title: AGS cell, siUSP22_3

city: Jinan

first: Jie

last: Zhang

address: 247 Beiyuan Street, Tianqiao District, Jinan, Shandong Province, China

institute: Sgandong University

description: Library name: SAMPLE6

data_processing:
(1) Discard a paired reads if either one read contains adapter  contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in  either one read;  (3) Discard a paired reads if the proportion of low quality (Phred quality  <=5) bases is over 50% in either one read.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Gastric cancer

growth_protocol: AGS cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Lysis of cells with Trizol regent and harvesting of RNA.
Using Illumina NovaSeq 6000 sequencing platform

treatment_protocol: AGS cells were transfected with siControl and siUSP22 for 48 h.

value: Gastric cancer

value: AGS cell

value: Gastric cancer cell


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L, tumor, castrated, Sx682, ICB, replicate 1

status: Public on Jun 01 2026

type: SRA

city: Notre Dame

first: Ziyu

last: Zeng

state: Indiana

address: 100 Galvin Life Sciences Center

department: Biological Sciences

country: USA

institute: University of Notre Dame

description: Library name: DKO_CSI_1

library_source: transcriptomic

data_processing:
(Bulk RNA-seq) Aligned to GRCm39 with STAR v2.7.11a. Differential expression via DESeq2 v1.48.2, rlog variance stabilization. Pathways analyzed with fgsea v1.34.2 and GSVA v2.2.0.
(scRNA-seq) Cell Ranger Multi v8.0.1 demultiplexing. Seurat v5.3.0: filtered 100-9069 genes/cell, <29430 UMI, <25% mitochondrial, doublets removed (scDblFinder). SCTransform normalization regressing cell cycle and mitochondrial content. Louvain clustering (resolution=1.0), 50 PCs for tSNE. Cell types annotated using SingleR + Azimuth + manual curation.
Assembly: GRCm39 (mm39)
Supplementary files format and content: comma-separated file containing bulk RNA-seq raw read counts for all samples; comma-separated file containing tpm normalized counts
Supplementary files format and content: h5 files for single-cell raw counts each individual sample, demultiplexed from cellranger multi; processed seurat object as R object (rds)

molecule: total RNA

organism: Mus musculus

source_name: prostate tumor

growth_protocol: Nkx3.1-CreERT2/+ mice with floxed Pten, Smad4, and Pygo2 alleles received tamoxifen (1 mg IP daily × 5 days) at 1-4 months to induce prostate tumorigenesis. Tumors harvested at 10 weeks (DKO) or 17 weeks (TKO) post-induction for RNA-seq.

extract_protocol:
Total RNA isolated using Direct-zol RNA MiniPrep Kit (Zymo R2050). For scRNA-seq: tumors dissociated with Mouse Tumor Dissociation Kit (Miltenyi 130-096-730), 1-2h 37°C, filtered through 40-μm strainer, dead cell depleted with EasySep Annexin V kit (STEMCELL 17899), TotalSeq-A hashtag A0303-A0308 applied.
Bulk RNA-seq: standard Illumina library prep
scRNA-seq: 10x Chromium Single Cell 3' v3 chemistry. Six tumor samples were individually labeled with TotalSeq-A hashtag oligonucleotides (BioLegend): DKO replicate 1 (A0303), DKO replicate 2 (A0304), TKO replicate 1 (A0305), TKO replicate 2 (A0306), TKO+CSI replicate 1 (A0307), TKO+CSI replicate 2 (A0308). After hashing, samples were pooled in equal proportions and loaded onto 10x Chromium Controller for library preparation with feature barcoding enabled.

treatment_protocol: CSI treatment: surgical castration + SX-682 medicated chow (1428.5 mg/kg, 200 mg/kg/day equivalent) + anti-PD1 (10 mg/kg) + anti-CTLA4 (10 mg/kg) IP twice weekly × 4 doses.

tag: tissue

value: prostate tumor

tag: genotype

value: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L

tag: treatment


title: N5_Spleen

city: Vienna

first: Peter

last: Pietschmann

state: Vienna

address: Währinger Gürtel 18-20

country: Austria

institute: Institute of Pathophysiology and Allergy Research

description: Library name: N5_M_MKRN250005727-1A_22

data_processing:
Base calling used CASAVA, and demultiplexing and FASTQ generation were performed with bcl2fastq (Illumina).
The Nothobranchius furzeri genome (Ensembl Release 113, 2024-08-14) and annotation were downloaded from Ensembl FTP repository (version 2024-08-14) . Read quality was assessed with FastQC v0.12.1 . Available online at:  and summarized using MultiQC v1.28 . Adapter trimming and quality filtering were performed with Trim Galore v0.6.10 . An average of ~40 million reads per sample were aligned to the Nfu genome using STAR v2.7.10b , and BAM files were indexed with samtools v1.13 . Read distribution was evaluated with RSeQC v5.0.2 and gene-level counts were obtained from STAR’s --quantMode GeneCounts output.
Assembly: Nothobranchius furzeri genome (Ensembl Release 113, 2024-08-14) and annotation were downloaded from Ensembl FTP repository (version 2024-08-14)
Supplementary files format and content: all_samples_counts.txt: rows represent Ensembl Gene Identifiers (Ensembl Release 113, 2024-08-14) obtained from STAR’s --quantMode GeneCounts output and columns are each sample analyzed

organism: Nothobranchius furzeri

source_name: Spleen

growth_protocol: Female Nothobranchius furzeri of the GRZ strain were grown in an overflow custom-made system maintained at 28°C on a 12h light/dark cycle.

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega GmbH). >10ng/ul of total RNA was used for the construction of sequencing libraries.
RNA sequencing analysis was performed at Novogene GmbH (Munich, Germany). Total RNA quality and integrity were verified using the Agilent 5400 Fragment Analyzer (Agilent Technologies). Libraries were prepared following standard Illumina protocols, quantified with the Qubit™ dsDNA HS Assay Kit (Invitrogen), and validated for fragment size and integrity on the Fragment Analyzer. Final quantification was performed by qPCR. Sequencing was conducted on an Illumina NovaSeq X Plus platform (paired-end 2 × 150 bp).

treatment_protocol: 16 weeks old female Nothobranchius furzeri were treated 3 weeks with 10µM alendronate (PHR1599, Sigma -Aldrich) and the placebo group with the same amount of distilled water added directly to the system water with a daily change of 10%.

value: Spleen

value: 10µM Alendronat


title: N5_Muscle

description: Library name: N5_Mu_MKRN250005729-1A_22

source_name: Muscle

value: Muscle


title: AGS cell, siUSP22_2

country: China

description: Library name: SAMPLE5

organism: Homo sapiens

tag: cell line

tag: cell type


title: N5_Liver

description: Library name: N5_L_MKRN250005728-1A_22

source_name: Liver

value: Liver


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L, tumor, untreated, replicate 2

description: Library name: DKO_2

value: untreated


title: N5_Kidney

description: Library name: N5_N_MKRN250005726-1A_22

source_name: Kidney

value: Kidney


title: AGS cell, siUSP22_1

description: Library name: SAMPLE4


title: N5_Heart

description: Library name: N5_H_MKRN250005730-1A_22

source_name: Heart

value: Heart


title: N4_Spleen

description: Library name: N4_M_MKRN250005722-1A_22


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L, tumor, untreated, replicate 1

description: Library name: DKO_1


title: AGS cell, siControl_3

description: Library name: SAMPLE3

value: siControl


title: N4_Muscle

description: Library name: N4_Mu_MKRN250005724-1A_22


title: N4_Liver

description: Library name: N4_L_MKRN250005723-1A_22


title: EM_2.5_rep4

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: Library name: J587

data_processing:
Raw FASTQ files were processed with the nf-core/rnaseq pipeline (3.21.0) using default parameters. STAR was used for alignment and Salmon was used for transcript quantification.
Assembly: GRCm39
Supplementary files format and content: text file

molecule: polyA RNA

source_name: liver

extract_protocol:
Approximately 10 mg of liver tissue was homogenized using a FastPrep-24 5G homogenizer and the RNA was extracted according to the manufacturer’s protocol using TRIZOL and purified using chloroform and EconoSpin Columns with RPE wash buffer. RNA purity was assessed with a NanoDrop 1000 spectrophotometer, and RNA integrity was determined using a 5200 Fragment Analyzer System.
Polyadenylated mRNA was enriched from 500 ng of total RNA and indexed SequencingcDNA libraries were generated from 500 ng of total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, San Diego, CA, USA), following the manufacturer’s specifications.

treatment_protocol: Mice were randomized into four experimental groups: (1) the vehicle-treated control group (CV); (2) the MI763F (2.5 mg/kg)-administered control group (CM 2.5 mg); (3) the EE-administered group (EV); (4) the MI763F (2.5 mg/kg) -administered EE group (EM 2.5 mg). Cholestasis was induced by subcutaneous injection of EE (10 mg/kg in propylene glycol) for seven days. MI763F was administered by oral gavage for six consecutive days (starting on day 2), at doses of 2.5 or 5 mg/kg.  The formulation used for MI763F consisted of 5% DMSO, 5% PEG300, and 90% corn oil.

