title: Jurkat cells, Coronin 3 (CORO1C) KO, biol rep 3

city: Basel

first: Jean

last: Pieters

address: Spitalstrasse 61

department: Biozentrum

institute: University of Basel

description:
Library name: Sample_S9
column name in TPM table: 6_1_cor3_KO

data_processing:
Raw reads were rimmed using Trimmomatic (4-nucleotide sliding windows, Phred threshold of 15)
Trimmed reads were aligned to the Homo sapiens genome using STAR, keeping only uniquely aligned reads.
Read counts were summarized using the "--quantmode GeneCounts" option of STAR, with the appropriate strandedness
Read counts were converted to TPM (transcipts per million) using R software with a method described in https://gist.github.com/slowkow/c6ab0348747f86e2748b
Assembly: GRCh38
Supplementary files format and content: csv file with TPM (normlized read counts) for each sample

source_name: Jurkat

growth_protocol: Jurkat T cells were cultured in RPMI-1640 (Sigma-Aldrich, CAT: R8758) media supplemented with 10% FBS (Gibco, CAT: 10207-106), 100 U/mL penicillin, and 100 µg/mL streptomycin (Sigma-Aldrich, CAT: P4333). Cells were harvested by centrifugation and subcultured every fifth day.

extract_protocol:
RNA extraction was perfumed using the RNeasy Micro kit (QIAGEN, catalog 74004)
Library preparation was performed starting from 200 ng total RNA, using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA).

treatment_protocol: Jurkat T cells knock-outs of Coronin 1 (CORO1A) and Coronin 3 (CORO1C)  ware generated by CRISPR-Cas9 genome editing.

value: Jurkat

value: T-cell

tag: genotype

value: Coronin 3 (CORO1C) Knock-out


title: Murine liver, JIB-4 treated_2

status: Public on Jul 13 2026

type: SRA

city: Tampa

first: Pragya

last: Kumar

state: FL

address: 4502 Montego Bay Court

country: USA

institute: University of South Florida

description: Library name: J2

library_source: transcriptomic

data_processing:
Standard processing by Novogene
Assembly: GRCm39/mm39
Supplementary files format and content: .xls file with fpkm values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted using Trizol and submitted to Novogene
Standard library preparation by Novogene

treatment_protocol: NSG mice were given 5 doses 55mg/kg JIB-04 by oral gavage, twice a week for the J1 and J2 samples. C1 and C2 samples were harvested from untreated mice

tag: tissue

value: Liver

value: WT

tag: treatment


title: Jurkat cells, Coronin 3 (CORO1C) KO, biol rep 2

country: Switzerland

description:
Library name: Sample_S8
column name in TPM table: 5_8_cor3_KO

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter hNP1 rep3

type: RNA

city: Nashville

first: Anthony

last: Flores

state: TN

address: 1161 21st Avenue S, MCN D7219

institute: Vanderbilt University Medical Center

hyb_protocol: NanoString nCounter hybridization performed on nCounter MAX/FLEX system at VANTAGE core facility, Vanderbilt University Medical Center, per NanoString manufacturer protocol (16 hr hybridization at 65 degrees C).

scan_protocol: NanoString nCounter MAX/FLEX system with nCounter Digital Analyzer. NanoString Technologies, Inc.

data_processing: Raw nCounter count data quality-assessed and normalized using nSolver v4.0 (positive control normalization followed by housekeeping gene normalization using tufA [M5005_Spy_0013], gyrA [M5005_Spy_0124], and guaB [M5005_Spy_0508]). Differential gene expression assessed using limma empirical Bayes in R v4.5.3 (|log2FC| >= log2(1.5), BH-FDR < 0.05). Gene module clustering: hierarchical clustering (k=4) on log2FC profiles across 12 pairwise contrasts for 86 endogenous probes. Cross-platform validation: NanoString log2FC vs RNA-seq DESeq2 log2FC for 97 mapped probes. One replicate (deltaSpxA1 hNP-1 rep1, SAMN60523470) excluded from DE analysis as PCA outlier. Analysis code: https://github.com/ar-flores/SpxA1-SpxA2-MultiOmic-GAS (DOI: https://doi.org/10.5281/zenodo.20476011)

label: other

organism: Streptococcus pyogenes MGAS10870

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 3 of 3. BioSample: SAMN60523481.

label_protocol: Not applicable. NanoString nCounter uses direct hybridization without labeling or amplification.

growth_protocol: GAS strains grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY) without agitation at 37 degrees C, 5% CO2, to mid-exponential phase (OD600 ~0.45).

extract_protocol: RNA extracted using RNeasy Mini Kit (Qiagen) with on-column DNase digestion per manufacturer protocol. RNA quality assessed by Bioanalyzer (Agilent). Hybridized to custom NanoString nCounter codeset (119 probes: 116 endogenous GAS targets + 3 housekeeping probes [tufA: M5005_Spy_0013; gyrA: M5005_Spy_0124; guaB: M5005_Spy_0508]) per NanoString manufacturer protocol. Probes designed against MGAS5005 (emm1) and mapped to MGAS10870 (emm3, NZ_CP067090.1) by k-mer similarity.

treatment_protocol: Cells exposed to sub-MIC bacitracin (BAC) or sub-MIC hNP-1 for 30 minutes at mid-exponential phase. Uninduced (UI) cells received vehicle control. Sub-MIC concentrations determined by MIC assay for each strain.

tag: strain

tag: biological replicate

tag: biosample accession


title: UW23

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description: Library name: UW23

library_source: genomic single cell

data_processing:
Read trimming, deduplication, and alignment was performed using the cellranger-atac count pipeline from 10X Genomics (v2.1.0) and the hg38 reference genome. Fragments files from cellranger-atac count into ArchR (v1.0.3) for downstream clustering and analysis.
Assembly: hg38
Supplementary files format and content: snATAC-seq fragments file

molecule: genomic DNA

source_name: brain

extract_protocol:
Nuclei were isolated from frozen human postmortem brain tissue following a modified sucrose gradient ultracentrifugation protocol. Briefly, 100–200 mg of frozen tissue (kept on dry ice until use) was thawed for ~5 min in 5 ml lysis buffer [0.32 M sucrose, 5 mM CaCl₂, 3 mM Mg(acetate)₂, 0.1 mM EDTA, 10 mM Tris–HCl (pH 8), 1 mM DTT, and 0.1% Triton X-100 in nuclease-free H₂O] on ice. Tissue was homogenized in a pre-chilled glass douncer (~30 strokes) and transferred to a 50 ml ultracentrifuge tube. The volume was brought to 12 ml with lysis buffer, and 21 ml sucrose buffer [1.8 M sucrose, 3 mM Mg(acetate)₂, 1 mM DTT, 10 mM Tris–HCl (pH 8)] was gently added from the bottom to form a density gradient. Tubes were balanced, placed in a SW32Ti swinging-bucket rotor (Beckman Coulter), and ultracentrifuged at 25,000 RPM (107,163 × g) for 2 h at 4 °C. The supernatant was discarded, and 500 μl of 1× PBS containing 1% BSA was added to the pellet. Pellets were incubated on ice for 10 min, resuspended, and transferred to 5 ml filter-cap tubes (12x75mm).
Single nucleus ATAC-seq libraries were prepared using the Chromium Next GEM Single Cell ATAC Kit (10x Genomics Cat#1000390). Nuclei were transposed with Tn5 transposase, partitioned into Gel Bead-in-Emulsions (GEMs) for barcoding and amplification, purified with SPRIselect beads (Beckman Coulter), and indexed by PCR. Libraries were size selected, quantified, and assessed on an Agilent Bioanalyzer.

value: brain

tag: cognitive status

value: no dementia

value: unsorted brain nuclei


title: Murine liver, JIB-4 treated_1

description: Library name: J1


title: Jurkat cells, Coronin 3 (CORO1C) KO, biol rep 1

description:
Library name: Sample_S7
column name in TPM table: 5_7_cor3_KO


title: UW22

description: Library name: UW22


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter hNP1 rep2

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 2 of 3. BioSample: SAMN60523480.


title: Murine liver, untreated_2

description: Library name: C2

value: untreated


title: Jurkat cells, Coronin 1 (CORO1A) KO, biol rep 3

description:
Library name: Sample_S6
column name in TPM table: 5_6_cor1_KO

value: Coronin 1 (CORO1A) Knock-out


title: UW21

description: Library name: UW21


title: Murine liver, untreated_1

description: Library name: C1


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter hNP1 rep1

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 1 of 3. BioSample: SAMN60523479.


title: Jurkat cells, Coronin 1 (CORO1A) KO, biol rep 2

description:
Library name: Sample_S5
column name in TPM table: 5_5_cor1_KO


title: UW20

description: Library name: UW20


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter BAC rep3

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 3 of 3. BioSample: SAMN60523478.

value: sub-MIC bacitracin


title: Jurkat cells, Coronin 1 (CORO1A) KO, biol rep 1

description:
Library name: Sample_S4
column name in TPM table: 5_4_cor1_KO


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter BAC rep2

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 2 of 3. BioSample: SAMN60523477.


title: UW19

description: Library name: UW19


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter BAC rep1

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 1 of 3. BioSample: SAMN60523476.


title: Jurkat cells, WT, biol rep 3

description:
Library name: Sample_S3
column name in TPM table: 5_3_WT


title: UW18

description: Library name: UW18


title: Jurkat cells, WT, biol rep 2

description:
Library name: Sample_S2
column name in TPM table: 5_2_WT


title: UW17

description: Library name: UW17


title: RAW264.7 cells, Let-7c, biol rep 2

city: Hangzhou

first: Yi

last: Xu

address: Qiutao Street 166

country: China

institute: Zhejiang University

description: Library name: Let7c2

data_processing:
Raw reads for each sample were generated. The sequencing-generated FASTQ files were evaluated for read quality and mapping rate with FastQC (version 0.11.9). Clean reads were aligned to the Mus_musculus_Ensembl_110 reference genome using Hisat2 (version 2.1.0). FPKM of each gene was calculated and the read count of each gene were obtained by HTSeq-count (version0.11.2). PCA analysis was performed using R (version 4.3.2) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2(version 1.4.2).
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 4.3.2), respectively. R (v 4.3.2) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: Mus_musculus_Ensembl_110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).  Then the libraries were constructed by Hangzhou Astrocyte Technology Co., Ltd(Hangzhou, China). The libraries were sequenced on the illumina NovaSeq X Plus and 150 bp paired-end reads were generated.
Sequencing libraries were prepared, and the quality of the libraries was assessed by Qubit (Thermo Fischer Scientific), 2100 Bioanalyzer (Aligent), and qPCR. Qualifying samples were sequenced by HiSeq (Illumina), and 150-bp paired-end reads were generated at a depth of 20×.

value: Murine macrophage

value: cell line

value: Transfected with let-7c-5p mimics.


