title: Mouse motor cortex, nonTg, 6mth, rep3

first: Oliver

middle: H

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

description: Library name: nonTg_6mth_rep3

data_processing:
Adapter sequences were removed with Cutadapt v4.4
Sequences were aligned to the mm39 genome using STAR v2.7.10b
Expression was quantified using Tetranscripts v2.2.3 with Refseq (Apr 2023) and RepeatMasker annotaitons
Differential analysis were performed using DESeq2
Variance stabilizing transformation was performed to allow subsequent visualization with heatmaps using the NMF package.
Assembly: mm39
Supplementary files format and content: Count tables with gene or TE feature, along with the counts for each feature

source_name: Motor cortex

growth_protocol: Animals (non-transgenic, or expressing a transgene containing TDP-43 cDNA with/without the Q331K mutation) were housed in the maximum isolation facility and then transferred to the conventional facility prior to the experiments. The cages, bedding and food were sterilized. Food and water were provided ad libitum. A light-dark cycle of 12h was used (7:00 on, 19:00 off). The temperature was maintained between 20-26˚C. For all experiments, mice were used at 1.5, 3, 6, 10 and 15mth timepoints

extract_protocol:
Animals were perfused with ice-cold PBS on ice. The MC was dissected on ice and flash-frozen in 100% ethanol and dry ice. The tissue samples were stored at -80 degrees for a few days. Samples were shipped to Azenta, and total RNA were extracted according to Azenta's sample preparation protocols
Strand-specific library preparation with rRNA deplettion was performed according to Azenta's library preparation protocol to be compatible with Illumina sequencing

value: Motor cortex

value: Non-transgenic control

tag: age

value: 6 months


title: Day1_QA-92-TQ17_replicate2

status: Public on Jun 23 2025

type: SRA

city: San Diego

first: Bin

last: Fang

state: CA

address: 10675 John Jay Hopkins Dr

department: Discovery Science

country: USA

institute: Novartis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were mapped to the mm10 mouse reference genome and a per-cell count matrix was generated using CellRanger pipeline (10X Genomics, version 5.0.1).The processed count matrix was used to filter out low quality cells with <700 detected genes or >10% mitochondrial reads. Doublets were identified using DoubletFinder with default parameters and excluded from downstream analysis.
Assembly: mm10
Supplementary files format and content: tab delimited text files with cell barcodes, gene ids, and raw counts.

molecule: polyA RNA

organism: Mus musculus

source_name: lung organoids

growth_protocol: Adult Hopx-GFP+ mice were sacrificed with isoflurane, perfused with PBS through the right ventricle, and the lungs were extracted. Trachea, connective tissue, and upper bronchiole was removed under dissection, microscope. Lungs were cut into small pieces (>2 mm2) and incubated in protease solution for 30 minutes at 37°C in a shaking incubator. Protease solution contained: 450 U/mL Collagenase Type I (Gibco; 17100–017), 4 U/mL Elastase (Worthington Biochemical Company; LS002279), Dispase 5 U/mL (BD Biosciences;354235), and 0.33 U/mL DNaseI (Roche; 10104159001) dissolved in DMEM/F12 (Gibco; 11320033). Digestion enzymes were inactivated with DMEM/F12 + 10% FBS, cells were centrifuged at 500g and resuspended in Trypsin/DNAse solution and incubated for 30 minutes at 37°C in a shaking incubator. Trypsin/DNase solution contained: 0.1% Trypsin-EDTA (Gibco, 25200056) + 0.13 U/mL DNaseI (Roche; 10104159001) in DMEM/F12. Trypsin/DNase solution was inactivated with DMEM/F12 + 10% FBS, cells were filtered through a 70 μM cell strainer, centrifuged at 300g (2x), resuspended in RBC cell lysis buffer (Sigma; R7757), and digestion enzymes inactivated with DMEM/F12 + 10% FBS. Cells were centrifuged at 500g, resuspended in DMEM/F12 + 2% FBS, counted on a hemacytometer, and diluted to 1 x 10^6 cells per mL. Cells were filtered through a 40 μM cell strainer, resuspended 1:1 in Matrigel Growth Factor Reduced (Corning; 354230), and 4-7 drops of 50 μL cells-medium/Matrigel mixture in each well of a 6-well plate. Once solidified 2 mL of ITS media was added per well and plates were incubated in a standard cell culture incubator. ITS media contained: DMEM/F12 + 5% FBS, 1/100 ITS-G (Gibco; 41400045), 1/100 Antibiotic-Antimycotic (Gibco; 15240096), 0.5 ng/mL TGFβ1 (R&D Systems; 240-B-002). Fresh ITS media was added on top after 4-5 days in culture.

