title: TG_EtOH_neur_enr_12d_plus30d_ATAC

description: transposase-accessible chromatin

data_processing:
RTA Version: v3.4.4 was used for base calls and quality scores.
The cellranger-arc-2.0.0 pipeline was used to generate FASTQ files, gene expression matrices, and ATAC fragment tables for each sample
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis
Genome_build: Mousrefdata-cellranger-arc-mm10-2020-A-2.0.0e Ensembl GRCm38.101
Supplementary_files_format_and_content: Multiomic filtered feature barcode matrices (*.HDF5), ATAC per fragment information files (*.tsv.gz), and ATAC per fragment information indices (*.tsv.gz.tbi)

growth_protocol: Mice (2-4 mice pooled per sample, including both males and females) were treated for up to 12 days with either ethanol vehicle or 1.5 nmol calcipotriol on each cheek

extract_protocol:
Some samples were further enriched for neuronal nuclei by labeling with rabbit polyclonal anti-NeuN antibody (ABN78, Sigma) followed by MACS purification
Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by the 10x Genomics ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD (CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevD.pdf).  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  GEX libraries were pooled and run over 0.05 of a NovaSeq6000 S4 flow cell using the XP workflow and running a 28x10x10x150 sequencing recipe in accordance with manufacturer’s protocol.  Target coverage was 500M reads per sample.  ATAC libraries were pooled and run over 0.167 of a NovaSeq6000 S1 flow cell using the XP workflow and running a 51x8x16x51 sequencing recipe in accordance with manufacturer’s protocol.  Target coverage was 250M reads per sample.

treatment_protocol: Fresh trigeminal ganglia from treated mice were immediately processed to yield nuclei suspensions

tag: strain

value: ethanol vehicle

value: steady state


title: cKK-E10_UNR_45_Day_0_Rep4

status: Public on Sep 11 2025

type: SRA

city: Waltham

first: Sudha

last: Chivukula

state: MA

address: 200 West

department: mRNA Center of Excellence

country: USA

institute: Sanofi

description:
Library name: Flu-N10-BF47CC-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-BF47CC-Pre-Pax_001

library_source: transcriptomic

data_processing:
The bcl files were demultiplexed using Illumina’s bcl2fastq software.
The fastq files were processed using Array Studio software (Qiagen) and aligned to the cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Differential gene expression analysis was performed using the Limma-Voom method, which transforms the raw read counts into log-counts per million (log-CPM) and models the mean-variance relationship of the data.
Assembly: cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.
Supplementary files format and content: Tab-delimited text file including log-CPM for each sample.

molecule: total RNA

organism: Macaca fascicularis

source_name: Blood

growth_protocol: Primary human skeletal muscle myoblasts were obtained from Lonza (Cat. No. CC-2580) and thawed and expanded following vendor recommendations. Briefly, cryopreserved cell stocks were thawed into SkGM-2 complete media (Lonza, Cat. No. CC-3245). Media was replaced 24 h after thawing and every 48 h thereafter. Cells were expanded/passaged to P6, at which point they were seeded on 24-well culture plates pre-coated with Collagen 1 at a density of 24,000 cells/cm2 in 1 mL of culture media. The next day, media in each well was replaced with 0.5 mL of fresh media before transfection mixes were prepared. Naive male and female Mauritius origin cynomolgus macaques (Macaca fascicularis) were selected from the Sanofi NHP colony at the NIRC. Animals weighed > 2 kg and were > 2 years of age at the start of the studies. Per NIRC SOPs, all animals underwent a pre-study health assessment performed by a licensed veterinarian, which included a complete blood count and clinical chemistry analysis before being cleared for entry into the study.

extract_protocol:
Muscle cells at each collection time-point, media was aspirated, and cultures were lysed on-plate using 350 µL of RLT buffer (Qiagen Cat. No. 79216) and immediately transferred to 1.5 mL tubes and stored at -80 °C. Total RNA was extracted from whole blood NHP samples collected in PAXgene Blood RNA Tubes (Qiagen, BD Diagnostics) pre- and 2 days post-immunization using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen) on an automated KingFisher Flex System (Thermo Scientific). The quality and yield of RNA were assessed on the 4200 TapeStation System (Agilent) and NanoDrop™ Eight Spectrophotometer (Thermo Scientific). Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).
Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).

treatment_protocol: Muscle cells were transfected at 2 µg of formulated RNA/million cells. For each treatment, 50 µL of transfection mix was added to the culture before an additional 0.5mL of media was added to thoroughly distribute the transfection mixture before plates were returned to the incubator for 1, 4, or 24 h. NHPs were randomized, (stratified randomization approach based on age, body weight, and sex by biostatistician) into groups of 4-6 per treatment group, were generally housed in pairs whenever possible and acclimated for at least 6 days prior to the start of the study. All NHPs were immunized with a dose of 0.5 mL of vaccine via the intramuscular (IM) route in the right forelimb on Day 0 and the left forelimb on D28 while under 10 mg/kg ketamine HCl /1 mg/kg acepromazine sedation.

tag: tissue

value: Blood

tag: cell type

value: PBMC

tag: genotype

tag: treatment

tag: timepoint

tag: dose

tag: biological replicate


title: MG_C_143_JJ

city: Amsterdam

first: Han

last: Jiao

address: 9 Meibergdreef, Endocrine Laboratory, Clin. Chemistry

country: Netherlands

institute: University of Amsterdam, Amsterdam, The Netherlands.

description:
Library name: Sample 94
column name in Raw_Counts_All_Samples.csv: MG_C_143_JJ

data_processing:
Sequencing data was filtered using SOAPnuke 68 by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: Rattus_norvegicus, GCF_000001895.5_Rnor_6.0
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
To study differences in microglial gene expression, bulk RNA sequencing was performed. RNA from microglial cells was isolated using the RNeasy Micro Kit (Qiagen, 74104), according to the manufacturer’s guidelines. mRNA was enriched from total RNA with the Dynabeads® mRNA Purification Kit (Invitrogen, 61006).
A strand-specific transcriptome library was constructed using the MGIEasy RNA Directional Library Prep Set (16 RXN) (MGI, 1000006385). Briefly, after cDNA synthesis, adaptor ligation was performed to ligate adaptors with the cDNAs. Subsequently, a PCR reaction was conducted to amplify the cDNAs, after which the library quality was checked using the Agilent 2100 Bioanalyzer (Agilent, G2939AA). Finally, single-stranded cyclized products were produced from single-stranded PCR products. To perform sequencing, single-stranded circle DNA molecules were replicated via rolling cycle amplification and a DNA nanoball (DNB) was generated. Sequencing was performed through combinatorial Probe-Anchor Synthesis (cPAS) on the DNBSEQ-G400 (MGI, G400).

value: Brain

value: Wistar

tag: Sex

value: Male

value: Microglia cells

value: WT

value: chow dark-feeding

tag: time


title: TG_MC903_neur_enr_12d_ATAC

city: St. Louis

first: Aaron

last: Ver Heul

state: MO

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University School of Medicine

description: transposase-accessible chromatin

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: trigeminal ganglia

value: calcipotriol

tag: disease state

value: atopic dermatitis-like disease


title: Control-1

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

data_processing:
Quality of raw RNAseq reads was accessed through FastQC v0.11.5. Reads were filtered with Trimmomatic-0.38 against adapters and rRNA sequences.
Filtered RNAseq reads were aligned to primary chromosomes of hg38 UCSC genome assembly with Hisat2 v2.1.0 and counted with HTSeq v2.0.1 against Gencode v43 basic annotation.
FPKM normalization and differential expression analysis was performed in edgeR v3.42.2 package for R. Gene modules were identified with WGCNA v1.72-1.
Assembly: Hg38 UCSC
Supplementary files format and content: Tables with raw and FPKM normalized counts per transcript. Differential expression analysis results (logFC > 0 for up-regulated genes in PMT, logFC < 0 for control). WGCNA gene modules.

molecule: polyA RNA

organism: Homo sapiens

source_name: bone tissue

extract_protocol:
Total RNA extraction was performed using AllPrep DNA/RNA Mini Kit (QIAGEN), following the manufacturer’s protocol. RNA quality was assessed using an Agilent 5200 Fragment Analyzer, using the Agilent HS RNA (15NT) kit.
The NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) was used to isolate intact poly(A)+ RNA from 1µg of previously isolated total RNA. Libraries were prepared using the Ultra II Directional RNA Library Prep Kit for Illumina and Unique Dual Index Primer Pairs were applied following the vendor protocols from New England Biolabs. Samples were sequenced in a single run on an Illumina NextSeq 550 using the NextSeq 500/550 High Output Kit v2.5 (300 Cycles) to produce 150–base pair-end reads with a mean sequencing depth of at least 60 million reads per sample.

value: bone tissue

tag: location

value: Mandibula

tag: age

value: female

tag: state

value: healthy

tag: patient


title: cKK-E10_UNR_45_Day_0_Rep1

description:
Library name: Flu-N10-AM900N-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AM900N-Pre-Pax_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: CTRL_PCreb_rep2

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

description:
CTRL_PCreb_rep2-CTRL_Input2.fc.signal.bw
CTRL_PCreb_rep2-CTRL_Input2.q_0.05_peaks.bchrfilt.narrowPeak.gz

data_processing:
Following quality controls (performed with FastQC v0.11.2), paired-end sequencing reads were aligned to the mouse reference genome (mm10/GRCm38) using Bowtie v2.3.5.1 [Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).]. Duplicated alignments (identified by Picard MarkDuplicates, https://broadinstitute.github.io/picard) and low-quality alignments/multi-mapping reads were excluded using SAMtools v1.6 [Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)]. Immunoprecipitation and corresponding control (Input DNA) datasets were treated identically. Peak calling was performed for each IP against its matched Input DNA using MACS v2.1.4 [Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] (command: callpeak -g mm --nomodel -f BAMPE -q 0.05). Input-normalized ChIP-seq fold-enrichment signal tracks were obtained using MACS v2.1.4 [Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] (command: callpeak -g mm --nomodel -f BAMPE -q 0.05 --SPMR -B and bdgcmp -m FE).
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig files of input-normalized signal tracks.
Supplementary files format and content: NarrowPeak files of called peaks.

source_name: Gastrocnemius muscle

growth_protocol: Animals were housed in pathogen-free environment. Morevoer, mice were fed standard chow diet with access to drinking water, while housed under a 12 hours light-dark cycle.

extract_protocol:
ChIP was performed on quadriceps from control and tumor-bearing mice, as previously described in Segatto et al., 2017 (PMID:29167426) and Savic et al., 2013 (PMID: 24279905). In brief, frozen tissues were pulverized using Covaris tissue TUBEs (Covaris 520001) with a chilled hammer on a metallic block placed in dry ice. The resulting powdered tissue was transferred to a glass vial and resuspended in 10ml 1xPBS, followed by cross-linking in 1% formaldehyde (Ted Pella Inc) for 15 minutes at RT. After blocking the cross-link with 0.125 M glycine for 5 minutes and washing with PBS containing protease and phosphatase inhibitors, the pellets were resuspended in Farnham buffer (5 mM PIPES pH 8.0; 85 mM KCl; 0.5% NP-40) and briefly homogenized with a homogenizer. Subsequently, cells were lysed in RIPA buffer (1× PBS; 1% NP-40; 0.5% sodium deoxycholate; 0.1% SDS). Chromatin was sonicated to achieve fragment lengths of approximately 0.5 kb and then subjected to immunoprecipitation using 5 μg of CREB or phospho-CREB1 antibodies and Protein G Dynabeads (Thermofisher). Washes were performed as described in Segatto et al., 2017 (PMID:29167426). The eluted DNA was reverse-crosslinked, digested with 20 μg of Proteinase K for 1hr at 55C and purified using Qiagen MinElute PCR purification kit.
Paired-end sequencing was performed on the Illumina NextSeq 1000 platform.