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter UI rep3

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 3 of 3. BioSample: SAMN60523475.

value: uninduced (vehicle control)


title: Jurkat cells, WT, biol rep 1

description:
Library name: Sample_S1
column name in TPM table: 5_1_WT


title: UW16_Pu

description: Library name: UW16_Pu


title: RAW264.7 cells, Let-7c, biol rep 1

description: Library name: Let7c1


title: M07e_KO_Replicate_3

city: Little Rock

first: Samrat

last: Roy Choudhury

state: AR

address: 13 Children's Way, Arkansas Children's Research Institute

institute: University of Arkansas for Medical Sciences

description:
Library name: Sample_18
M07e_KO_C_R3

data_processing:
The bioinformatics analysis pipeline began with quality control, where raw fastq reads were processed using in-house Perl scripts to remove adapter-containing, poly-N, and low-quality reads, yielding high-quality clean data with Q20, Q30, and GC content calculated. Clean reads were then mapped to the reference genome using HISAT2 v2.0.5, leveraging splice junctions for improved alignment accuracy. Gene expression levels were quantified with featureCounts v1.5.0-p3, and FPKM was used for normalization. Differential expression analysis was performed using DESeq2 (v1.20.0) for biological replicates, applying a negative binomial model and Benjamini-Hochberg correction (adjusted P ≤ 0.05), while edgeR (v3.22.5) was used for conditions without replicates, normalizing read counts and identifying significant genes with a corrected P ≤ 0.05 and absolute fold change ≥ 2.
Assembly: hg38
Supplementary files format and content: FPKM values of gene counts per sample

growth_protocol: CD34+ hematopoietic stem cells (HSCs) were expanded in StemSpan SFEM II media supplemented with 1% L-glutamine, 1% penicillin-streptomycin, and growth factors: TPO (50 ng/µL), EPO (5 ng/µL), SCF (100 ng/µL), IL-3 (10 ng/µL), IL-6 (10 ng/µL), and FLT-3L (10 ng/µL). Megakaryocyte (MK) progenitors were derived by treating CD34+ HSCs with StemSpan™ Megakaryocyte Expansion Supplement (100X) following the manufacturer’s instructions. Flow cytometry confirmed the purity of HSCs (CD34+) and MK progenitors (CD41+). M07e cells were grown in RPMI-1640, supplemented with 20% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin and 10 ng/mL GM-CSF. K-562 cells were were grown in RPMI-1640, supplemented with 20% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA was extracted from AML cell lines and primary cells using the AllPrep DNA/RNA Kits, Qiagen, following the manufacturer’s instructions. DNA purity and concentration were assessed using a Qubit fluorometer. The integrity of the extracted DNA was evaluated using a bioanalyzer.
mRNA library was prepared by (1) mRNA enrichment by poly (A) capture or rRNA removel, (2) RNA fragmentation, (3) cDNA reverse transcription, and (4) RNA library preparation.

value: Acute Megakaryoblastic Leukemia Cells

value: DNMT3B knockout


title: RAW264.7 cells, Negative Control, biol rep 4

description: Library name: NC4

value: Negative Control


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter UI rep1

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 1 of 3. BioSample: SAMN60523473.


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter hNP1 rep3

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 3 of 3. BioSample: SAMN60523472.


title: UW16_v2

description: Library name: UW16_v2


title: RAW264.7 cells, Negative Control, biol rep 3

description: Library name: NC3


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter hNP1 rep2

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 2 of 3. BioSample: SAMN60523471.


title: M07e_KO_Replicate_1

description:
Library name: Sample_16
M07e_KO_C_R1


title: UW15_Pu

description: Library name: UW15_Pu


title: RAW264.7 cells, Negative Control, biol rep 2

description: Library name: NC2


title: M07e_C_Replicate_3

description:
Library name: Sample_15
M07e_C_R3


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter hNP1 rep1

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 1 of 3. BioSample: SAMN60523470. NOTE: Excluded from differential expression analysis as PCA outlier. Data included for transparency.


title: UW15

description: Library name: UW15


title: RAW264.7 cells, Negative Control, biol rep 1

description: Library name: NC1


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter BAC rep3

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 3 of 3. BioSample: SAMN60523469.


title: M07e_C_Replicate_2

description:
Library name: Sample_14
M07e_C_R2


title: LIM1215-GFP, uninfected rep 1

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

description: Library name: 1_GFP_uninf_R

data_processing:
Base calling was performed using Dragen BCLConvert (v3.7.4).
RNA sequencing read alignment was performed in R (v4.1.2) using the Rsubread package (v2.6.4). A genome index was built using the custom combined human and EMCV genome using the buildindex function and alignment was performed using sunjunc, with default settings.
Exon- and intron-level differential gene expression analyses followed the methods of the index package (v1.0)
A custom GTF file consisting of human and EMCV data was used for mapping. This GTF file was processed using the Annotations scripts from the Intron-reads repository (https://github.com/charitylaw/Intron-reads) in order to define exon and gene body regions. Counts were obtained using featureCounts from Rsubread (v2.8.1), with isPairedEnd and useMetaFeatures set to TRUE, allowMultiOverlap set to FALSE and strandSpecific. Intron counts were obtained by subtracting exon counts from gene body counts.
Assembly: Combined hg38 and EMCV (DQ288856.1) genomes
Supplementary files format and content: CSV file containing raw read counts mapped to introns or exons

growth_protocol: LIM1215 cells were maintained in RPMI (Sigma Aldrich) supplemented with 10% v/v foetal calf serum (FCS) and 2 mM L-glutamine (Gibco).

extract_protocol:
Cytoplasmic RNA was extracted using Cytoplasmic & Nuclear RNA Purification Kit (Norgen) according to manufacturer’s instructions.
Total RNA libraries were prepared, starting with 500 ng of total RNA, according to the Illumina Tru-Seq Stranded Total RNA-Seq protocol (protocol 1000000040499) with RiboZero depletion, using unique dual indexes. 150 base paired-end sequencing was performed on a NextSeq 2000 P3 chip, loading pooled libraries at a concentration of 1,000 pM (protocol 1000000109376). Approximately 100 million reads were obtained per sample.

treatment_protocol: Cells were infected with EMCV (MOI = 0.01) for 48 hr, or treated with IFN for 6 hr.

value: GFP

value: uninfected


title: UW14

description: Library name: UW14


title: Unwounded skin tissue 3

status: Public on Jul 14 2026

city: Maebashi

first: Akihiko

last: Uchiyama

state: Gunma

department: Dermatology

country: Japan

institute: Gunma University

description: Library name: N2_S15genesresults

data_processing:
Reads were aligned to the mm10 assembly of the mouse genome (NCBI Build 38, obtained from the UCSC Genome Browser website) using STAR aligner. Gene-level raw count data were used for downstream analyses. RNA-seq data were analyzed using the iDEP Genomics Suite (https://bioinformatics.sdstate.edu/idep/). Relative log expression (RLE) plots were used to assess data normalization and quality.
Differential gene expression analysis was performed using the Wald test for pairwise comparisons. For human samples, publicly available RNA-seq datasets comparing PG lesional skin and normal skin were analyzed. In mouse samples, brequinar-treated skin was compared with vehicle-treated skin and with unwounded skin. Gene Ontology (GO) terms (p < 0.01, fold change > 4 for human and p < 0.05, fold change > 1.5 for mouse) were obtained using ToppGene (https://toppgene.cchmc.org/).
Assembly: mm 10
Supplementary files format and content: csv file including normalized count value for all samples

source_name: Skin

extract_protocol:
Total RNA from skin tissue and cells were isolated using a RNeasy Mini Kit (Qiagen, Valencia, California). Total 100 ng
Library preparation was carried out using the KAPA mRNA HyperPrep kit (KAPA BIOSYSTEMS, KK8580) according to the manufacturer’s protocols. Library quality was assessed using an Agilent 4200 TapeStation (Agilent, CA, US). Paired-end sequencing was performed on a NextSeq 2000 platform (Illumina).

value: Skin


title: Smart-seq2 of tdTomato-positive neurons from Run3-2

city: Guangzhou

first: Can-Yuan

last: Zhang

state: Guangdong

address: No.1023-1063 South Shatai Road, Baiyun District, Guangzhou City, Guangdong Province, P.R.China

department: Department of Neurobiology, School of Basic Medical Sciences

institute: Southern Medical University

description:
Library name: Run3-2
Smart-seq2 RNA-seq library generated from FACS-isolated tdTomato-positive neurons in the LH+ Run group.

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed with Trimmomatic v0.39 to remove low-quality reads and trim adapter sequences.
Clean reads were aligned to the Mus musculus mm10 reference genome using STAR v2.7.5c.
Gene-level expression was quantified using StringTie v2.1.7 to obtain gene-level FPKM values and gene count matrices.
Differential expression analysis was performed using DESeq2 for comparisons based on the gene count matrix. edgeR was used for differential analysis of groups without duplicate samples.
Gene Ontology enrichment analysis was performed using topGO v2.24.0.Unsupervised hierarchical clustering was performed using log2(FPKM + 1) values across samples. Genes used for clustering were selected based on expression and variability criteria. Supervised hierarchical clustering was performed using differentially expressed genes with FPKM > 1.
Assembly: mm10
Supplementary files format and content: All_FPKM.txt

source_name: Hippocampal DG

extract_protocol:
The RNA from tdTomato+ neurons was converted to cDNA using the Smart-seq2 protocol.
RNA from tdTomato-positive neurons was reverse-transcribed into cDNA using the Smart-seq2 protocol. Amplified cDNA and final sequencing libraries were prepared by Beijing Geek Gene and subjected to quality and quantity control before sequencing.

value: Hippocampal DG

value: tdTomato+ neurons

value: Run

tag: batch

value: batch 1


title: M07e_C_Replicate_1

description:
Library name: Sample_13
M07e_C_R1

value: WT


title: lung-derived CD45+ immune cells post control CAR T treatment #2 TCR

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: Library name: Ctrl2_TCR

data_processing:
The Cell Ranger v6 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix and TCR filtered contig annotations for single cells in each sample

source_name: lung

growth_protocol: CD45+ immune cells isolated from lung were used directly for experiments.

extract_protocol:
CD45+ immune cells were sorted and loaded onto the Chromium Controller according to their respective cell counts to target 10,000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 5’ v2 Library and Gel Bead Kit (10x Genomics)

value: lung

value: CD45+ immune cells

value: wild type

value: Sort-purified CD45+ immune cells


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter BAC rep2

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 2 of 3. BioSample: SAMN60523468.

value: sub-MIC bacitracin


title: UW13

description: Library name: UW13

value: brain

value: no dementia

value: unsorted brain nuclei


title: Smart-seq2 of tdTomato-positive neurons from Run2-2

description:
Library name: Run2-2
Smart-seq2 RNA-seq library generated from FACS-isolated tdTomato-positive neurons in the LH+ Run group.