value: liver

value: Humanized PXR-CAR-CYP3A4/3A7

value: MI763F (2.5 mg/kg) + ethinylestradiol-administered group


title: EM_2.5_rep3

description: Library name: J586


title: N4_Kidney

description: Library name: N4_N_MKRN250005721-1A_22


title: N4_Heart

description: Library name: N4_H_MKRN250005725-1A_22


title: AGS cell, siControl_1

description: Library name: SAMPLE1


title: N3_Spleen

description: Library name: N3_M_MKRN250005717-1A_22


title: AGS cell, siControl_2

description: Library name: SAMPLE2


title: EM_2.5_rep2

description: Library name: J585


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 095 | Full ROI

city: Boston

first: Emmanuel

last: Ogbonna

state: MA

address: 200 Longwood Ave

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_B5_scan1 | 095 | Full ROI
FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

source_name: tuberculosis-infected human lung tissue

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

value: tuberculosis-infected human lung tissue

tag: batch

tag: histopathological region

value: TLS

tag: patient id


title: N3_Liver

description: Library name: N3_L_MKRN250005718-1A_22


title: N3_Muscle

description: Library name: N3_Mu_MKRN250005719-1A_22


title: EM_2.5_rep1

description: Library name: J584


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 094 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 094 | Full ROI
FFPE


title: N3_Heart

description: Library name: N3_H_MKRN250005720-1A_22


title: N3_Kidney

description: Library name: N3_N_MKRN250005716-1A_22


title: EV_rep4

description: Library name: J583

value: ethinylestradiol-administered group


title: N2_Spleen

description: Library name: N2_M_MKRN250005712-1A_22


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 093 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 093 | Full ROI
FFPE


title: N2_Kidney

description: Library name: N2_N_MKRN250005711-1A_22


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 092 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 092 | Full ROI
FFPE


title: N2_Liver

description: Library name: N2_L_MKRN250005713-1A_22


title: EV_rep3

description: Library name: J582


title: N2_Muscle

description: Library name: N2_Mu_MKRN250005714-1A_22


title: N2_Heart

description: Library name: N2_H_MKRN250005715-1A_22


title: EV_rep1

description: Library name: J580


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 091 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 091 | Full ROI
FFPE


title: N1_Muscle

description: Library name: N1_Mu_MKRN250005709-1A_22


title: CM_2.5_rep4

description: Library name: J575

value: MI763F (2.5 mg/kg)-administered control group


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 090 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 090 | Full ROI
FFPE


title: N1_Kidney

description: Library name: N1_N_MKRN250005706-1A_22


title: N1_Liver

description: Library name: N1_L_MKRN250005708-1A_22


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 089 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 089 | Full ROI
FFPE


title: N1_Heart

description: Library name: N1_H_MKRN250005710-1A_22


title: CM_2.5_rep3

description: Library name: J574


title: CM_2.5_rep2

description: Library name: J573


title: WGS_N2_NtrC_His_NWH071_rep1

city: Bloomington

first: James

last: McKinlay

address: 1001 E 3rd Street

institute: Indiana University

description: Library name: WGS_N2_NtrC_His_NWH071_rep1

library_source: genomic

data_processing:
Reads were mapped to the V. natriegens ATCC 14048 genome (GCA_001456255.1) using CLC Genomics Workbench (CLC Bio, QIAGEN). ChIP and input sequences were normalized based on the total number of reads, and ChIP enrichment (ChIP/input) was analyzed and plotted using customized R scripts.
Assembly: V. natriegens ATCC 14048 genome (NCBI RefSeq: GCA_001456255.1)
Supplementary files format and content: Files ending with .csv files have comma-separated values files of ChIP-seq/ WGS results.  The bacterium has two chromosomes so each processed data file refers to a different chromosome (   ch1    vs    ch2   ).

molecule: genomic DNA

organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

source_name: Vibrio natriegens ATCC 14048

growth_protocol: Cultures were grown in anoxic VMDC175 medium (M9-derived coculture medium (PMID: 27898053) plus 100 mM MOPS (pH 7) and an additional 175 mM NaCl) with 25 mM glucose, 1 mM MgSO4, and 0.1 mM CaCl2. Either 10 mM NH4Cl or a 100% N2 headspace were included as the sole nitrogen source.   Cultures were incubated at 30C, laid horizontally with shaking at 150 rpm.

extract_protocol:
gDNA was extracted from the pooled 2-mL samples using the QIAGEN DNeasy Blood and Tissue kit to be used as the ‘input’ for normalization after whole-genome sequencing. Chromatin was immunoprecipitated from cross-linked cell pellets as described [PMID: 40759902], except Protein G Mag SepharoseTM Xtra magnetic beads (Cytiva, 45-002-513) and anti-His antibodies (Genscript, A00186-100) were used to pull down His-tagged NtrC. Chromatin from a strain with untagged NtrC was used as a control for nonspecific enrichment.
Library preparation for genomic and ChIP DNA was performed using the NEBNext Ultrall kit (NEB, E7645L) and sequenced at the Indiana University Center for Genomics and Bioinformatics using an Illumina NextSeq2000, generating paired-end reads. Reads were mapped to the V. natriegens ATCC 14048 genome (GCA_001456255.1) using CLC Genomics Workbench (CLC Bio, QIAGEN). ChIP and input sequences were normalized based on the total number of reads, and ChIP enrichment (ChIP/input) was analyzed and plotted using customized R scripts.

treatment_protocol: Five 10-mL anaerobic cultures were grown to exponential phase (0.3-0.5 OD660). Samples (2 ml) were then extracted and pooled for whole-genome sequencing. These pooled samples were pelleted by centrifugation at 4C, supernatants discarded, pellets frozen in dry ice, and then stored at -80C. The remaining anaerobic cultures received an injection of 37% formaldehyde (1% final) and were crosslinked for 30 min at room temperature. Tubes were then unsealed, cultures pooled, and crosslinking quenched with 125 mM glycine. Cells were then pelleted by as above, resuspended in 1 mL ice-cold TBS buffer (20 mM TRIS, 0.9% NaCl, pH 7.4), transferred to a 1.5 ml tube and pelleted again by centrifugation at 4C. This wash step was repeated, then cell pellets were frozen using dry ice, and stored at -80C.

value: Vibrio natriegens ATCC 14048

value: bacterial cell

value: Grown in anoxic VMDC175 medium (M9-derived coculture medium (PMID:27898053) + 100 mM MOPS (pH 7) + additional 175 mM NaCl) with 25 mM glucose, 1 mM MgSO4, 0.1 mM CaCl2, under 100% N2 headspace. Cultures were incubated at 30C, laid horizontally with shaking at 150 rpm.


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 088 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 088 | Full ROI
FFPE


title: WGS_N2_NtrC_His_NWH071_rep2

description: Library name: WGS_N2_NtrC_His_NWH071_rep2


title: WGS_N2_NtrC_NWH061_rep1

description: Library name: WGS_N2_NtrC_NWH061_rep1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 087 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 087 | Full ROI
FFPE

value: uninvolved lung


title: ChIP_N2_NtrC_His_NWH071_rep2

description: Library name: ChIP_N2_NtrC_His_NWH071_rep2


title: CM_2.5_rep1

description: Library name: J572


title: ChIP_N2_NtrC_His_NWH071_rep1

description: Library name: ChIP_N2_NtrC_His_NWH071_rep1


title: WGS_ammonium_NtrC_His_NWH071_rep2

description: Library name: WGS_ammonium_NtrC_His_NWH071_rep2

value: Grown in anoxic VMDC175 medium (M9-derived coculture medium (PMID:27898053) + 100 mM MOPS (pH 7) + additional 175 mM NaCl) with 25 mM glucose, 1 mM MgSO4, 0.1 mM CaCl2, and 10 mM NH4Cl. Cultures were incubated at 30C, laid horizontally with shaking at 150 rpm.


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 086 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 086 | Full ROI
FFPE


title: ChIP_N2_NtrC_NWH061_rep1

description: Library name: ChIP_N2_NtrC_NWH061_rep1


title: CV_rep3

description: Library name: J570

value: propylene glycol (vehicle) treated control group


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 084 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 084 | Full ROI
FFPE


title: WGS_ammonium_NtrC_NWH061_rep1

description: Library name: WGS_ammonium_NtrC_NWH061_rep1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 085 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 085 | Full ROI
FFPE


title: WGS_ammonium_NtrC_His_NWH071_rep1

description: Library name: WGS_ammonium_NtrC_His_NWH071_rep1


title: CV_rep2

description: Library name: J569


title: ChIP_ammonium_NtrC_His_NWH071_rep2

description: Library name: ChIP_ammonium_NtrC_His_NWH071_rep2


title: CV_rep4

description: Library name: J571


title: ChIP_ammonium_NtrC_His_NWH071_rep1

description: Library name: ChIP_ammonium_NtrC_His_NWH071_rep1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 083 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 083 | Full ROI
FFPE


title: ChIP_ammonium_NtrC_NWH061_rep1

description: Library name: ChIP_ammonium_NtrC_NWH061_rep1


title: CV_rep1

description: Library name: J568


title: Daily 10PM bat6, Seasonal fall bat5

city: College Station

first: Michael

last: Smotherman

state: Texas

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description: Library name: 100622061

data_processing:
Quality checking of reads and trimming used TrimGalore 0.6.7
Alignment of trimmed reads to genome used STAR Aligner 2.7.10b
HTSeq-Count 2.0.1 was used to generate counts based on read alignment
Assembly: Tadarida brasiliensis genome, NCBI Accession number: PRJNA972445 under Bat1K BioProject PRJNA489245
Supplementary files format and content: HTSeq-Count output text (.txt) files, counts based on species' genome

organism: Tadarida brasiliensis

source_name: whole eyes

extract_protocol:
Promega Maxwell automated workflow for extraction, conducted at MedGenome Inc
Library prep used Takara SMART-Seq v4 Ultra-low Input RNA kit, conducted at MedGenome Inc

treatment_protocol: Extracted tissue were flash frozen using liquid nitrogen and stored at -80°C before being shipped to sequencing

value: whole eyes

tag: Sex

value: male


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 082 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 082 | Full ROI
FFPE


title: Daily 10PM bat5

description: Library name: 100622051


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 081 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 081 | Full ROI
FFPE


title: CAC_FPL, H6

city: lanzhou

first: Hu

last: Chen

state: Gansu

address: Lanzhou University, Lanzhou City, Gansu Province, China, lanzhou, Gansu, 730000, China

institute: Lanzhou University

description: Library name: sample 27

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt（https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
Assembly: HISAT2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor-bearing colon segment