treatment_protocol: 106 C26 murine adenocarcinoma cells in 100 μl of PBS were subcutaneously injected in the right flank of 2-month-old male Balb/c mice. Starting from day 4 post tumor inoculation, C26-bearing animals were injected intraperitoneally with rolipram (3 mg/kg) or vehicle (1,86% ethanol in saline).

value: Gastrocnemius muscle

value: CTRL


title: MG_C_142_JJ

description:
Library name: Sample 93
column name in Raw_Counts_All_Samples.csv: MG_C_142_JJ


title: TG_MC903_neur_enr_3d_ATAC

description: transposase-accessible chromatin


title: cKK-E10_UNR_15_Day_2_Rep6

description:
Library name: Flu-N10-YS15H-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-YS15H-D2-Pax_001

value: Blood


title: TG_EtOH_neur_enr_12d_ATAC

description: transposase-accessible chromatin

value: ethanol vehicle

value: steady state


title: MG_C_140_JJ

description:
Library name: Sample 91
column name in Raw_Counts_All_Samples.csv: MG_C_140_JJ

value: Brain

value: Wistar

value: chow ad libitum


title: cKK-E10_UNR_15_Day_2_Rep5

description:
Library name: Flu-N10-RE11M-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-RE11M-D2-Pax_001

value: PBMC


title: TG_MC903_bulk_12d_ATAC

description: transposase-accessible chromatin


title: CTRL_PCreb_rep1

description:
CTRL_PCreb_rep1-CTRL_Input.fc.signal.bw
CTRL_PCreb_rep1-CTRL_Input.q_0.05_peaks.bchrfilt.narrowPeak.gz


title: cKK-E10_UNR_15_Day_2_Rep4

description:
Library name: Flu-N10-GA955J-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-GA955J-D2-Pax_001


title: MG_C_139_JJ

description:
Library name: Sample 90
column name in Raw_Counts_All_Samples.csv: MG_C_139_JJ

value: Male

value: Microglia cells

value: WT


title: CTRL_Input2


title: CTRL_Input


title: C26_Pcreb_rep2

description:
C26_PCreb_rep2-C26_Input2.fc.signal.bw
C26_PCreb_rep2-C26_Input2.q_0.05_peaks.bchrfilt.narrowPeak.gz


title: MG_C_137_JJ

description:
Library name: Sample 88
column name in Raw_Counts_All_Samples.csv: MG_C_137_JJ


title: TG_MC903_neur_enr_12d_plus30d_GEX

description: gene expression

value: calcipotriol

value: atopic dermatitis-like disease


title: cKK-E10_UNR_15_Day_2_Rep2

description:
Library name: Flu-N10-AT257G-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AT257G-D2-Pax_001


title: TG_MC903_neur_enr_12d_plus30d_ATAC

description: transposase-accessible chromatin


title: cKK-E10_UNR_15_Day_2_Rep3

description:
Library name: Flu-N10-BM674C-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-BM674C-D2-Pax_001


title: TG_EtOH_bulk_12d_ATAC

description: transposase-accessible chromatin


title: C26_Pcreb_rep1

description:
C26_PCreb_rep1-C26_Input.fc.signal.bw
C26_PCreb_rep1-C26_Input.q_0.05_peaks.bchrfilt.narrowPeak.gz


title: cKK-E10_UNR_15_Day_2_Rep1

description:
Library name: Flu-N10-AS30B-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AS30B-D2-Pax_001


title: TG_EtOH_neur_enr_12d_plus30d_GEX

description: gene expression


title: cKK-E10_UNR_45_Day_0_Rep2

description:
Library name: Flu-N10-AP892D-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AP892D-Pre-Pax_001


title: MG_C_136_JJ

description:
Library name: Sample 87
column name in Raw_Counts_All_Samples.csv: MG_C_136_JJ


title: MG_C_141_JJ

description:
Library name: Sample 92
column name in Raw_Counts_All_Samples.csv: MG_C_141_JJ


title: C26_Input2


title: MG_C_135_JJ

description:
Library name: Sample 86
column name in Raw_Counts_All_Samples.csv: MG_C_135_JJ


title: cKK-E10_UNR_15_Day_0_Rep6

description:
Library name: Flu-N10-YS15H-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-YS15H-Pre-Pax_001


title: MG_C_138_JJ

description:
Library name: Sample 89
column name in Raw_Counts_All_Samples.csv: MG_C_138_JJ


title: TG_MC903_neur_enr_12d_GEX

description: gene expression


title: MG_C_134_JJ

description:
Library name: Sample 85
column name in Raw_Counts_All_Samples.csv: MG_C_134_JJ

value: chow light-feeding


title: Heart, TGFb, patient 2

city: Salzburg

first: Wolfgang

last: Esser-Skala

address: Hellbrunner Strasse 34

country: Austria

institute: University of Salzburg

data_processing:
(1) Sample quality was verified using FastQC, trimming of the reads was checked with trimmomatic. (2) Alignment against the human reference genome was performed using STAR. (3) Gene expression quantification using read counts of exonic gene regions was carried out with featureCounts. (4) Gencode v45 was used as gene annotation reference.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing counts for the respective sample or for all samples

source_name: Heart

extract_protocol:
75,000 to 100,000 human fibroblasts were homogenized in 100 μl of Lysis/Binding Buffer (Ambion), vortexed and stored at -80°C until further processing. Poly-A RNA was extracted with Dynabeads Oligo dT (Ambion) and eluted in 8 μL Tris Cl pH 7.5.
RNA was reverse transcribed with PrimeScript Reverse Transcription reagent kit (Takara). Double stranded cDNA was obtained by second strand synthesis using the SSS kit (Invitrogen) starting with 3 ng of cDNA. Purified cDNA was then converted to sequencing library using the Illumina Nextera XT DNA library prep with 1 ng of cDNA and 12 cycles of PCR amplification.

value: Heart

value: fibroblast

value: TGFb


title: cKK-E10_UNR_15_Day_0_Rep5

description:
Library name: Flu-N10-RE11M-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-RE11M-Pre-Pax_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: TG_EtOH_neur_enr_12d_GEX

description: gene expression


title: cKK-E10_UNR_15_Day_0_Rep4

description:
Library name: Flu-N10-GA955J-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-GA955J-Pre-Pax_001

value: Blood


title: cKK-E10_UNR_15_Day_0_Rep3

description:
Library name: Flu-N10-BM674C-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-BM674C-Pre-Pax_001


title: MG_C_130_JJ

description:
Library name: Sample 82
column name in Raw_Counts_All_Samples.csv: MG_C_130_JJ

value: chow dark-feeding


title: TG_EtOH_bulk_12d_GEX

description: gene expression

value: ethanol vehicle

value: steady state


title: TG_MC903_bulk_12d_GEX

description: gene expression


title: MG_C_133_JJ

description:
Library name: Sample 84
column name in Raw_Counts_All_Samples.csv: MG_C_133_JJ

value: Brain

value: Wistar


title: Heart, TGFb, patient 1


title: cKK-E10_UNR_15_Day_0_Rep1

description:
Library name: Flu-N10-AS30B-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AS30B-Pre-Pax_001

value: PBMC


title: MG_C_132_JJ

description:
Library name: Sample 83
column name in Raw_Counts_All_Samples.csv: MG_C_132_JJ

value: Male


title: Heart, mock-treated, patient 2

value: mock


title: cKK-E10_UNR_5_Day_2_Rep6

description:
Library name: 8733-2103-Flu-N19-BZ838-D2_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BZ838-D2_001


title: C26_Input

description:
C26_PCreb_rep1-C26_Input.fc.signal.bw
C26_PCreb_rep1-C26_Input.q_0.05_peaks.bchrfilt.narrowPeak.gz

value: Gastrocnemius muscle


title: MG_C_128_JJ

description:
Library name: Sample 80
column name in Raw_Counts_All_Samples.csv: MG_C_128_JJ

value: Microglia cells

value: WT


title: cKK-E10_UNR_15_Day_0_Rep2

description:
Library name: Flu-N10-AT257G-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AT257G-Pre-Pax_001


title: av045_18, vehicle, TG

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software
RNA-seq reads were aligned and quantified to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights
Genome_build: Mouse Ensembl GRCm38.101
Supplementary_files_format_and_content: transcript quantification file - plain text

growth_protocol: Mice were treated for 12 days with either ethanol vehicle or 1.5 nmol calcipotriol on each cheek

extract_protocol:
RNA was extracted from trigeminal ganglia using the Nucleospin RNA purification kit
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Fresh trigeminal ganglia from treated mice were immediately processed for RNA

value: male

value: vehicle

value: trigeminal ganglia


title: av045_20, vehicle, TG


title: Heart, Kat5 inhibitor, patient 2

value: Heart

value: fibroblast

value: Kat5 inhibitor


title: MG_C_129_JJ

description:
Library name: Sample 81
column name in Raw_Counts_All_Samples.csv: MG_C_129_JJ

value: chow dark-feeding


title: cKK-E10_UNR_5_Day_2_Rep5

description:
Library name: 8733-2103-Flu-N19-BZ653-D2_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BZ653-D2_001

value: Blood

value: Naive male and female Mauritius origin cynomolgus macaques


title: TG_MC903_neur_enr_3d_GEX

description: gene expression

value: calcipotriol

value: atopic dermatitis-like disease


title: MG_C_123_JJ

description:
Library name: Sample 78
column name in Raw_Counts_All_Samples.csv: MG_C_123_JJ

value: Brain

value: Wistar


title: Sed_G_Replicate3

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

institute: University of Louisville

description: Library name: STC804_15_B23_Control_Re_L1_ds.07c02afbb2664c99a752570381ad4088

data_processing:
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
Assembly: mm10/GRCm38.93
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Kidney

growth_protocol: Wild type C57BL/6J male mice were subjected to sedentary or exercise condtions.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Plus Mini Kit (Cat no. 74134)
The TruSeq Stranded mRNA Library Prep Kit (Illumina Cat# 20020594 was used for library prep

treatment_protocol: Exercised mice were subjected to either 1 day, 1 week, or 2 weeks of forced treadmill running at 70% capacity for 40 minutes. Kidney cortex pieces were flash frozen at time of euthanisia.

value: Kidney

value: Control


title: MG_C_126_JJ

description:
Library name: Sample 79
column name in Raw_Counts_All_Samples.csv: MG_C_126_JJ

value: Male

value: Microglia cells

value: chow light-feeding


title: Sed_G_Replicate4

description: Library name: STC804_16_B24_Control_Re_L1_ds.4faeef3090c84746a4eba91bb5fc3835


title: Heart, mock-treated, patient 1

value: mock


title: av045_14, calcipotriol, TG

value: male

value: trigeminal ganglia


title: av045_15, calcipotriol, TG


title: MG_C_122_JJ

description:
Library name: Sample 77
column name in Raw_Counts_All_Samples.csv: MG_C_122_JJ

value: WT


title: MG_C_121_JJ

description:
Library name: Sample 76
column name in Raw_Counts_All_Samples.csv: MG_C_121_JJ


title: Sed_G_Replicate2

description: Library name: STC804_14_B21_Control_Re_L1_ds.b870ded9e7b045abad50df9701670033


title: av045_10, vehicle, TG

value: female

value: vehicle

value: steady state


title: av045_19, vehicle, TG


title: cKK-E10_UNR_5_Day_2_Rep3

description:
Library name: 8733-2103-Flu-N19-BW352-D2_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BW352-D2_001

value: Blood

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques


title: Sed_G_Replicate1

description: Library name: STC804_13_B20_Control_Re_L1_ds.0bb5b042880342ba9a04dc8543ea32e2


title: av045_13, calcipotriol, TG

value: calcipotriol

value: atopic dermatitis-like disease


title: cKK-E10_UNR_5_Day_2_Rep1

description:
Library name: 8733-2103-Flu-N19-BB512G-D2_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BB512G-D2_001


title: av045_9, vehicle, TG


title: cKK-E10_UNR_5_Day_2_Rep2

description:
Library name: 8733-2103-Flu-N19-BV065-D2_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BV065-D2_001


title: Ex_1w_F_Replicate4

description: Library name: STC804_12_B17_1wk_Re_L1_ds.2b41cb51b4f24965874eaeed8282b8cd