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter BAC rep1

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 1 of 3. BioSample: SAMN60523467.


title: M07e_Replicate_3

description:
Library name: Sample_9
M_07e_R3

value: Acute Megakaryoblastic Leukemia Cells


title: UW12

description: Library name: UW12

source_name: brain


title: Smart-seq2 of tdTomato-positive neurons from Run1-2

description:
Library name: Run1-2
Smart-seq2 RNA-seq library generated from FACS-isolated tdTomato-positive neurons in the LH+ Run group.


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter UI rep3

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 3 of 3. BioSample: SAMN60523466.

value: uninduced (vehicle control)


title: M07e_Replicate_2

description:
Library name: Sample_8
M_07e_R2


title: UW11

description: Library name: UW11


title: Smart-seq2 of tdTomato-positive neurons from NR3-2

description:
Library name: NR3-2
Smart-seq2 RNA-seq library generated from FACS-isolated tdTomato-positive neurons in the LH+ NR group.

value: Non Run


title: M07e_Replicate_1

description:
Library name: Sample_7
M_07e_R1


title: UW10

description: Library name: UW10


title: GM27

city: New York

first: Edridge

middle: Kevin

last: D'Souza

state: NY

address: 1130 St Nicholas Ave

department: Hematology/Oncology

institute: Columbia University

description:
Library name: GM27
Single nucleus RNA sequencing

data_processing:
Raw snRNA data were analyzed by aligning demultiplexed FASTQ files to HRCh38-2020-A human transcriptome using CellRanger v7.1.0
Ambient RNA was removed using CellBender v0.2.2 and doublets were flagged for downstream removal using Scrublet (Wolock et al., 2019)
Expression matrices were processed in R v4.2.0 using Seurat v4.3.0.1. Barcodes were filtered to keep cells with 200-12000 genes and <15% mitochondrial gene load, and to retain predicted singlets as well as predicted doublets in the G2M/S phase.
Downstream analysis followed the Seurat NormalizeData pipeline, and sample integration used the Seurat CCA Integration pipeline.
Assembly: GRCh38-2020-A transcriptome
Supplementary files format and content: Gene expression matrix (raw output from CellRanger)

molecule: nuclear RNA

source_name: Hepatic metastasis

extract_protocol:
We obtained fresh frozen tissue specimens from the New York Presbyterian/Columbia University Medical Center under IRB approval (#AAAT6521, AAAS9513) and prepared them as previously described for sequencing (Wang, Y. et al., Nat. Genet. 2023; Luthria, K. et al., Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res. 2024). We embedded samples in Tissue-Tek Optimal Cutting Temperature (OCT) Compound (Sakura Finetek; #4583) and obtained 4-5 sections of 20 µm thickness per sample using a Leica CM1950 cryostat (Leica Biosystems, Wetzlar, Germany). We placed the samples in 5 mL tubes (Eppendorf, Hamburg, Germany), washed with ice cold PBS (Thermo Fisher, #10010023), centrifuged for 2 minutes at 400g, then discarded the supernatant and resuspended in 1 mL ST buffer [146 mM NaCl, 10 mM Tris-HCl pH7.5, 1 mM CaCl2, and 21 mM MgCl2 in ultrapure water] with 0.03% Tween-20 (Sigma Aldrich, #P7949) and 0.1% BSA (New England Biolabs, #B9000S) plus or minus 40 U/mL RNAse OUT inhibitor (Thermo Fisher, #10777019). We pipetted each suspension 15 times with a 1 mL pipette to mechanically dissociate tissue, then incubated for 5 minutes on ice before repeating the pipetting and finally quenching with 4 mL ST buffer plus or minus 40 U/mL RNAse OUT (Thermo Fisher, #10777019). We pre-wetted sequential 70-micron nylon mesh filters (Fisher Scientific, #NC0446099), then filtered samples into a 50 mL conical tube and washed the filter with 5 mL ST buffer. We centrifuged for 5 minutes at 500g and discarded supernatant to isolate the dissociated nuclei, which were resuspended in 100-400 µl ST buffer, filtered with a 40 µm mesh filter (Fisher Scientific), stained with 50 µg/ml Hoechst 33342 (Thermo Fisher, #H3570), and then counted with a Neubauer counting chamber (Bulldog Bio, Inc., Portsmouth, NH).
We loaded 0.9-1.5e3 nuclei in ST buffer without RNAse inhibitor using a Chromium controller and 5’ chemistry v2 capture (10X Genomics, #1000263). We prepared cDNA libraries according to manufacturer instructions for reverse transcription and cleanup, and performed an extra cycle of cDNA amplification to compensate for the reduced total RNA content when analyzing single nuclei compared to single cells. We prepared final sequencing libraries with the 10X Library Construction Kit (#1000190) and Dual Index Kit TT Set A (#1000215) and quantified them using D1000 and D5000 reagents (Agilent, #5067-5583 and #5067-5589) on an Agilent 2200 TapeStation system. We then mixed samples and sequenced to a target depth of at least 20,000 reads per droplet using NovaSeq S4 (Illumina, San Diego, CA) with at least 2x100bp read length.

value: Hepatic metastasis

value: Tumor (nuclei)

tag: treatment stage

tag: patient id

tag: response

value: PR


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter UI rep2

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 2 of 3. BioSample: SAMN60523465.


title: RAW264.7 cells, Let-7c, biol rep 4

description: Library name: Let7c4

value: Murine macrophage

value: cell line

value: Transfected with let-7c-5p mimics.


title: CD41_MK_Replicate 3

description:
Library name: Sample_6
CD41_R3

source_name: CD41+ Megakaryocyte Progenitor Cells

value: CD41+ Megakaryocyte Progenitor Cells

value: Megakaryocyte Progenitor Cells

value: WT


title: UW9_Pu

description: Library name: UW9_Pu


title: Smart-seq2 of tdTomato-positive neurons from NR1-2

description:
Library name: NR1-2
Smart-seq2 RNA-seq library generated from FACS-isolated tdTomato-positive neurons in the LH+ NR group.

value: Hippocampal DG

value: tdTomato+ neurons

value: batch 1


title: RAW264.7 cells, Let-7c, biol rep 3

description: Library name: Let7c3


title: Streptococcus pyogenes MGAS10870 delta-spxA1 NanoString nCounter UI rep1

source_name: NanoString nCounter, delta-spxA1 MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 1 of 3. BioSample: SAMN60523464.


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter hNP1 rep3

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 3 of 3. BioSample: SAMN60523463.

value: wild-type


title: Streptococcus pyogenes MGAS10870 delta-spxA2 NanoString nCounter UI rep2

source_name: NanoString nCounter, delta-spxA2 MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 2 of 3. BioSample: SAMN60523474.


title: CD41_MK_Replicate 2

description:
Library name: Sample_5
CD41_R2


title: UW9

description: Library name: UW9

value: brain

value: no dementia

value: unsorted brain nuclei


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter hNP1 rep2

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 2 of 3. BioSample: SAMN60523462.


title: RAW264.7 cells, Let-7c, biol rep 5

description: Library name: Let7c5


title: CD41_MK_Replicate 1

description:
Library name: Sample_4
CD41_R1


title: UW8

description: Library name: UW8


title: RNA_deg_Ctrl11_Act4

city: Schlieren

first: Ataman

last: Sendoel

address: Wagistrasse 12

department: Institute of Regenerative Medicine

institute: University of Zurich

description:
Library name: Ctrl11_Act2
RNA sequencing from control 120h gastruloids treated with Acinomycin D for 4h, Replicate 2

data_processing:
Bioinformatic analysis of single-cell sequencing data: Raw sequencing data in the form of BCL files, were demultiplexed using Illumina bcl2fastq v2.20 with default settings. Up to one mismatch in the sample barcode sequences was allowed. Resulting fastq files were processed using the BD Rhapsody Pipeline (version 1.9.1) hosted at the Seven Bridges’ cloud platform (https://www.sevenbridges.com/). A custom mouse reference genome, based on Gencode vM25 (GRCm38.p6), was generated and combined with the 669 sgRNAs sequences. Based on STAR aligner, a custom STAR reference genome was created and the Refined Putative Cell Calling option was disabled during the pipeline execution. For downstream analysis, unique molecular identifier (UMI) count data was corrected by BD Genomics Recursive Substitution Error Correction (RSEC).  Bioinformatic analysis of dial-out data: PCR dial-out data was processed using an in-house custom Python script as previously described. Three 9-nucleotide cell barcodes were extracted from the 97 possible barcodes from Read 1. Up to one mismatch was allowed for each barcode (Hamming distance of 1). The script retrieved the 8-nucleotide UMI sequences from Read 1 as per the BD manual. For valid barcodes, sgRNAs were identified in Read 2 by performing an exact match search for the 20-nucleotide sgRNA sequence. Following UMI deduplication sgRNA UMI counts per cell were computed. In case of multiple sgRNAs detected for an individual cell, specific sgRNA assignment was only performed if the cells UMI count exceeded the 99th percentile.  Processing of single-cell RNA sequencing data: The Scrublet Python package was used for duplet detection and removal on each individual sample. Expected doublet rates were adjusted based on estimates by the BD Rhapsody scanner. Genes expressed at least 5 cells were retained. Following filtering, 4 datasets from 2 different screen replicates were combined in Seurat using the Harmony package. Data from Cnot8 KO, Cnot7 KO and Control organoids comes from a single cartridge/whole transcriptome assembly, with no need for integration. Only cells containing detected sgRNAs and classified as singlets were selected for further analysis. Cells were filtered based on the following criteria: UMI counts > 500, UMI counts lower than the 0.99 quantile (to remove outliers) and mitochondrial gene content < 20%. Filtered datasets were then processed using Seurat’s standard pipeline.
Bulk RNA sequencing data analysis: Paired-end RNA-seq data was processed using the Nextflow RNA-seq pipeline (https://github.com/nf-core/rnaseq) version 3.14.0 as previously described. In short, the FastQC program was used for quality control, followed by quality and adapter trimming using TrimGalore. Read alignment was performed to the Gencode vM25 (GRCm38.p6) reference by STAR. Reads were quantified using Salmon. Quality control of analysis pipelines was done by MultiQC.    Ribosome profiling data analysis: UMI- tools in combination with a custom “regular expression pattern” were used to extract ribosome footprints from fastq files. Footprints above minimal length cutoff of 20 nt were extracted, along with sample barcode 5 nt in length. For further processing adapter sequences (AGATCGGAAG) were moved to the 7 nt UMI sequence of the fastq header. Removal of reads aligning to rRNAs and tRNAs was performed using bowtie2 v2.2.5. All remaining reads were aligned to the Gencode vM25 (GRCm38.p6) reference genome by STAR v2.7.11a allowing up to one mismatch (--outFilterMismatchNmax 1) and a maximum of 20 multimappers (--outFilterMultimapNmax 20). UMI deduplication of the aligned bam files was performed using the UMI-tools dedup command. Reads mapping to the CDS regions of the genome in forward strand were counted by featureCounts program.
Nanopore data bioinformatic analysis and poly(A) length estimation: Raw nanopore reads in .pod5 format were basecalled and mapped to the reference mouse genome GRCm38 (primary assembly, obtained from the GENCODE website) using the Dorado software [https://github.com/nanoporetech/dorado] version 0.8.3 with the model rna004_130bps_sup@v5.1.0. Dorado is the software package developed and supported by Oxford Nanopore Technologies for the processing of raw nanopore data obtained on their platform. Dorado uses a deep learning-based algorithm for basecalling (transforming nanopore current data to nucleotide sequence), minimap2 aligner [PMID: 29750242] for read alignment to the genome, and a separate heuristic algorithm for estimating poly(A) tail length in each read. Importantly, successfully estimated tail lengths are stored as the “pt:i” tags in the output .bam files, while the basecalled sequences of reads contain only short fragments of poly(A) tails which are not informative for actual length of the poly(A) tails. Identification of the poly(A) tails in the reads was configured to tolerate non-adenine gaps up to 3 nt in length: tail_interrupt_length = 3. We further retained only uniquely mapped reads with mapping quality above or equal to one (in minimap2 output, quality=0 indicates that a read is a multimapper that aligns equally well to more than one genomic loci) and present “pt:i” tag. In total, ~8.1 mln reads were retrieved from four samples (two bioreplicates for each of the two conditions: Cnot8 KO and Control), with ~1.7 to ~2.5 mln reads per sample. Read counting was performed by featureCounts.
For a subset of analyses, the WTA reads were aligned and quantified with STARsolo (STAR v2.7.11b) against the Gencode vM25 (GRCm38.p6) genome, using the BD Rhapsody bead cell-barcode and UMI configuration (CB_UMI_Complex mode with single-mismatch whitelist matching).
Assembly: Gencode Mouse vM25 (GRCm38.p6)
Supplementary files format and content: Comma-separated value files and matrix files with count numbers, *_counts.csv.gz files contain Cell Barcode, Gene Symbol and RSEC adjusted counts.
Supplementary files format and content: Some single-cell WTA gene-expression matrices are provided in the standard STARsolo output format - three files per sample: *_matrix.mtx.gz (genes x cells, integer UMI counts) with *_barcodes.tsv.gz (composite cell barcodes) and _features.tsv.gz (Ensembl gene ID, gene symbol, feature type). Dial-out sgRNA files (_DO.csv.gz) give the per-cell sgRNA assignment with columns: cell_barcode, cell_index, sgRNA, umi_count, sgrna_detected.