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Following purification, the mRNA was fragmented into short fragments using ivalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Tumor-bearing colon segment

value: WT

value: FOLFOX i.p.- comlpex probiotics+loperamide i.g.- AOM/DSS


title: Daily 10PM bat4, Seasonal fall bat4

description: Library name: 100622041


title: CAC_FPL, H5

description: Library name: sample 26


title: Daily 10PM bat3, Seasonal fall bat3

description: Library name: 100622031


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 080 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 080 | Full ROI
FFPE


title: Daily 10PM bat2, Seasonal fall bat2

description: Library name: 100622021


title: Daily 10PM bat1, Seasonal fall bat1

description: Library name: 100622011


title: CAC_FPL, H4

description: Library name: sample 25


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 079 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 079 | Full ROI
FFPE


title: Seasonal summer bat6

description: Library name: 62724041

value: Summer


title: Seasonal summer bat5

description: Library name: 62724031


title: CAC_FPL, H3

description: Library name: sample 24


title: Seasonal summer bat4

description: Library name: 62724021


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 078 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 078 | Full ROI
FFPE


title: Seasonal summer bat3

description: Library name: 62724011


title: CAC_FPL, H2

description: Library name: sample 23


title: Seasonal summer bat2

description: Library name: 70323041


title: Seasonal summer bat1

description: Library name: 70323031


title: CAC_FPL, H1

description: Library name: sample 22


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 076 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 076 | Full ROI
FFPE


title: Seasonal spring bat5

description: Library name: 40323051

value: Spring


title: Seasonal spring bat6

description: Library name: 40323061


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 077 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 077 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: Seasonal spring bat4

description: Library name: 40323041


title: CAC_FP, G5

description: Library name: sample 21

value: FOLFOX i.p.- comlpex probiotics i.g.- AOM/DSS


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 075 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 075 | Full ROI
FFPE

value: TLS


title: Seasonal spring bat3

description: Library name: 40323031


title: Seasonal spring bat2

description: Library name: 40323021


title: CAC_FP, G4

description: Library name: sample 20


title: Seasonal spring bat1

description: Library name: 40323011


title: CAC_FP, G3

description: Library name: sample 19


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 074 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 074 | Full ROI
FFPE


title: Seasonal winter bat9

description: Library name: 12725041

value: Winter


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 073 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 073 | Full ROI
FFPE


title: EV_rep2

description: Library name: J581

value: liver

value: Humanized PXR-CAR-CYP3A4/3A7

value: ethinylestradiol-administered group


title: Seasonal winter bat8

description: Library name: 12725021


title: CAC_FP, G2

description: Library name: sample 18


title: Seasonal winter bat7

description: Library name: 12725011


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 072 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 072 | Full ROI
FFPE


title: Seasonal winter bat6

description: Library name: 11723061


title: CAC_FP, G1

description: Library name: sample 17


title: Seasonal winter bat5

description: Library name: 11723051


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 071 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 071 | Full ROI
FFPE


title: N1_Spleen

description: Library name: N1_M_MKRN250005707-1A_22

value: Spleen

value: 10µM Alendronat


title: CAC_F, F5

description: Library name: sample 16

value: FOLFOX i.p.- normal saline i.g.- AOM/DSS


title: Seasonal winter bat4

description: Library name: 11723041

value: whole eyes


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 070 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 070 | Full ROI
FFPE


title: Seasonal winter bat3

description: Library name: 11723031

value: male


title: CAC_F, F4

description: Library name: sample 15

value: Tumor-bearing colon segment


title: Seasonal winter bat1

description: Library name: 11723011


title: Seasonal winter bat2

description: Library name: 11723021


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 069 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 069 | Full ROI
FFPE


title: I3_Dmos_25

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description: Library name: L20

data_processing:
All bioinformatic analyses were performed using RNAlysis. For sRNA-seq data, sRNA reads were aligned to PRJNA13758 ce11 genome assembly using ShortStack111 and aligned anti-sense reads were quantified using FeatureCounts. We included all reads with > 5 RPM without imposing any constraint on the length and 5′ nucleotide. For mRNA, we pseudo-aligned reads using Kallisto. We then performed differential expression analysis using DESeq2.
Assembly: PRJNA13758 ce11
Supplementary files format and content: mRNA_kallisto_output.xlsx

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: C. elegans strains were maintained on standard Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 20 degree, unless stated otherwise

extract_protocol:
Total RNA was isolated from day 1 adults (~72 hours following L1 synchronization) using standard phenol-chloroform method with TRIzolTM (Invitrogen). RNA quality was accessed using Agilent 4150 BioAnalyzer instrument and High Sensitivity RNA ScreenTapes.
To sequence the mRNA, RNA libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® coupled with NEBNext® Poly(A) mRNA Magnetic Isolation Module. The cDNA libraries were pooled and paired-end sequencing was performed on the Nextseq 2000 platform.  For sRNA sequencing, we treated the RNA samples with RNA 5′ Polyphosphatase (epicentre) and the libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) or TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. RNA ranging from ~140 to 160 nt was size-selected by gel extraction using 4% agarose E-Gel (Life Technologies). The pooled samples were the sequenced using the Illumina HiSeq 2500 instrument.

treatment_protocol: For experiment at 25 degree, worms were move from 20 to 25 degree at L4 stage

value: Whole worm

value: pigSi3; rde-4(ne299)


title: CAC_F, F3

description: Library name: sample 14

value: WT


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 068 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 068 | Full ROI
FFPE


title: I2_Dmos_25

description: Library name: L19


title: I1_Dmos_25

description: Library name: L18


title: CAC_F, F2

description: Library name: sample 13


title: F4_Dmos_20

description: Library name: L17


title: F3_Dmos_20

description: Library name: L16


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 067 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 067 | Full ROI
FFPE


title: F1_Dmos_20

description: Library name: L15


title: CAC, B5

description: Library name: sample 11

value: normal saline i.p./i.g.- AOM/DSS


title: CAC_F, F1

description: Library name: sample 12


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 066 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 066 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: P1-T6-1120B

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

data_processing:
Cut and adapt the barcodes and remove poly A and T
Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Hisat2
Using Galaxy: Hisat2 (2.2.1): Default settings except under splice alignment options use GTF file with known splice sites.
Run FeatureCounts
Using Galaxy: FeatureCounts (1.6.2): Default settings except single stranded, GFT File, and Output: Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)
DESEQ2
Using R: Deseq2 Version 2.11
Assembly: dm6/ BDGP6.87.gtf

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Flies were raised at 25C.  With a larval density corresponding to 5 females and 4 males parents per vial.  Parents were placed in a new vial every 4 days for 2 weeks to minimize overcrowding and keep the larval density relatively constant.  All flies were kept in a 12:12 Light Dark cycle.

extract_protocol:
Neurons were identified through anatomical location and GFP expression and then harvested into a patch pipet on an electrophysiology rig from alive flies.  Cells were harvested into .5ul Nuclease Free water to cause the cells to lyse.
cDNA was made and amplified using the Clontech SMARTer Ultra low RNA kit (version 2 HV). 15 rounds of amplification was perfromed on the samples.   This was then sheared to 200bp and put into an IXI Chip-seq protocol  (automated system) and barcoded following another 12 rounds of amplification. 12 samples were run in a lane and each sample was run across two lanes.

treatment_protocol: Virgin Males were raised in isolation for 4-6 days. Males were then paired with a female for the paired/trained group and then naïve (control) males were virgin.

value: Brain

value: P1 Neuron

value: UAS>stop>GFP/+; fruFLP/NP2631-Gal4

value: mated


title: CAC, B4

description: Library name: sample 10


title: P1-C2-1125B

value: naïve


title: P1-T6-1120A


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 065 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 065 | Full ROI
FFPE

value: TLS


title: P1-C2-1125A


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 064 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 064 | Full ROI
FFPE


title: P1-C2-1119B


title: P1-C2-1119A


title: CAC, B3

description: Library name: sample 9


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 063 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 063 | Full ROI
FFPE


title: P1-C1-1105B


title: CAC, B2

description: Library name: sample 8


title: P1-C1-1105A


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 062 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 062 | Full ROI
FFPE


title: CAC, B1

description: Library name: sample 7


title: P1-T9-1119A


title: P1-T9-1119B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 061 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 061 | Full ROI
FFPE


title: P1-T7-1120B


title: Negative control, A6

description: Library name: sample 6

source_name: colon

value: colon

value: normal saline i.p./i.g.