value: Kidney

value: 1 wk


title: MG_C_119_JJ

description:
Library name: Sample 75
column name in Raw_Counts_All_Samples.csv: MG_C_119_JJ

value: Brain

value: Wistar

value: Male

value: chow dark-feeding


title: cKK-E10_UNR_5_Day_0_Rep6

description:
Library name: 8733-2103-Flu-N19-BZ838-Baseline_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BZ838-Baseline_001


title: MG_C_118_JJ

description:
Library name: Sample 74
column name in Raw_Counts_All_Samples.csv: MG_C_118_JJ

value: Microglia cells

value: chow ad libitum


title: av045_8, vehicle, TG

value: trigeminal ganglia


title: Ex_1w_F_Replicate3

description: Library name: STC804_11_B16_1wk_Re_L1_ds.b86be11917934a0f831ba8097348a488


title: MG_C_117_JJ

description:
Library name: Sample 73
column name in Raw_Counts_All_Samples.csv: MG_C_117_JJ

value: WT


title: Heart, Kat5 inhibitor, patient 1

value: Heart

value: fibroblast

value: Kat5 inhibitor


title: cKK-E10_UNR_5_Day_0_Rep5

description:
Library name: 8733-2103-Flu-N19-BZ653-Baseline_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BZ653-Baseline_001

value: Blood

value: PBMC


title: av045_5, calcipotriol, TG

value: female

value: calcipotriol


title: cKK-E10_UNR_5_Day_2_Rep4

description:
Library name: 8733-2103-Flu-N19-BY447-D2_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BY447-D2_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: MG_C_115_JJ

description:
Library name: Sample 72
column name in Raw_Counts_All_Samples.csv: MG_C_115_JJ


title: av045_4, calcipotriol, TG

value: atopic dermatitis-like disease


title: cKK-E10_UNR_5_Day_0_Rep4

description:
Library name: 8733-2103-Flu-N19-BY447-Baseline_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BY447-Baseline_001


title: cKK-E10_UNR_5_Day_0_Rep3

description:
Library name: 8733-2103-Flu-N19-BW352-Baseline_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BW352-Baseline_001


title: Ex_1w_F_Replicate1

description: Library name: STC804_9_B13_1wk_Re_L1_ds.d7fe878b687b4b97a1a713b398d8b685

value: Kidney

value: 1 wk


title: av045_3, calcipotriol, TG


title: Ex_24h_F_Replicate4

description: Library name: STC804_8_B11_24h_Re_L1_ds.97afaaa4552a4378ab204a136cba73af


title: Ex_24h_F_Replicate3

description: Library name: STC804_7_B10_24h_Re_L1_ds.97b722a8ba2949298635c110a7a947f3


title: MG_C_114_JJ

description:
Library name: Sample 71
column name in Raw_Counts_All_Samples.csv: MG_C_114_JJ

value: Brain

value: Wistar

value: Male


title: cKK-E10_UNR_5_Day_0_Rep1

description:
Library name: 8733-2103-Flu-N19-BB512G-Baseline_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BB512G-Baseline_001


title: cKK-E10_UNR_5_Day_0_Rep2

description:
Library name: 8733-2103-Flu-N19-BV065-Baseline_001
Column name in count_nhp.txt: 8733-2103-Flu-N19-BV065-Baseline_001


title: MG_C_113_JJ

description:
Library name: Sample 70
column name in Raw_Counts_All_Samples.csv: MG_C_113_JJ

value: Microglia cells

value: chow ad libitum


title: Bulk RNA-seq of K562 cells culturedin CAGEs or wells for 3 days (Cell_Culturing)

city: Boston

first: Ignas

last: Mazelis

address: 210 Longwood Avenue

department: System Biology

institute: Harvard Medical School

description: Library name: K562 cultures

data_processing:
BCL sequencing files received from Illumina BaseSpace portal were converted to raw FASTQ files for each of the 4 (R1, R2, R3, R4) sequencing reads without read trimming or masking by using bcl2fastq software (Illumina, v2.20.0.422). Raw FASTQ files were processed using a custom pipeline (available at https://github.com/AllonKleinLab/paper-data/tree/master/Mazelis2025_CAGEs). In brief, sequencing reads were demultiplexed based on Read1 index sequence (stored as read3) (index used: AGAGGATA [iPSC_cells], ATAGAGAG [iPSC_CAGEs], CTCCTTAC [K562_cells], TATGCAGT [K562_CAGEs],  CGGAGAGA [L929 cells] AGGCTTAG [L929 CAGEs]), and were filtered based on expected structure (all barcodes matching a barcode whitelist with hamming distance of 1). The demultiplexed reads were then processed using Trimmomatic (1) (with parameters: LEADING 28; SLIDINGWINDOW 4:20; MINLEN 20), followed by Poly-A length trim to 4 nt and selecting reads that are longer than MINLEN. For surviving reads, the fraction of length composed out of same base repeats (only considering > 5) was determined, rejecting reads whose fraction is greater than 0.5.
Bulk Count matrices were generated using STARsolo pipeline (2) (STAR 2.7.9a) with the with parameters (--soloFeatures Gene, GeneFull, --genomeSAsparseD 3, --outSAMtype BAM SortedByCoordinate, --outSAMattributes CB CR UR UB UY GN GX, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloUMIfiltering MultiGeneUMI_CR, --soloUMIdedup 1MM_CR, --soloMultiMappers EM, --soloCellFilter EmptyDrops_CR, --quantMode TranscriptomeSAM GeneCounts) Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly was used.
Count matrices were downampled to 5M total counts. EdgeR analysis was carried out using assumed biological CV (bcv) of 0.35.
Assembly: Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly
Supplementary files format and content: h5ad sample x genes expression matrix for different samples

source_name: Bone marrow

growth_protocol: K562 and L1210 cells were cultured in IMDM (Thermo Fisher, 10566016) + 10% FBS (ATCC, 30-2020) + 1x penicillin/streptomycin (Thermo Fisher, 10378016) in T25 flasks (Corning). Cell lines were cultured until they reached ~80-90% confluency. For passaging, suspension cells (K562, L1210) were resuspended gently and collected into a 15 mL tube. 5 mL of 37ºC pre-warmed complete media was used to wash the flask and was added into the same 15 mL tube. Cells were centrifuged at 300g for 4 min, followed by media aspiration and resuspension in 5 mL of fresh pre-warmed complete media. Cells were counted using an automatic cell counter and 500,000 cells were seeded into 5 mL of 37ºC pre-warmed complete media in a 25cm2 flask. Induced pluripotent stem cells were cultured in a 6-well plate on a layer of Matrigel (Corning) in mTeSR media (STEMCELL Technologies, 100-0276). To passage the culture, cells were detached by removing media, rinsing twice with DPBS, adding 1mL of Accutase (STEMCELL Technologies, 07920) and incubating at 37ºC for 7 min. Next, cells were resuspended in 5mL of plain DMEM and centrifuged in a swinging bucket centrifuge for 4 min at 300g. Supernatant was aspirated and the cell pellet was resuspended in 1mL of DMEM. 2mL of Matrigel in DMEM solution was added to a single 6-well plate well. The plate was incubated in 37ºC for 30 min. Any remaining solution was aspirated and 500K of iPSC cells in DMEM were seeded into 2mL of mTeSR (STEMCELL Technologies, 100-0276) with 10μg/mL Y-27632 (Dihydrochloride) (STEMCELL Technologies, 72302). After a day of culturing, media was changed with fresh mTeSR without Y-27632. Media changes were performed daily for 3-4 days, till cells reached 80-90% confluency. For encapsulation experiments, cells were washed twice with ice cold DPBS with 0.1% BSA

extract_protocol:
Cells were washed twice with DPBS with 0.1% BSA and were encapsulated into CAGEs at a final concentration of 20e6 cells/mL in core mix. Next, for some samples the CAGE core dextran was removed using dextranase enzyme. 100μL of washed and packed CAGEs or 20,000 cells were transferred to a 24-well plate and cultured for 3 (K562 and L929) or 4 (iPSCs) days in 1mL of complete media (IMDM (Thermo Fisher, 10566016) + 10% FBS (ATCC, 30-2020) + 1x penicillin/streptomycin (Thermo Fisher, 10378016) or mTeSR 3D media (STEMCELL Technologies, #03950) with 1X CloneRTM2 cloning supplement (STEMCELL Technologies, 100-0691)) without pluronics. No media changes were performed for cell lines and, in the case of iPSCs, mTeSR 3D media feed supplement (STEMCELL Technologies, #03950) was added every day. Cells in wells and CAGEs were analyzed using bulk RNA-seq. First, all samples were washed three times with ice-cold DPBS. 40,000 cells or 40.5μL of CAGEs were lyzed using 0.45% Igepal CA-630 on ice in a final volume of 63.5μL. Reverse-transcription reaction was set on ice and performed in PCR strip tubes in100μL reactions (63.5μL of lysate, 2.5μL of 10μM RT R2-poly(T) primer housing a 8nt UMI and no barcode,  20μL of 5X SMARTseq3 RT buffer (100mM Tris pH 8.3, 150mM NaCl, 12.5mM MgCl2, 5mM GTP, 40mM DTT), 0.5μL of 10mM dNTPs (NEB, N0447L), 2.5μL of 40U/μL Recombinant RNase Inhibitor (Takara Bio, 2313A), 1.5μL of 50μM TSO, 5μL of Maxima H- reverse transcriptase (ThermoFisher, EP0753). To set up the reaction, lysates were mixed with theRT primer on ice in a PCR tubes sand samples were incubated on ice for 10 min to allow the RT primer to diffuse in, followed by heating at 70ºC for 5 min and cooling down on ice. Next, RT master mix, composed out of the remaining reagents was added to each tube, ensuring a thought mixing of capsules with pipetting. Tubes were incubated on ice for 5 min and the reaction was carried out at 42ºC for 90 min, followed by cycling between 50ºC and 42ºC incubation of 2 mins for 15 cycles. After the RT reaction, 2μL of 10M NaOH were added to all reactions followed by 20 min incubation at 37ºC to dissolve the CAGEs [NaOH was also added to samples with no CAGEs]. cDNA was purified into 20μL of water using 0.8X AMPure XP beads (Beckman Coulter, A63881). Next cDNA was amplified using 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) PCR WITH 2.5μL of 10μM TSO FW primer and 2.5μL of 10μM R2 FW primer. After the reaction, amplified cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and was eluted into a 15μL Elution Buffer. DNA concentration was measured using QuBit fluorometer and cDNA fragment length profile was assessed using Agilent Tapestation D5000 kits (Agilent, 5067).
To construct Illumina sequencing libraries, 50 ng of barcoded and amplified cDNA was fragmented, blunted and dA-tailed by mixing it with 3.5 μL of NEBNext Ultra II FS Reaction buffer (NEB), 1 μL of fully mixed NEBNext Ultra II FS Enzyme mix (NEB) and nuclease free water to a final volume of 17.5 μL. The reaction mix was vortexed for 10 s, spanned down and placed into a preheated PCR machine for incubation at 37°C for 10 min; 65°C for 30 min; hold 4°C (lid at 75ºC). Fragmented DNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and eluted into 16μL of water. Single-stranded DNA adapter, containing Illumina’s TruSeq read 1 (Adp. TruSeq R1 FW and RV) sequences were annealed together at the final concentration of 1.5 μM by mixing 1.5 μL of forward ligation primer and reverse ligation primer (each at 100 μM) with 97 μL of nuclease-free water and heating the solution to 95°C for 2 min and cooling it at room temperature for 5 min. 16 μL of the purified fragmented DNA was mixed with 1.25 μL of 1.5 μM annealed adapters, 1.5μL of 10X T4 DNA ligase buffer, 15 μL of NEBNext Ultra II Ligation Master Mix (NEB, E7805S kit) and 0.5 μL of NEBNext Ultra II Ligation Master Enhancer (NEB, E7805S kit). The ligation reaction was carried out by incubating in the thermocycler for 15 min at 20°C (lid at 30ºC). After ligation, the reaction mix was diluted to 100 μL and was purified using AMPure XP beads (Beckman Coulter, A63881) with 0.8X volume ratio and eluted into 40 μL nuclease-free water. Indexing PCR was carried out by mixing purified DNA with 25 μL of 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) and 2.5 μL of 20μM P7_IDX_R2 primer, 6 sets of 2.5μL of 20μM indexing primer that houses an 8bp library index and water to 50μL. PCR cycling program: 98 °C, 2 min; 3 cycles of 98 °C, 20 s; 55 °C, 30 s; 72 °C, 20 s and 9 cycles 98 °C, 20 s; 65 °C, 30 s; 72 °C, 20 s; with a 1 min final extension at 72 °C, and 4 °C, hold at the end. Following final library indexing, DNA was double-side purified using 0.6x-0.8x SPRIselect (Beckman Coulter, B23318) magnetic beads and eluted into 15μL.