source_name: Gastruloids

growth_protocol: Mouse embryonic stem cell culture: The dual T/Brachyury-mCherry, SOX1-GFP reporter (SBR) mouse ES cell line was cultured in in tissue culture treated 6 well plates (Thermo Scientific, 140675), in DMEM with Glutamax (Gibco, 7001569) supplemented with 10% FCS (XXX), Penicillin-Streptomycin (100U/ml, 100µg/ml respectively), non-essential amino acids (0.1 mM, Gibco, 11140050), sodium pyruvate (1mM, Thermo Scientific, 11360070), , beta-mercaptoethanol (0.11 mM, Gibco, 21985023) , 3 µM CHIR99021 (SML1046), 1 µM PD0325901 (S1036), 100u/mL LIF (produced in house). Cells were split every 48-72h, by accutase treatment followed by centrifugation at 200 g, 4min and seeding between 75 000 and 150 000 cells per well.

extract_protocol:
Gastruloids were generated as described previously. In short, murine embryonic stem cells (mESCs) are washed twice with PBS, followed by a detachment using Accutase (AT-104) for 4 min at 37C, 5% CO2. Cells were collected in 4.5 ml of embryonic stem cell medium with 10% fetal calf serum. Cells were centrifuged 200xg, 4min, 4°C and then resuspended in 10 ml PBS, followed by a second spin and PBS wash. Finally, cells were resuspended in 1 ml of N2B27 and counted using a hemocytometer. 40 µl of N2B27 with 300 cells per well were seeded in low adhesion 96 well plates (CLS7007-24EA) and incubated for 48h at 37C, 5% CO2. After 48 hours gastruloids were pulsed with 150uL of N2B27 supplemented with 3uM CHIR99021 (SML1046-5MG). Medium was refreshed using N2B27 every 24 hours for the extend of culture (between 120-144h). 120h gastruloids were harvested using P1000 cut-tips and subjected to single cell sequencing. In short gastruloids were collected in 15 ml tubes, washed once with PBS and incubated with accutase for 15 mins at 37C. Cell suspensions were resuspended using low adhesion tips and centrifuged 200xg, 4min, 4C. For sorting, cells were resuspended in FACS buffer (2% FCS and 0.5 ng/ul DAPI in PBS), passed through a 35 µm filter cap into 5 ml FACS tubes and sorted for GFP+ populations using a BD FACSAria III cell sorter using a 70 µM nozzel. Sorted cells were then spun down 15 min at 400xg, 4°C and then resuspended in BD sample buffer. Unsorted gastruloids were harvested and processed the same way, resuspended in sample buffer and then passed through 35 µm cell filters 3 times. Single cell suspensions were prepared for sequencing using the BD Rhapsody Single-Cell Analysis System with the BD Rhapsody Cartridge Kit (633733). Bead based reverse transcription, amplification and sequencing library production was performed following manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 2.0).                                                                   Samples for Nanopore direct RNA-seq: Samples for Nanopore direct RNA-sequencing were harvested at 72 h of gastruloid development. Gastruloids were harvested using cut P1000 tips, collected in 15 ml tubes and washed 2 times in PBS+CHX. Supernatant was removed, and organoids were flash frozen in liquid nitrogen. Frozen organoids were then resuspended in ribosome lysis buffer (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase, 100µg/mL CHX), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and flash frozen in liquid nitrogen, before being stored at -80 °C before downstream processing.                    Samples for ribosome profiling: Ribosome profiling experiments were performed as previously described, with minor modifications for gastruloids. In short, gastruloids were harvested at indicated time points using cut P1000 tips and collected into 15 ml tubes. Gastruloids were washed 2 times in PBS+CHX, supernatant was removed, and organoids were flash frozen in liquid nitrogen. Frozen organoids were then resuspended in ribosome lysis buffer (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase, 100µg/mL CHX), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and flash frozen in liquid nitrogen, before being stored at -80 °C before downstream processing. Samples for RNA degradation: Gastruloids at 96 h of development were treated with 10 µM Actinomycin D (ThermoScientific, 11805017) in N2B27 and gastruloids were harvested after 0, 2 and 4 h of treatment. Gastruloids were harvested at indicated time points using cut P1000 tips and flash frozen. Frozen organoids were then resuspended in ribosome lysis buffer without cyclohexamide (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and RNA was purified using the DirectZol RNA kit. Purified RNA was submitted for library preparation and sequencing to Novogene.
Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). Library construction protocol for RNA-seq: RNA was isolated from lysates gastruloids at indicated time points as described in the Ribosome profiling section using TRIzol®  LS Reagent (Invitrogen, 10296028) and column purified with a Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared and sequenced at Novogene. Library construction protocol for Other:  As previously described, the sgRNA-containing region was amplified from the BD Rhapsody beads using a nested KAPA Polymerase reaction. In the first polymerase reaction (PCR1), the Rhapsody beads from each separate cartridges were resuspended and distributed into 4 separate 50 µL reactions  (100 µl KAPA HiFi HotStart ReadyMix (Roche 07958935001), 6 µl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 6 µl reverse primer (5′-TCTTGTGGAAAGGACGA-3′, 10 μM), 12 μl Bead RT/PCR Enhancer reagent from BD Biosciences and 72 μl nuclease-free water for a total volume of 200 μl). PCR1 conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 25 cycles of denaturation 95 °C for 30 s, annealing 53 °C for 30 s, extension 72 °C for 20 s and a final extension of 10 min at 72 °C. The 4 x 50 µl PCR1 product was pooled, and beads were removed using a magnet. Amplicons were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instructions. 3 μl of cleaned up PCR1 was used as template for PCR 2 (25 µL KAPA HiFi HotStart Ready Mix, 2 μl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 2 μl reverse primer (CAGACGTGTGCTCTTCCGATCTCTTGTGGAAAGGACGAAACA*C*C*G-3′, 10 μM), 18 μl nuclease-free water) for a total volume of 50 μl. PCR2 conditions were as follows: initial denaturation at 95 °C for 3 min, followed by 10 cycles of denaturation 95 °C for 30 s, annealing 60 °C for 3 min, extension 72 °C for 60 s, and a final extension of 5 min at 72 °C. Agencourt AMPure XP beads were used to clean up PCR2 product according to the manufacturer’s instructions  before the indexing PCR. Indexing PCR was performed according to BD Biosciences ‘mRNA Targeted Library Preparation’ protocol (doc ID: 210968 rev. 3.0). Library construction protocol for Ribo-seq: Ribosome profiling was conducted with some adjustments of the original method (64, 65). For RNA digestion, cell lysates were incubated with 1 U/µg of RNase 1 (Epicentre/Lucigen, 10U/µL) for 45 minutes at room temperature. Reaction was stopped by adding 4 µL of SUPERase Inhibitor (20 U/µL, SUPERase-InTM RNase Inhibitor Thermo Scientific AM2694). To eliminate free nucleotides and isolate ribosome-protected fragments, the RNase I-treated samples were processed using Amersham MicroSpin S-400 HR columns (Cytiva, 27514001). RNA extraction was performed utilizing TRIzol® LS Reagent (Invitrogen 10296028) in combination with the Direct-zolTM RNA MiniPrep kit (Zymo Research, R2052). Total RNA concentration was measured using QubitTM RNA broad range kit (Invitrogen, Q10210). Ribosome footprints were excised and extracted from a 15% TBE-UREA gel (Invitrogen, EC68852BOX) using the 20nt, 22nt, 27nt, 30nt and 60nt oligonucleotides mix as markers (1 µL of 10 µM dilution in 19µL RNase-free H2O). Extraction was performed overnight with RNA extraction buffer (300mM NaOAc pH=5.5, 1mM EDTA, 0.25% v/v SDS). T4 PNK (NEB, M0201S) end-healing reaction was performed on the ribosome footprints for 1 hour at 37˚C. Linker ligation reaction followed using T4 RnI truncated K227Q (NEB, M0351L) in combination with 20 µM of preadenylated linker for 3 hours at 22˚C (50% w/v PEG-8000, 10X T4 RNA ligase, preadenylated linker, T4 RnI truncated K227Q). Ribosomal RNA was depleted using biotinylated rRNA depletion oligos (2 µM) by mixing 10 µL of sample with 10 µL of oligo mix and incubated for 2 minutes at 80˚C, followed by a gradual decrease in temperature to 25˚C. MyOne Streptavidin dynabeads (Life Technologies, 65001) were used to recover the samples. Reverse transcription was performed on the Ribosomal RNA-free samples using SuperScriptTM IV Reverse Transcriptase (Invitrogen, 18090050). Footprints were excised and extracted from a 15% TBE-UREA gel. Extraction was performed overnight with DNA extraction buffer (10mM Tris-HCl pH=8, 300mM NaCl, 1mM EDTA). cDNA was circularized using CircLigase II (100 U/µL, Biosearch, CL4115K) for 1 hour at 60˚C. cDNA was amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific, F530S) using an individual index per sample. 6-12 cycle amplicons were visualized using an 8% TBE non-denaturing polyacrylamide gel to determine optimal cycle number. PCR was carried out with 7-9 cycles and analyzed on an 8% TBE non-denaturing polyacrylamide gel (Invitrogen, EC61252BOX). DNA was excised from gel and extracted using DNA extraction buffer by incubating overnight with gentle shaking. DNA was recovered and precipitated in 10 mM Tris-HCl pH=8. DNA was quantified using Qubit TM 1X dsDNA High Sensitivity Assay (Invitrogen, Q33230) and quality was verified using the Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Samples were pooled and prepared for sequencing.               Nanopore direct RNA-seq: RNA was isolated from ribosome profiling lysate buffer lysates using Direct-zol RNA Kit, according to manufacturer’s instruction. Nanopore direct RNA-sequencing library preparation was performed using the Direct RNA Sequencing Kit (SQK-RNA004) according to manufacturer’s instructions. Samples were loaded onto MinION flow cells (FLO-MIN114).

