKAVSEKEVDSGNDIYGNPIKRIQYEIKQIKMFKGPEKDIEFIYTAPSSAVCGVSLDVGGKKEYLIAGKAEGDGKMHIT
Supplementary files format and content: csv file that includes raw counts of each variant from each library

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: The transformed yeast was grown in SDCAA selective medium (2% dextrose, 0.67% yeast nitrogen base, 0.5% Bacto casamino acids, 1.47% sodium citrate, and 0.429% citric acid monohydrate, adjusted to pH 4.5) overnight at 30°C to an OD600 of 10.0 (108 cells/ml)

extract_protocol:
The sorted N-TIMP2 library fractions (high and low affinity) were isolated from the yeast cells using the E.Z.N. A. Yeast Plasmid Mini Kit (Omega Bio-tek, Norcross, GA, U.S.A.) according to the manufacturer’s protocol.
The library, purchased from GenScript (Piscataway, NJ), was constructed using NNS degenerate codons (where N represents A, C, T, or G nucleotides, and S represents C or G) at positions 4, 35, 38, 68, 71, 97, and 99 on the basis of the N-TIMP2WT gene (PDB ID code 1BUV), giving random mutationsat a single position for each clone. This single position N-TIMP2 mutagenesis library was expressed in a YSD system with the Saccharomyces cerevisiae EBY100 yeast strain according to an established protocol. For the construction of a yeast-displayed N-TIMP2 library with a free N-terminus, the pCHA-VRC01-scFv vector  was used. In this construct, the C-terminus of the N-TIMP2 library was fused to the N-terminus of Aga-2, leaving the N-terminus of the displayed N-TIMP2 protein variants exposed to the solvent. The pCHA vector was linearized with the restriction enzymes BamHI-HF and Nhe-HF and, together with the N-TIMP2 library, were transformed by homologous recombination into a competent EBY100 S. cerevisiae yeast strain using a MicroPulser electroporator.. A library size of 5.45 × 10^6 transformants was obtained, as determined by plating serial dilutions on SDCAA plates (2% dextrose, 0.67% yeast nitrogen base, 0.5% Bacto casamino acids, 1.54% Na2HPO4, 1.856% Na2HPO4·H2O, 18.2% sorbitol, and 1.5% agar).

value: yeast cells


title: WT-Mock-1


title: WT-Mock-2


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 75h, replicate 2

description:
Library name: Salt_t3_B
Salt_t3_B


title: P4KO-6


title: MMP3 Low affinity sub-population rep 3

description: Library name: MMP3_L_3


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 75h, replicate 1

description:
Library name: Salt_t3_A
Salt_t3_A


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 17h, replicate 3

description:
Library name: Salt_t1_C
Salt_t1_C


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 33h, replicate 1

description:
Library name: Salt_t2_A
Salt_t2_A


title: P4KO-2


title: MMP3 Low affinity sub-population rep 1

description: Library name: MMP3_L_1


title: NIH3T3, control siRNA, MHV68-infected, replicate 2, CPSF30 (ChIP)

city: Berkeley

first: Britt

last: Glaunsinger

address: 565 Li Ka Shing Center

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

description:
Library name: CPSF30_controlsiRNA_MHV68_rep2_ChIP
CPSF30_controlsiRNA_MHV68_ChIP_replicateAverage.bw

data_processing:
Basecalls were performed using bcl2fastq v.2.17 for NovaSeq output
ChIP-seq reads were trimmed using HTStream v.1.3.3 with default settings for paired-end reads, including trimming adapter sequences, PhiX screening, “N” nucleotide trimming, and removing low-quality reads.
The mm10, yeast (GCA_000146045.2), and MHV68 (U97553.2) genomes were manually indexed using the bowtie2-build command. ChIP-seq reads were then separately aligned to the three genomes with bowtie2 v.2.5.4 using the following parameters: --maxins 1500, -k 25, --no-mixed, and --no-discordant to allow for multiple mapping locations per read.
Allo algorithm v.1.1.2 was used to redistribute multimapping reads, including those that map to highly repetitive RNA Pol III-transcribed genes. The resulting bam files were further filtered to discard any unmapped reads and supplementary alignments (samtools -F 2048), ensure reads are properly paired (samtools -f 2), and blacklist regions on the mm10 genome (bedtools intersect -v)
Peak calling was performed with MACS2 v.2.2.9.1 on Polr3A ChIP-seq data with default settings except for setting --min-length to 150 to capture small Pol III-transcribed genes. Bedtools intersect with the -u option was performed on the mm10 RepeatMasker file and called peaks to identify the precise loci that were bound by Polr3A. Consensus Polr3A-bound genes were then identified using bedtools intersect between replicates with the -f 1, -r, and -u options.
All consensus Polr3A-bound genes in the mock and MHV68-infected conditions were concatenated into one file for differential binding analysis with DiffBind v.3.8 using spike-in normalization scale factors proportional to the total number of spike-in reads. Differentially bound regions were defined as having an FDR<0.05 and a log2FC>1.5 or log2FC<-1.5.
Coverage profiles generated for all ChIP-seq datasets were produced using DeepTools v. 3.5.5. BigWig files were first generated with the bamCoverage command for each bam file from each sample mapped to the mm10 genome with the following parameters --binSize 10, --smoothLength 30, --extendReads, --centerReads, --normalizeUsing None, and --scaleFactor with their respective spike-in normalized scale factor (reciprocal of the ones used in DiffBind).
Assembly: mm10, yeast (GCA_000146045.2), MHV68 (U97553.2)
Supplementary files format and content: bigWig, narrowPeak (except for Input samples), csv file with differential binding values