extract_protocol:
At designated times (day 0, day 1, day 3, day 11) cells were removed from Matrigel. Briefly, media was removed and washed with ice cold PBS. TrypLE Express (Gibco; 12604013) was added to wells and incubated at 37°C, followed by scraping of Matrigel bubbles to collect in a 15 mL conical tube. Cells were mechanically disrupted by pipetting ~10 times and incubated at 37°C for an additional 10 minutes. Cells were mechanically disrupted again and enzyme was inactivated with DMEM/F12 + 10% FBS + 1/100 Penicillin-Streptomycin (Gibco; 15140122). Cells were centrifuged at 300g at 4°C, resuspended to 1000 cells/ μL in DMEM/F12 + 10% FBS, and filtered through a Flowmi 40 μM cell strainer (Sigma; BAH136800040).
The Chromium Next GEM Single Cell 3’ reagent kit v3.1 from 10X Genomics (protocol CG000204 Rev C) was used in scRNA-seq library preparation. Single-cells were partitioned into nanoliter-scale Gel Beads-inemulsion (GEMs) using Chromium Controller. Upon cell lysis, the poly-A tails of mRNA are captured on the beads containing an Illumina read 1 sequencing primer, 16nt 10X barcode, 12nt UMI and 30nt poly (dT) sequence. Reverse transcription occurs followed by amplification of full-length cDNA from polyA mRNA. Enzymatic fragmentation and size-selection was used to optimize cDNA amplicon size. End repair, Atailing, Adaptor ligation and PCR create the final sequencing libraries that contain the P5 and P7 primers used in Illumina bridge amplification.
The libraries were sequenced using NextSeq 550 High Output Kit v2.5 (150 cycles).

treatment_protocol: Compounds (DMSO, DB-11-BE87, or QA-92-TQ17) were added at time of plating (10 μM final concentration). Day 0 samples have no treatment.

tag: tissue

value: lung organoids

tag: cell type

value: lung cells

tag: genotype

tag: treatment

value: TGFB1 + QA-92-TQ17


title: Wild-type, endometriosis model, replicate 2

city: Houston

first: Nuri

last: Sung

state: Texas

address: One Baylor plaza, Houston, Rm807

department: Molecular and Cellular biology

institute: Baylor college of Medicine

description: Library name: BO_72136

library_source: transcriptomic

data_processing:
Galaxy server version24.2.4.dev0
Adapter trimming was performed using Trimmomatic in Galaxy.
Reads were aligned to the Mus musculus genome (GRCm39).
Gene-level quantification was performed using featureCounts.
Differential expression analysis was performed with DESeq2.
Assembly: GRCm39
Supplementary files format and content: Gene-level count matrix (rows: genes, columns: samples) generated by featureCounts. Differential expression results includeGeneID,Gene name,Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj,-log10.

molecule: total RNA

source_name: mouse endometriosis

growth_protocol: Uterine horns from female mice (either wild-type or DNMT3A knock-out) were dissected and then cut into 20 small fragments. These tissue fragments were pipetted into 1 ml of 1X PBS to create a suspension. The suspension was then loaded into a 1 ml syringe and intraperitoneally injected into wild-type recipient mice that had received estrogen pellets one week earlier.

extract_protocol:
RNA was extracted using the RNeasy Mini Plus kit (Qiagen). For constructing sequencing libraries, 1.3 µg of RNA was used.
The Sample Quality was checked by using the NanoDrop spectrophotometer, Invitrogen Qubit 2.0 quantitation assay and Agilent Bioanalyzer. Library was prepared by using Illumina TruSeq Stranded mRNA library preparation protocol.

value: mouse endometriosis

value: WT

tag: time

value: 4 weeks


title: Wild-type, endometriosis model, replicate 1

description: Library name: BO_72135


title: DE WT rep 1 ATAC

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

library_source: genomic

data_processing:
The sequencing reads were aligned to the human hg19 and T2T reference genome using BWA mem using the default parameter.
Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Narrow peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Assembly: hg19 and T2T (CHM13v2.0)
Supplementary files format and content: bigWig coverage files and MACS2 narrow peak call files

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: ZIP8K8 iPSCs (Tandon et al., 2018) were maintained in mTeSR Plus (Stemcell Technologies, #100-0276) supplemented with 100U/ml Penicillin and 100µg/ml Streptomycin (Thermo Fisher Scientific, #15140122) on pre-coated culture ware (1:100 diluted Matrigel (Corning, #354234) in KnockOut DMEM (Thermo Fisher Scientific, #10829–018)) at 20-80% confluency by splitting every two to three days. Clump-based cell splitting was performed by incubating the cells in EDTA pH 8.0 (Thermo Fisher Scientific, #15575–038) and DPBS (Thermo Fisher Scientific, #14190-250) in a final concentration of 5 mM for 3 minutes at 37°C and 5% CO2. Single-cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10µM Y-27632 (Tocris, #1254) for 15 min at 37°C and 5% CO2. All centrifugation steps were performed at 300 x g for 5 minutes at room temperature (RT) unless otherwise specified. Cell counting was performed using an automated cell-counter (Thermo Fisher Scientific) on a single-cell suspension diluted 1:1 in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, #15250-061). Definitive endoderm differentiation was performed using the STEMdiff Trilineage Differentiation media (Stemcell Technologies, #05230). Single-cell suspensions of mTeSR Plus-maintained ZIP8K8 iPSCs were seeded into 6-well plates at the cell-number recommended by the manufacturer’s instructions. Fresh STEMdiff Trilineage Endoderm Differentiation media was given to the cells every 24h during the duration of the differentiation protocol. On day 5 cells were collected using a single-cell split prepared for FACS analysis.