value: Gastruloids

value: SBR

value: mESCs/gastruloid cells


title: CD34_HSC_Replicate_3

description:
Library name: Sample_3
CD34_R3

source_name: CD34+ Hematopoietic Stem Cells

value: CD34+ Hematopoietic Stem Cells

value: Hematopoietic Stem Cells


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter hNP1 rep1

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), sub-MIC human neutrophil peptide-1 (hNP-1). Biological replicate 1 of 3. BioSample: SAMN60523461.


title: RNA_deg_Ctrl11_Act2

description:
Library name: Ctrl11_Act1
RNA sequencing from control 120h gastruloids treated with Acinomycin D for 2h, Replicate 2


title: M07e_KO_Replicate_2

description:
Library name: Sample_17
M07e_KO_C_R2

value: Acute Megakaryoblastic Leukemia Cells

value: DNMT3B knockout


title: UW16_Ce

description: Library name: UW16_Ce


title: UW7

description: Library name: UW7


title: Smart-seq2 of tdTomato-positive neurons from NR2-2

description:
Library name: NR2-2
Smart-seq2 RNA-seq library generated from FACS-isolated tdTomato-positive neurons in the LH+ NR group.

value: Non Run


title: RNA_deg_Ctrl11_Act0

description:
Library name: Ctrl11_Act0
RNA sequencing from control 120h gastruloids treated with Acinomycin D for 0h, Replicate 2


title: CD34_HSC_Replicate_2

description:
Library name: Sample_2
CD34_R2


title: UW6_Pu

description: Library name: UW6_Pu


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter BAC rep3

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 3 of 3. BioSample: SAMN60523460.

value: sub-MIC bacitracin


title: RNA_deg_Ctrl2_Act4

description:
Library name: Ctrl2_Act4
RNA sequencing from control 120h gastruloids treated with Acinomycin D for 4h, Replicate 1


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter BAC rep2

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 2 of 3. BioSample: SAMN60523459.


title: CD34_HSC_Replicate_1

description:
Library name: Sample_1
CD34_R1

value: WT


title: UW6_Ce

description: Library name: UW6_Ce


title: MB231 cells, shPAK5-3

city: Weifang

first: Zhenhai

last: Yu

address: No.288 Shengli East Street

institute: Weifang Medical University

data_processing:
After the library was constructed, the library was first diluted to 1.5ng/ul using a Qubit 2.0 Fluorometer for initial quantification.
The insert size of the library was detected using Agilent 2100 bioanalyzer, and the effective library concentration was accurately quantified by qRT-PCR after the insert size was as expected (effective library concentration above 2nM)
After passing the library inspection, the different libraries are pooled according to the effective concentration and the target downstream data volume required for Illumina sequencing.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: MB231 cells

extract_protocol:
RNA was extracted from tissues or cells using standard extraction methods, and then the RNA samples were strictly controlled. RNA purity was checked using the NanoPhotometer® spectrophotometer(IMPLEN, CA, USA).RNA integrity was 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: MB231 cells

value: breast cancer cells

value: PAK5 knockdown


title: RNA_deg_Ctrl2_Act2

description:
Library name: Ctrl2_Act2
RNA sequencing from control 120h gastruloids treated with Acinomycin D for 2h, Replicate 1


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter BAC rep1

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), sub-MIC bacitracin. Biological replicate 1 of 3. BioSample: SAMN60523458.

value: wild-type


title: UW6_v2

description: Library name: UW6_v2

value: brain


title: RNA_deg_Ctrl2_Act0

description:
Library name: Ctrl2_Act0
RNA sequencing from control 120h gastruloids treated with Acinomycin D for 0h, Replicate 1


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter UI rep3

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 3 of 3. BioSample: SAMN60523457.

value: uninduced (vehicle control)


title: MB231 cells, shPAK5-1


title: UW4_v2

description: Library name: UW4_v2

source_name: brain

value: no dementia

value: unsorted brain nuclei


title: RNA_deg_C8c4_Act2

description:
Library name: C8c4_Act2
RNA sequencing from Cnot8 KO 120h gastruloids treated with Acinomycin D for 2h, Replicate 2

value: Gastruloids

value: SBR

value: Cnot8 KO


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter UI rep2

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 2 of 3. BioSample: SAMN60523456.


title: Streptococcus pyogenes MGAS10870 wild-type NanoString nCounter UI rep1

source_name: NanoString nCounter, wild-type MGAS10870 (emm3), uninduced (vehicle control). Biological replicate 1 of 3. BioSample: SAMN60523455.


title: MB231 cells, shNC-3


title: MB231 cells, shPAK5-2


title: UW3

description: Library name: UW3


title: RNA_deg_C8c4_Act0

description:
Library name: C8c4_Act0
RNA sequencing from Cnot8 KO 120h gastruloids treated with Acinomycin D for 0h, Replicate 2

value: mESCs/gastruloid cells


title: RNA_deg_C8c4_Act4

description:
Library name: C8c4_Act4
RNA sequencing from Cnot8 KO 120h gastruloids treated with Acinomycin D for 4h, Replicate 2


title: UW5

description: Library name: UW5


title: Whole cells obtained after 5-days culture of EPCRHigh HSCs with R162, ATAC

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-ku

institute: Kumamoto University

library_source: genomic

data_processing:
The demultiplexing, barcode processing and fragment generation were made using the CellRanger-ARC software v2.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?).
Assembly: mm10
Supplementary files format and content: h5 files are Hierarchical Data Formats files of cellranger_arc count matrix output
Supplementary files format and content: tsv.gz files are gzipped tab delimited bed files of atac fragments
Library strategy: scMultiome

source_name: bone marrow

extract_protocol:
After HSCs were cultured for 5 days, whole cells were collected by a centrifuge.
Nuclei were isolated from collected cells, following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol (10x Genomics, Pleasanton, CA), and then resuspended in a cell concentration of 5000 cells/µl. Cells were processed using a Chromium Next GEM Chip J Single Cell Kit (10xGenomics, PN-1000230), Chromium Next GEM Single Cell Multiome Reagent Kit A (10x Genomics, PN-1000284), and Chromium Next GEM Single Cell Multiome ATAC Kit A (10x Genomics, PN-1000281), following the manufacturer’s User Guide. Targeted nuclei recovery was around 9,000. The single cell RNA and ATAC sequencing libraries were prepared using Dual Index Kit TT Set A (10x Genomics, 1000215) and Single Index Kit N Set A (10x Genomics, 1000212), respectively. The resulting libraries were sequenced by PE50 sequencing using a DNBSEQ-G400 system (MGI Tech, Shenzhen, China).

value: bone marrow

value: Hematopoietic stem cells


title: MB231 cells, shNC-2


title: UW2

description: Library name: UW2


title: RNA_deg_C8c2_Act4

description:
Library name: C8c2_Act4
RNA sequencing from Cnot8 KO 120h gastruloids treated with Acinomycin D for 4h, Replicate 1


title: Whole cells obtained after 5-days culture of EPCRHigh HSCs with R162, GEX


title: MB231 cells, shNC-1


title: RNA_deg_C8c2_Act2

description:
Library name: C8c2_Act2
RNA sequencing from Cnot8 KO 120h gastruloids treated with Acinomycin D for 2h, Replicate 1


title: UW1

description: Library name: UW1


title: Whole cells obtained after 5-days culture of EPCRHigh HSCs without R162, ATAC


title: FAPs, fibrogenic culture, fibro

city: San Francisco

first: Steven

middle: Michael

last: Garcia

state: CA

address: 1700 Owens St.

department: Orthopaedic Surgery

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: integrated metadata files and matrix files

source_name: cultured FAPs

extract_protocol:
Muscle was trimmed of excess fat, tendon, and connective tissue. Muscle was then mechanically and enzymatically digested in 1 mg/ml collagenase III (Worthington Biochemical Corporation, #NC0021929) in Dulbecco's Modified Eagle Medium (DMEM), 10% FBS (fetal bovine serum, Gibco, #10437028) and 1% Penicillin/Streptomycin (Gibco, #11550043) at 37°C for 70 minutes with intermittent manual needle trituration with an 18-gauge needle. Digests were washed with PBS and further digested with 0.25% trypsin at 37°C for 12–15 min. Suspensions were passed through 40 µm nylon mesh, erythrocytes were lysed with ACK lysing buffer (Quality Biological, #188-156-101) for 5–7 min on ice and washed in PBS with 2% FBS. Cells were washed and resuspended in 100 µl flow cytometry buffer (PBS with 2% FBS, 5 mM EDTA, 2 mM HEPES) per 1 gram of starting tissue weight. Antibody cocktail consisting of: anti-CD31 (eBioscience, #48-0319-42, eFluor 450) (2 µl per gram of starting muscle weight), anti-CD45 (eBioscience, #48-0459-42, eFluor 450) (2 µl), anti-CD56 (Miltenyi Biotec, #130-114-548, APC-Vio770) (8 µl), anti-CD34 (BD, #555823, PE-Cy5) (6 µl) and anti-PDGFRα (BioLegend, 323506, PE) (8 µl) was then added to the cells for 30 minutes on ice. Cells were washed and resuspended in flow cytometry buffer with 1:1000 sytox blue (ThermoFisher, #S34857). Viable CD31-/CD45-/CD56-/CD34+/PDGFRa+ FAPs were collected and spiked into a collection of all cells (sytox negative) to obtain samples with >50% FAPs. Cells were resuspended in 0.04% BSA in PBS at 1000 cells per μl to prepare for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina 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 sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: For cultured FAPs: FAPs were isolated from fresh tissue digests with the surface marker combination CD31-/CD45-/CD56-/CD34+/PDGFRα+. Primary cells were cultured in growth media: Ham's F-10 Nutrient Mix (Gibco, #11550043) containing 1% Penicillin/Streptomycin (Gibco, #11550043), 10% FBS (Gibco, #10437028), and 10ng/mL bFGF (Gibco, #PHG0264). Cell media was changed every 2-3 days and cells were passaged at 70-80% confluency. For adipogenic differentiation, FAPs were grown to 80% confluency in growth media and then switched to adipogenic media (StemPro Adipogenesis Differentiation Kit, Gibco, # A1007001). Media was changed every 2 days. For fibrogenic differentiation, FAPs were grown to 80% confluency in growth media and then switched to growth media containing, 10 ng/ml of TGFβ1 (Invitrogen, #PHG9204). Media was changed every 2 days.