growth_protocol: NIH3T3 (ATCC CRL-1658) mouse fibroblast cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) with 10% fetal calf serum (FBS; VWR). Cells were cultured at 37C at 5% CO2

extract_protocol:
NIH3T3 mouse fibroblast cells plated in a 10-cm TC-treated dish were cross-linked in 1% formaldehyde in DPBS (Gibco) for 5 minutes at room temperature, quenched in 0.125 M glycine, and washed twice with DPBS (Gibco). Cross-linked cells were harvested and lysed with 1 ml ChIP lysis buffer (50 mM HEPES [pH 7.9], 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) by rotation for 10 min. Nuclei were collected by centrifugation at 1,700 × g for 5 min at 4°C, washed once with ChIP shearing buffer (50 mM Tris-Cl, pH 7.5, 10 mM EDTA, 0.1% SDS), and then resuspended in 1 ml of ChIP shearing buffer. Chromatin was then sheared for 5 min using a Covaris S220 focused ultrasonicator at 140 power, a 5% duty cycle, and 200 bursts/cycle. Chromatin was spun at 15,000 × g for 5 min at 4°C, and the pellet was discarded. 40 μg of chromatin was incubated with 10 μg rabbit polyclonal anti-POLR3A (Abcam ab96328), anti-CPSF30 (Proteintech 15023-1-AP), or rabbit IgG (Abcam ab37415) overnight. 25 μl of mixed protein A and G Dynabeads (Thermo Fisher) was added, and the tubes were rotated for 2 hours at 4°C. Dynabeads were then washed with low-salt immune complex (20 mM Tris [pH 8.0], 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 0.1% SDS), high-salt immune complex (20 mM Tris [pH 8.0], 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 0.1% SDS), lithium chloride immune complex (10 mM Tris [pH 8.0], 0.25 M LiCl, 1% NP-40, 1% deoxycholic acid, 1 mM EDTA), and Tris-EDTA for 5 min each at 4°C with rotation. DNA was eluted from the beads using 100 μl of elution buffer (150 mM NaCl, 50 μg/ml proteinase K) and incubated at 50°C for 2 h and then at 65°C overnight. DNA was purified using an Oligo Clean and Concentrator kit (Zymo) and eluted in 50 μl of nuclease-free water. DNA was used for prepping libraries for ChIP-seq.
Libraries for ChIP-seq were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) with NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors DNA Set 1). Equal amounts of sample eluted DNA and spike-in DNA (yeast spike-in DNA – Cell Signaling) were used within each experiment and amplified for 3-10 cycles based on NEB recommendations and sequenced on a NovaSeq X 10B (Illumina) with 150 paired-end reads.

treatment_protocol: Transfections of siRNAs into NIH3T3 fibroblasts were completed as follows: Cells were maintained in DMEM with 10% FBS and grown to 90% confluence. Cells were removed and washed once with Dulbecco’s phosphate-buffered saline (DPBS) (Gibco). Nucleofections were done using the Neon Transfection System (Thermo Fisher). Then, 2 × 106 cells were resuspended in 100 μL of buffer R, to which control non-targeting, Brf1, CPSF30, CPSF73, or Nudt21 pools of siRNA (ON-TARGETplus SMARTpool siRNA – Horizon Discovery) were added to a final concentration of 200nM.  This was loaded into a Neon 100-μL pipette tip and Neon tube with 3 mL of buffer E2 with electroporation parameters set to 1,300 V, 20 ms, 2 pulses. Following electroporation, cells were plated in 10 mL of DMEM with 10% FBS in 10 cm TC-treated plates and were incubated at 37°C for 24 hours. MHV68 was amplified in NIH3T12 fibroblast cells, and the viral 50% tissue culture infective dose (TCID50) was measured on NIH#T3 fibroblasts by limiting dilution. NIH 3T3 or MC57G fibroblasts were infected at the indicated multiplicity of infection (MOI) by adding the required volume of the virus to cells in 5 mL of serum-free DMEM in 10-cm TC-treated plates. Infection was allowed to proceed for one hour to allow for viral entry, followed by removal of the virus-containing media and replacement with fresh DMEM with 10% FBS. Cells were harvested 24 hours post-infection.

value: Mouse fibroblast

value: control siRNA

value: MHV68 infection

tag: chip antibody

value: CPSF4 (Proteintech, #15023-1-AP)


title: NIH3T3, Brf1 siRNA, MHV68-infected, replicate 2, CPSF30 (ChIP)

description:
Library name: CPSF30_Brf1siRNA_MHV68_rep2_ChIP
CPSF30_Brf1siRNA_MHV68_ChIP_replicateAverage.bw

value: Brf1 siRNA


title: P4KO-1


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 17h, replicate 2

description:
Library name: Salt_t1_B
Salt_t1_B


title: NIH3T3, Brf1 siRNA, mock-treated, replicate 2, CPSF30 (ChIP)

description:
Library name: CPSF30_Brf1siRNA_mock_rep2_ChIP
CPSF30_Brf1siRNA_mock_ChIP_replicateAverage.bw