extract_protocol:
Two replicates each of undifferentiated iPSCs and endoderm differentiated cells were harvested using a single-cell suspension (see growth protocol) and prepared for FACS analysis. ZIP8K8 single-cell suspensions were quenched DPBS-10% Fetal bovine serum (FBS, PAN Biotech, #P30-2602)). Next, cells were centrifuged at 4°C. Cells were then resuspended in DPBS-10% FBS containing the surface marker anti-CXCR4 antibody (Biologend, #306506) in a 1:200 dilution and incubated for 15 min at 4 °C in the dark. Next, cells were washed once again with DPBS-10% FBS and centrifuged at 4°C before FACS. Finally, cells were resuspended in DPBS-10% FBS and passed through a 70µm cell strainer (Corning, #431751). FACS analysis was performed on the FACSCelesta Flow Cytometer (Beckton Dickinson). For each replicate 50,000 cells were collected by sorting either NCAM negative iPSCs or positive Endoderm differentiated cells.
ATAC-seq libraries were prepared as described previously (Corces et al., 2017) with minor adjustments. In brief, 50,000 cells were centrifuged at 4°C for 5 minutes at 500 x g. The cell pellet was resuspended in 50ul of a water-based buffer containing 10mM TRIS-HCL pH 7.4 (Thermo Fisher Scientific, #J67501-AK), 10mM NaCl (Thermo Fisher Scientific, #AM9759), 3mM MgCl2 (#AM9530G), 0.1% Igepal (Sigma-Aldrich, #I8896) and 0.1% Tween-20.The lyse the cells the solution was incubated on ice for 3 minutes after which the reaction was quenched with 1ml of the resuspension buffer without lysing reagent (10mM TRIS-HCL pH7.4, 10mM NaCl, 3mM MgCl2, and 0.1% Tween-20). Nuclei were collected by centrifuging the solution for at 4°C for 10 minutes at 500 x g. The supernatant was carefully removed and the nuclei resuspended in 50ul of the DPBS-based transposition mixture consisting of a 2X water-based buffer with 20mM TRIS-HCL pH 7.4, 10mM MgCl2, 20% Dimethyl Formamide (Sigma-Aldrich, #PHR1553), and 0.1% Tween-20, 1% H2O, and 100mM Transposase (EpiCypher, #15-1017). The transposition reaction was incubated in a thermomixer at 37°C for 30 minutes at 1,000 RPM. The reaction was purified using the Zymo Clean & Concentrator 5 Kit following the manufacturer’s instructions for fragmented DNA and eluted in 20ul. The sequencing library was prepared by amplifying the 20ul purified DNA with a total of 50uM Nextera indexing primers using the NEB Q5 Hot Start High Fidelity 2X Master Mix (#M0494L) for 5 minutes at 72°C, 30 seconds of 98°C, and 9 cycles of 30 seconds 98°C, 30 seconds of 63°C, and 1 minutes of 72°C, followed by cooling down to 4°C. The final libraries were purified using Agencourt AMPure XP beads, and diluted to 4nM for sequencing.

value: cell line

tag: cell line

value: Definitive Endoderm


title: Day1_QA-92-TQ17_replicate1

description: 10x Genomics


title: Mouse motor cortex, nonTg, 6mth, rep2

city: New York

description: Library name: nonTg_6mth_rep2


title: iPSC HELLS KO rep2 ATAC

value: iPSC

value: HELLS KO


title: iPSC WT rep 2 ATAC


title: Old_Female

city: New Haven

first: Vishwa

middle: Deep

last: Dixit

state: CT

address: 310 Cedar Street, BML330

department: Pathology

institute: Yale School of Medicine

description:
Library name: Sample 4
10X Genomics

data_processing:
The Cell Ranger Single-Cell Software 3.0.2 available at 10x website was used to perform sample demultiplexing and resulting fastq files were aligned on mm10 genome reference (10x website, https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) with cellranger count tool. Data analysis was performed using Seurat v4.3.0 R package, including quality control, dimension reduction, clustering, cell-type identification and comparative analyses between conditions. In the step of quality control, poor-quality cells with the number of expressed genes < 363 (363 corresponding to the first mode in the bimodal distribution of number of expressed genes) were filtered out. We also excluded cells if their mitochondrial gene percentages were over 10%. After combining cells from all samples, we first normalized the raw count matrix using Log-Normalization with scale.factor 10,000 and then defined top variable genes using “mean.var.plot” methods.
Assembly: mm10
Supplementary files format and content: barcodes and features in tabulation-separated values files and matrix files

source_name: epidydymal white adipose tissue

extract_protocol:
Visceral adipose tissue (VAT) was digested in 0.8mg/mL collagenase II (Worthington Biochemicals), 3% BSA (Sigma), 1.2mM Calcium Chloride, 1.0mM Magnesium Chloride, 0.8mM Zinc Chloride, and 1x HBSS (Life Technologies 14185-052) for 40-45 minutes in a 37°C water bath with vigorous shaking. The Stromal Vascular Fraction (SVF) was filtered on a 100um cell strainer. Red blood cell lysis was performed using ACK lysis buffer, and cells were filtered a second time with a 70um cell strainer. Following adipose tissue digestion, stromal vascular fraction (SVF) cells isolated from VAT were then stained with viability dye, CD45.2, CD45, CD3, CD19, SiglecF, F4/80, CD11b, and were were sorted using a BD FACSAria II.
Library was generated according to manufacturer's instructions (Chromium Next GEM Automated Single Cell 3' cDNA Kit v3, 10X Genomics)