value: Bone marrow

tag: cell line

value: Lymphoblasts


title: MG_C_111_JJ

description:
Library name: Sample 68
column name in Raw_Counts_All_Samples.csv: MG_C_111_JJ

value: WT


title: Ex_24h_F_Replicate1

description: Library name: STC804_5_B7_24h_Re_L1_ds.dfbfb095313c4b95b56a77345005d564


title: Bulk RNA-seq of iPSC cells culturedin CAGEs or wells for 4 days (Cell_Culturing)

description: Library name: iPSC cultures

source_name: Induced pluropotent stem cells

value: Induced pluropotent stem cells

value: stem-cells


title: Ex_24h_F_Replicate2

description: Library name: STC804_6_B9_24h_Re_L1_ds.a96b442e9f0d4ccaaa79cc3aa367a8d5


title: inC-RNA-seq of L1210 single-cell derived colonies cultured in the presence of epigenetic drugs (CAGE_Colonies)

description: Library name: L1210_Clone_seq

data_processing:
BCL sequencing files received from Illumina BaseSpace portal were converted to raw FASTQ files for each of the 4 (R1, R2, R3, R4) sequencing reads without read trimming or masking by using bcl2fastq software (Illumina, v2.20.0.422). Raw FASTQ files were processed using a custom pipeline (available at https://github.com/AllonKleinLab/paper-data/tree/master/Mazelis2025_CAGEs). In brief, sequencing reads were demultiplexed based on Read1 index sequence (stored as read3) (index used: "Control_A_1":"ATAGAGAG", "Control_A_2":"AGAGGATA", "Control_A_3":"CTCCTTAC", "Control_A_4":"TATGCAGT", "Control_A_1":"TACTCCTT", "Control_A_2":"AGGCTTAG", "Control_A_3":"ATTAGACG", "Control_A_4":"CGGAGAGA", "Vorinostat1_1":"CTAGTCGA",  "Vorinostat1_2":"AGCTAGAA","Vorinostat1_3":"ACTCTAGG","Vorinostat1 4":"TCTTACGC","Vorinostat2_1":"CTTAATAG","Vorinostat2_2":"ATAGCCTT","Vorinostat2_3":"TAAGGCTC","Vorinostat2_4":"TCGCATAA","Decitabine1_1":"GTAACGTT","Decitabine1_2":"ACTGAGTT","Decitabine1_3":"ATACTCTT","Decitabine1_4":"GACAACTT","Decitabine2_1":"GAACGATT","Decitabine2_2":"AAGATTGT","Decitabine2_3":"AATCGGGT","Decitabine2_4":"TTGAGGGT","Azacytidine1_1":"AAGCTTCT", "Azacytidine1_2":"TATTGCCT","Azacytidine1_3":"CAGTCCCT","Azacytidine1_4":"ATGCGGAT","Azacytidine2_1":"CAAGTCAT","Azacytidine2_2":"ATATGCAT","Azacytidine2_3":"ATGGAAAT","Azacytidine2_4":"CTGCGTTG","Control_C_1":"AAGCGTAC", "Control_C_2":"TAGTGGAC","Control_C_3":"CGGACAAC","Control_C_4":"ATGGATTA","Control_C_1":"CCACATTA","Control_C_2":"GCAGGGTA","Control_C_3":"ATCCGCTA","Control_C_4":"TTCACATA","Control_B_1"…"TGAAATGA","Control_B_2":"AAACTCGA","Control_B_3":"ACCCACGA","Control_B_4":"CGACGTCA","Control_B_1":"TGTGCTCA","Control_B_2":"CTGGTGCA","Control_B_3":"TACCGGCA","Control_B_4":"ATGAAGCA"), and were filtered based on expected structure (all barcodes matching a barcode whitelist with hamming distance of 1). The demultiplexed reads were then processed using Trimmomatic (1) (with parameters: LEADING 28; SLIDINGWINDOW 4:20; MINLEN 20), followed by Poly-A length trim to 4 nt and selecting reads that are longer than MINLEN. For surviving reads, the fraction of length composed out of same base repeats (only considering > 5) was determined, rejecting reads whose fraction is greater than 0.5. Count matrices were generated using InDrops pipeline.
Count matrices were filtered by selecting barcodes with >2000 UMIs and fraction of mitochondrial counts being below 0.4. Mouse and human cells were filered based on gene expression. Read mapping and cell filtering based on counts and mitochondrial fraction were carried out as described above. Raw counts were then normalized to 10,000 counts per cell (CP10K). Highly variable genes were selected using Scanpy's implementation of the Seurat v3 approach (sc.pp.highly_variable_genes with flavor='seurat_v3'; 4,000 genes for K562 cells and 5,000 genes for L1210 cells; using unnormalized counts for variance calculations). Visualization by UMAP embedding. For visualization only, batch effects from library preparation and cell seeding were corrected using Harmony (Korsunsky et al., 2019) using the scanpy implementation, with the following non-default parameters: theta=4.0, lambda=10.0, and sigma=0.05. Harmony was applied to the 15 NMF program usages per cell. A nearest neighbor graph was constructed using the Harmony-corrected program usages with n_neighbors=10, and scanpy’s UMAP was then applied to the batch-corrected embedding with default parameters. Heatmaps of NMF gene loadings. For heatmaps of gene contributions to NMF programs, the NMF loading matrix (“H” matrix in scikit-learn) was normalized by dividing each gene's loading by its mean non-zero expression level (calculated as mean expression when expressed / fraction of cells expressing). The genes shown in the final heatmaps were filtered to remove mitochondrial genes and non-coding genes to improve interpretability, and ordered by descending normalized loading values. NMF usage means, CVs and Fano Factors. NMF program usage values were first normalized for each cell such that the sum of usages across all programs equaled 1. The mean, CV, and Fano factor of each program's usage across colonies was then calculated at each timepoint. To calculate mock colony CV and Fano factors, we corrected for systematic differences in means over time by regressing the CVs using the power law relationship observed between mean and CV. For comparisons across conditions, each metric was normalized to its value in control colonies at the same timepoint.
Assembly: Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly
Supplementary files format and content: h5ad cell x genes matrices

source_name: Blood cell line

growth_protocol: K562 and L1210 cells were pre-treated with drugs separately by seeding 150,000 (L1210) and 200,000 (K562) cells into 6-well plate wells (Corning). Cells were grown in 2mL of IMDM with 10% FBS, 1X Pen/Strep in the presence of 0.05 μM Dec, 0.7μM Aza, 0.4μM Vor (MedChemExpress) or no drugs (3 repeats) for 48 hours. Next, cells were collected and K562 and L1210 cell-lines were pooled based on the drug condition at a 1:1 ratio. Cell suspensions were encapsulated into CAGEs using a final cell concentration of 1.4e6 cells/mL. Each drug condition was encapsulated for 2 hours, collecting the droplets into four 30 min fractions. One fraction of each condition was sampled instantly by lysing the cells inside the CAGEs and freezing the lysate containing CAGEs at -80ºC in 3X SSCI with 10% DMSO and 0.05U/μL Murine RNAse Inhibitor. Remaining fractions of packed hydrogel CAGEs were seeded into a different 24-well plate well into 1mL of IMDM with 10% FBS and 1x Pen/Strep, 0.1% F127 and 0.1% L31 with appropriate drug. 10,000 K562 and L1210 cells from appropriate drug conditions were seeded outside the CAGEs for the first two days. Every two days, media was exchanged with fresh media with appropriate drugs and one well of each condition was sampled for inC-RNA-seq by lysing the cells and freezing at -80ºC as described above.

extract_protocol:
After all the time points were collected, CAGEs were thawed, washed, and treated with Turbo DNAse I and Proteinase K. Finally, CAGEs were washed three times with 3X SSCI buffer and three times with HI10. Resulting CAGEs were subjected to the inC-RNA-seq protocol.  Reverse-transcription reaction was set on ice and performed in PCR strip tubes. A standard 100μL reaction was composed out of 60.5μL of packed capsules, 2.5μL of 10μM RT poly(T) primer housing a 10nt UMI and 6nt barcode (Table S3, RT), 3μL of 10% Igepal CA-630 (Millipore Sigma, I8896-50ML), 20μL of 5X SMARTseq3 RT buffer (100mM Tris pH 8.3, 150mM NaCl, 12.5mM MgCl2, 5mM GTP, 40mM DTT), 0.5μL of 10mM dNTPs (NEB, N0447L), 2.5μL of 40U/μL Recombinant RNase Inhibitor (Takara Bio, 2313A), 1.5μL of 50μM TSO, 5μL of Maxima H- reverse transcriptase (ThermoFisher, EP0753). Different timepoints were pooled and were kept separate from other timepoints. Reaction volumes were scaled according to the amount of capsules used and number of reactions performed. To set up the reaction, capsules, RT primer and Igepal CA-630 (Millipore Sigma, I8896-50ML) were mixed on ice in a PCR tube, with each housing a different RT barcode. Capsules were incubated on ice for 10 min to allow the RT primer to diffuse in, followed by heating at 70ºC for 5 min and cooling down on ice. Next, RT master mix, composed out of the remaining reagents was added to each tube, ensuring a thought mixing of capsules with pipetting. Tubes were incubated on ice for 5 min and the reaction was carried out at 42ºC for 90 min, followed by cycling between 50ºC and 42ºC incubation of 2 mins for 15 cycles. Reactions were left at room temperature overnight and processed the next day. After the RT reaction, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with ice-cold TI100 (pH 8.0) with 2 min incubations on ice. Finally capsules were washed twice with TI10 (pH 8.0). Next, Capsule dU PCR was performed to carry out cDNA amplification. After the cDNA amplification, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with TI100 (pH 8.0), twice with TI10 (pH 8.0). Washed capsules were subjected to tree rounds of split-and-pool barcoding. Following split-and-pool barcoding, capsules were split into 8 tubes and were dissolved  using 10M NaOH. DNA was purified using MinElute PCR purification kit and barcoded cDNA was eluted into 20μL of the elution buffer. Barcoded and purified DNA was amplified using PCR. After the reaction, amplified barcoded cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and was eluted into a 15μL Elution Buffer.
To construct Illumina sequencing libraries, 50 ng of barcoded and amplified cDNA was fragmented, blunted and dA-tailed by mixing it with 3.5 μL of NEBNext Ultra II FS Reaction buffer (NEB), 1 μL of fully mixed NEBNext Ultra II FS Enzyme mix (NEB) and nuclease free water to a final volume of 17.5 μL. The reaction mix was vortexed for 10 s, spanned down and placed into a preheated PCR machine for incubation at 37°C for 10 min; 65°C for 30 min; hold 4°C (lid at 75ºC). Fragmented DNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and eluted into 16μL of water. Single-stranded DNA adapter, containing Illumina’s TruSeq read 1 (Adp. TruSeq R1 FW and RV) sequences were annealed together at the final concentration of 1.5 μM by mixing 1.5 μL of forward ligation primer and reverse ligation primer (each at 100 μM) with 97 μL of nuclease-free water and heating the solution to 95°C for 2 min and cooling it at room temperature for 5 min. 16 μL of the purified fragmented DNA was mixed with 1.25 μL of 1.5 μM annealed adapters, 1.5μL of 10X T4 DNA ligase buffer, 15 μL of NEBNext Ultra II Ligation Master Mix (NEB, E7805S kit) and 0.5 μL of NEBNext Ultra II Ligation Master Enhancer (NEB, E7805S kit). The ligation reaction was carried out by incubating in the thermocycler for 15 min at 20°C (lid at 30ºC). After ligation, the reaction mix was diluted to 100 μL and was purified using AMPure XP beads (Beckman Coulter, A63881) with 0.8X volume ratio and eluted into 40 μL nuclease-free water. Indexing PCR was carried out by mixing purified DNA with 25 μL of 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) and 2.5 μL of 20μM P7 binding primer, 48 sets of 2.5μL of 20μM indexing primer that houses an 8bp library index and water to 50μL. PCR cycling program: 98 °C, 2 min; 3 cycles of 98 °C, 20 s; 55 °C, 30 s; 72 °C, 20 s and 9 cycles 98 °C, 20 s; 65 °C, 30 s; 72 °C, 20 s; with a 1 min final extension at 72 °C, and 4 °C, hold at the end. Following final library indexing, DNA was double-side purified using 0.6x-0.8x SPRIselect (Beckman Coulter, B23318) magnetic beads and eluted into 15μL.