value: cultured FAPs


title: Whole cells obtained after 5-days culture of EPCRHigh HSCs without R162, GEX


title: RNA_deg_C8c2_Act0

description:
Library name: C8c2_Act0
RNA sequencing from Cnot8 KO 120h gastruloids treated with Acinomycin D for 0h, Replicate 1


title: FAPs, standard culture, std

description: 10x Genomics


title: PGK1_OE_replicate3

city: ChongQing

first: yuanze

last: zhou

address: No.30, Gaotanyan Main Street, Shapingba District

institute: The First Hospital Affiliated to Army Medical University (Southwest Hospital)

description:
Library name: PGK1_OE_replicate3
P-OE-3

data_processing:
Data quality control was performed using fastp to remove reads with adapters. Paired reads were removed under the following conditions: when the the number of N in any sequencing read exceeded 10% of the length of that read, and when any sequencing read contained low-quality bases (Q<=20) exceeding 50% of the length of that read. Subsequent analyses were based on clean reads. The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index, and clean reads were aligned to the reference genome.
Assembly: hg38
Supplementary files format and content: geneID_symbol_readcount.txt file includes raw counts for each Sample
Supplementary files format and content: geneID_symbol_fpkm.txt file includes FPKM values for each Sample

source_name: Connective tissue

extract_protocol:
The mRNA was prepared by VAHTS mRNA Capture Beads 2.0 (N403-C4, Vazyme Biotech Co., Ltd.) following manufacturer's protocols
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit (NR616-02, Vazyme Biotech Co., Ltd.) following manufacturer's protocols

value: Connective tissue

value: PGK1 OE Cell

value: PGK1 OE


title: PGK1_OE_replicate2

description:
Library name: PGK1_OE_replicate2
P-OE-2


title: Whole blood, VI, rep 5

city: Durham

first: Nathaniel

middle: P

last: Hernandez

state: NC

address: 3 Genome Ct

department: Anesthesiology

institute: Duke University

description:
Library name: Nackley_20
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

data_processing:
Sequencing reads were processed using the miRquant small RNA-seq pipeline. Adapter-trimmed reads were mapped using a two-tier Bowtie and SHRiMP strategy against the Rattus norvegicus RGSC 3.4 (rn4) reference genome. Small RNA expression was quantified as reads per million mapped reads (RPM).
Assembly: RGSC 3.4 (rn4)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV file containing normalized miRNA expression values reported as reads per million (RPM), with rows representing individual small RNAs and columns representing individual biological samples.

organism: Rattus norvegicus

source_name: Whole blood

extract_protocol:
Whole blood was collected in PAXgene Blood RNA tubes (BD Biosciences). Total RNA was isolated using the PAXgene Blood miRNA Kit (Qiagen). RNA quantity and quality were assessed using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was normalized to approximately 250 ng/µL with RNase-free water prior to library preparation.
Small RNA libraries were prepared using the TriLink Small RNA Library Prep Kit according to the manufacturer's protocol. Libraries were sequenced on an Illumina HiSeq 2000 platform at the Next Generation Sequencing and Bioinformatics Core, University of Texas Health Science Center at San Antonio. Each biological sample was sequenced with three technical replicates.

value: Whole blood

value: WT

value: Vehicle and ICI118551/SR59230A


title: PGK1_OE_replicate1

description:
Library name: PGK1_OE_replicate1
P-OE-1


title: FAPs, adipogenic culture, adipo

description: 10x Genomics


title: Gast_144_C7c2

description:
Library name: G144_C7c2
RNA sequencing from sorted brachyury-P2A-mCherry cells

value: Cnot7 KO


title: Gast_144_C7c1

description:
Library name: G144_C7c1
RNA sequencing from sorted brachyury-P2A-mCherry cells


title: Whole blood, VV, rep 5

description:
Library name: Nackley_19
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Vehicle and Vehicle


title: muscle, ham, 32m

description: 10x Genomics

source_name: muscle

value: muscle

tag: location

value: hamstring


title: PGK1_WT_replicate3

description:
Library name: PGK1_WT_replicate3
v511-3

value: WT Cell

value: PGK1 WT


title: Gast_144_C8c4

description:
Library name: G144_C8c4
RNA sequencing from sorted brachyury-P2A-mCherry cells

value: Gastruloids

value: SBR

value: Cnot8 KO


title: Whole blood, OI, rep 5

description:
Library name: Nackley_18
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: muscle, ham, 24m_ham

description: 10x Genomics


title: PGK1_WT_replicate2

description:
Library name: PGK1_WT_replicate2
v511-2


title: Gast_144_C8c2

description:
Library name: G144_C8c2
RNA sequencing from sorted brachyury-P2A-mCherry cells

value: mESCs/gastruloid cells


title: Whole blood, OV, rep 5

description:
Library name: Nackley_17
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: OR486 and Vehicle


title: PGK1_WT_replicate1

description:
Library name: PGK1_WT_replicate1
v511-1

value: Connective tissue


title: Whole blood, VI, rep 4

description:
Library name: Nackley_16
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: Gast_125_CTRL_RNA

description:
Library name: Gast_125_CTRL_RNA
RNA sequencing from Control, Replicate 3

value: CTRL


title: CD4-GPA-tEPOR, donor 3

first: Matthew

last: Porteus

address: 265 Campus Drive

department: Pediatrics

description: Library name: SL156_4_d14

data_processing:
Base calling performed by Novogene using standard Illumina pipeline (NovaSeq X Plus).
Reads were quantified against the GENCODE v44 (GRCh38) transcriptome, including custom GFP, CD4-GPA, and CD4-GPA-tEPOR transgene sequences, using Salmon v1.10.3.
Mitochondrial genes were removed prior to downstream analysis.
Transcript-level counts were aggregated to gene level using tximport; transgene counts were added manually. Differential expression was assessed with DESeq2 (design: donor + treatment), comparing each treatment (CCR5-GFP, CD4-GPA, CD4-GPA-tEPOR) to mock.
Assembly: GRCH38
Supplementary files format and content: CSV file containing gene-level raw read count matrix, generated from Salmon transcript-level quantifications aggregated with tximport; includes manually added counts for custom transgene sequences (GFP, CD4-GPA, CD4-GPA-tEPOR).

source_name: In vitro-differentiated erythroid cells derived from cord blood CD34+ hematopoietic stem/progenitor cells

extract_protocol:
Qiagen RNeasy Plus Micro Kit; REF 74034
RNA-seq libraries were prepared by Novogene. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, followed by fragmentation and first- and second-strand cDNA synthesis using random hexamer priming. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, and amplification, then were quantified by Qubit, real-time PCR, and bioanalyzer prior to sequencing on an Illumina platform (paired-end, 150 bp).

tag: individual

value: donor 3

value: D14 differentiated erythroids


title: Whole blood, VV, rep 4

description:
Library name: Nackley_15
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Whole blood

value: WT


title: Gast_125_C8_RNA

description:
Library name: Gast_125_C8_RNA
RNA sequencing from Cnot8 KO, Replicate 2

source_name: Gastruloids


title: muscle, cuff, 79f_cuff

description: 10x Genomics

value: supraspinatus


title: CD4-GPA, donor 3

description: Library name: SL156_3_d14

value: In vitro-differentiated erythroid cells derived from cord blood CD34+ hematopoietic stem/progenitor cells


title: Whole blood, OI, rep 4

description:
Library name: Nackley_14
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: Gast_124_C7_RNA

description:
Library name: Gast_124_C7_RNA
RNA sequencing from Cnot7 KO Replicate 1

value: Cnot7 KO


title: muscle, cuff, 72_cuff

description: 10x Genomics

value: muscle


title: GFP, donor 3

description: Library name: SL156_2_d14


title: Gast_124_CTRL_RNA

description:
Library name: Gast_124_CTRL_RNA
RNA sequencing from Control, Replicate 3


title: Whole blood, OV, rep 4

description:
Library name: Nackley_13
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: muscle, delt, 56m_delt

description: 10x Genomics

value: deltoid


title: Mock, donor 3

description: Library name: SL156_1_d14

value: Mock


title: Whole blood, VI, rep 3

description:
Library name: Nackley_12
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Vehicle and ICI118551/SR59230A


title: CD4-GPA-tEPOR, donor 2

description: Library name: SL155_4_d14

value: donor 2


title: muscle, cuff, 56m_cuff

description: 10x Genomics


title: Gast_124_C7_RNA1

description:
Library name: Gast_124_C7_RNA1
RNA sequencing from Cnot7 KO Replicate 1

value: Gastruloids

value: SBR


title: Gast_124_C8_RNA

description:
Library name: Gast_124_C8_RNA
RNA sequencing from Cnot8 KO, Replicate 2

value: mESCs/gastruloid cells

value: Cnot8 KO


title: Whole blood, VV, rep 3

description:
Library name: Nackley_11
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Vehicle and Vehicle


title: muscle, delt, 48f_delt

description: 10x Genomics


title: CD4-GPA, donor 2

description: Library name: SL155_3_d14


title: Gast_123_CTRL_RNA

description:
Library name: Gast_123_CTRL_RNA
RNA sequencing from Control, Replicate 3

value: CTRL


title: Whole blood, OI, rep 3

description:
Library name: Nackley_10
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: muscle, cuff, 48f_cuff

description: 10x Genomics


title: GFP, donor 2

description: Library name: SL155_2_d14

value: D14 differentiated erythroids


title: Gast_123_C8_RNA

description:
Library name: Gast_123_C8_RNA
RNA sequencing from Cnot8 KO, Replicate 2


title: Mock, donor 2

description: Library name: SL155_1_d14


title: Whole blood, OV, rep 3

description:
Library name: Nackley_9
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Whole blood