title: MMP3 High affinity sub-population rep 4

description: Library name: MMP3_H_4


title: NIH3T3, control siRNA, mock-treated, replicate 2, CPSF30 (ChIP)

description:
Library name: CPSF30_controlsiRNA_mock_rep2_ChIP
CPSF30_controlsiRNA_mock_ChIP_replicateAverage.bw


title: P4KO-4


title: MMP3 High affinity sub-population rep 3

description: Library name: MMP3_H_3


title: Streptomyces sp. Je 1-4 4N24, artificial sea water, 17h, replicate 1

description:
Library name: Salt_t1_A
Salt_t1_A


title: P4Cre-7


title: NIH3T3, Brf1 siRNA, MHV68-infected, replicate 1, CPSF30 (ChIP)

description:
Library name: CPSF30_Brf1siRNA_MHV68_rep1_ChIP
CPSF30_Brf1siRNA_MHV68_ChIP_replicateAverage.bw


title: Streptomyces sp. Je 1-4 4N24, deionized water, 175h, replicate 3

description:
Library name: Fresh_t4_C
Fresh_t4_C

value: deionized water


title: P4Cre-6


title: MMP3 High affinity sub-population rep 2

description: Library name: MMP3_H_2


title: NIH3T3, control siRNA, MHV68-infected, replicate 1, CPSF30 (ChIP)

description:
Library name: CPSF30_controlsiRNA_MHV68_rep1_ChIP
CPSF30_controlsiRNA_MHV68_ChIP_replicateAverage.bw


title: Streptomyces sp. Je 1-4 4N24, deionized water, 175h, replicate 2

description:
Library name: Fresh_t4_B
Fresh_t4_B


title: MMP3 High affinity sub-population rep 1

description: Library name: MMP3_H_1


title: P4Cre-4


title: Streptomyces sp. Je 1-4 4N24, deionized water, 175h, replicate 1

description:
Library name: Fresh_t4_A
Fresh_t4_A


title: P4KO-3


title: NIH3T3, Brf1 siRNA, mock-treated, replicate 1, CPSF30 (ChIP)

description:
Library name: CPSF30_Brf1siRNA_mock_rep1_ChIP
CPSF30_Brf1siRNA_mock_ChIP_replicateAverage.bw


title: MMP3 Low affinity sub-population rep 2

description: Library name: MMP3_L_2


title: P4Cre-5


title: MMP1 Low affinity sub-population rep 4

description: Library name: MMP1_L_4


title: P4Cre-3


title: MMP1 Low affinity sub-population rep 3

description: Library name: MMP1_L_3


title: Streptomyces sp. Je 1-4 4N24, deionized water, 75h, replicate 3

description:
Library name: Fresh_t3_C
Fresh_t3_C


title: NIH3T3, Brf1 siRNA, MHV68-infected, CPSF30 (input)

description:
Library name: CPSF30_Brf1siRNA_MHV68_input
CPSF30_Brf1siRNA_MHV68_input.bw


title: P4Cre-2


title: NIH3T3, Brf1 siRNA, mock-treated, CPSF30 (input)

description:
Library name: CPSF30_Brf1siRNA_mock_input
CPSF30_Brf1siRNA_mock_input.bw


title: MMP1 Low affinity sub-population rep 2

description: Library name: MMP1_L_2


title: Streptomyces sp. Je 1-4 4N24, deionized water, 75h, replicate 2

description:
Library name: Fresh_t3_B
Fresh_t3_B


title: Streptomyces sp. Je 1-4 4N24, deionized water, 75h, replicate 1

description:
Library name: Fresh_t3_A
Fresh_t3_A


title: P4Cre-1


title: MMP1 Low affinity sub-population rep 1

description: Library name: MMP1_L_1


title: Streptomyces sp. Je 1-4 4N24, deionized water, 33h, replicate 3

description:
Library name: Fresh_t2_C
Fresh_t2_C


title: INPUT_SLIF

description: ChIP-seq input from mESC grown in serum/LIF media

data_processing:
Reads were aligned to the mm10 version of Mus musculus genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates. Coverage at 100 bp windows genome-wide was calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads). 2800000000 was a number chosen arbitrarily.
Assembly: mm10
Supplementary files format and content: BigWig files were created based on coverage at 100 bp windows genome-wide, which was calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads). 2800000000 was a number chosen arbitrarily.

source_name: mESC

extract_protocol:
Native ChIP was performed with 2×10^6 cells. Cells were trypsinized, washed and subjected to hypotonic lysis (50 mM TrisHCl pH 7.4, 1 mM CaCl2, 0.2% Triton X-100, 10 mM NaButyrate, and protease inhibitor cocktail (Roche)) with micrococcal nuclease for 5 min at 37 °C to recover mono- to tri-nucleosomes. Nuclei were lysed by brief sonication and dialyzed into RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100) for 2 hr at 4 °C. Soluble material was incubated with 3 μg of antibody bound to 50 μl protein A Dynabeads (Invitrogen) and incubated overnight at 4 °C, with 5% reserved as input DNA. Magnetic beads were washed as follows: 3x RIPA buffer, 2x RIPA buffer + 300 mM NaCl, 2x LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% NaDeoxycholate), 1x TE + 50 mM NaCl. Chromatin was eluted and treated with RNaseA and Proteinase K. ChIP DNA was purified and dissolved in H2O.
ChIP-seq libraries were prepared from 5-10 ng ChIP DNA following the Illumina TruSeq protocol. The quality of the libraries was assessed using a D1000 ScreenTape on a 2200 TapeStation (Agilent) and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher). Libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina NextSeq 500 (paired-end, 33 base pair reads). Typical sequencing depth was at least 20 million reads per sample.