value: Blood cell line

value: Lymphoblast


title: Ex_2w_F_Replicate4

description: Library name: STC804_4_B6_2wk_Re_L1_ds.0ba5ac67315b4465987d4caebaaf03a9

value: 2 wk


title: SM102_MNR_135_Day_2_Rep5

description:
Library name: N16_s202_S101_001
Column name in count_nhp.txt: N16_s202_S101_001

value: Blood

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques


title: Ex_1w_F_Replicate2

description: Library name: STC804_10_B15_1wk_Re_L1_ds.37f95078620e4e66a3fd7016d8cb0fd5

value: Kidney

value: 1 wk


title: MG_C_109_JJ

description:
Library name: Sample 66
column name in Raw_Counts_All_Samples.csv: MG_C_109_JJ

value: Brain

value: Wistar


title: SM102_MNR_135_Day_2_Rep4

description:
Library name: N16_s201_S89_001
Column name in count_nhp.txt: N16_s201_S89_001


title: MG_C_107_JJ

description:
Library name: Sample 65
column name in Raw_Counts_All_Samples.csv: MG_C_107_JJ

value: Male

value: Microglia cells

value: chow light-feeding


title: KPCic5

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

description: Library name: BA717KPC7_4_24ADCre_KPCic5

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using Burrows-Wheeler aligner BWA-MEM version 0.7.15 (github.com/lh3/bwa.git) with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
The aligned reads were then converted to BAM files using Picard tools 2.9.0 (http:// broadinstitute.github.io/picard). Duplicate reads were removed using Picard tools.
StringTie was used for assembling RNA-seq alignments into potential transcripts, and also getting count and normalize reads with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
Differentially expressed genes were defined with edgeR
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include cov, FPKM, and TPM values for each sample

source_name: lung adenocarcinoma

growth_protocol: Animals were infected with Adeno-Cre to induce tumor formation at 8 weeks of age. Tumors were extracted 5 months later.

extract_protocol:
Tumors were removed from mice and tissue was snap-frozen in liquid nitrogen. RNA was extracted using the PureLink RNA Mini kit (Invitrogen).
Library construction and sequencing was carried out by HaploX Gene Tech Limited (Hong Kong)

value: lung adenocarcinoma


title: Ex_2w_F_Replicate3

description: Library name: STC804_3_B5_2wk_Re_L1_ds.ef1db9a14bf54955a0f4a0948fbf29c6


title: SM102_MNR_135_Day_2_Rep3

description:
Library name: N16_s199_S160_001
Column name in count_nhp.txt: N16_s199_S160_001


title: Ex_2w_F_Replicate2

description: Library name: STC804_2_B2_2wk_Re_L1_ds.30c68c7e7d194a20a8105b353df2d254


title: KP5

description: Library name: BA705KPADCRET4_KP5


title: MG_C_106_JJ

description:
Library name: Sample 64
column name in Raw_Counts_All_Samples.csv: MG_C_106_JJ

value: WT


title: Bulk RNA-seq of L929 cells culturedin CAGEs or wells for 3 days (Cell_Culturing)

description: Library name: L929 cultures

source_name: connective mouse tissue

value: connective mouse tissue

value: Fibroblasts


title: KP4

description: Library name: BA599KPADCRET3_KP4


title: MG_C_112_JJ

description:
Library name: Sample 69
column name in Raw_Counts_All_Samples.csv: MG_C_112_JJ

value: chow ad libitum


title: Ex_2w_F_Replicate1

description: Library name: STC804_1_B1_2wk_Re_L1_ds.7fb3660f24924fc6bcfdf10e2e124d20


title: MG_C_105_JJ

description:
Library name: Sample 63
column name in Raw_Counts_All_Samples.csv: MG_C_105_JJ


title: SM102_MNR_135_Day_2_Rep1

description:
Library name: N16_s174_S145_001
Column name in count_nhp.txt: N16_s174_S145_001


title: SM102_MNR_135_Day_2_Rep6

description:
Library name: N16_s203_S113_001
Column name in count_nhp.txt: N16_s203_S113_001


title: MG_C_103_JJ

description:
Library name: Sample 62
column name in Raw_Counts_All_Samples.csv: MG_C_103_JJ


title: MG_C_110_JJ

description:
Library name: Sample 67
column name in Raw_Counts_All_Samples.csv: MG_C_110_JJ


title: KPCic4

description: Library name: 722_KPCic4


title: KPCic2

description: Library name: 721_T1_KPCic2


title: SM102_MNR_135_Day_0_Rep5

description:
Library name: N16_s162_S96_001
Column name in count_nhp.txt: N16_s162_S96_001


title: MG_C_102_JJ

description:
Library name: Sample 61
column name in Raw_Counts_All_Samples.csv: MG_C_102_JJ

value: chow dark-feeding


title: Tongue Sarcoma Tumor, Hic1;hSS2, S19, RNA-seq

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

data_processing:
Illumina sequencing outputs generated bcl files that were demultiplexed by bcl2fastq2.
Demultiplexed read sequences were aligned to the Mouse Genome (mm10) reference sequence using TopHat58 splice junction mapper with Bowtie 259 or STAR60 aligners (RNA-seq Alignment app, Illumina Basespace)
Assembly was performed and differential expression were estimated using Cufflinks61 and Cuffdiff62, respectively (Cufflinks Assembly & DE app; Illumina Basespace).
Assembly: mm10
Supplementary files format and content: Rpkm

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology

extract_protocol:
Tissues or sorted cells were homogenized in RNAzol lysis reagent and further processed as per manufacturers instructions to obtain RNA for library preparation and subsequent NGS.
TruSeq Stranded mRNA library kit protocol

treatment_protocol: Adult animals (for tSRC and WT sample collections) 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days. For embryonic age (E) 12.5 collections, timed-pregnant females were administered a single dose of TAM at a concentration of 300 mg/kg along with 150 mg/kg progesterone (Sigma P3972-5G) in sunflower oil via oral gavage.

value: Tongue sarcoma tumor

value: Hic1; hSS2


title: Stifle Sarcoma Tumor, Hic1;hSS2, S18, RNA-seq, rep2

value: Stifle sarcoma tumor


title: MG_C_101_JJ

description:
Library name: Sample 60
column name in Raw_Counts_All_Samples.csv: MG_C_101_JJ


title: MG_C_100_JJ

description:
Library name: Sample 59
column name in Raw_Counts_All_Samples.csv: MG_C_100_JJ


title: SM102_MNR_135_Day_0_Rep6

description:
Library name: N16_s166_S144_001
Column name in count_nhp.txt: N16_s166_S144_001

value: Blood

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques


title: SM102_MNR_135_Day_0_Rep3

description:
Library name: N16_s078_S38_001
Column name in count_nhp.txt: N16_s078_S38_001


title: KPCic1

description: Library name: 720_KPCic1


title: KP3

description: Library name: 704_KP3


title: SM102_MNR_135_Day_2_Rep2

description:
Library name: N16_s196_S124_001
Column name in count_nhp.txt: N16_s196_S124_001


title: SM102_MNR_135_Day_0_Rep4

description:
Library name: N16_s152_S166_001
Column name in count_nhp.txt: N16_s152_S166_001


title: Stifle Sarcoma Tumor, Hic1;hSS2, S20, RNA-seq, rep2


title: KP2

description: Library name: 685_KP2


title: MG_C_99_JJ

description:
Library name: Sample 58
column name in Raw_Counts_All_Samples.csv: MG_C_99_JJ

value: Brain


title: Stifle Sarcoma Tumor, Hic1;hSS2, S18, RNA-seq, rep1


title: SM102_MNR_135_Day_0_Rep1

description:
Library name: N16_s055_S15_001
Column name in count_nhp.txt: N16_s055_S15_001


title: MG_C_96_JJ

description:
Library name: Sample 57
column name in Raw_Counts_All_Samples.csv: MG_C_96_JJ

value: Wistar


title: Tongue Sarcoma Tumor, Hic1;hSS2, S22, RNA-seq


title: KP1

description: Library name: 594_KP1


title: SM102_MNR_45_Day_2_Rep6

description:
Library name: N16_s204_S125_001
Column name in count_nhp.txt: N16_s204_S125_001


title: Tongue Sarcoma Tumor, Hic1;hSS2, S11, RNA-seq


title: MG_C_95_JJ

description:
Library name: Sample 56
column name in Raw_Counts_All_Samples.csv: MG_C_95_JJ

value: Male


title: KPCic3

description: Library name: 721_T2_KPCic3


title: Pool of P14 cells - KO Naive, WT Naive, KO liver, WT liver, KO spleen, WT spleen - CITE rep2

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Library name: Pool2_CITE_seq

library_source: other

data_processing:
Cell Ranger count to for alignment and assignment of CITE-seq reads to specific hashes
Cell Ranger aggr to combine samples
Assembly: GRCm39
Supplementary files format and content: 10x Genomics Cell Ranger output
Library strategy: CITE-seq

molecule: other

source_name: Spleen, liver, and blood

extract_protocol:
A 10x Genomics Chip N was used to generate single-cell emulsions.
The 10x Genomics Chromium Next GEM Single Cell 5' HT protocol was performed per the manufacturer's instructions.

treatment_protocol: For infected samples, mice were infected intravenously with 2e6 PFU of LCMV clone 13. For naive cells, uninfected P14 donors were bled to isolate naive cells.

value: Spleen, liver, and blood

value: P14 transgenic CD8+ T cells

value: WT and CD7 KO (pooled)


title: Stifle Sarcoma Tumor, Hic1;hSS2, S12, RNA-seq


title: Tongue Sarcoma Tumor, Hic1;hSS2, S21, RNA-seq


title: SM102_MNR_45_Day_2_Rep4

description:
Library name: N16_s198_S148_001
Column name in count_nhp.txt: N16_s198_S148_001


title: Tongue Sarcoma Tumor, Hic1;hSS2, S10, RNA-seq


title: Pool of P14 cells - KO Naive, WT Naive, KO liver, WT liver, KO spleen, WT spleen - GEX rep2

description: Library name: Pool2_gene_expression

library_source: transcriptomic single cell

data_processing:
Cell Ranger count to for alignment and assignment of CITE-seq reads to specific hashes
Cell Ranger aggr to combine samples
Assembly: GRCm39
Supplementary files format and content: 10x Genomics Cell Ranger output


title: SM102_MNR_45_Day_2_Rep5

description:
Library name: N16_s200_S172_001
Column name in count_nhp.txt: N16_s200_S172_001


title: Stifle Sarcoma Tumor, Hic1;hSS2, S20, RNA-seq, rep1


title: MG_C_93_JJ

description:
Library name: Sample 54
column name in Raw_Counts_All_Samples.csv: MG_C_93_JJ

value: Microglia cells

value: WT

value: chow light-feeding


title: Pool of P14 cells - KO Naive, WT Naive, KO liver, WT liver, KO spleen, WT spleen - GEX rep1

description: Library name: Pool1_gene_expression


title: SM102_MNR_135_Day_0_Rep2

description:
Library name: N16_s061_S21_001
Column name in count_nhp.txt: N16_s061_S21_001


title: MG_C_90_JJ

description:
Library name: Sample 51
column name in Raw_Counts_All_Samples.csv: MG_C_90_JJ


title: SM102_MNR_45_Day_2_Rep2

description:
Library name: N16_s193_S88_001
Column name in count_nhp.txt: N16_s193_S88_001


title: Naive cells from uninfected spleen rep3

description:
Library name: Naive_3
23059FL-10-01-06

data_processing:
Alignment was performed and raw gene counts generated with STAR v2.7.6
Normalized counts were generated by DESeq2
Assembly: GRCm38
Supplementary files format and content: Normalized counts from DESeq2

source_name: Spleen

extract_protocol:
Qiagen AllPrep kit was used to extract DNA and RNA from sorted cells. Only RNA was used in this study.
Takara SMART-seq mRNA kit

treatment_protocol: C57BL/6J mice were infected with 2e6 PFU of LCMV clone 13. Cells were isolated >45 days after infection.