value: epidydymal white adipose tissue


title: Old_Male

description:
Library name: Sample 2
10X Genomics


title: Young_Female

description:
Library name: Sample 3
10X Genomics


title: Day1_DMSO_replicate3

description: 10x Genomics

value: TGFB1 + DMSO


title: iPSC HELLS KO rep1 ATAC


title: iPSC WT rep 1 ATAC


title: Day1_DMSO_replicate2

description: 10x Genomics


title: DNMT3A knockout, endometriosis model, replicate 1

description: Library name: BO_72138

value: DNMT3A knock-out


title: Mouse motor cortex, nonTg, 3mth, rep1

description: Library name: nonTg_3mth_rep1

value: 3 months


title: Wild-type, endometriosis model, replicate 3

description: Library name: BO_72137


title: Day1_DMSO_replicate4

description: 10x Genomics


title: DE HELLS KO rep2 ATAC


title: DE WT WGBS

description: WGBS

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20.
Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for autsomes and coverage (10-150 reads).
Assembly: T2T (CHM13v2.0)
Supplementary files format and content: bigWig file of coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

growth_protocol: ZIP8K8 or ZIP34K14 iPSCs (Tandon et al., 2018, Rosebrock et al., 2022) were maintained in mTeSR Plus (Stemcell Technologies, #100-0276) supplemented with 100U/ml Penicillin and 100µg/ml Streptomycin (Thermo Fisher Scientific, #15140122) on pre-coated culture ware (1:100 diluted Matrigel (Corning, #354234) in KnockOut DMEM (Thermo Fisher Scientific, #10829–018)) at 20-80% confluency by splitting every two to three days. Clump-based cell splitting was performed by incubating the cells in EDTA pH 8.0 (Thermo Fisher Scientific, #15575–038) and DPBS (Thermo Fisher Scientific, #14190-250) in a final concentration of 5 mM for 3 minutes at 37°C and 5% CO2. Single-cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10µM Y-27632 (Tocris, #1254) for 15 min at 37°C and 5% CO2. All centrifugation steps were performed at 300 x g for 5 minutes at room temperature (RT) unless otherwise specified. Cell counting was performed using an automated cell-counter (Thermo Fisher Scientific) on a single-cell suspension diluted 1:1 in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, #15250-061). Definitive endoderm differentiation was performed using the STEMdiff Trilineage Differentiation media (Stemcell Technologies, #05230). Single-cell suspensions of mTeSR Plus-maintained ZIP8K8 iPSCs were seeded into 6-well plates at the cell-number recommended by the manufacturer’s instructions. Fresh STEMdiff Trilineage Endoderm Differentiation media was given to the cells every 24h during the duration of the differentiation protocol. On day 5 cells were collected using a single-cell split prepared for FACS analysis. For the cell cycle arrest cells were treated with 2 µg/ml nocodazole (Sigma-Aldrich, #M1404-10MG) for 16 hours.