value: mESC

value: serum/LIF media


title: NIH3T3, control siRNA, MHV68-infected, CPSF30 (input)

description:
Library name: CPSF30_controlsiRNA_MHV68_input
CPSF30_controlsiRNA_MHV68_input.bw


title: MMP1 High affinity sub-population rep 4

description: Library name: MMP1_H_4


title: NIH3T3, control siRNA, mock-treated, CPSF30 (input)

description:
Library name: CPSF30_controlsiRNA_mock_input
CPSF30_controlsiRNA_mock_input.bw


title: Streptomyces sp. Je 1-4 4N24, deionized water, 33h, replicate 2

description:
Library name: Fresh_t2_B
Fresh_t2_B


title: MMP1 High affinity sub-population rep 3

description: Library name: MMP1_H_3


title: INPUT_2i

description: ChIP-seq input from mESC grown in 2i media

value: 2i media


title: NIH3T3, control siRNA, mock-treated, replicate 1, CPSF30 (ChIP)

description:
Library name: CPSF30_controlsiRNA_mock_rep1_ChIP
CPSF30_controlsiRNA_mock_ChIP_replicateAverage.bw


title: NIH3T3, MHV68-infected, replicate 2, Polr3A (ChIP)

description:
Library name: Polr3A_MHV68_rep2_ChIP
Polr3A_MHV68_rep2_ChIP.narrowPeak
Inf_vs_Uninf_DiffBind.csv
Polr3A_MHV68_ChIP_replicateAverage.bw
Polr3A_MHV68_ChIP_replicateAverage_viralGenome.bw

value: WT

value: Polr3A (Abcam, #ab96328)


title: MMP1 High affinity sub-population rep 2

description: Library name: MMP1_H_2


title: H3K27me3_SLIF

description: ChIP-seq of H3K27 trimethylation from mESC grown in serum/LIF media


title: Streptomyces sp. Je 1-4 4N24, deionized water, 17h, replicate 3

description:
Library name: Fresh_t1_C
Fresh_t1_C

value: liquid culture


title: Streptomyces sp. Je 1-4 4N24, deionized water, 33h, replicate 1

description:
Library name: Fresh_t2_A
Fresh_t2_A


title: NIH3T3, mock-treated, replicate 2, Polr3A (ChIP)

description:
Library name: Polr3A_mock_rep2_ChIP
Polr3A_mock_rep2_ChIP.narrowPeak
Inf_vs_Uninf_DiffBind.csv
Polr3A_mock_ChIP_replicateAverage.bw


title: H3K27me3_2i

description: ChIP-seq of H3K27 trimethylation from mESC grown in 2i media


title: MMP1 High affinity sub-population rep 1

description: Library name: MMP1_H_1


title: Streptomyces sp. Je 1-4 4N24, deionized water, 17h, replicate 2

description:
Library name: Fresh_t1_B
Fresh_t1_B


title: presort rep 4

description: Library name: Pre_4


title: H3K27ac_SLIF

description: ChIP-seq of H3K27 acetylation from mESC grown in serum/LIF media


title: Streptomyces sp. Je 1-4 4N24, deionized water, 17h, replicate 1

description:
Library name: Fresh_t1_A
Fresh_t1_A


title: H3K27ac_2i

description: ChIP-seq of H3K27 acetylation from mESC grown in 2i media


title: NIH3T3, mock-treated, replicate 1, Polr3A (ChIP)

description:
Library name: Polr3A_mock_rep1_ChIP
Polr3A_mock_rep1_ChIP.narrowPeak
Inf_vs_Uninf_DiffBind.csv
Polr3A_mock_ChIP_replicateAverage.bw


title: presort rep 3

description: Library name: Pre_3


title: NIH3T3, MHV68-treated, Polr3A (input)

description:
Library name: Polr3A_MHV68_input
Polr3A_MHV68_input.bw
Polr3A_MHV68_input_viralGenome.bw


title: HPAEC_HYPOXIA_siNOX1-3

city: Pittsburgh

middle: Jeffrey

last: Goossen

state: PA

address: 200 Lothrop Street

department: Molecular Pharmacology

institute: University of Pittsburgh

description:
Library name: Sample 12
Column name in "Gene_Counts_RNASeq.xlsx": HX_siNOX1_3

data_processing:
Novogene plant and animal eukaryotic mRNA-seq with reference (WBI-Quantification) occurred with NovaSeq PE150, Q30>85%, 6 G of raw data per sample.
Unstranded and paired 150 bp sequencing data was filtered, trimmed, aligned to the human reference genome (GRCh38), and counted on the gene level. After filtering low-count genes, the most variable genes (2000 genes) were used for principal component analysis (PCA) using base R functions. Differentially expressed genes (DEGs) were identified using DESeq2 (adjusted p-value < 0.05 unless specified otherwise). Pathway enrichment analysis was performed using ClusterProfiler and Gene Ontology biological processes. Pathways with false detection rates (FDR) < 0.05 were considered significant, and redundant pathways (>50% overlapping) were removed using the simplify function in ClusterProfiler.
Assembly: GRCh38
Supplementary files format and content: Gene_Counts_RNASeq.xlsx INCLUDES RAW COUNTS FOR EACH SAMPLE
Supplementary files format and content: COLUMN NAMES LISTED ABOVE IN "DESCRIPTON"

source_name: Human Pulmonary Artery Endothelial Cells (HPAECs)

growth_protocol: Human pulmonary artery endothelial cells (HPAEC) were obtained from Lonza (CC-2530) and cultured in EBM-2 medium containing EGM-2 components (Lonza, CC-3162) at 5% CO2, 37°C.