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 060 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 060 | Full ROI
FFPE


title: P1-T7-1120A


title: P1-T7-1119B


title: Negative control, A5

description: Library name: sample 5


title: P1-T7-1119A


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 059 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 059 | Full ROI
FFPE


title: P1-C10-1113B


title: P1-C10-1113A


title: Head and Neck case 17

city: Seattle

first: Joel

middle: Markus

last: Vaz

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
Library name: SCC17
Column Name in SCC_raw_counts.csv: SCC17

data_processing:
Raw RNA-seq reads were aligned to the hg38 reference genome using STAR v2.7.7a with two-pass mode and gene-level quantification enabled (--quantMode GeneCounts). BAM files were sorted and indexed using SAMtools. Gene expression counts were obtained using featureCounts (Subread package) with GENCODE v40 GTF, allowing multimapping reads (-M) and paired-end assignment (-p). The resulting raw gene count matrix was used for downstream analysis.
Assembly: hg38
Supplementary files format and content: comma separated file includes raw counts for each sample

source_name: Head and Neck Squamous Cell Carcinoma

extract_protocol:
Total RNA was isolated from human tissue specimens using the AllPrep DNA/RNA Mini Kit (Qiagen, Cat. No. 80204) in accordance with the manufacturer’s protocol. Briefly, fresh or snap-frozen tissue was transferred to 2 mL tubes containing ceramic beads (Omni International, Cat. No. 19-646-3) and homogenized in RLT buffer using the Bead Ruptor 12 (Omni International) at 3-4 M/s for 5 seconds, repeated for one to two cycles to ensure complete disruption. Following a centrifugation, the resulting supernatant was processed through the kit’s spin columns to sequentially purify genomic DNA and total RNA. RNA was eluted in RNase-free water, and concentration and purity were measured using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific). RNA integrity was assessed using the Agilent TapeStation. Purified RNA samples were stored at -80°C until downstream analyses
RNA libraries for RNA sequencing were prepared using Novogene and following the Illumina manufacturer’s protocol. Paired-end sequencing was performed on an Illumina HiSeq 2500 platform following library quality control and poly(A) enrichment, using a read length of 150 base pairs.

value: Head and Neck Squamous Cell Carcinoma

value: Tissue


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 058 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 058 | Full ROI
FFPE


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 057 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 057 | Full ROI
FFPE


title: Head and Neck case 16

description:
Library name: SCC16
Column Name in SCC_raw_counts.csv: SCC16


title: Negative control, A2

description: Library name: sample 2


title: Head and Neck case 15

description:
Library name: SCC15
Column Name in SCC_raw_counts.csv: SCC15


title: Head and Neck case 14

description:
Library name: SCC14
Column Name in SCC_raw_counts.csv: SCC14


title: Negative control, A4

description: Library name: sample 4


title: Negative control, A3

description: Library name: sample 3


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 056 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 056 | Full ROI
FFPE


title: Head and Neck case 13

description:
Library name: SCC13
Column Name in SCC_raw_counts.csv: SCC13


title: Negative control, A1

description: Library name: sample 1


title: Head and Neck case 12

description:
Library name: SCC12
Column Name in SCC_raw_counts.csv: SCC12


title: Head and Neck case 11

description:
Library name: SCC11
Column Name in SCC_raw_counts.csv: SCC11


title: Kdm6a Inhibition Input Control

city: Shanghai

first: Lei

last: Wang

address: No. 639, Zhizaoju Road

institute: Shanghai Ninth People's Hospital

description: Library name: sh_Input

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2 (2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCm38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 054 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 054 | Full ROI
FFPE


title: Acinic Cell Carcinoma

description:
Library name: SCC9
Column Name in SCC_raw_counts.csv: SCC9

source_name: Acinic Cell Carcinoma

value: Acinic Cell Carcinoma


title: Head and Neck case 10

description:
Library name: SCC10
Column Name in SCC_raw_counts.csv: SCC10


title: Head and Neck case 8

description:
Library name: SCC8
Column Name in SCC_raw_counts.csv: SCC8


title: Kdm6a Inhibition IP Sample

description: Library name: sh

value: Active Motif 39055


title: Control for Kdm6a Overexpression Input Control

description: Library name: puro_Input


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 052 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 052 | Full ROI
FFPE


title: Head and Neck case 6

description:
Library name: SCC6
Column Name in SCC_raw_counts.csv: SCC6


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 053 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 053 | Full ROI
FFPE


title: Head and Neck case 7

description:
Library name: SCC7
Column Name in SCC_raw_counts.csv: SCC7


title: Control for Kdm6a Overexpression IP Sample

description: Library name: puro


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 051 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 051 | Full ROI
FFPE


title: Head and Neck case 2

description:
Library name: SCC3
Column Name in SCC_raw_counts.csv: SCC3


title: Control for Kdm6a Inhibition Input Control

description: Library name: Zs_Input


title: Head and Neck case 1

description:
Library name: SCC2
Column Name in SCC_raw_counts.csv: SCC2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 050 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 050 | Full ROI
FFPE


title: Control for Kdm6a Inhibition IP Sample

description: Library name: Zs


title: Spleen/PLN from obese donor D478

city: NYC

first: Alexey

last: Koshkin

state: New York

department: Department of Pathology and Cell Biology

institute: Columbia University Medical center, department of Pathology and Cell Biology

description:
Library name: DS042_library
Bulk RNA-seq from spleen/PLN of obese donor D478 in batch B

data_processing:
Data Preprocessing Whole-Transcriptome Profiling by RNA-Seq D8+ TRM (DAPI- CD45+ CD3+ CD8+ CD45RA- CCR7- CD69+ 70 cells) from pancreas, small  intestine, lymph node and spleen were individually sorted. Analysis was restricted to CD8 TRM  because they are the predominant TRM lineage in pancreas. RNA was isolated from cell pellets  using the RNeasy Mini Kit (QIAGEN) and quantitated using an Agilent 2100 Bioanalyzer (Agilent  Technologies), and library preparation and RNA-seq was performed by the Columbia Genome Center as previously described4. To analyze the effect of obesity on TRM gene expression, RNA-Seq reads from sorted CD8+ 259 TRM were mapped, filtered and read counts computed as we previously described7 260 . Data from samples that were included in our previous study7 261 (GEO: GSE135582) were merged with 24 additional samples and batch correction was performed using ComBat-seq21  4. Kumar, B.V., et al. Human Tissue-Resident Memory T Cells Are Defined by Core  Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell Rep 20, 2921-  2934 (2017) 7. Weisberg, S.P., et al. Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the  Human Pancreas through the PD-1/PD-L1 Pathway. Cell Rep 29, 3916-3932 e3915 (2019) . 21. Zhang, Y., Parmigiani, G. & Johnson, W.E. ComBat-seq: batch eject adjustment for RNA-seq  count data. NAR Genom Bioinform 2, lqaa078 (2020).
Assembly: Homo sapiens
Supplementary files format and content: Counts_Table_bulkRNAseq_GEO.txt

source_name: spleen/PLN

extract_protocol:
Human Tissue Samples Human samples Tissues were obtained from deceased organ donors as part of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement with LiveOnNY as described previously (Carpenter et al., 2018, Gordon et al., 2017, Granot et al., 2017, Kumar et al., 2017, Miron et al., 2018, Senda et al., 2019). Donors were free of cancer, chronic diseases, seronegative for hepatitis B, C, and HIV, and represented diverse ages. Use of organ donor tissues does not qualify as “human subjects” research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals.
library preparation and RNA-seq was performed by the Columbia Genome Center as previously described

value: spleen/PLN

tag: sample group

value: obese

value: B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 055 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 055 | Full ROI
FFPE


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 049 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 049 | Full ROI
FFPE


title: Kdm6a Overexpression Input Control

description: Library name: 3x_Input


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 048 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 048 | Full ROI
FFPE


title: PLN from obese donor D478

description:
Library name: DS043_library
Bulk RNA-seq from PLN of obese donor D478 in batch B

source_name: PLN

value: PLN


title: Pancreas from obese donor D478

description:
Library name: DS041_library
Bulk RNA-seq from pancreas of obese donor D478 in batch B

source_name: pancreas

value: pancreas


title: Kdm6a Overexpression IP Sample

description: Library name: 3x


title: Spleen/PLN from lean donor D408

description:
Library name: DS032_library
Bulk RNA-seq from spleen/PLN of lean donor D408 in batch B

value: lean


title: Jejunum from lean donor D408

description:
Library name: DS031_library
Bulk RNA-seq from jejunum of lean donor D408 in batch B

source_name: jejunum

value: jejunum


title: ISO_0725

city: Tarrytown

first: Qingqing

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description:
Library name: ISO_0725
scATAC-seq data

data_processing:
Cellranger-atac v2.1.0 (10x Genomics) was used to perform demultiplexing and read alignment of scATAC-seq raw data from all treatments and timepoints
Single cell data were filtered based on the number of unique fragments per cell and enrichment of ATAC-seq accessibility at TSSs, as described in Satpathy et al, 2019. TSS positions were acquired from the TxDb.Hsapiens.UCSC.hg38.knownGene Bioconductor package.
Cell clustering based on cell genome accessibility were performed as described in ref.Kourtis et al, 2022, with the minimum cluster size set to 150 for the first round of clustering, and a final resolution of 0.8. For subclustering of T cells, the minimum cluster size was set to 100 and a final resolution of 0.8.
Gene activity score, TF motif enrichment calculation and pseudotime analyses were performed as described in Kourtis et al, 2022
Assembly: mm10
Supplementary files format and content: MetaData.txt file, phenotypic metadata for cells in dataset
Supplementary files format and content: peakSet.txt file, peaks called from the datasets
Supplementary files format and content: fragments.tsv.gz files; ATAC-seq fragments captured by the assay, analyzed by Cell ranger

source_name: Tumor

growth_protocol: hCD3/hPSMA humanized male mice (8-12 week old) were implanted with 2.5x106 TrampC2/hPSMA tumor cells by subcutaneous injection in the right flank. hCD3/hCD20 humanized female mice (8-12 weeks old) were implanted with 0.5x106 MC38/hCD20 tumor cells by subcutaneous injection in the right flank.