value: OR486 and Vehicle


title: muscle, delt, 43m_delt

description: 10x Genomics


title: Gast_123_C7_RNA

description:
Library name: Gast_123_C7_RNA
RNA sequencing from Cnot7 KO Replicate 1


title: Whole blood, VI, rep 2

description:
Library name: Nackley_8
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: WT


title: muscle, cuff, 43m_cuff

description: 10x Genomics

value: supraspinatus


title: CD4-GPA-tEPOR, donor 1

description: Library name: SL154_4_d14

value: In vitro-differentiated erythroid cells derived from cord blood CD34+ hematopoietic stem/progenitor cells

value: donor 1


title: Pseudomonas fluorescens GL-S-306, infected with phage KNP; enriched

city: Heverlee

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 20

department: Biosystems

country: Belgium

institute: KU Leuven

description: Library name: Sample 9

data_processing:
Real time basecalling and demultiplexing by the Guppy software (v3.2.10) in high accuracy mode.
read processing, mapping and identification of the viral transcription start sites (TSS) and termination sites (TTS) was performed according to the ONT-cappable-seq2 automated data-analysis workflow (https://github.com/LoGT-KULeuven/ONT-cappable-seq2)
Assembly: KIL3b (KU130131), KIL5 (KU130130), pphageB21 (MZ868714.1), f2 (NC_013638), KNP (NC_047827)
Supplementary files format and content: .txt files contain information on the location and efficiency of transcription start and termination sites of the phages

organism:
Pseudomonas fluorescens
Pseudomonas phage KNP

source_name: bacterial cells infected with phage

growth_protocol: An overnight culture of the bacterial host was diluted in 30 ml of fresh culture medium and grown to an OD600 of 0.3. At this point phages were added  and samples were taken throughout the entire infection cycle of the phage

extract_protocol:
All samples were pooled together and homogenized. The resulting sample was subjected to hot phenol treatment and ethanol precipitation to extract and purify the RNA
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109)

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

value: bacterial cell

value: enriched for primary transcripts

tag: infection stage

value: infected with phage KNP


title: Whole blood, VV, rep 2

description:
Library name: Nackley_7
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: GFP, donor 1

description: Library name: SL154_2_d14


title: Pseudomonas fluorescens SBW25, infected with phage f2; control

description: Library name: Sample 8

organism:
Pseudomonas fluorescens
Pseudomonas phage phi2

value: no enrichment

value: infected with phage f2


title: Whole blood, OV, rep 2

description:
Library name: Nackley_5
Female Sprague-Dawley rat whole blood collected after 14 days of treatment


title: Mock, donor 1

description: Library name: SL154_1_d14

source_name: In vitro-differentiated erythroid cells derived from cord blood CD34+ hematopoietic stem/progenitor cells.

value: Mock


title: Pseudomonas fluorescens SBW25, infected with phage f2; enriched

description: Library name: Sample 7


title: Streptococcus pyogenes MGAS10870 LiaSQ146A (SpxA2-OE) CovR ChIP-exo, biological replicate 3

first: Anthony

last: Flores

description:
Library name: spxA2OE_ChIPexo_rep3
CovR ChIP-exo in LiaSQ146A (SpxA2-OE) MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 3 of 3. FRiP=0.24. ChIP target: CovR (control of virulence response regulator).

data_processing:
Peaks called on merged BAM files using MACS3 v3.0.4: genome size 1,840,000 bp, --nomodel, --extsize 50, --shift -25, --keep-dup all, p-value 1e-10. High-confidence peaks retained at score > 5,000.
Differential CovR binding assessed using DiffBind v3.20 with DESeq2 v1.50.2 in R v4.5.3. Consensus peaks at score > 3,000 threshold; summit-centered 150bp windows for read counting; library-size normalization. FDR < 0.05 significant.
CovR binding motif occurrence assessed using FIMO v5.5.9 (MEME Suite). Dimer motif (WTWTTATAAWAAAAWNATDA) and monomer motif (ATTARA) from Horstmann et al. 2023. Fisher exact test for enrichment between peak classes.
Analysis code is available at https://github.com/ar-flores/SpxA1-SpxA2-MultiOmic-GAS  (DOI: https://doi.org/10.5281/zenodo.20476011)
Assembly: NZ_CP067090.1 (Streptococcus pyogenes MGAS10870, NCBI RefSeq)
Supplementary files format and content: BAM files: aligned reads per biological replicate (9 total), sorted and indexed. narrowPeak files: MACS3 peak calls (score > 5,000) per condition (3 files). CSV files: DiffBind consensus peaks, differential binding results, and FIMO motif hits (ST1-ST5).
Supplementary files format and content: ST1_all_700_peaks.csv: consensus peak coordinates with DESeq2-normalized counts per sample. ST2/ST3: differentially bound sites with log2FC, FDR, gene annotations. ST4: FIMO motif hits per peak. ST5: SpxA2OE vs SpxA2KO results.

organism: Streptococcus pyogenes

source_name: bacterial cells

growth_protocol: GAS strains were grown without agitation in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY) at 37 degrees C under 5% CO2 to mid-exponential phase (OD600 ~0.45).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature, quenched with glycine. Cells were lysed and chromatin sheared by sonication. CovR immunoprecipitation performed using a polyclonal anti-CovR antibody (N-terminal domain). ChIP-exo library preparation and lambda-exonuclease digestion performed by the Cornell ChIP-exo core facility.
ChIP-exo libraries prepared and sequenced by the Cornell ChIP-exo core facility on an Illumina NextSeq 500 platform (75nt paired-end reads).

treatment_protocol: Not applicable — no treatment applied prior to cross-linking.

value: bacterial cells

value: LiaSQ146A (SpxA2-OE)


title: Whole blood, VV, rep 1

description:
Library name: Nackley_3
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Vehicle and Vehicle


title: Streptococcus pyogenes MGAS10870 LiaSQ146A (SpxA2-OE) CovR ChIP-exo, biological replicate 2

description:
Library name: spxA2OE_ChIPexo_rep2
CovR ChIP-exo in LiaSQ146A (SpxA2-OE) MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 2 of 3. FRiP=0.21. ChIP target: CovR (control of virulence response regulator).


title: Patient 43, endometrium, healthy control

city: Bogota

first: Maria

middle: Camila

last: Rincon

state: Bogota

department: Biomedical Engineering

country: Colombia

institute: Universidad de los Andes

description:
Library name: P43
39 year old, Ovarian Cyst Naturally Reabsorbed

data_processing:
RNA-seq reads were mapped using HISAT2 (v.2.2.1) to the human reference genome hg38 from the Broad Institute public database (20 Broad Institute 2024). SAM files were sorted using Picard (v2.27.4). Read counts for each sample and each gene were calculated from the mapped sequences using Stringtie (v.1.3.5). The counts expression matrix was assembled using the script prepDE.py available with Stringtie. The obtained expression matrix was normalized using the VST method implemented in DESeq2
Assembly: hg38
Supplementary files format and content: FASTQ files includes raw counts for each Sample
Supplementary files format and content: csv files include TMP values for each Sample

source_name: Endometrium

extract_protocol:
Total RNA was extracted from preserved endometrium biopsies using the Monarch® Total RNA Miniprep Kit (New England Biolabs, Ipswich, MA, USA) following the instructions given for extraction from tissues (25-30mg of the sample).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Endometrium

tag: subject status

value: healthy control


title: KMD26_Pre

type: genomic

city: Palo Alto

first: Shota

last: Nishitani

address: 3165 Porter Dr.

department: Department of Psychiatry and Behavioral Sciences

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPIC v2 BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using the BeadArray Scanner (iScan) under standard settings

data_processing: Raw IDAT files were processed using the minfi package (Bioconductor) in R, with EPIC v2 manifest and annotation (IlluminaHumanMethylationEPICv2manifest and IlluminaHumanMethylationEPICv2anno.20a1.hg38). Background correction was performed using the Noob method (preprocessNoob). Beta values, methylated signals, unmethylated signals, and detection p-values were extracted for each probe and sample.

label: Cy3 and Cy5

source_name: KMD Delirium

label_protocol: Bisulfite conversion

extract_protocol: QIAamp DNA Mini Kit (QIAGEN)

value: blood

tag: group

value: non-POD

tag: gender

value: female

tag: age

tag: anesthesia type

value: general

tag: anesthesia duration (m)

tag: operative time (m)

tag: blood loss (ml)

tag: sampling day

value: Pre


title: Streptococcus pyogenes MGAS10870 delta-spxA2 RNA-seq, biological replicate 2

city: Nashville

address: 1161 21st Avenue S, MCN D7219

institute: Vanderbilt University Medical Center

description:
Library name: spxA2KO_RNAseq_rep2
Wild-type MGAS10870 (emm3) or isogenic delta-spxA2 deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 2 of 3. Original filename: JMF481B_R1/R2_001.fastq.gz.

data_processing:
Raw paired-end FASTQ reads were quality filtered and trimmed using CLC Genomics Workbench v23 (Qiagen).
Trimmed reads were aligned to the MGAS10870 reference genome (NZ_CP067090.1, GenBank) using CLC Genomics Workbench v23 with default RNA-seq mapping parameters.
Raw read counts per gene were extracted using CLC Genomics Workbench v23.
Differential gene expression analysis was performed using DESeq2 v1.50 in R v4.5.3. Significance thresholds: |log2FC| >= log2(1.5), Bonferroni-corrected p < 0.05 and BH-FDR-adjusted padj < 0.05.
TPM (transcripts per million) values were calculated for each sample using CLC Genomics Workbench v23.
Analysis code is available at https://github.com/ar-flores/SpxA1-SpxA2-MultiOmic-GAS  (DOI: https://doi.org/10.5281/zenodo.20476011)
Assembly: NZ_CP067090.1 (Streptococcus pyogenes MGAS10870, NCBI RefSeq)
Supplementary files format and content: RNAseq_counts_matrix.txt: tab-delimited text file containing raw read counts per gene for all 9 samples (rows = genes annotated to NZ_CP067090.1; columns = sample names)
Supplementary files format and content: Per-sample TPM and RPKM files (e.g., *_TPM_matrix.txt): tab-delimited text file containing TPM- or RPKM-normalized expression values per gene for each individual sample

extract_protocol:
Cells were harvested by centrifugation, resuspended in RNAprotect Bacteria Reagent (Qiagen), and RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion. RNA quality was assessed by Bioanalyzer (Agilent). Libraries were prepared and sequenced by Genewiz (Azenta Life Sciences).
Strand-non-specific paired-end RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Libraries were sequenced on an Illumina NovaSeq 6000 platform (2x150bp paired-end reads).

treatment_protocol: Not applicable — no treatment applied prior to RNA extraction.