extract_protocol:
At the end of treatment, cells were lysed for RNA isolation and purification (RNeasy MinElute cleanup kit, QIAGEN). Total RNA samples ( ≥ 0.2 μg ≥ 10 μL ≥ 20 ng/μL) were sent to NovoGene (Sacramento, CA) for mRNA library preparation and sequencing.
RNA libraries for RNASeq were prepped with poly A enrichment by NovoGene.

treatment_protocol: For gene silencing, HPAECs were transfected with short interfering RNAs (siRNA) as previously described11, 36. In short, siRNA targeting either NOX1 (ThermoFisher, Assay ID: s25726 [UniGene ID: Hs.592227] and s25728 [UniGene ID:Hs.592227]) or ATF4 (ThermoFisher, Assay ID: 122168 [UniGene ID: Hs496487]) were used at a final concentration of 10 nM according to the manufacturer’s protocol (ThermoFisher, Lipofectamine RNAiMax, 13778150). As a transfection control (Ctr) scrambled RNA was used (ThermoFisher). For transfection, HPAECs were seeded at a 60-70% density and transfected on the following day with NOX1/ATF4 siRNA (10 nmol/l) or scrambled control siRNA (10nmol/l) using Lipofectamine RNAiMax (ThermoFisher, Lipofectamine RNAiMax, 13778150) according to the manufacturer’s protocol. Cells were serum starved (1% FBS) for 16 h and subsequently subjected to normoxic (Nx; 21% O2) or hypoxic (Hx; 1% O2) conditions. Gene silencing was confirmed by Western blot yielding 60-80% knockdown.

value: HPAECs

value: Endothelial Cells

value: siNOX1 - HYPOXIA


title: B-ALL_PAX5P80R_1308_S12

city: Toulouse

first: Bastien

last: Gerby

address: 2 Avenue Hubert Curien

country: France

institute: INSERM

description: Sample 12

data_processing:
Paired-end sequencing was performed on an Illumina NextSeq 500 using 2 x 75 bp reads
Low quality reads were trimmed and adaptor sequence was removed using fastp (v)
Short reads were then mapped to mm39 genome using RNA-STAR (v2.7.8a) with doublepass parameter
Low quality mapping and duplicated reads were removed and the remaining reads were count using featurecount (v) with default paired-end parameter.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: B-ALL cells

growth_protocol: Pax5 KO and Pax5 Wt fetal liver lymphoid cells and B-ALL GFP+ PAX5 P80R cells were purified by cell sorting and resuspended in RLT buffer

extract_protocol:
RNA was isolated with the RNeasy plus micro kit (Qiagen).
Smart-seqv4 libraries were prepared as previously described using the Takara SMART-Seq v4 full-length transcriptiome analysis kit according to the manufacture’s guidelines.

value: B-ALL cells

value: PAX5 P80R


title: presort rep 2

description: Library name: Pre_2

value: yeast cells


title: B-ALL_PAX5P80R_1302_S11

description: Sample 11


title: NIH3T3, mock-treated, Polr3A (input)

description:
Library name: Polr3A_mock_input
Polr3A_mock_input.bw

value: Mouse fibroblast


title: presort rep 1

description: Library name: Pre_1


title: B-ALL_PAX5P80R_1301_S10

description: Sample 10


title: NIH3T3, MHV68-infected, replicate 1, Polr3A (ChIP)

description:
Library name: Polr3A_MHV68_rep1_ChIP
Polr3A_MHV68_rep1_ChIP.narrowPeak
Inf_vs_Uninf_DiffBind.csv
Polr3A_MHV68_ChIP_replicateAverage.bw
Polr3A_MHV68_ChIP_replicateAverage_viralGenome.bw

value: MHV68 infection


title: HPAEC_HYPOXIA_siNOX1-1

description:
Library name: Sample 10
Column name in "Gene_Counts_RNASeq.xlsx": HX_siNOX1_1

value: Human Pulmonary Artery Endothelial Cells (HPAECs)


title: HPAEC_HYPOXIA_siNOX1-2

description:
Library name: Sample 11
Column name in "Gene_Counts_RNASeq.xlsx": HX_siNOX1_2


title: B-ALL_PAX5P80R_1300_S9

description: Sample 9


title: PAX5_WT4_S8

description: Sample 8

source_name: Pro-B/Pre-BI

value: Pro-B/Pre-BI

value: PAX5 WT


title: HPAEC_HYPOXIA_siCTR-3

description:
Library name: Sample 9
Column name in "Gene_Counts_RNASeq.xlsx": HX_siCtr3

value: WT - HYPOXIA


title: HPAEC_HYPOXIA_siCTR-1

description:
Library name: Sample 7
Column name in "Gene_Counts_RNASeq.xlsx": HX_siCtr1