extract_protocol:
Freshly sorted, live mouse T cells were washed with PBS containing 0.04% BSA, and the cell count was determined. Nuclei were isolated using the 10x Genomics Low Cell Input Nuclei Isolation protocol. Briefly, cells were centrifuged at 300×g for 5 min at 4°C and resuspended in 50µL PBS + 0.04% BSA. After centrifugation, 45µL of the supernatant was removed, and 45µL of chilled Lysis Buffer was added. The suspension was gently mixed and incubated on ice for 3-5 min. Chilled Wash Buffer was added without mixing, followed by centrifugation at 500×g for 5 min. Supernatant was removed, and 45 µL of chilled Diluted Nuclei Buffer was added. After a second centrifugation, the pellet was resuspended in 7µL of chilled Diluted Nuclei Buffer. Nuclei concentration was counted and used immediately for transposition
Single-cell ATAC-seq libraries were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10x Genomics, Pleasanton, CA) per manufacturer’s instructions. Transposed nuclei were loaded with gel beads and reagents onto a Chromium Next GEM Chip H and processed on the Chromium X instrument to generate barcoded Gel Beads-in-emulsion (GEMs). GEMs underwent thermal cycling for barcoding, followed by recovery, Dynabead and SPRIselect cleanup, sample indexing PCR, and dual-sided SPRI size selection. Final libraries were quantified with the Qubit dsDNA HS assay (Thermo Fisher Scientific) and assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Libraries were sequenced on a NovaSeq (Illumina, San Diego, CA), producing approximately 200 million paired-end 150 bp reads per sample.

treatment_protocol: On indicated timepoints, mice were euthanized and tumors excised. Tumors were weighed and processed using the mouse tumor dissociation kit (Miltenyi 130-096-730) per manufacturer’s protocol with the following modifications: Enzyme R was used at 40% of the recommended volume. Tumors were minced in petri dishes using razors (VWR 55411-050), transferred to 5mL tubes containing enzyme mix, and incubated in a 37oC water bath for 40 min vortexing every 5 min. Dissociated tumors were forced through a 70uM mesh filter (Miltenyi 130-098-462) to generate single cell suspension for flow cytometry.

value: Tumor

value: T cells

value: hCD3/hPSMA humanized

value: Isotype control


title: Pancreas from lean donor D408

description:
Library name: DS030_library
Bulk RNA-seq from pancreas of lean donor D408 in batch B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 046 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 046 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: Spleen/PLN from obese donor D472

description:
Library name: DS029_library
Bulk RNA-seq from spleen/PLN of obese donor D472 in batch B


title: Pancreas from obese donor D472

description:
Library name: DS027_library
Bulk RNA-seq from pancreas of obese donor D472 in batch B


title: EpiDrug_0725

description:
Library name: EpiDrug_0725
scATAC-seq data

value: Decitabine


title: Jejunum from obese donor D472

description:
Library name: DS028_library
Bulk RNA-seq from jejunum of obese donor D472 in batch B


title: Combo_0725

description:
Library name: Combo_0725
scATAC-seq data

value: PSMAxCD3 bispecific antibody + decitabine


title: Spleen/PLN from lean donor D382

description:
Library name: DS025_library
Bulk RNA-seq from spleen/PLN of lean donor D382 in batch B


title: Bispec_0725

description:
Library name: Bispec_0725
scATAC-seq data

value: PSMAxCD3 bispecific antibody


title: Jejunum from lean donor D382

description:
Library name: DS024_library
Bulk RNA-seq from jejunum of lean donor D382 in batch B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 043 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 043 | Full ROI
FFPE


title: Jejunum from lean donor D346

description:
Library name: DS022_library
Bulk RNA-seq from jejunum of lean donor D346 in batch B


title: Pancreas from lean donor D346

description:
Library name: DS021_library
Bulk RNA-seq from pancreas of lean donor D346 in batch B


title: ISO_0714

description:
Library name: ISO_0714
scATAC-seq data


title: protein65

city: Houston

first: Stephen

last: Wong

address: 6565 Fannin St

institute: Houston Methodist

description:
Library name: DSP-1001660022162-A-C08-Y
DSP-1001660022162-A-C08.stats.txt
DSP-1001660022162-A-C08.dcc

library_source: other

data_processing:
Spatial proteogenomic and transcriptomic data were generated on the GeoMx DSP platform and processed with the GeoMxWorkflows R package (v1.0+) following the standard NanoString pipeline. Raw DCC files were imported with corresponding PKC files and sample annotations using readNanoStringGeoMxSet. Segment-level QC required: minimum total reads ≥1,000, trimmed reads ≥80%, stitched reads ≥80%, aligned reads ≥75%, sequencing saturation ≥50%, negative control counts ≥1, NTC counts ≤9,000, nuclei count ≥20, and segment area ≥1,000 μm². Probe-level QC was performed with setBioProbeQCFlags (minimum probe ratio 0.1; maximum percentage failing Grubbs test 20%; local outlier removal enabled), and probes failing these metrics or flagged as global Grubbs outliers were excluded. Probe counts were aggregated to genes with aggregateCounts. For each segment, the limit of quantification (LOQ) was defined as the geometric mean of negative controls plus 2 SD, with a minimum LOQ of 2 counts. Segments with <5% gene detection were removed, and genes detected above LOQ in <10% of segments were excluded (negative control probes retained for normalization). The final dataset comprised 7,709 genes across 65 high-quality segments. Spatial multi-omics data from all metastases samples were obtained from both PanCK+ tumor cell regions and CD45+ immune cell regions. Sample identifiers were standardized by combining scan names with ROI identifiers to ensure proper matching between expression data and metadata across both data modalities. Low-expression gene filtering was applied independently to brain and bone datasets using stringent criteria: genes were retained only if they showed ≥1 count in ≥3 samples per tissue type to ensure adequate gene coverage.
The PKC are
(v1.0) Human Procode NGS Core Protein (Lot Number: 519184)
(v1.1) Human Procode NGS IPA Protein (Lot Number: 512044)
(v1.0) Human NGS Whole Transcriptome Atlas RNA (Lot Number: HW0050423)
In the following link
https://brukerspatialbiology.com/products/geomx-digital-spatial-profiler/geomx-dsp-configuration-files/
Assembly: GRCh38
Supplementary files format and content: .csv, dcc
Supplementary files format and content: The RNA_Pro__Exp.csv, WTAONLY_Exp_NEW.csv files were generated from the .dcc file, the readout of gene expression and the protein (the first row =  the sample id,  and the first column = RNA/protein name).
Supplementary files format and content: When dcc was generated from merged/multiple samples, the file is linked to the first sample records and listed in the corresponding sample description field
Library strategy: Spatial Transcriptomics

molecule: protein

extract_protocol:
We retrospectively collected metastatic tissue samples from six breast cancer patients with one or more metastatic lesions. The samples included two bone metastases, two brain metastases, one pericardial metastasis, and one chest wall metastasis. Formalin-fixed, paraffin-embedded (FFPE) tissue sections (5 μm) were mounted on standard microscope slides and processed for spatial proteogenomics analysis using the NanoString GeoMx Digital Spatial Profiler (DSP). To enable tissue compartmentalization and spatial segmentation, sections were stained with a panel of three fluorescently labeled morphological markers: anti-pancytokeratin (PanCK-AF532) to identify epithelial tumor cells, anti-CD45 (CD45-AF594) to delineate immune cell populations, and Syto13 nucleic acid stain to visualize nuclei and define cellular boundaries. Staining was performed according to standard immunofluorescence protocols with overnight incubation at 4°C.
DNA barcodes corresponding to RNA and protein targets were photocleaved and collected from each segmented AOI using sequential UV light exposure. Collected barcodes were processed using the GeoMx library preparation protocol with unique dual indexing (i7/i5) for each AOI to enable multiplexed analysis.

value: Brain


title: Spleen/PLN from lean donor D453

description:
Library name: DS020_library
Bulk RNA-seq from spleen/PLN of lean donor D453 in batch B

value: spleen/PLN


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 041 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 041 | Full ROI
FFPE


title: Combo_0714

description:
Library name: Combo_0714
scATAC-seq data


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 040 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 040 | Full ROI
FFPE


title: Pancreas from obese donor D443

description:
Library name: DS017_library
Bulk RNA-seq from pancreas of obese donor D443 in batch B

value: obese


title: Spleen/PLN from lean donor D466

description:
Library name: DS016_library
Bulk RNA-seq from spleen/PLN of lean donor D466 in batch B

value: B


title: Bispec_0714

description:
Library name: Bispec_0714
scATAC-seq data


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 039 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 039 | Full ROI
FFPE


title: Jejunum from lean donor D466

description:
Library name: DS015_library
Bulk RNA-seq from jejunum of lean donor D466 in batch B


title: ISO_0707

description:
Library name: ISO_0707
scATAC-seq data


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 038 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 038 | Full ROI
FFPE


title: Pancreas from lean donor D466

description:
Library name: DS014_library
Bulk RNA-seq from pancreas of lean donor D466 in batch B


title: 2DR5F401HE_S106

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DR5F401HE_S106_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq rat S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

organism: Rattus norvegicus

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Rat S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Heart

tag: strain

value: Sprague-Dawley

value: female

tag: age

value: 9 weeks

tag: concentration (ppm)

tag: sample status

value: Used in Analysis

tag: qc issue


title: 2DR5F401LI_S114

description: Library name: 2DR5F401LI_S114_R1_001

source_name: Liver Left Lobe

value: Liver Left Lobe


title: S3-LCM64

city: San Diego

first: Young Chul

last: Kim

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

description: Library name: S3-LCM64

data_processing:
nf-core/rnaseq analysis pipeline (v3.16.0) with the Nextflow workflow manager (v23.10.0)
Assembly: GRCm38, Ensembl release 101
Supplementary files format and content: txt file with log10 (TPM) of genes for each sample

source_name: Kidney

extract_protocol:
Total RNA was isolated from 70-80 microdissected SGLT2-negative LTL-positive tubules per sample using Arcturus PicoPure frozen RNA isolation kit and additional gDNA digestion was performed via Arcticzymes Heat & Run gDNA removal kit.
Quality and quantity of total RNA were determined by High Sensitive Tape Analysis, and cDNA library was prepared using SMARTer Stranded Total RNA-seq Kit v3-Pico Input Mammalian with 0.5 ng total RNA (DV200>30%).