value: Spleen

value: Naive (CD44-CD62L+) CD8+ T cells

value: Uninfected


title: MG_C_91_JJ

description:
Library name: Sample 52
column name in Raw_Counts_All_Samples.csv: MG_C_91_JJ


title: Stifle Sarcoma Tumor, Hic1;hSS2, S9, RNA-seq

value: Hic1; hSS2


title: MG_C_92_JJ

description:
Library name: Sample 53
column name in Raw_Counts_All_Samples.csv: MG_C_92_JJ


title: SM102_MNR_45_Day_2_Rep1

description:
Library name: N16_s186_S99_001
Column name in count_nhp.txt: N16_s186_S99_001


title: Tongue Sarcoma Tumor, Hic1;hSS2, S7, RNA-seq

value: Tongue sarcoma tumor


title: MG_C_94_JJ

description:
Library name: Sample 55
column name in Raw_Counts_All_Samples.csv: MG_C_94_JJ


title: Naive cells from uninfected spleen rep2

description:
Library name: Naive_2
23059FL-10-01-05


title: MG_C_89_JJ

description:
Library name: Sample 50
column name in Raw_Counts_All_Samples.csv: MG_C_89_JJ

value: chow dark-feeding


title: Naive cells from uninfected spleen rep1

description:
Library name: Naive_1
23059FL-10-01-04


title: SM102_MNR_45_Day_0_Rep6

description:
Library name: N16_s133_S77_001
Column name in count_nhp.txt: N16_s133_S77_001

value: Blood

value: PBMC


title: Stifle Sarcoma Tumor, Hic1;hSS2, S19, RNA-seq, rep2

value: Stifle sarcoma tumor


title: SM102_MNR_45_Day_0_Rep5

description:
Library name: N16_s132_S76_001
Column name in count_nhp.txt: N16_s132_S76_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: Tongue Sarcoma Tumor, Hic1;hSS2, S20, RNA-seq


title: PD-1+ Tim3+ CD7hi cells isolated from liver rep3

description:
Library name: Liver_CD7hi_3
23059FL-10-01-14

source_name: Liver

value: Liver

value: PD-1+ CD8+ T cells

value: LCMV clone 13


title: MG_C_87_JJ

description:
Library name: Sample 49
column name in Raw_Counts_All_Samples.csv: MG_C_87_JJ

value: Brain

value: Wistar

value: Male


title: Pool of P14 cells - KO Naive, WT Naive, KO liver, WT liver, KO spleen, WT spleen - CITE rep1

description: Library name: Pool1_CITE_seq

value: Spleen, liver, and blood

value: P14 transgenic CD8+ T cells

value: WT and CD7 KO (pooled)


title: SM102_MNR_45_Day_2_Rep3

description:
Library name: N16_s195_S112_001
Column name in count_nhp.txt: N16_s195_S112_001


title: MG_C_85_JJ

description:
Library name: Sample 48
column name in Raw_Counts_All_Samples.csv: MG_C_85_JJ

value: Microglia cells

value: WT


title: Tongue Sarcoma Tumor, Hic1;hSS2, S8, RNA-seq

value: Tongue sarcoma tumor

value: Hic1; hSS2


title: SM102_MNR_45_Day_0_Rep4

description:
Library name: N16_s129_S73_001
Column name in count_nhp.txt: N16_s129_S73_001

value: Blood


title: PD-1+ Tim3+ CD7hi cells isolated from liver rep1

description:
Library name: Liver_CD7hi_1
23059FL-10-01-16


title: PD-1+ Tim3+ CD7hi cells isolated from liver rep2

description:
Library name: Liver_CD7hi_2
23059FL-10-01-15


title: MG_C_84_JJ

description:
Library name: Sample 47
column name in Raw_Counts_All_Samples.csv: MG_C_84_JJ

value: chow light-feeding


title: MG_C_83_JJ

description:
Library name: Sample 46
column name in Raw_Counts_All_Samples.csv: MG_C_83_JJ


title: Stifle Sarcoma Tumor, Hic1;hSS2, S21, RNA-seq

value: Stifle sarcoma tumor


title: SM102_MNR_45_Day_0_Rep3

description:
Library name: N16_s053_S13_001
Column name in count_nhp.txt: N16_s053_S13_001

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques


title: SM102_MNR_45_Day_0_Rep2

description:
Library name: N16_s037_S156_001
Column name in count_nhp.txt: N16_s037_S156_001


title: PD-1+ Tim3+ CD7lo cells isolated from liver rep3

description:
Library name: Liver_CD7lo_3
23059FL-10-01-17

value: Liver

value: PD-1+ CD8+ T cells


title: Stifle Sarcoma Tumor, Hic1;hSS2, S19, RNA-seq, rep1


title: SM102_MNR_45_Day_0_Rep1

description:
Library name: N16_s036_S144_001
Column name in count_nhp.txt: N16_s036_S144_001


title: MG_C_82_JJ

description:
Library name: Sample 45
column name in Raw_Counts_All_Samples.csv: MG_C_82_JJ

value: Brain


title: PD-1+ Tim3+ CD7lo cells isolated from liver rep2

description:
Library name: Liver_CD7lo_2
23059FL-10-01-09

value: LCMV clone 13


title: SM102_MNR_15_Day_2_Rep6

description:
Library name: N16_s197_S136_001
Column name in count_nhp.txt: N16_s197_S136_001


title: PD-1+ Tim3+ CD7lo cells isolated from liver rep1

description:
Library name: Liver_CD7lo_1
23059FL-10-01-18


title: inC-RNA-seq of K562 single-cell derived colonies cultured in the presence of epigenetic drugs (CAGE_Colonies)

description: Library name: K562_Clone_seq

value: Blood cell line

value: Lymphoblast

value: 0.05 μM Dec, 0.7μM Aza, 0.4μM Vor (MedChemExpress) or no drugs (3 repeats)


title: Sepsis 3

city: Charleston

first: Liu

last: Liu

state: South Carolina

address: 173 Ashley Ave. CRI 610

institute: Medical University of South Carolina

description:
Library name: SAMPLE6
10x Genomics
Combination1.Seuratobject.rds

data_processing:
Raw sequencing reads were processed by Novogene, including alignment to the GRCh38 human reference genome using Cell Ranger (10x Genomics), UMI collapsing, and barcode filtering to generate gene expression matrices. Downstream analysis was performed in R using Seurat, including quality control, normalization, clustering, and cell type annotation. The final processed data are provided as a Seurat RDS object containing all six samples.
Assembly: GRCh38
Supplementary files format and content: Processed data are provided as a Seurat RDS object containing gene expression matrices and cell-level annotations for all six samples.

source_name: hippocampus

extract_protocol:
RNA extraction and library preparation were performed by Novogene (San Jose, CA) following standard 10x Genomics Chromium Single Cell 3′ v3.1 protocols.
Single-nucleus 3′ RNA libraries were prepared by Novogene (San Jose, CA) using the 10x Genomics Chromium Single Cell 3′ v3.1 platform following the manufacturer’s instructions. Library construction included barcoding of individual nuclei, cDNA synthesis, amplification, and preparation for Illumina sequencing.

value: hippocampus

value: male

tag: subject status

value: sepsis patient


title: MG_C_81_JJ

description:
Library name: Sample 44
column name in Raw_Counts_All_Samples.csv: MG_C_81_JJ

tag: strain

value: Wistar

value: Male

value: Microglia cells

value: WT

value: chow ad libitum


title: SM102_MNR_15_Day_2_Rep4

description:
Library name: N16_s191_S159_001
Column name in count_nhp.txt: N16_s191_S159_001

tag: tissue

value: Blood

value: PBMC


title: Sepsis 2

description:
Library name: SAMPLE5
10x Genomics
Combination1.Seuratobject.rds

value: Female


title: SM102_MNR_15_Day_2_Rep5

description:
Library name: N16_s192_S171_001
Column name in count_nhp.txt: N16_s192_S171_001

tag: cell type

value: Naive male and female Mauritius origin cynomolgus macaques


title: MG_C_80_JJ

description:
Library name: Sample 43
column name in Raw_Counts_All_Samples.csv: MG_C_80_JJ

value: Brain

tag: genotype


title: MG_C_79_JJ

description:
Library name: Sample 42
column name in Raw_Counts_All_Samples.csv: MG_C_79_JJ

tag: treatment


title: PD-1+ Tim3+ CD7hi cells isolated from spleen rep3

description:
Library name: Spleen_CD7hi_3
23059FL-10-01-07

value: Spleen

value: PD-1+ CD8+ T cells

value: LCMV clone 13


title: PD-1+ Tim3+ CD7hi cells isolated from spleen rep2

description:
Library name: Spleen_CD7hi_2
23059FL-10-01-08


title: Sepsis 1

description:
Library name: SAMPLE4
10x Genomics
Combination1.Seuratobject.rds


title: PD-1+ Tim3+ CD7hi cells isolated from spleen rep1

description:
Library name: Spleen_CD7hi_1
23059FL-10-01-10


title: Tongue Sarcoma Tumor, Hic1;hSS2, S18, RNA-seq

value: Tongue sarcoma tumor

value: Hic1; hSS2


title: MG_C_78_JJ

description:
Library name: Sample 41
column name in Raw_Counts_All_Samples.csv: MG_C_78_JJ

value: chow dark-feeding


title: SM102_MNR_15_Day_2_Rep1

description:
Library name: N16_s185_S87_001
Column name in count_nhp.txt: N16_s185_S87_001

tag: timepoint


title: SM102_MNR_15_Day_2_Rep2

description:
Library name: N16_s187_S111_001
Column name in count_nhp.txt: N16_s187_S111_001

tag: dose


title: MG_C_76_JJ

description:
Library name: Sample 39
column name in Raw_Counts_All_Samples.csv: MG_C_76_JJ


title: SM102_MNR_15_Day_2_Rep3

description:
Library name: N16_s188_S123_001
Column name in count_nhp.txt: N16_s188_S123_001

tag: biological replicate


title: MG_C_77_JJ

description:
Library name: Sample 40
column name in Raw_Counts_All_Samples.csv: MG_C_77_JJ

tag: Sex


title: Con 2

description:
Library name: SAMPLE2
10x Genomics
Combination1.Seuratobject.rds

value: hippocampus

value: age-matched control


title: PD-1+ Tim3+ CD7lo cells isolated from spleen rep2

description:
Library name: Spleen_CD7lo_2
23059FL-10-01-12


title: MG_C_75_JJ

description:
Library name: Sample 38
column name in Raw_Counts_All_Samples.csv: MG_C_75_JJ

value: Wistar

value: Male

value: chow light-feeding

tag: time


title: PD-1+ Tim3+ CD7lo cells isolated from spleen rep3

description:
Library name: Spleen_CD7lo_3
23059FL-10-01-11


title: SM102_MNR_15_Day_0_Rep6

description:
Library name: N16_s161_S84_001
Column name in count_nhp.txt: N16_s161_S84_001


title: PD-1+ Tim3+ CD7lo cells isolated from spleen rep1

description:
Library name: Spleen_CD7lo_1
23059FL-10-01-13


title: LINC01432 LNA ASO3-2

first: Jessica

last: Silva-Fisher

address: 425 Euclid

institute: Washington University in St. Louis

description: Library name: LIB088056

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl GRCh38.113 primary assembly with STAR version 2.7.11b.  Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8.
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.10.0.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 5.04.
Assembly: GRCh38.113 reference genome
Supplementary files format and content: Comma Separated Values text file with raw counts for each sample

source_name: RPMI 8226

extract_protocol:
RNA isolation
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.