extract_protocol:
Proliferating and G2-arrested iPSCs were harvested using a single-cell suspension (see growth protocol) and snap-frozen for further use. A subset of G2-arrested cells was taken for cell cycle analysis to verify the arrest. Fort the cell cycle analysis cells were collected using a single-cell split and quenched with DPBS. 1M cells were transferred into a protein lo-bind Eppendorf tube (#) and centrifuged. The supernatant was discarded and the cell pellet resuspended in 100ul PBS-T (0.2% Tween 20, Thermo Fisher Scientific, #J20605.AP) To permeabilize and fix the cells 1ml of 70% EtOH was added dropwise for a final concentration 1ml/1M cells and incubated at 4°C for two hours or overnight. For one wash the cell suspension was then centrifuged and resuspended in 1ml PBS-T. After centrifuging the cell pellet was in 1ml Dapi solution of 0.1% Triton-PBS (Triton-X-100. Thermo Fisher Scientific, #85111) and 1ug/ml Dapi (Invitrogen, #D1306) and incubated at RT for 30 minutes in the dark. The cells were washed with 1ml PBS-T. Finally, the cells were resuspended in 200ul DPBS-10% FBS and filtered for FACS analysis.  Endoderm differentiated cells were harvested using a single-cell suspension (see growth protocol) and prepared for FACS analysis. ZIP8K8 single-cell suspensions were quenched DPBS-10% Fetal bovine serum (FBS, PAN Biotech, #P30-2602)). Next, cells were centrifuged at 4°C. Cells were then resuspended in DPBS-10% FBS containing the surface marker anti-CXCR4 antibody (Biologend, #306506) in a 1:200 dilution and incubated for 15 min at 4 °C in the dark. Next, cells were washed once again with DPBS-10% FBS and centrifuged at 4°C before FACS. Finally, cells were resuspended in DPBS-10% FBS and passed through a 70µm cell strainer (Corning, #431751). NCAM positive cells were sorted and snap-frozen for further use. FACS analysis was performed on the FACSCelesta Flow Cytometer (Beckton Dickinson).
Genomic DNA was extracted using Phenol-chloroform purification. In brief cell pellets were resuspended in 200ul DPBS an200ul cold phenol-chloroform was added (1:1 ratio), after mixing by vortexing the cell solution was centrifuged for 10 minutes at full speed. The aqueous layer was transferred to a fresh DNA-lo bind Eppendorf tube and supplemented with 10ul of 5M NaOH, 2ul glycogen, and 500ul 100% EtOH. After gentle vortexing the solution was incubated at -20°C over night. The next day, ethanol precipitation was performed by centrifuging the cell solution at 4°C for one hour at full speed. After discarding of the supernatant, the pellet was resuspended on 1ml of cold 70% EtOH and centrifuged again at 4°C for one hour at full speed. Finally, after discarding the supernatant and drying the pellet for 10 minutes the DNA was resuspended in 25ul of low EDTA TE buffer (Swift Biosciences, #90296). In a fresh lo-bind DNA tube dilute 300ng genomic DNA in 50ul low EDTA TE buffer and transfer to a Covaris tube (#520045) for fragmentation.  Next the DNA was fragmented using the following sonication settings: 10 % cycle, PIP of 175, and 200 bursts/cycle for 2 x 45 second. The fragmented DNA was then transferred to a DNA lo-bind tube and purified using the Zymo Clean & Concentrator 5 Kit (#D4013) following the manufacturer’s instructions for fragmented DNA. The final product was eluted in in 20ul low EDTA TE buffer. The purified genomic DNA was the bisulfite converted using the Zymo EZ DNA Methylation-Gold Kit (#D5005) by following the manufacturer’s instructions. The final product was eluted in in 15ul low EDTA TE buffer. Finally, the sequencing library was prepared using Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). The libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and diluted to 4nM for sequencing.

value: iPSC-derived DE


title: Young_Male

description:
Library name: Sample 1
10X Genomics


title: RPTEC-TERT1 cell control, biol rep 4

city: London

first: Maria

last: Caluianu

address: Gower Street

country: United Kingdom

institute: University College London

description: Library name: Sample4

data_processing:
nf-core/rnaseq pipeline v3.12.0
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: RPTEC-TERT1 cells (ATCC, #CRL-4031™) were cultured in DMEM:F12 Medium (ATCC® 30-2006™), supplemented with hTERT RPTEC Growth Kit (ATCC® ACS-4007™) (1% Supplement A and 1.6% Supplement B), 2% FBS, and 0.1 mg/mL Geneticin™ Selective Antibiotic (G418 Sulfate) (Thermo Fisher, #10131035). Cells were cultured at 37 °C with 5% CO2.

extract_protocol:
RPTEC-TERT1 Control, KO1, and KO2 clones were cultured to 70-80% confluency before RNA extraction with the RNeasy Plus Mini kit (QIAGEN, #74136). 1.0 µg of total RNA was used for the construction of the libraries
RNA for RNA-seq libraries was prepared with with the Watchmaker RNA Library Prep Kit with Polaris™ Depletion following manufacturer's protocol

value: Proximal tubule


title: Day1_DMSO_replicate1

description: 10x Genomics


title: Mouse motor cortex, nonTg, 1pt5mth, rep3

description: Library name: nonTg_1pt5mth_rep3

value: Motor cortex

value: Non-transgenic control

value: 1.5 months


title: Mouse motor cortex, nonTg, 6mth, rep1

description: Library name: nonTg_6mth_rep1

value: 6 months


title: Mouse motor cortex, nonTg, 3mth, rep3

description: Library name: nonTg_3mth_rep3


title: Mouse motor cortex, nonTg, 1pt5mth, rep2

description: Library name: nonTg_1pt5mth_rep2


title: B6N-86-5day-4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: B6N-86-5day-4

data_processing:
fastp (v0.20.0) used for trimming + filtering of raw data
Kallisto (0.46.1) used for transcript abundance quantification
Assembly: GRCm39
Supplementary files format and content: Tab-delimited transcript abundances

source_name: liver

growth_protocol: The mice, aged 12 weeks, were provided ad libitum access to chow (18% proteins, 4.5% fibers, 4.5% fat, 6.3% ashes, Provimi Kliba SA) during the long-acting glucagon treatment.