treatment_protocol: Experimental mice were treated with vehicle, dapagliflozin (10mg/kg diet) or semaglutide (3nmol/kg body weight per day) for 2 weeks.

value: Kidney

value: Sglt1 KO

value: Vehicle


title: GSK591-3

city: Guangzhou, Guangdong

first: Siqi

last: Jiang

address: No.56 Lingyuanxi Road

institute: Sun Yat-sen University

description: Library name: GSK591-3

data_processing:
After the completion of the library construction, the quality of the library was tested, and on-machine sequencing could be carried out only after the test results met the requirements. The detection methods were as follows :(1) The Qubit dye method was used for preliminary quantification, the fragment analyzer was used to detect the insert size of the library, and the next experiment could be carried out only after the insert size met the expectations; (2) The effective concentration of the library was accurately quantified by Q-PCR method (the effective concentration of the library was >2nM), and the library examination was completed. After the library test is qualified, different libraries are pooled according to the target data volume and sequenced by Illumina platform. Filter the offline Data to get Clean Data, sequence match with the specified reference genome, and carry out variable splicing analysis on the Mapped Data obtained; According to the expression levels of genes in different samples or different sample groups, differential expression analysis, functional annotation and functional enrichment of differential expression genes were performed.
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: Portable Document Format and Microsoft Office Excel

extract_protocol:
CKs were negative controls, GSK591s were treated with GSK591, and collect total RNA for RNA-seq.
mRNA with polyA tail was enriched by Oligo(dT) magnetic beads. Then the RNA was broken into short fragments by fragmentation buffer, and the first cDNA was synthesized with six-base random hexamers based on the fragment RNA template. Buffer solution, dNTPs(dTTP, dATP, dGTP and dCTP) and DNA polymerase were then added to synthesize the double-stranded cDNA, which was then purified by DNA purification magnetic beads. The purified double-stranded cDNA was then end-repaired, A tail was added and a sequencing joint was connected. Then the fragment size was selected by DNA purification magnetic beads, and the final cDNA library was obtained by PCR enrichment.

value: squamous cell carcinoma

value: treated with GSK591(replication3)


title: EpiDrug_0707

description:
Library name: EpiDrug_0707
scATAC-seq data

value: Tumor

value: T cells

value: hCD3/hPSMA humanized

value: Decitabine


title: GSK591-2

description: Library name: GSK591-2

value: treated with GSK591(replication2)


title: GSK591-1

description: Library name: GSK591-1

value: treated with GSK591(replication1)


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 037 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 037 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: Combo_0707

description:
Library name: Combo_0707
scATAC-seq data

value: PSMAxCD3 bispecific antibody + decitabine


title: CK3

description: Library name: CK3

value: negetive control(replication3)


title: Bispec_0707

description:
Library name: Bispec_0707
scATAC-seq data

value: PSMAxCD3 bispecific antibody


title: CK1

description: Library name: CK1

value: negetive control(replication1)


title: 2349-NPC-ASDDM-Pool5-b

city: Ann Arbor

first: Carlos

last: Aguilar

state: MI

address: 2800 Plymouth Rd.,

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

description:
Library name: 2349NPCb
Column names in processed data files: 2349bNPC

data_processing:
FASTQ samples were assessed for quality using the FASTQC toolkit.
The reads were then trimmed to 30 bases using cutadapt (v4.6).
Trimmed reads were aligned to the GRCh38 reference genome via the STAR aligner (v 2.7.5b). Transcripts were quantified via RSEM (v1.3.3).
TPM (transcripts per million) values from RSEM were filtered for input into differential expression and pathway enrichment analysis.
Downstream analysis was restricted to genes with TPM >=1 in at least one of the samples analyzed, and variance in TPM > 0.01 across the set of samples. Analysis was further restricted to ENSGID’s from Gencode (v43) that were assigned the following gene types in the Gencode GTF annotation: protein_coding, rRNA, ribozyme, sRNA, IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, Mt_rRNA, Mt_tRNA, TR_C_Genne, TR_D_gene, TR_J_gene, TR_V_gene. Limma’s voom function in R (https://bioconductor.org/packages/release/bioc/html/limma.html) was applied to transform the TPM to a log2 scale and apply quantile normalization.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Tab-delimited text file includes FPKM for each Sample.
Supplementary files format and content: Tab-delimited text file includes TPM for each Sample.
Supplementary files format and content: Tab-delimited text file includes metadata manifest information for each sample.

source_name: Neuron progenitor cells

growth_protocol: Prior to differentiation, all iPSC lines were cultured and maintained in mTeSR+ (Stem Cell Technologies) at 37 degrees C and 5% CO2 on Cultrex (R&D Systems, Bio-Techne) coated plates with 10 µM ROCK inhibitor (Y27632, Selleck Chemicals).

extract_protocol:
Total RNA was extracted from NPCs using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quality was assessed using a Bioanalyzer (Agilent Technologies).
Library preparation was performed using the KAPA Stranded mRNA-Seq Kit (Roche) following manufacturer’s instructions.

treatment_protocol: iPSC-derived NPCs were generated in Essential 6 Medium (Thermo Fisher) supplemented with small chemical inhibitors of TGF, SMAD, and Wnt pathways. iPSCs were treated with 500 nM LDN193189 (Tocris), 10 µM SB431542 (Tocris), and 2 µM XAV939 (Tocris) for the first three days and then 500 nM LDN193189 and 10µM SB431542 for the remaining nine days of differentiation. Medium was freshly made and replaced daily. NPCs were collected at Day12 for RNA-sequencing.

value: Neuron progenitor cells

value: WT

tag: group

value: ASDDM


title: Therapy control repeat 3 (S9)

city: Evanston

first: Anna

last: Metlushko

state: IL

address: 2236 Sherman Avenue, Unit K-2

institute: Northwestern University

description: Library name: PDL_T3_S9

data_processing:
Adapters were trimmed from reads using cutadapt version 4.2
Trimmed reads were aligned using STAR version 2.7.5
Gene counting was performed using htseq-count version 2.0.2
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw gene counts

source_name: cortical neuron

growth_protocol: Based on U.S. Provisional Patent No. 63/548,029

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Total RNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: cortical neuron

value: wildtype

value: Peptide amphiphile


title: 2349-NPC-ASDDM-Pool5-a

description:
Library name: 2349NPCa
Column names in processed data files: 2349aNPC

tag: genotype


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 035 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 035 | Full ROI
FFPE

source_name: tuberculosis-infected human lung tissue


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 034 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 034 | Full ROI
FFPE


title: 2220-NPC-ASDDM-Pool2-b

description:
Library name: 2220NPCb
Column names in processed data files: 2220bNPC


title: 2220-NPC-ASDDM-Pool2-a

description:
Library name: 2220NPCa
Column names in processed data files: 2220aNPC


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 1

description:
Library name: 23248XR-01-31
Raw_counts.txt
Normalized_counts.txt

data_processing:
FastQC was employed to check the quality of raw reads.Sequences of poor quality were removed.
HiSAT2 was used for alignment of trimmed reads using mm39 build and GRCm39 GTF file. FeatureCounts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Assembly: mm39
Supplementary files format and content: Raw_counts.txt (raw counts from FeatureCounts for all samples compiled in a table with library name as headers), Normalized_counts.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers),
Supplementary files format and content: RTT271_counts.txt (count table of RTT271 construct in RNA library for injected samples), MECP2_E2_CDS_Tau_counts.txt (count table for Tau overexpression contruct in Tau-driven Mecp2 overexpression and control lines).

source_name: Cortex

extract_protocol:
RNA was isolated from samples using Qiazol phase separation followed by cleanup with RNeasy 96 Kit per manufacturer’s instruction. Isolated RNA sample quality was assessed by both RNA Tapestation assay and High Sensitivity RNA Tapestation assay (Agilent Technologies Inc., California, USA and quantified by Infinite F Nano+ 200 Pro Tecan® (Tecan, Switzerland)
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 450bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus (Illumina, California, USA) with a read length configuration of 150 PE for 60M PE reads per sample (30M in each direction).