title: PAX5_WT3_S7

description: Sample 7


title: HPAEC_HYPOXIA_siCTR-2

description:
Library name: Sample 8
Column name in "Gene_Counts_RNASeq.xlsx": HX_siCtr2


title: HPAEC_NORMOXIA_siNOX1-3

description:
Library name: Sample 6
Column name in "Gene_Counts_RNASeq.xlsx": NX_siNOX1_3

value: siNOX1 - NORMOXIA


title: AIS Patient 4

city: Doha

first: Abdelali

last: Agouni

address: Al Tarfa

country: Qatar

institute: Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University

hyb_protocol: The hybridization process was carried out at 48 °C at 60 rpm for 16 h in Affymetrix GeneChip® Hybridization Oven 640 (Central Expressway Santa Clara, CA). The chips were subsequently washed and stained using Affymetrix GeneChip® Fluidics Station 450 (Central Expressway Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix Gene Array scanner 3000 7G.

data_processing: The CEL files were imported into the Transcriptome Analysis Console (TAC) for quality control, normalization, and annotation using the miRNA 4.0 library files.

label: biotin

source_name: AIS patient exosomal miRNA

label_protocol: Isolated RNA samples were labeled using the FlashTag® Biotin HSR RNA Labeling Kit for Affymetrix® GeneChip® miRNA 4.0 Arrays

growth_protocol: Blood samples obtained from patients and controls through venipuncture and collected in K2 EDTA tubes (Vacutainer; Becton Dickinson) were processed within 2 h of the blood draw. Cell-free plasma was collected by centrifuging the blood at 1500 g for 15 min at 4 °C and stored immediately at −80 °C until further downstream processing.

extract_protocol: Isolation of total RNA from the concentrated pooled EV-rich samples was achieved using miRNeasy Serum/Plasma Kit from Qiagen (#1071073, Qiagen GmbH, Hilden, Germany)

treatment_protocol: Size exclusion chromatography-based Izon qEVoriginal 35 nm Smart columns (Izon Science, Christchurch, New Zealand) were used to isolate and purify EVs from the cell free plasma

tag: subject status

value: AIS patient

value: Peripheral blood


title: PAX5_WT2_S6

description: Sample 6


title: AIS Patient 5


title: TNF-α + IFN-γ + L. bulgaricus 2038

city: Tokyo

first: Kyosuke

last: Kobayashi

address: 1-29-1 Nanakuni, Hachioji

department: Wellness Science Labs

country: Japan

institute: Meiji Holdings Co., Ltd.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes. • Transfer 80 μL of hyb solution to each array, then tape holes. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The array datasets were normalized using the signal space transformation-robust multi-chip analysis algorithm implemented in Affymetrix’s transcriptome analysis console software (version 4.0).

source_name: TNF-α + IFN-γ + L. bulgaricus 2038

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: iPS cells were differentiated into intestinal organoids and cultured on cell culture inserts for 8 days.

extract_protocol: Total RNA from cells was prepared using Agencourt RNAdvance Tissue Kit (Beckman Coulter, Brea, CA, USA).

treatment_protocol: In TNF-α + IFN-γ group, cytokines were added and the cells were incubated for 42 hours. In the lactic acid bacteria (LABs)-added group, after 24 hours of cytokine stimulation, LABs were added and the cells were incubated for 18 hours.

value: induced pluripotent stem cell-derived crypt-villus structural small intestine


title: HPAEC_NORMOXIA_siNOX1-2

description:
Library name: Sample 5
Column name in "Gene_Counts_RNASeq.xlsx": NX_siNOX1_2


title: PAX5_WT1_S5

description: Sample 5


title: TNF-α + IFN-γ + S. thermophilus 1131

source_name: TNF-α + IFN-γ + S. thermophilus 1131


title: PAX5_KO4_S4

description: Sample 4

source_name: CLP/Pre-pro-B

value: CLP/Pre-pro-B

value: PAX5 KO


title: HPAEC_NORMOXIA_siNOX1-1

description:
Library name: Sample 4
Column name in "Gene_Counts_RNASeq.xlsx": NX_siNOX1_1

value: HPAECs

value: Endothelial Cells


title: HPAEC_NORMOXIA_siCTR-2

description:
Library name: Sample 2
Column name in "Gene_Counts_RNASeq.xlsx": NX_siCtr2

value: WT - NORMOXIA


title: PAX5_KO3_S3

description: Sample 3


title: HPAEC_NORMOXIA_siCTR-3

description:
Library name: Sample 3
Column name in "Gene_Counts_RNASeq.xlsx": NX_siCtr3


title: PAX5_KO2_S2

description: Sample 2


title: AIS Patient 1


title: AIS Patient 3


title: Control Subject 5

source_name: Control subject exosomal miRNA

value: Control subject


title: Control Subject 4


title: HPAEC_NORMOXIA_siCTR-1

description:
Library name: Sample 1
Column name in "Gene_Counts_RNASeq.xlsx": NX_siCtr1


title: TNF-α + IFN-γ

source_name: TNF-α + IFN-γ


title: AIS Patient 2


title: Control Subject 3


title: 7_DR0101_Day 365_lib54418

status: Public on Mar 09 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count (v0.4.1). Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38 release 91
Supplementary files format and content: Gene count matrix in text file

source_name: CD4 T cell

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from 50 to 120 ml whole blood samples by Ficoll gradient method, and autologous plasma was also saved to make T cell medium (TCM; consisting of RPMI with 10% autologous human plasma and 1% sodium pyruvate, glutamine, and penicillin/streptomycin; Invitrogen) for each donor.