extract_protocol:
Total RNA was isolated from liver tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol with minor modifications. Briefly, approximately 50–100 mg of liver tissue was homogenized in 1 mL of TRIzol reagent using a Polytron homogenizer. The homogenate was incubated at room temperature for 5 minutes to ensure complete dissociation of nucleoprotein complexes. Subsequently, 0.2 mL of chloroform was added per 1 mL of TRIzol, and the mixture was vigorously shaken for 15 seconds, followed by incubation at room temperature for 3 minutes. Samples were centrifuged at 12,000 × g for 15 minutes at 4°C to separate the phases. The aqueous phase containing RNA was carefully transferred to a new RNase-free tube, and RNA was precipitated by adding 0.5 mL of isopropanol per 1 mL of TRIzol used. After incubation at room temperature for 10 minutes, samples were centrifuged at 12,000 × g for 10 minutes at 4°C to pellet the RNA. The RNA pellet was washed once with 1 mL of 75% ethanol (prepared with DEPC-treated water), followed by centrifugation at 7,500 × g for 5 minutes at 4°C. The supernatant was discarded, and the RNA pellet was air-dried for 5–10 minutes. The pellet was resuspended in 20–50 µL of DEPC-treated water and incubated at 55–60°C for 10 minutes to ensure complete dissolution. To remove any contaminating genomic DNA, RNA samples were treated with DNase I (RNase-free) according to the manufacturer’s instructions. Briefly, 1 µg of RNA was incubated with 1 U of DNase I in the presence of 1× reaction buffer and 1 U/µL RNase inhibitor at 37°C for 30 minutes. The reaction was terminated by adding EDTA to a final concentration of 2.5 mM and incubating at 65°C for 10 minutes. RNA concentration and purity were determined using a spectrophotometer (NanoDrop), with an A260/A280 ratio of ~2.0 indicating high-purity RNA. RNA integrity was verified by agarose gel electrophoresis or using a Bioanalyzer. RNA samples were stored at -80°C until further use.
The Illumina Truseq kit was used to generate libraries.

treatment_protocol: The long-acting glucagon was dissolved in phosphate buffer (50 mM, pH 7.0) with 5% mannitol, which was also used as vehicle control. The long-acting glucagon was carried out at the dose of 100 nmol/kg in a volume of 5 mL/kg, daily subcutaneously injected for 6 days.

value: liver

value: long-acting glucagon


title: iPSC DNMT3A DNMT3B DKO WGBS

description: WGBS

value: DNMT3A + DNMT3B DKO


title: Mouse motor cortex, nonTg, 3mth, rep2

description: Library name: nonTg_3mth_rep2


title: Day1_DB-11-BE87_replicate1

description: 10x Genomics

value: lung organoids

value: lung cells

value: TGFB1 + DB-11-BE87


title: Mouse motor cortex, nonTg, 1pt5mth, rep1

description: Library name: nonTg_1pt5mth_rep1


title: Day1_DB-11-BE87_replicate2

description: 10x Genomics


title: B6N-86-5day-3

description: Library name: B6N-86-5day-3

value: WT


title: B6N-86-5day-2

description: Library name: B6N-86-5day-2


title: iPSC DNMT3B KO WGBS

description: WGBS

value: cell line

value: iPSC

value: DNMT3B KO


title: Day0_replicate4

description: 10x Genomics

source_name: lung

value: lung


title: B6N-86-5day-1

description: Library name: B6N-86-5day-1


title: Day0_replicate3

description: 10x Genomics


title: SW480-Wild - Bisulfite

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
The pooled Bis-seq sequencing samples underwent sequencing on a NovaSeq 6000 S1 run using paired-end sequencing mode.
Subsequently, the sequences were mapped and methylation sites were identified utilizing the Dragen v4.0.3 pipeline software  against the reference genome hg38.   The Ensembl genome features were employed for annotating the methylated sites
Assembly: hg38
Supplementary files format and content: Differential analysis for the identified methylation sites was conducted using the MethylKit  function calculateDiffMeth.    Differentially methylated sites were determined by a minimum 15% change in methylation with a q-value of < 0.01 and a coverage of at least 10X.

source_name: Colon origin

growth_protocol: Both cell lines are grown in RPMI with 10% FBS and 5% CO2 at 37C.

extract_protocol:
PacBio® Nanobind® HMW DNA extraction kits following suppliers protocols.
Library was prepeared following NovaSeq6000 Denature and Dilute Libraries Guide provided by the supplier (Document #1000000106351 v03, Illumina).

treatment_protocol: No treatments were given to the cells included for sequenceing analysis.

value: Colon origin

value: SW480 Colorectal cancer

value: Epithelial

value: myc+; myb+; ras+; fos+; sis+; p53+; abl-; ros-; src-


title: B6N-vehicle-4

description: Library name: B6N-vehicle-4

value: Vehicle


title: Day0_replicate2

description: 10x Genomics


title: DE HELLS KO WGBS

description: WGBS

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20.
Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for autsomes and coverage (10-150 reads).
Assembly: hg19 and T2T (CHM13v2.0)
Supplementary files format and content: bigWig file of coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