value: Cortex

value: MeCP2:-/Y rtt271a

tag: treatment

value: injected rtt271 1e11

tag: animal id


title: Therapy PA + PS2 repeat 3 (S8)

description: Library name: IKVAV_plus_PEDOT-S-OH_T3_S8

treatment_protocol: Based on U.S. Provisional Patent No. 63/548,029

tag: cell line

tag: cell type


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 033 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 033 | Full ROI
FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

tag: batch

tag: histopathological region


title: 2140-NPC-TDN-Pool1-b

description:
Library name: 2140NPCb
Column names in processed data files: 2140bNPC

value: TDN


title: Therapy PA repeat 3 (S7)

description: Library name: IKVAV_T3_S7


title: 2140-NPC-TDN-Pool1-a

description:
Library name: 2140NPCa
Column names in processed data files: 2140aNPC


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 032 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 032 | Full ROI
FFPE

tag: patient id


title: RNA32

description: Library name: DSP-1001660022159-B-F04

source_name: Bone

value: Bone


title: Therapy control repeat 2 (S6)

description: Library name: PDL_T2_S6


title: 1928-NPC-ASDN-Pool2-a

description:
Library name: 1928NPCa
Column names in processed data files: 1928aNPC

value: ASDN


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 031 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 031 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: hippocampal tissues of AAV2/9-Syn-cre injected Bcas2F/F mice 1

city: Beijing

first: Hai

middle: xia

last: Ma

address: Changchun street NO.45

institute: Xuanwu Hospital

description: Library name: BKO_1

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: FPKM, count values for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: hippocampus

value: Bcas2 knockdown


title: 1853-NPC-TDN-Pool5-a

description:
Library name: 1853NPCa
Column names in processed data files: 1853aNPC


title: 1485-NPC-ASDN-Pool1-b

description:
Library name: 1485NPCb
Column names in processed data files: 1485bNPC


title: Therapy PA repeat 2 (S4)

description: Library name: IKVAV_T2_S4


title: 1485-NPC-ASDN-Pool1-a

description:
Library name: 1485NPCa
Column names in processed data files: 1485aNPC


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 030 | Full ROI

city: Boston

first: Emmanuel

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_B5_scan1 | 030 | Full ROI
FFPE


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 029 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 029 | Full ROI
FFPE


title: 1428-NPC-TDN-Pool1-b

description:
Library name: 1428NPCb
Column names in processed data files: 1428bNPC


title: Therapy control repeat 1 (S3)

description: Library name: PDL_T1_S3


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 028 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 028 | Full ROI
FFPE


title: 1358-NPC-ASDN-Pool2-b

description:
Library name: 1358NPCb
Column names in processed data files: 1358bNPC


title: Therapy PA + PS2 repeat 1 (S2)

description: Library name: IKVAV_plus_PEDOT-S-OH_T1_S2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 027 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 027 | Full ROI
FFPE


title: 1358-NPC-ASDN-Pool2-a

description:
Library name: 1358NPCa
Column names in processed data files: 1358aNPC


title: Therapy PA repeat 1 (S1)

description: Library name: IKVAV_T1_S1


title: 1206-NPC-ASDDM-Pool2-a

description:
Library name: 1206NPCa
Column names in processed data files: 1206aNPC

value: CHD8 mutation


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 026 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 026 | Full ROI
FFPE


title: 1164-NPC- ASDN- Pool1-b

description:
Library name: 1164NPCb
Column names in processed data files: 1164bNPC

value: Neuron progenitor cells


title: Therapy control repeat 3 (S23)

description: Library name: PDL_T3_S23


title: 1164-NPC- ASDN- Pool1-a

description:
Library name: 1164NPCa
Column names in processed data files: 1164aNPC

value: WT


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 025 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 025 | Full ROI
FFPE


title: 1128-NPC-TDN-Pool1-b

description:
Library name: 1128NPCb
Column names in processed data files: 1128bNPC


title: 1928-NPC-ASDN-Pool2-b

description:
Library name: 1928NPCb
Column names in processed data files: 1928bNPC


title: Head and Neck case 5

description:
Library name: SCC5
Column Name in SCC_raw_counts.csv: SCC5

value: Head and Neck Squamous Cell Carcinoma

value: Tissue


title: Therapy PA + PS2 repeat 3 (T3_S22)

description: Library name: IKVAV_plus_PEDOT-S_OH_T3_S22

value: cortical neuron

value: wildtype


title: hippocampal tissues of AAV-vehicle injected Bcas2F/F mice 3

description: Library name: WT_3


title: 1853-NPC-TDN-Pool5-b

description:
Library name: 1853NPCb
Column names in processed data files: 1853bNPC


title: Adenoid Cystic Carcinoma

description:
Library name: SCC4
Column Name in SCC_raw_counts.csv: SCC4

source_name: Adenoid Cystic Carcinoma

value: Adenoid Cystic Carcinoma


title: 1128-NPC-TDN-Pool1-a

description:
Library name: 1128NPCa
Column names in processed data files: 1128aNPC


title: Therapy PA + PS2 repeat 2 (S5)

description: Library name: IKVAV_plus_PEDOT-S-OH_T2_S5

value: Peptide amphiphile


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 024 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 024 | Full ROI
FFPE


title: 1116-NPC-ASDDM-Pool2-b

description:
Library name: 1116NPCb
Column names in processed data files: 1116bNPC

value: ASDDM


title: 1116-NPC-ASDDM-Pool2-a

description:
Library name: 1116NPCa
Column names in processed data files: 1116aNPC


title: Therapy PA repeat 3 (S21)

description: Library name: IKVAV_T3_S21


title: PLN from lean donor D466

description:
Library name: DS044_library
Bulk RNA-seq from PLN of lean donor D466 in batch B

value: PLN

value: lean

value: B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 023 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 023 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: Spleen/PLN from obese donor D333

description:
Library name: DS033_library
Bulk RNA-seq from spleen/PLN of obese donor D333 in batch B

value: spleen/PLN

value: obese


title: Therapy control repeat 2 (S91)

description: Library name: PDL_T3_S91


title: SUM-44 LacZ-B control

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
shASH2L_vs_LacZ.txt
275Sum44_vs_271Sum44.txt
277Sum44_vs_271Sum44.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the Human (HG19) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: SUM-44PE breast cancer cells

growth_protocol: Cells were cultured at 37°C in 10% CO2 and passaged using Trypsin (Invitrogen Catalog # 15400-054) diluted to 1x with Hanks Buffered Salt Solution (Corning Cellgro Catalog #20-021-CV) supplemented with 1 ml/L sodium bicarbonate and 25 μg/ml gentamicin. SUM-44 cells were cultured in serum-free Ham’s F-12 medium supplemented with 1 μg/ml hydrocortisone, 1 mg/ml bovine serum albumin, 10 mM HEPES, 5 mM ethanolamine, 5 μg/ml transferrin, 10 nM triiodothyronine, 50 nM sodium selenite, 25 μg/ml gentamicin, 2.5 μg/ml fungizone, and 5 μg/ml insulin.

extract_protocol:
Total RNA was prepared using a Qiagen RNeasy Plus Mini Kit (74136, lot 151036409)
A total of 100-200 ng of total RNA was used to prepare RNA-seq libraries using the TruSeq RNA Sample Prep kit following the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: Target cells were transduced with virus in growth media supplemented with 5 μg/ml polybrene using 0.5-1.0 ml virus per 1 million cells. Cells were selected for resistance marker expression and maintained in puromycin-containing growth media beginning 24-48 hours after infection. Cells were cultured in selection media at least 5 days to allow expression of the construct. 3 μg/ml puromycin was used for selection and maintenance of shRNA-transduced SUM-44 cells.

tag: passage

tag: source

value: pleural effusion cells from metastatic ER+ breast cancer patient

tag: knockdown

value: control LacZ


title: SUM-44 LacZ-C control

description:
shASH2L_vs_LacZ.txt
275Sum44_vs_271Sum44.txt
278Sum44_vs_271Sum44.txt


title: SUM-44 LacZ-A control

description:
shASH2L_vs_LacZ.txt
275Sum44_vs_271Sum44.txt
276Sum44_vs_271Sum44.txt


title: Therapy PA + PS2 repeat 2 (S90)

description: Library name: IKVAV_plus_PEDOT-S_OH_T12_S90


title: SUM-44 ASH2L 276-B

description:
shASH2L_vs_LacZ.txt
277Sum44_vs_271Sum44.txt

value: ASH2L Sigma pLKO TRC0000019276


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 021 | Full ROI

last: Ogbonna

address: 200 Longwood Ave

description:
Library name: LSP16102_B5_scan1 | 021 | Full ROI
FFPE

value: TLS


title: SUM-44 ASH2L 276-A

description:
shASH2L_vs_LacZ.txt
276Sum44_vs_271Sum44.txt


title: Therapy PA repeat 2 (S89)

description: Library name: IKVAV_T2_S89


title: SUM-44 ASH2L 275-C

value: ASH2L Sigma pLKO TRC0000019275


title: SUM-44 ASH2L 275-B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 019 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 019 | Full ROI
FFPE


title: SUM-44 ASH2L 275-A

description:
shASH2L_vs_LacZ.txt
275Sum44_vs_271Sum44.txt


title: Therapy PA + PS2 repeat 1 (S87)

description: Library name: IKVAV_plus_PEDOT-S_OH_T1_S87


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 018 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 018 | Full ROI
FFPE


title: Therapy PA repeat 1 (S86)

description: Library name: IKVAV_T1_S86


title: JORRP Patient 95

type: RNA

first: shilan

last: li

address: No. 56 Nanlishi Road, Xicheng District

department: Department of Otolaryngology – Head and Neck Surgery

institute: Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health

description: Papilloma

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.  scan protocol After hybridization, slides were scanned on the Agilent Microarray Scanner G5761A (Agilent technologies, Santa Clara, CA, US).