tag: cell type

tag: genotype


title: Whole blood, OI, rep 1

description:
Library name: Nackley_2
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

tag: tissue

value: Whole blood

value: WT

tag: treatment


title: Patient 27, endometrium, healthy control

description:
Library name: P27
44 year old, Cellular Atypia, Low-grade Epithelial Cervical Neoplasia, Cancer Cured by Surgery Approach


title: Streptococcus pyogenes MGAS10870 delta-spxA2 RNA-seq, biological replicate 1

description:
Library name: spxA2KO_RNAseq_rep1
Wild-type MGAS10870 (emm3) or isogenic delta-spxA2 deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 1 of 3. Original filename: JMF481A_R1/R2_001.fastq.gz.

tag: batch


title: Whole blood, OV, rep 1

description:
Library name: Nackley_1
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: OR486 and Vehicle


title: Streptococcus pyogenes MGAS10870 delta-spxA2 CovR ChIP-exo, biological replicate 3

description:
Library name: spxA2KO_ChIPexo_rep3
CovR ChIP-exo in delta-spxA2 MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 3 of 3. FRiP=0.24. ChIP target: CovR (control of virulence response regulator).


title: Patient 21, endometrium, unexplained infertility

description:
Library name: P21
37 year old, Myomas in the uterus

value: unexplained infertility


title: Streptococcus pyogenes MGAS10870 delta-spxA1 RNA-seq, biological replicate 3

description:
Library name: spxA1KO_RNAseq_rep3
Wild-type MGAS10870 (emm3) or isogenic delta-spxA1 deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 3 of 3. Original filename: JMF509C_R1/R2_001.fastq.gz.


title: Parental Neural Progenitor Stem Cell KO clone 2_2

city: Cleveland

first: Tyler

middle: J

last: Alban

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description: Library name: PARKIN_KO_2_2

data_processing:
Post-sequencing FASTQ files were aligned to gene code release M25 (GRCm38.p6) with STAR aligner with default parameters version 2.7.11a. Quality control was performed using RSeqQC to assess the quality of RNA alignment from BAM files. Mapped reads for each gene were counted using the featureCounts read summarization program, with annotations from Human GENECODE (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: comma-separated text file with raw counts for each sample: raw_count_matrix.csv

source_name: NPC

extract_protocol:
Total RNA was isolated using Rneasy mini kits (Qiagen Sciences, Germantown, MD)
cDNA library was prepared using SMART-Seq v4 ultra-low input cDNA Library Construction Kit (Takara Bio, San Jose, CA) or TruSeq Library kit (Illumina, San Diego, CA)

tag: cell line

value: NPC

value: KO


title: Streptococcus pyogenes MGAS10870 delta-spxA2 CovR ChIP-exo, biological replicate 2

description:
Library name: spxA2KO_ChIPexo_rep2
CovR ChIP-exo in delta-spxA2 MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 2 of 3. FRiP=0.22. ChIP target: CovR (control of virulence response regulator).


title: muscle, delt, 72_delt

description: 10x Genomics

value: muscle

tag: location

value: deltoid


title: Streptococcus pyogenes MGAS10870 delta-spxA1 RNA-seq, biological replicate 2

description:
Library name: spxA1KO_RNAseq_rep2
Wild-type MGAS10870 (emm3) or isogenic delta-spxA1 deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 2 of 3. Original filename: JMF509B_R1/R2_001.fastq.gz.

value: bacterial cells


title: Streptococcus pyogenes MGAS10870 delta-spxA2 CovR ChIP-exo, biological replicate 1

description:
Library name: spxA2KO_ChIPexo_rep1
CovR ChIP-exo in delta-spxA2 MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 1 of 3. FRiP=0.23. ChIP target: CovR (control of virulence response regulator).


title: Patient 12, endometrium, unexplained infertility

description:
Library name: P12
37 year old, Poly-cystic Ovary Syndrome


title: Parental Neural Progenitor Stem Cell KO clone 2_1

description: Library name: PARKIN_KO_2_1


title: Streptococcus pyogenes MGAS10870 delta-spxA1 RNA-seq, biological replicate 1

description:
Library name: spxA1KO_RNAseq_rep1
Wild-type MGAS10870 (emm3) or isogenic delta-spxA1 deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 1 of 3. Original filename: JMF509A_R1/R2_001.fastq.gz.


title: Parental Neural Progenitor Stem Cell KO clone 1_2

description: Library name: PARKIN_KO_1_2


title: Streptococcus pyogenes MGAS10870 wild-type CovR ChIP-exo, biological replicate 3

description:
Library name: WT_ChIPexo_rep3
CovR ChIP-exo in wild-type MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 3 of 3. FRiP=0.23. ChIP target: CovR (control of virulence response regulator).

value: wild-type


title: hiPSC-differentiated cells, D16, PD/SU-treated SULF1/2 DKO

city: Stockholm

first: Carmen

last: Abaurre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 3
10x Genomics

data_processing:
BCL files received from NGI were converted to FASTQ with Illumina bcl2fastq v2.20 (RRID:SCR_015058), which was run with default parameters. Raw and filtered matrices were constructed with 10x Genomics Cell Ranger v8.0.1 using default parameters. All samples were subjected to CellBender v.0.3.2 nuclei calling and ambient RNA correction, which uses raw CellBender matrices as input. CellBender was run with default parameters and the CellBender-corrected expression matrix was used for all downstream analysis. Only nuclei with a minimum cell probability of 0.5 were retained in the nuclei matrix. Feature selection, PCA, dimensionality reduction, graph generation and embedding, clustering, annotation and regulon analysis were carried out as described in the Methods section.
Assembly: GRCh38-2020-A-2.0.0 from 10X Genomics website
Supplementary files format and content: SULF_differentiated.h5ad: HD5F object obtained after entire analysis pipeline with Scanpy, described in the manuscript's Methods.
Supplementary files format and content: (SAMPLE)_raw_feature_bc_matrix.h5.gz: CellRanger-generated filtered counts matrix for each individual sample.
Supplementary files format and content: (SAMPLE)_filtered_feature_bc_matrix.h5.gz: CellRanger-generated filtered counts matrix for each individual sample.
Supplementary files format and content: (SAMPLE)_cellbender.h5.gz: CellBender-corrected counts matrix generated for each individual sample.

source_name: KOLF 2.1J iPSC

growth_protocol: hiPSC lines were maintained on Laminin 521-coated plates (Biolamina, LN521) in Essential 8 Flex medium (E8 Flex, Thermo Fisher Scientific) under standard conditions (37° C, 5% CO₂) until differentiation was initiated.

extract_protocol:
Cultured cells at D16 were dissociated using TriplE, counted, and 300,000–400,000 cells were resuspended in 500 μL lysis buffer (2% BSA, 1:200 RNase inhibitor, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tergitol). To minimize mechanical stress, pipetting was limited to 1–2 gentle mixes, and lysis occurred on ice for 5 min, followed by dilution with 1 mL resuspension buffer (2% BSA in nuclease-free water with RNase inhibitor). The lysate was filtered through a 70 μm filter and centrifuged at 500 × g for 10 min at 4 °C. The supernatant was discarded, and the pellet was resuspended in 50-100 μL resuspension buffer to obtain optimal nuclei concentration. Nuclei quality was assessed visually, and concentration was determined by manual counting with Trypan Blue staining.
RNA library was constructed following the manufacturer's protocol (10X Genomics Chromium Gem-X Single Cell 3' Kit v4). Nuclei suspensions from each sample were loaded in separate lanes of the same Chromium Chip G, with a target of 20,000 nuclei per sample, and GEMs were generated in a Chromium X controller. After library preparation, next-generation sequencing was conducted by SciLifeLab National Genomics Infrastructure (NGI) on an Illumina NovaSeq XPlus instrument.

treatment_protocol:
All three iPSC lines were plated at a density of 200,000 cells/cm² in 12-well plates pre-coated with Geltrex™ (Life Technologies) and Laminin-511 (Biolamina, LN511) and maintained in E8 Flex medium. Once the cells reached confluency (typically after 48–72 h), differentiation was initiated. Cells were cultured in Neurobasal medium supplemented with B27 (Life Technologies), 2 mM L-glutamine (Invitrogen), and N2 supplement, along with the appropriate small molecules and growth factors, until D16 of differentiation.
Only SULF1/2 DKO cells were treated with FGF inhibitors PD0325901 (1 µM) and SU5402 (5 µM) (Sigma) from D4 to D14.

value: KOLF 2.1J iPSC

value: hiPSC-differentiated

value: SULF1/2 DKO

tag: genetic modification

tag: growth

value: E8 flex media

value: Midbrain dopaminergic differentiation + PD/SU

tag: time

value: Day 16


title: Streptococcus pyogenes MGAS10870 wild-type RNA-seq, biological replicate 3

description:
Library name: WT_RNAseq_rep3
Wild-type MGAS10870 (emm3) or isogenic wild-type deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 3 of 3. Original filename: JMF14C_R1/R2_001.fastq.gz.


title: Streptococcus pyogenes MGAS10870 wild-type CovR ChIP-exo, biological replicate 2

description:
Library name: WT_ChIPexo_rep2
CovR ChIP-exo in wild-type MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 2 of 3. FRiP=0.23. ChIP target: CovR (control of virulence response regulator).


title: hiPSC-differentiated cells, D16, SULF1/2 DKO

description:
Library name: Sample 2
10x Genomics

value: Midbrain dopaminergic differentiation


title: Parental Neural Progenitor Stem Cell KO clone 1_1

description: Library name: PARKIN_KO_1_1


title: Streptococcus pyogenes MGAS10870 wild-type RNA-seq, biological replicate 2

description:
Library name: WT_RNAseq_rep2
Wild-type MGAS10870 (emm3) or isogenic wild-type deletion mutant grown in THY to mid-exponential phase (OD600 ~0.45). Biological replicate 2 of 3. Original filename: JMF14B_R1/R2_001.fastq.gz.


title: CD4-GPA, donor 1

city: Stanford

institute: Stanford University

description: Library name: SL154_3_d14

value: In vitro-differentiated erythroid cells derived from cord blood CD34+ hematopoietic stem/progenitor cells

tag: individual

value: donor 1

value: D14 differentiated erythroids


title: Pseudomonas fluorescens GL-S-306, infected with phage KNP; control

description: Library name: Sample 10

value: bacterial cell

value: no enrichment

tag: infection stage

value: infected with phage KNP


title: Parental Neural Progenitor Stem Cell clone 2

description: Library name: Parental_2

value: NPC

value: WT


title: muscle, delt, 42_delt

description: 10x Genomics

value: muscle

value: deltoid


title: Whole blood, OI, rep 2

description:
Library name: Nackley_6
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

value: Whole blood


title: muscle, cuff, 42_cuff

description: 10x Genomics

value: supraspinatus


title: Streptococcus pyogenes MGAS10870 wild-type CovR ChIP-exo, biological replicate 1

description:
Library name: WT_ChIPexo_rep1
CovR ChIP-exo in wild-type MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 1 of 3. FRiP=0.23. ChIP target: CovR (control of virulence response regulator).

value: bacterial cells

value: wild-type