growth_protocol: ZIP8K8 iPSCs (Tandon et al., 2018) were maintained in mTeSR Plus (Stemcell Technologies, #100-0276) supplemented with 100U/ml Penicillin and 100µg/ml Streptomycin (Thermo Fisher Scientific, #15140122) on pre-coated culture ware (1:100 diluted Matrigel (Corning, #354234) in KnockOut DMEM (Thermo Fisher Scientific, #10829–018)) at 20-80% confluency by splitting every two to three days. Clump-based cell splitting was performed by incubating the cells in EDTA pH 8.0 (Thermo Fisher Scientific, #15575–038) and DPBS (Thermo Fisher Scientific, #14190-250) in a final concentration of 5 mM for 3 minutes at 37°C and 5% CO2. Single-cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10µM Y-27632 (Tocris, #1254) for 15 min at 37°C and 5% CO2. All centrifugation steps were performed at 300 x g for 5 minutes at room temperature (RT) unless otherwise specified. Cell counting was performed using an automated cell-counter (Thermo Fisher Scientific) on a single-cell suspension diluted 1:1 in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, #15250-061). Definitive endoderm differentiation was performed using the STEMdiff Trilineage Differentiation media (Stemcell Technologies, #05230). Single-cell suspensions of mTeSR Plus-maintained ZIP8K8 iPSCs were seeded into 6-well plates at the cell-number recommended by the manufacturer’s instructions. Fresh STEMdiff Trilineage Endoderm Differentiation media was given to the cells every 24h during the duration of the differentiation protocol. On day 5 cells were collected using a single-cell split prepared for FACS analysis. For the cell cycle arrest cells were treated with 2 µg/ml nocodazole (Sigma-Aldrich, #M1404-10MG) for 16 hours.

value: Definitive Endoderm

value: HELLS KO


title: Mouse motor cortex, nonTg, 15mth, rep2

description: Library name: nonTg_15mth_rep2

value: Motor cortex

value: Non-transgenic control

value: 15 months


title: Day0_replicate1

description: 10x Genomics

value: lung cells


title: Mouse motor cortex, nonTg, 15mth, rep1

description: Library name: nonTg_15mth_rep1


title: SW480-PCAT2-KI - Bisulfite


title: V1TxS-2

city: Philadelphia

first: Craig

last: Bassing

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Library name: V1TxS-2

data_processing:
RNA-Seq reads were trimmed using bbduk as part of bbmap (version 38.92) (https://sourceforge.net/projects/bbmap/). Reads were then aligned to mm10 using STAR (version 2.7.9a) (https://pubmed.ncbi.nlm.nih.gov/23104886/). bamCoverage from the deeptools package (version 3.5.1) (https://pubmed.ncbi.nlm.nih.gov/27079975/) yielded the bigwig coverage files and was run using flags to separate the coverage tracks by stranded-ness and to normalize to counts per million (cpm). Normalized bigwig coverage files were uploaded to the UCSC genome browser (https://pubmed.ncbi.nlm.nih.gov/12045153/). Gene expression levels were quantified using TPMcalculator (version 0.0.3) (https://pubmed.ncbi.nlm.nih.gov/30379987/) with the GENCODE annotation for the mm10 genome (version M23_GRCm38.p6). For normalization and identification of significantly differentially expressed genes, the raw read counts were analyzed with the limma-voom package from Bioconductor (version 3.54.2)(Law et al., 2014).
Assembly: mm10
Supplementary files format and content: bigwig coverage files as produced by bamCoverage. The coverage is seperated into reads originating from the forward (fwd) or reverse (rev) strand.

source_name: Rag1-/- DN thymocytes

extract_protocol:
(B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice.
RNA sequencing library preparation was prepared using Rib0-Zero rRNA Removal Kit and TruSeq Stranded Total RNA library Prep kit following manufacturer’s protocol (Illumina, RS-122-2101)

value: Rag1-/- DN thymocytes


title: B6N-vehicle-2

description: Library name: B6N-vehicle-2

value: liver

value: WT


title: iPSC WT G2 arrest WGBS

description: WGBS

value: cell line

value: iPSC


title: Mouse motor cortex, nonTg, 10mth, rep3

description: Library name: nonTg_10mth_rep3

value: 10 months


title: Mouse motor cortex, nonTg, 10mth, rep2

description: Library name: nonTg_10mth_rep2


title: B6N-vehicle-3

description: Library name: B6N-vehicle-3


title: B6N-vehicle-1

description: Library name: B6N-vehicle-1


title: iPSC HELLS KO WGBS

description: WGBS


title: Mouse motor cortex, nonTg, 15mth, rep3

description: Library name: nonTg_15mth_rep3


title: wt-treated-4

description: Library name: wt-86-581

growth_protocol: The liver glucagon receptor knockout mice and wild-type control, aged 6-8 weeks, were fed a high fat diet (60% (kal%) fat, diet no. 3436, Provimi Kliba SA) for 16 weeks prior to long-acting glucagon treatment.

value: long-acting glucagon


title: ko-treated-4

description: Library name: ko-86-544

value: KO


title: Mouse motor cortex, nonTg, 10mth, rep1

description: Library name: nonTg_10mth_rep1


title: S5PC_2

description: Library name: S5PC_2


title: iPSC HELLS KO G2 arrest WGBS

description: WGBS


title: iPSC WT WGBS

description: WGBS


title: MDA-MB-453 cells treated with IL1β and TNFα

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description:
cell_metadata.txt
counts_matrix.txt