scan_protocol: the arrays were scanned using the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Raw data were extracted with Feature Extraction software (version 10.7.1.1, Agilent Technologies), and basic analysis was performed using Genespring software (version 14.8, Agilent Technologies).

source_name: JORRP Patient 95

label_protocol: Sample labeling, microarray hybridization, and washing were performed according to the manufacturer's protocols.

extract_protocol: In brief, total RNA was quantified with the NanoDrop ND-2000 (Thermo Scientific), and RNA integrity was evaluated using the Agilent Bioanalyzer 2100 (Agilent Technologies).

value: Papilloma

tag: location

value: Beijing children hospital


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 017 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 017 | Full ROI
FFPE


title: JORRP Patient 94

description: Papilloma

source_name: JORRP Patient 94


title: HTR2B-cko-MCAO3d

first: Yueman

last: Zhang

address: 160 Pujian Rd

institute: Department of Anesthesiology,  Renji Hospital, School of Medicine Shanghai Jiao Tong University, China

description: Library name: sample 2

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
Starsolo was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;  Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Brain

extract_protocol:
brain cells were sorted with BD FACS
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: Brain

value: brain cells

value: tMCAO


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 016 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 016 | Full ROI
FFPE


title: JORRP Patient 93

description: Papilloma

source_name: JORRP Patient 93


title: HTR2B-fl/fl-MCAO3d

description: Library name: sample 1


title: JORRP Patient 92-2

description: Papilloma

source_name: JORRP Patient 92-2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 015 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 015 | Full ROI
FFPE


title: JORRP Patient 90

description: Papilloma

source_name: JORRP Patient 90


title: JORRP Patient 91

description: Papilloma

source_name: JORRP Patient 91


title: JORRP Patient 89

description: Papilloma

source_name: JORRP Patient 89


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 014 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 014 | Full ROI
FFPE


title: JORRP Patient 88-2

description: Papilloma

source_name: JORRP Patient 88-2


title: JORRP Patient 66

description: Papilloma

source_name: JORRP Patient 66


title: JORRP Patient 76-2

description: Papilloma

source_name: JORRP Patient 76-2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 013 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 013 | Full ROI
FFPE

source_name: tuberculosis-infected human lung tissue


title: Split_4C-rep7-blastomere3

city: Xuhui, Shanghai

first: Jie

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

description:
Library name: 4C_Split_7_B3
Column name in counts_allsample.txt: 4C_Split_7_B3

data_processing:
Raw reads were firstly processed through Trim Galore (v0.6.10) with the default parameters. In this step, clean reads were obtained by removing reads containing adapter and low-quality reads from raw data. Reference genome (GRCm38) and gene model annotation files (Release M25) were downloaded from GENCODE database (http://gencodegenes.org/mouse/release_M25.html). Paired-end clean reads were aligned to the reference genome using STAR (v2.7.3a). The abundance of transcripts and genes was estimated from the aligned reads using RSEM (v1.2.28). RSEM provided quantification of gene expression metrics including expected read counts, TPM (transcripts per million), and FPKM (fragments per kilobase of transcript per million mapped reads).
Assembly: GRCm10/mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: embryo

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent  (Invitrogen, Carlsbad, CA, USA)following the manufacturer's procedure. SMARTer cDNA synthesis starts with picogram amounts of total RNA.
To construct Smart-seq2 libraries from 2-cell or 4-cell mouse embryos/blastomeres, individual embryos (or blastomeres) are gently lysed to release mRNA, which is then reverse transcribed using an oligo-dT primer and a template-switching oligo to generate full-length cDNA.  The resulting cDNA is pre-amplified by PCR, purified using magnetic beads, and quantified.  Next, the cDNA is fragmented and tagged with sequencing adapters using a tagmentation (Nextera or Tn5) reaction. The final libraries are cleaned up, assessed for quality and concentration, and then subjected to high-throughput sequencing.

value: embryo

value: 4-cell (Split)

value: WT


title: Split_4C-rep7-blastomere2

description:
Library name: 4C_Split_7_B2
Column name in counts_allsample.txt: 4C_Split_7_B2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 012 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 012 | Full ROI
FFPE


title: JORRP Patient 92

description: Blood

source_name: JORRP Patient 92

value: Blood


title: Split_4C-rep7-blastomere1

description:
Library name: 4C_Split_7_B1
Column name in counts_allsample.txt: 4C_Split_7_B1


title: JORRP Patient 43

description: Papilloma

source_name: JORRP Patient 43


title: JORRP Patient 88

description: Blood

source_name: JORRP Patient 88


title: young_bleo_4

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Library name: S20

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore (Trim Galore) (v0.4.5) with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20 –rrbs.
Reads are aligned to mm10 with Bismark (Krueger and Andrews, 2011) (v0.22.1) using Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4) with default settings (multi-seed length of 20bp with 0 mismatches).
Alignments below a MAPQ threshold are removed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10.
MethylDackel (MethylDackel) (v0.4.0) then calls methylation rates with parameters -d 5 -D 2000 –mergeContext.
Assembly: mm10
Supplementary files format and content: bedGraph of methylation calls from MethylDackel

source_name: Lung fibroblasts

extract_protocol:
Lungs were minced with a razor blade and tissue was digested with 0.2 mg/mL of Liberase DL and 100 U/mL DNase I (Roche, Indianapolis, IN, USA) for 40 min at 37 °C. Digestion was stopped with medium containing 10% FBS and cells were passed through a 40 µm cell strainer (ThermoFisherScientific, Waltham, MA). Cells were incubated with 2 mL with red cell lysis buffer for 90 seconds. Cells were centrifuged before undergoing FACS sorting using antibodies against CD45:PerCpCy5.5 (1:200, Biolegend, San Diego, CA, USA, Cat# 103132), CD31:PE (1:200, Biolegend, San Diego, CA, USA, Cat#102408), EpCAM:APC (1:200,Biolegend, San Diego, CA, USA, Cat#118214). They were also stained with DAPI (1:1000, Biolegend, San Diego, CA, USA, Cat#422801). DAPI-positive, GFP-positive cells were sorted by FACS using the BD FACS Aria II (BD Biosciences, San Jose, CA, USA).
25-75 ng of genomic DNA was digested for 16-18 hours with the MspI restriction enzyme. The digested DNA was purified by phenol-chloroform extraction, then ethanol precipitated in the presence of glycogen and sodium acetate. The precipitated DNA was resuspended in 10mM Tris-Cl pH8.5 (Buffer EB) and processed for end-repair, A-tailing, and ligation of hairpin adapters with methylated cytosines. The ligated DNA was next ran on a 1.8% Low-Range Ultra Agarose Gel in TBE buffer, and fragments of 100-200bp and 200-300bp were excised and separately purified using Qiagen Gel Extraction kit. A 2ul aliquot of each fragment was used to verify proper adapter ligation and size selection by PCR. Samples passing this QC were then subjected to bisulfite conversion with the EZ DNA Methylation Kit, but with the following changes: the samples were incubated in a thermal cycler using the following conditions: 55 cycles: 95C for 30 sec, 50C for 15 min. Hold at 4C. The bisulfite converted samples were cleaned up according to the manufacturer’s protocol and eluted in 40ul of nuclease free water. The samples were next amplified using Roche High Fidelity FastStart system with the following protocol: 94C for 5 minutes; 18 cycles of: denaturing at 94C for 20 seconds, annealing at 60C for 30 seconds, extension at 72C for 1 min. A final extension was done at 72C for 3 minutes and the reactions were kept at 4C until they were cleaned. This final library cleanup was done with Agencourt’s AMPure XP SPRI beads according to the following protocol: The beads were brought to room temperature with gentle agitation for a minimum of 30 minutes. A 1.2X volume (for short fragments) and 1.1X volume (for long fragments) of SPRI beads was added to each sample fragment, and the PCR products were purified per manufacturer’s recommendation using 500ul of 80% ethanol for washes. Each library was eluted into 33ul of elution buffer (10mM Tris-Cl pH 8.5). The libraries were quantified using Qubit’s High Sensitivity ds DNA kit, and the quality was assessed with Agilent’s High Sensitivity D1000 ScreenTape assay.

treatment_protocol: Col1a1-GFP mice on a FVB background  were obtained from Derek Radisky (Mayo Clinic, Jacksonville, Florida, USA) and were maintained in breeding colonies. Mice were allowed to mature to either 6-8 weeks (young) or > 18 months (aged) of age. Nine mice in each group (aged and young) were treated with 50 µl of either intratracheal bleomycin (1.2 U/kg, APP Pharmaceutical, Schaumburg, IL) (five mice per group) or saline (four mice per group), delivered using a MicroSprayer (Penn-Century). Mice were euthanized at day 30 post-intratracheal treatment. Fibroblasts were isolated by FACS sorting for GFP.

value: Lung fibroblasts

tag: age

value: young

value: bleo


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 011 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 011 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: Split_4C-rep6-blastomere4

description:
Library name: 4C_Split_6_B4
Column name in counts_allsample.txt: 4C_Split_6_B4


title: JORRP Patient 76

description: Blood

source_name: JORRP Patient 76


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 010 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 010 | Full ROI
FFPE


title: JORRP Patient 46

description: Blood

source_name: JORRP Patient 46


title: OSA-8

description: glossopalatine arch mucosa

value: glossopalatine arch mucosa