value: RPMI 8226

value: Multiple Myeloma


title: MG_C_74_JJ

description:
Library name: Sample 37
column name in Raw_Counts_All_Samples.csv: MG_C_74_JJ

value: Microglia cells

value: WT


title: SM102_MNR_15_Day_0_Rep5

description:
Library name: N16_s156_S119_001
Column name in count_nhp.txt: N16_s156_S119_001

source_name: Blood

value: Blood

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques


title: Con 1

description:
Library name: SAMPLE1
10x Genomics
Combination1.Seuratobject.rds

value: Female


title: Con 3

description:
Library name: SAMPLE3
10x Genomics
Combination1.Seuratobject.rds

value: male


title: Stem-like cells isolated from spleen rep3

description:
Library name: Stem_like_3
23059FL-10-01-01

value: Spleen

value: PD-1+ CD8+ T cells

value: LCMV clone 13


title: MG_C_73_JJ

description:
Library name: Sample 36
column name in Raw_Counts_All_Samples.csv: MG_C_73_JJ

source_name: Brain

value: Brain


title: Stem-like cells isolated from spleen rep2

description:
Library name: Stem_like_2
23059FL-10-01-02


title: Control LNA ASO1-2

description: Library name: LIB088053


title: MG_C_71_JJ

description:
Library name: Sample 35
column name in Raw_Counts_All_Samples.csv: MG_C_71_JJ

value: chow ad libitum


title: SM102_MNR_15_Day_0_Rep4

description:
Library name: N16_s148_S118_001
Column name in count_nhp.txt: N16_s148_S118_001


title: Stem-like cells isolated from spleen rep1

description:
Library name: Stem_like_1
23059FL-10-01-03


title: SM102_MNR_15_Day_0_Rep3

description:
Library name: N16_s077_S37_001
Column name in count_nhp.txt: N16_s077_S37_001


title: Control LNA ASO1-1

description: Library name: LIB088052


title: SM102_MNR_15_Day_0_Rep2

description:
Library name: N16_s062_S22_001
Column name in count_nhp.txt: N16_s062_S22_001


title: MG_C_69_JJ

description:
Library name: Sample 34
column name in Raw_Counts_All_Samples.csv: MG_C_69_JJ

value: Wistar

value: chow dark-feeding


title: SM102_MNR_15_Day_0_Rep1

description:
Library name: N16_s056_S16_001
Column name in count_nhp.txt: N16_s056_S16_001


title: MG_C_67_JJ

description:
Library name: Sample 33
column name in Raw_Counts_All_Samples.csv: MG_C_67_JJ

value: Male


title: SM102_MNR_5_Day_2_Rep6

description:
Library name: N16_s183_S158_001
Column name in count_nhp.txt: N16_s183_S158_001


title: CELF2_LNA-ASO2

description: Library name: LIB088059

data_processing:
RNA-seq
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl GRCh38.113 primary assembly with STAR version 2.7.11b.  Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8.
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.10.0.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 5.04.
Assembly: GRCh38.113 reference genome
Supplementary files format and content: Comma Separated Values text file with raw counts for each sample

value: 5nM CELF2 LNA ASO


title: CELF2_LNA-ASO1

description: Library name: LIB088058

value: Multiple Myeloma


title: MG_C_65_JJ

description:
Library name: Sample 32
column name in Raw_Counts_All_Samples.csv: MG_C_65_JJ

value: Microglia cells

value: chow light-feeding


title: MG_C_60_JJ

description:
Library name: Sample 30
column name in Raw_Counts_All_Samples.csv: MG_C_60_JJ

value: WT


title: Aombp1_24 h

city: Kunming

last: Bai

address: No. 2 Cuihu North Road, Huashan Street, Wuhua District

country: China

institute: Yunan University

description:
Library name: sample 6
RNA-Seq

data_processing:
High-throughput sequencing data were analyzed using the OmicShare online platform (www.majorbio.com)
Assembly: GCF_000225545.1
Supplementary files format and content: TPM, gene counts

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: WT (represented by AO) and ΔAombp1 (represented by Aombp1) strains were cultured in PD broth at 28℃ with agitation (180 r/min) for 5 days.

extract_protocol:
After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)
RNA libraries for RNA-Seq were prepared by Illumina MiSeq platform at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China)

treatment_protocol: Three replicatesMycelia were collected, washed three times with 0.1 M phosphate buffer (pH 6.8–7.2), divided into four groups, and induced with approximately 600 nematodes for 0, 12, and 24 h, respectively; three replicates were used for each sample. were used for each sample.

value: Fungal hyphae

tag: time point


title: AO_12 h

description:
Library name: sample 2
RNA-Seq


title: Aombp1_12 h

description:
Library name: sample 5
RNA-Seq


title: Control_LNA ASO2

description: Library name: LIB088053

value: Control LNA ASO


title: LINC01432 LNA ASO3-1

description: Library name: LIB088055

value: RPMI 8226


title: AO_24 h

description:
Library name: sample 3
RNA-Seq


title: SM102_MNR_5_Day_2_Rep4

description:
Library name: N16_s179_S110_001
Column name in count_nhp.txt: N16_s179_S110_001

data_processing:
The bcl files were demultiplexed using Illumina’s bcl2fastq software.
The fastq files were processed using Array Studio software (Qiagen) and aligned to the cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Differential gene expression analysis was performed using the Limma-Voom method, which transforms the raw read counts into log-counts per million (log-CPM) and models the mean-variance relationship of the data.
Assembly: cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.
Supplementary files format and content: Tab-delimited text file including log-CPM for each sample.

value: Blood

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques


title: Control_LNA-ASO1

description: Library name: LIB088052


title: MG_C_64_JJ

description:
Library name: Sample 31
column name in Raw_Counts_All_Samples.csv: MG_C_64_JJ

data_processing:
Sequencing data was filtered using SOAPnuke 68 by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: Rattus_norvegicus, GCF_000001895.5_Rnor_6.0
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample


title: MG_C_56_JJ

description:
Library name: Sample 28
column name in Raw_Counts_All_Samples.csv: MG_C_56_JJ


title: AO_0 h

description:
Library name: sample 1
RNA-Seq

value: 0 h


title: H3K27R_wing_H3K27me3_rep_2

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
Library name: RNAseq_6
H3K27R_H3K27me3_rpkm_spikein.bw
H3K27R_H3K27me3_peaks.broadPeak

data_processing:
Reads were mapped to the dm6 genome assembly using Bowtie2. Unmapped, multiply aligning, mitochondrial, and scaffold reads were removed. Nonspecific CUT&RUN signal was subtracted from H3K27me3 samples using IgG control for each genotype. MACS2 was used to identify broad H3K27me3 peaks after merging replicates for each genotype.
Assembly: dm6
Supplementary files format and content: Bigwig files were formed from merged replicates and spike-in normalized with SNAP-CUTANA K-MetStat nucleosomes.
Library strategy: CUT&Run

organism: Drosophila melanogaster

source_name: 3rd instar wing disc

growth_protocol: Animals were reared at 25ºC, a temperature at which GAL80 represses GAL4. Plates with molasses and yeast paste were exchanged at three-hour intervals to stage discs at time of dissection.  Embryos were aged on plates for 24 hours and picked into vials as first-instar larvae. Larvae were reared until 44 hours after egg laying (AEL), then shifted to 32ºC to inactivate GAL80 and express transgenes for 72 hours.

extract_protocol:
Imaginal wing and eye-antennal discs were harvested from crawling third-instar larvae. Larvae were staged to within 116 and 119 hours after egg laying. For each replicate, twenty discs were dissected into ice cold 1X PBS solution. Two biological replicates were dissected for each genotype.. Samples were washed three times in Wash Buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5 mM spermidine (Sigma S0266-1G), and Pierce EDTA-free Protease Inhibitor (ThermoFisher PIA32955)) and incubated with activated concanavalin-A (ConA) paramagnetic beads (EpiCypher SKU: 21-1401) for ten minutes in PCR strip tubes. Samples were resuspended in cold Antibody Buffer (Wash Buffer + 0.05% digitonin (Sigma Millipore 300410250MG) and 2mM EDTA (Fisher S311500)). 2 uL of SNAP-CUTANA K-MetStat nucleosomes (EpiCypher SKU: 19-1002) diluted 1:100 in Wash Buffer were added to each sample for spike-in normalization. Antibody was added to samples at a 1:50 concentration and incubated overnight at 4ºC (Rabbit anti-H3K27me3 (Cell Signaling Technology #9733S) or rabbit IgG control (ThermoFisher #10500C)). The following day, discs were washed with Digitonin Buffer (Wash Buffer + 0.05% digitonin (Sigma Millipore 300410250MG)), then incubated with pAG-MNase (EpiCypher SKU: 15-1016) for ten minutes to allow protein A/G binding to antibody. 1 uL of cold 100 mM CaCl2 was added to samples to activate pAG-MNase and incubated on nutator for 2 hours at 4ºC. Reaction was quenched with Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A , 50 µg/mL Glycogen). Chromatin was eluted from samples at 37ºC for ten minutes, then DNA was purified with the Qiagen MinElute Reaction Cleanup Kit (Qiagen #28204).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina

value: 3rd instar wing disc


title: MG_C_57_JJ

description:
Library name: Sample 29
column name in Raw_Counts_All_Samples.csv: MG_C_57_JJ

value: Brain


title: SM102_MNR_5_Day_2_Rep3

description:
Library name: N16_s178_S98_001
Column name in count_nhp.txt: N16_s178_S98_001

extract_protocol:
Muscle cells at each collection time-point, media was aspirated, and cultures were lysed on-plate using 350 µL of RLT buffer (Qiagen Cat. No. 79216) and immediately transferred to 1.5 mL tubes and stored at -80 °C. Total RNA was extracted from whole blood NHP samples collected in PAXgene Blood RNA Tubes (Qiagen, BD Diagnostics) pre- and 2 days post-immunization using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen) on an automated KingFisher Flex System (Thermo Scientific). The quality and yield of RNA were assessed on the 4200 TapeStation System (Agilent) and NanoDrop™ Eight Spectrophotometer (Thermo Scientific). Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).
Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).


title: MG_C_53_JJ

description:
Library name: Sample 27
column name in Raw_Counts_All_Samples.csv: MG_C_53_JJ

extract_protocol:
To study differences in microglial gene expression, bulk RNA sequencing was performed. RNA from microglial cells was isolated using the RNeasy Micro Kit (Qiagen, 74104), according to the manufacturer’s guidelines. mRNA was enriched from total RNA with the Dynabeads® mRNA Purification Kit (Invitrogen, 61006).
A strand-specific transcriptome library was constructed using the MGIEasy RNA Directional Library Prep Set (16 RXN) (MGI, 1000006385). Briefly, after cDNA synthesis, adaptor ligation was performed to ligate adaptors with the cDNAs. Subsequently, a PCR reaction was conducted to amplify the cDNAs, after which the library quality was checked using the Agilent 2100 Bioanalyzer (Agilent, G2939AA). Finally, single-stranded cyclized products were produced from single-stranded PCR products. To perform sequencing, single-stranded circle DNA molecules were replicated via rolling cycle amplification and a DNA nanoball (DNB) was generated. Sequencing was performed through combinatorial Probe-Anchor Synthesis (cPAS) on the DNBSEQ-G400 (MGI, G400).