extract_protocol:
CD4+CD154+Tetramer+ cells were sorted by BD FACSAria Fusion at single-cell purity directly into individual wells of a 96-well PCR plate with 5μl reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). Index sorting was performed, thus the phenotype of surface staining could be traced and confirmed for each individual cell.
Reverse transcription was performed, followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 1 million reads per sample.

treatment_protocol: PBMCs were divided into 10 to 15 million in 2 ml of TCM in each well of 12-well plate, then were activated with peptide-MHC-II tetramers at (5 µg/ml) in the presence of anti-CD40 (clone HB-14, Miltenyi Biotec) at 37°C, 5% CO2 in a humidified incubator for 5 hours. Specific tetramers conjugated to either PE-Cy7 or PE Dazzle 594 were used according to the HLA class II haplotype of the individual. Cells were washed and then stained with anti-CD154-PE (clone 5C8, Miltenyi Biotec). An 1/10th fraction of the cells was saved for the purpose of calculating the total CD4+ T cells used as described before, and the rest of cells were processed with anti-PE MicroBeads and MS column (Miltenyi Biotec) to magnetically enrich CD154-PE+/Tetramer-PE-Cy7+ and/or Tetramer-PE-Dazzle 594+ cells.

value: CD4 T cell

tag: donorid

tag: tetramer

tag: qc pass

value: FALSE

tag: visit

value: Day 365


title: 7_DR0401_Day 365_lib54415


title: control

source_name: control


title: 7_DR0401_Day 365_lib54417

value: TRUE


title: 7_DR0101_Day 365_lib54413


title: 7_DR0401_Day 365_lib54414


title: NBS8-iPSCs control

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

source_name: fibroblasts with Nijmegen Breage Syndrome (NBS)

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

growth_protocol: hiPSCs were maintained in feeder-free conditions, cultivated on Matrigel extracellular matrix and fed with mTeSR™ Plus. They were kept in an incubator at 37°C, 5% CO2 and 5% O2, in a humid atmosphere.

extract_protocol:
The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufacturer's protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).
The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion  (RNase-free DNase Set, Quiagen) has been applied on the columns during  isolation.

treatment_protocol: Benzo [a] pyrene diol epoxide (BPDE) was dissolved in DMSO at a concentration of 40mM. This solution was diluted in the culture medium to a final concentration of 75 nM. Cells were incubated for 24h with BPDE, after which the cells were harvested for RNA extraction.

value: iPSCs with Nijmegen Breage Syndrome (NBS)


title: Control Subject 1

tag: tissue


title: Control Subject 2


title: 7_DR0401_Day 365_lib54409


title: 7_DR0401_Day 365_lib54408


title: UJ-iPSCs BPDE treated

description: replicate 1

source_name: Urine-derived renal progenitor cell (UdRPC)

value: iPSCs reprogrammed from UdRPCs


title: 7_DR0401_Day 365_lib54407


title: UJ-iPSCs control

description: replicate 1


title: 7_DR0101_Day 365_lib54406


title: iPSC-12 iPSCs control

description: replicate 1

source_name: commercial induced pluripotent stem cells cell (iPSCs)


title: PAX5_KO1_S1

description: Sample 1

tag: genotype


title: NBS8-iPSCs BPDE treated

description: replicate 1

tag: cell type


title: 7_DR0401_Day 365_lib54401


title: 7_DR0401_Day 365_lib54416


title: 7_DR0401_Day 365_lib54411


title: 7_DR0401_Day 365_lib54403


title: iPSC-12 iPSCs BPDE treated

description: replicate 1

value: commercial induced pluripotent stem cells cell (iPSCs)


title: 7_DR0401_Day 365_lib54402


title: 7_DR0401_Day 365_lib54398


title: 7_DR0401_Day 365_lib54412


title: 7_DR0101_Day 365_lib54400


title: 7_DR0101_Day 365_lib54395


title: 7_DR0401_Day 365_lib54399


title: 7_DR0401_Day 365_lib54393


title: 7_DR0401_Day 365_lib54394


title: 7_DR0401_Day 365_lib54397


title: 7_DR0401_Day 365_lib54392


title: 7_DR0401_Day 365_lib54404


title: 7_DR0401_Day 365_lib54410


title: 7_DR0401_Day 365_lib54391


title: 7_DR0401_Day 365_lib54390


title: 7_DR0101_Day 365_lib54405


title: 7_DR0401_Day 365_lib54389


title: 7_DR0401_Day 365_lib54387


title: 7_DR0401_Day 365_lib54388


title: 7_DR0401_Day 365_lib54384


title: 7_DR0101_Day 365_lib54386


title: 7_DR0401_Day 365_lib54385


title: 7_DR0401_Day 365_lib54382


title: 7_DR0101_Day 365_lib54383


title: 7_DR0101_Day 365_lib54380


title: 7_DR0401_Day 365_lib54377


title: 7_DR0401_Day 365_lib54381


title: 7_DR0401_Day 365_lib54379


title: 7_DR0401_Day 365_lib54376


title: 7_DR0101_Day 365_lib54378


title: 7_DR0401_Day 365_lib54396


title: 7_DR0401_Day 365_lib54375


title: 7_DR0401_Day 365_lib54374


title: 7_DR0401_Day 365_lib54373


title: 7_DR0401_Day 365_lib54372


title: 7_DR0401_Day 365_lib54370


title: 7_DR0401_Day 365_lib54371


title: 7_DR0101_Day 365_lib54369


title: 7_DR0401_Day 365_lib54367


title: 7_DR0401_Day 365_lib54366


title: 7_DR0401_Day 365_lib54364


title: 7_DR0401_Day 365_lib54361


title: 7_DR0401_Day 365_lib54362


title: 7_DR0401_Day 365_lib54358


title: 7_DR0401_Day 365_lib54357


title: 7_DR0101_Day 365_lib54363


title: 7_DR0401_Day 365_lib54365


title: 7_DR0401_Day 365_lib54359


title: 7_DR0401_Day 365_lib54356


title: 7_DR0401_Day 365_lib54368


title: 7_DR0401_Day 365_lib54353


title: 7_DR0401_Day 365_lib54355


title: 7_DR0101_Day 365_lib54354


title: 7_DR0401_Day 365_lib54351


title: 7_DR0401_Day 365_lib54349


title: 7_DR0401_Day 365_lib54350


title: 7_DR0401_Day 365_lib54348


title: 7_DR0101_Day 365_lib54345


title: 7_DR0401_Day 365_lib54344


title: 7_DR0401_Day 365_lib54346


title: 7_DR0101_Day 365_lib54343


title: 7_DR0401_Day 365_lib54340


title: 7_DR0401_Day 365_lib54338


title: 7_DR0401_Day 365_lib54341


title: 7_DR0401_Day 365_lib54339


title: 7_DR0401_Day 365_lib54337


title: 7_DR0401_Day 365_lib54336


title: 7_DR0101_Day 365_lib54360


title: 7_DR0101_Day 365_lib54335


title: 7_DR0401_Day 365_lib54334


title: 7_DR0401_Day 365_lib54332


title: 7_DR0401_Day 365_lib54333


title: 7_DR0401_Day 365_lib54327


title: 7_DR0101_Day 365_lib54326


title: 7_DR0401_Day 365_lib54330


title: 7_DR0401_Day 365_lib54328


title: 7_DR0401_Day 365_lib54347


title: 7_DR0401_Day 365_lib54331


title: 7_DR0401_Day 365_lib54324


title: 7_DR0401_Day 365_lib54325


title: 7_DR0401_Day 365_lib54323


title: 7_DR0401_Day 365_lib54352


title: 2_DR0701_Day 365_lib52324


title: 2_DR0701_Day 365_lib52322


title: 2_DR0701_Day 365_lib52323


title: 2_DR0701_Day 365_lib52318


title: 2_DR0701_Day 365_lib52321


title: 2_DR0701_Day 365_lib52319


title: 7_DR0401_Day 365_lib54342


title: 2_DR0701_Day 365_lib52314


title: 2_DR0701_Day 365_lib52315


title: 2_DR0701_Day 365_lib52313


title: 2_DR0701_Day 365_lib52310


title: 2_DR0701_Day 365_lib52309


title: 2_DR0701_Day 365_lib52317


title: 2_DR0701_Day 365_lib52316


title: 2_DR0701_Day 365_lib52308


title: 2_DR0701_Day 365_lib52311


title: 2_DR0701_Day 365_lib52305


title: 2_DR0701_Day 365_lib52312


title: 7_DR0401_Day 365_lib54329


title: 2_DR0701_Day 365_lib52300


title: 2_DR0701_Day 365_lib52306


title: 2_DR0701_Day 365_lib52304


title: 2_DR0701_Day 365_lib52298


title: 2_DR0701_Day 365_lib52307


title: 2_DR0701_Day 365_lib52320


title: 2_DR0701_Day 365_lib52303


title: 2_DR0701_Day 365_lib52297


title: 2_DR0701_Day 365_lib52296


title: 2_DR0701_Day 365_lib52302


title: 2_DR0701_Day 365_lib52289


title: 2_DR0701_Day 365_lib52287


title: 2_DR0701_Day 365_lib52295


title: 2_DR0701_Day 365_lib52299


title: 2_DR0701_Day 365_lib52294


title: 2_DR0701_Day 365_lib52292


title: 2_DR0701_Day 365_lib52293


title: 2_DR0701_Day 365_lib52291


title: 2_DR0701_Day 365_lib52290


title: 2_DR0701_Day 365_lib52301


title: 2_DR0701_Day 365_lib52281


title: 2_DR0701_Day 365_lib52283


title: 2_DR0701_Day 365_lib52275


title: 2_DR0701_Day 365_lib52272


title: 2_DR0701_Day 365_lib52279


title: 2_DR0701_Day 365_lib52273


title: 2_DR0701_Day 365_lib52286


title: 2_DR0701_Day 365_lib52271


title: 2_DR0701_Day 365_lib52270


title: 2_DR0701_Day 365_lib52277


title: 2_DR0701_Day 365_lib52285


title: 2_DR0701_Day 365_lib52278


title: 2_DR0701_Day 365_lib52269


title: 2_DR0701_Day 365_lib52268


title: 2_DR0701_Day 365_lib52288


title: 2_DR0701_Day 365_lib52274


title: 2_DR0701_Day 365_lib52280


title: 2_DR0701_Day 365_lib52263


title: 2_DR0701_Day 365_lib52282


title: 2_DR0701_Day 365_lib52264


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