value: Wistar

value: chow ad libitum


title: H3K27R_wing_IgG

description: Library name: RNAseq_4


title: AoMbp1

description:
Library name: Sample 2
DAP-Seq

data_processing:
DNA affinity purification sequencing involves the in vitro construction and expression of transcription factor (TF, Transcription Factor) proteins, which are then combined with target genomic fragments. The genomic DNA fragments bound by the target protein are enriched. By integrating with high-throughput sequencing technology, the DNA products after DAP are sequenced and analyzed to identify the DNA binding sites of the target protein across the entire genome, thereby obtaining high-throughput data results through efficient sequencing methods.
Assembly: Genome builded by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).
Supplementary files format and content: peaks

growth_protocol: The cDNA sequence encoding protein AoMbp1 is constructed in Halo Tag plasmid, the construct vector pAoMbp1-halo was identified by sequencing,and for protein expression

extract_protocol:
The DNA was extracted by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).
The DNA libraries were sequenced on the Illumina sequencing platform by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

treatment_protocol: Through the combination with high-throughput sequencing technology, DNA products after DAP were sequenced and analyzed, DNA binding sites of target proteins were searched from the whole genome, and high-throughput data results were obtained by efficient sequencing methods.


title: SM102_MNR_5_Day_2_Rep1

description:
Library name: N16_s173_S133_001
Column name in count_nhp.txt: N16_s173_S133_001


title: Ao-input

description:
Library name: Sample 1
DAP-Seq


title: H3K27M_wing_H3K27me3_rep_2

description:
Library name: RNAseq_3
H3K27M_H3K27me3_rpkm_spikein.bw
H3K27M_upregulated_genes.bed


title: Aombp1_0 h

description:
Library name: sample 4
RNA-Seq


title: SM102_MNR_5_Day_2_Rep5

description:
Library name: N16_s180_S122_001
Column name in count_nhp.txt: N16_s180_S122_001


title: MG_C_52_JJ

description:
Library name: Sample 26
column name in Raw_Counts_All_Samples.csv: MG_C_52_JJ

value: Male


title: WingDisc_H3K27M_Nup153RNAi_Rep_3

description:
Library name: mRNAseq_36
H3K27M_Nup153.bw

data_processing:
Alignment of reads to the Drosophila melanogaster dm6 reference genome was done with HISAT2 v2.1.0 with a mapping quality threshold of ≥ 30. Reads below this threshold were rejected as were reads that mapped to the mitochondrial or scaffold DNA.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized,

extract_protocol:
Imaginal wing and eye-antennal discs were harvested from crawling third-instar larvae. Larvae were staged to within 116 and 119 hours after egg laying. For each replicate, ten discs were dissected into ice cold 1X PBS solution. Three biological replicates were dissected for each genotype. After dissection, discs were incubated in Trizol for 5 minutes to dissolve tissue, then frozen at -20ºC. RNA was isolated using standard Trizol RNA isolation procedure.
Libraries were prepared using the Illumina TrueSeq RNA prep kit V2.


title: SM102_MNR_5_Day_0_Rep5

description:
Library name: N16_s136_S80_001
Column name in count_nhp.txt: N16_s136_S80_001


title: WingDisc_H3K27M_Nup153RNAi_Rep_2

description:
Library name: mRNAseq_35
H3K27M_Nup153.bw


title: SM102_MNR_5_Day_0_Rep4

description:
Library name: N16_s134_S78_001
Column name in count_nhp.txt: N16_s134_S78_001


title: SM102_MNR_5_Day_0_Rep6

description:
Library name: N16_s146_S94_001
Column name in count_nhp.txt: N16_s146_S94_001


title: H3K27M_wing_IgG

description: Library name: RNAseq_1


title: H3K27M_wing_H3K27me3_rep_1

description:
Library name: RNAseq_2
H3K27M_H3K27me3_rpkm_spikein.bw
H3K27M_upregulated_genes.bed


title: srcCalvXX_Bcat_end2

description: Single cell RNA-seq sarcoma cells

data_processing:
Samples were demultiplexed using cellranger mkfastq with bclfastq2.
Samples were aligned and output matrices generated using cellranger count for alignment.
cellranger aggregate for alignment, matrix etc
Assembly: mm10 with appended tdTomato and EGFP sequences
Supplementary files format and content: gene matrices, cell barcode and gene list are included as .mtx, .tsv and .tsv files, respectively

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2;Cttnb1Ex3FL/+ sarcoma cells 8 weeks endpoint calvaria XX 2

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology.

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium library preparation pipeline and subsequent NGS.
10X Chromium Single Cell 3' v2

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experments were performed.

value: Mesenchymal Progenitors

value: Calvaria


title: SM102_MNR_5_Day_2_Rep2

description:
Library name: N16_s177_S86_001
Column name in count_nhp.txt: N16_s177_S86_001


title: MG_C_50_JJ

description:
Library name: Sample 24
column name in Raw_Counts_All_Samples.csv: MG_C_50_JJ

value: Microglia cells

value: chow dark-feeding


title: MG_C_49_JJ

description:
Library name: Sample 23
column name in Raw_Counts_All_Samples.csv: MG_C_49_JJ

value: WT


title: MG_C_51_JJ

description:
Library name: Sample 25
column name in Raw_Counts_All_Samples.csv: MG_C_51_JJ


title: H3K27R_wing_H3K27me3_rep_1

description:
Library name: RNAseq_5
H3K27R_H3K27me3_rpkm_spikein.bw
H3K27R_H3K27me3_peaks.broadPeak


title: MG_C_48_JJ

description:
Library name: Sample 22
column name in Raw_Counts_All_Samples.csv: MG_C_48_JJ

value: chow light-feeding


title: WingDisc_H3K27R_Nup153RNAi_Rep_3

description:
Library name: mRNAseq_33
H3K27R_Nup153.bw


title: srcTongueXX_Lgr5_end

description: Single cell RNA-seq sarcoma cells

source_name: Lgr5CreERT2/+;Rosa26SSM2/SSM2 sarcoma cells 20 weeks endpoint tongue XX

value: Tongue


title: WingDisc_H3K27M_Nup153RNAi_Rep_1

description:
Library name: mRNAseq_34
H3K27M_Nup153.bw


title: WingDisc_H3K27R_Nup153RNAi_Rep_2

description:
Library name: mRNAseq_32
H3K27R_Nup153.bw


title: MG_C_44_JJ

description:
Library name: Sample 21
column name in Raw_Counts_All_Samples.csv: MG_C_44_JJ


title: WingDisc_H3K27R_Nup153RNAi_Rep_1

description:
Library name: mRNAseq_31
H3K27R_Nup153.bw


title: SM102_MNR_5_Day_0_Rep1

description:
Library name: N16_s035_S132_001
Column name in count_nhp.txt: N16_s035_S132_001


title: srcCalvXX_Bcat_end1

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2;Cttnb1Ex3FL/+ sarcoma cells 8 weeks endpoint calvaria XX 1


title: MG_C_42_JJ

description:
Library name: Sample 20
column name in Raw_Counts_All_Samples.csv: MG_C_42_JJ


title: srcStifleXX_end

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint stifle XX

value: Stife (hindlimb-knee)


title: WingDisc_H3K27M_Ash1RNAi_Rep_3

description:
Library name: mRNAseq_30
H3K27M_Ash1.bw


title: srcTongueXX_end4

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XX 4


title: cKK-E10_MNR_135_Day_2_Rep4

description:
Library name: N14_s064_S92_001
Column name in count_nhp.txt: N14_s064_S92_001

value: Blood


title: cKK-E10_MNR_135_Day_2_Rep3

description:
Library name: N14_s063_S80_001
Column name in count_nhp.txt: N14_s063_S80_001

value: PBMC


title: cKK-E10_MNR_135_Day_2_Rep2

description:
Library name: N14_s058_S20_001
Column name in count_nhp.txt: N14_s058_S20_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: WingDisc_H3K27M_Ash1RNAi_Rep_2

description:
Library name: mRNAseq_29
H3K27M_Ash1.bw


title: srcTongueXX_end3

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XX 3


title: WingDisc_H3K27M_Ash1RNAi_Rep_1

description:
Library name: mRNAseq_28
H3K27M_Ash1.bw


title: SM102_MNR_5_Day_0_Rep3

description:
Library name: N16_s051_S11_001
Column name in count_nhp.txt: N16_s051_S11_001


title: MG_C_39_JJ

description:
Library name: Sample 18
column name in Raw_Counts_All_Samples.csv: MG_C_39_JJ


title: SM102_MNR_5_Day_0_Rep2

description:
Library name: N16_s038_S167_001
Column name in count_nhp.txt: N16_s038_S167_001


title: srcTongueXX_end1

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XX 1


title: MG_C_41_JJ

description:
Library name: Sample 19
column name in Raw_Counts_All_Samples.csv: MG_C_41_JJ


title: MG_C_38_JJ

description:
Library name: Sample 17
column name in Raw_Counts_All_Samples.csv: MG_C_38_JJ


title: MG_C_36_JJ

description:
Library name: Sample 15
column name in Raw_Counts_All_Samples.csv: MG_C_36_JJ


title: cKK-E10_MNR_135_Day_0_Rep4

description:
Library name: N14_s023_S75_001
Column name in count_nhp.txt: N14_s023_S75_001


title: WingDisc_H3K27R_Ash1RNAi_Rep_3

description:
Library name: mRNAseq_27
H3K27R_Ash1.bw


title: cKK-E10_MNR_135_Day_0_Rep5

description:
Library name: N14_s031_S76_001
Column name in count_nhp.txt: N14_s031_S76_001


title: cKK-E10_MNR_135_Day_2_Rep1

description:
Library name: N14_s057_S8_001
Column name in count_nhp.txt: N14_s057_S8_001


title: WingDisc_H3K27R_Ash1RNAi_Rep_2

description:
Library name: mRNAseq_26
H3K27R_Ash1.bw


title: srcStifleXY_end2

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint stifle XY 2


title: WingDisc_H3K27R_Ash1RNAi_Rep_1

description:
Library name: mRNAseq_25
H3K27R_Ash1.bw


title: srcTongueXX_end2

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XX 2


title: cKK-E10_MNR_135_Day_0_Rep3

description:
Library name: N14_s009_S2_001
Column name in count_nhp.txt: N14_s009_S2_001


title: MG_C_35_JJ

description:
Library name: Sample 14
column name in Raw_Counts_All_Samples.csv: MG_C_35_JJ


title: MG_C_37_JJ

description:
Library name: Sample 16
column name in Raw_Counts_All_Samples.csv: MG_C_37_JJ


title: srcStifleXY_end1

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint stifle XY 1


title: srcTongueXY_end3

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XY 3


title: WingDisc_H3K27M_AsxRNAi_Rep_3

description:
Library name: mRNAseq_24
H3K27M_Asx.bw

value: Act5C-GAL4, alphaTub84B-GAL80ts/UAS-tH3 K27M; AsxRNAi


title: MG_C_34_JJ

description:
Library name: Sample 13
column name in Raw_Counts_All_Samples.csv: MG_C_34_JJ


title: WingDisc_H3K27M_AsxRNAi_Rep_2

description:
Library name: mRNAseq_23
H3K27M_Asx.bw

value: 3rd instar wing disc


title: cKK-E10_MNR_135_Day_0_Rep2

description:
Library name: N14_s008_S85_001
Column name in count_nhp.txt: N14_s008_S85_001


title: srcTongueXY_end2

description: Single cell RNA-seq sarcoma cells

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XY 2


title: MG_C_33_JJ

description:
Library name: Sample 12
column name in Raw_Counts_All_Samples.csv: MG_C_33_JJ

value: Brain


title: cKK-E10_MNR_135_Day_0_Rep1

description:
Library name: N14_s003_S25_001
Column name in count_nhp.txt: N14_s003_S25_001