data_processing:
10X Genomics Cell Ranger (v3.1.0) (PMID: 28091601) was used to process the fastq files to cell and gene count tables using unique molecule identifiers (UMI) with the GRCh38 genome (compiled by 10X Genomics, refdata-gex-GRCh38-2020-A).
The Seurat (v4.0.4) (ref2) pipeline was used for downstream quality control and analysis. Cellranger-filtered data was read into Seurat. Host genes were removed if identified in fewer than 10 cells. Cells were filtered out if they contained >= 50,000 UMI, <= 3000 genes, >= 5000 genes, or >= 15% of UMIs coming from mitochondria.
The two samples were integrated for visualization only using Seurat with normalization by the sctransform with the difference between S and G2M scores regressed out. The top 30 principal components were used to perform Uniform Manifold Approximation and Projection (UMAP).
Prior to differential expression and plotting gene expression, data was normalized by dividing gene counts by total counts per cell and multiplied by 10,000 followed by natural-log transformation.
Assembly: GRCh38 genome (compiled by 10X Genomics, refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Text file containing UMIs by gene by cell (counts_matrix.txt) and text file containing metadata for each cell (cell_metadata.txt)

growth_protocol: MDA-MB-453 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere incubator with 5% CO2 at 37C

extract_protocol:
Freshly collected MDA-MB-453 cells after the treatment were detached by 0.25% Trypsin/EDTA and live cells were counted by using trypan blue.  The counted cells were then resuspended with PBS supplemented with 0.1% Bovine-serum albumin (BSA).
Library was performed based on the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: The cells were treated with 10ng/ml of IL1β and TNFα or vehicle control (water) for 24 hours

value: Human Triple-Negative Breast Cancer

value: IL1β+TNFα, 24 hours


title: Mouse motor cortex, TgTDP43, 6mth, rep2

description: Library name: TgTDP43_6mth_rep2

value: 6 months


title: S5PC_1

description: Library name: S5PC_1


title: ko-treated-3

description: Library name: ko-86-557


title: wt-treated-3

description: Library name: wt-86-580


title: Mouse motor cortex, TgTDP43, 6mth, rep1

description: Library name: TgTDP43_6mth_rep1


title: S513TKO_1

description: Library name: S513TKO_1


title: Mouse motor cortex, TgTDP43, 6mth, rep3

description: Library name: TgTDP43_6mth_rep3


title: S513TKO_2

description: Library name: S513TKO_2


title: Mouse motor cortex, TgTDP43, 3mth, rep3

description: Library name: TgTDP43_3mth_rep3

value: 3 months


title: ko-control-4

description: Library name: ko-ve-552

value: Vehicle


title: R1_7

description: Library name: R1_7


title: Mouse motor cortex, TgTDP43, 3mth, rep2

description: Library name: TgTDP43_3mth_rep2

value: Motor cortex


title: V1TxS-1

description: Library name: V1TxS-1


title: wt-control-4

description: Library name: wt-ve-582


title: No KD (Dox-) 1

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Assembly: hg38
Supplementary files format and content: differential analysis and raw counts

source_name: LNCaP Cell Line

extract_protocol: RNA was extracted from cells with Trizol reagent. Two rounds of phenol chloroform extraction were performed, and mRNA was precipitated with isopropanol and washed with 75% ethanol. Following desiccation, mRNA was resuspended in the TE buffer and frozen at -80C prior to library preparation. Illumina TruSeq RNA Sample Prep Kit  was used for the construction of sequencing libraries.

value: LNCaP

tag: knockdown


title: No KD (Dox-) 3


title: R1_6

description: Library name: R1_6


title: Mouse motor cortex, TgTDP43, 3mth, rep1

description: Library name: TgTDP43_3mth_rep1


title: No KD (Dox-) 2


title: MDA-MB-453 cells treated with Vehicle

description:
cell_metadata.txt
counts_matrix.txt

value: Vehicle (Water), 24 hours


title: ko-control-3

description: Library name: ko-ve-543


title: MEP50 KD (Dox+) 3


title: R1_4

description: Library name: R1_4


title: Mouse motor cortex, TgTDP43, 1pt5mth, rep2

description: Library name: TgTDP43_1pt5mth_rep2

value: 1.5 months


title: wt-control-3

description: Library name: wt-ve-571


title: R1_3

description: Library name: R1_3

value: Rag1-/- DN thymocytes


title: MEP50 KD (Dox+) 2


title: MEP50 KD (Dox+) 1


title: wt-control-2

description: Library name: wt-ve-563

value: liver


title: Mouse motor cortex, TgTDP43, 15mth, rep3

description: Library name: TgTDP43_15mth_rep3

value: 15 months


title: Mouse motor cortex, TgTDP43, 1pt5mth, rep1

description: Library name: TgTDP43_1pt5mth_rep1


title: ko-control-2

description: Library name: ko-ve-554


title: EbKO_1

description: Library name: EbKO_1


title: Mouse motor cortex, TgTDP43, 15mth, rep1

description: Library name: TgTDP43_15mth_rep1


title: Testis, adult, 1 day old, GEX, rep3

city: Heidelberg

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

institute: Centre for Organismal Studies Heidelberg

data_processing:
The 10x genomics Cell Ranger ARC v2.0.2 pipeline was used in Cluster mode on a slurm-enabled system.
Assembly: BDGP6.32, Ensemble release 107
Supplementary files format and content: All processed files are direct outputs from the Cell Ranger ARC pipeline.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Testis

extract_protocol:
Flash-frozen nuclei were pooled per replicate. Tissue was dounced in 1x lysis buffer (10x Genomics protocol CG000366, RevD), followed by 3x centrigugation and filtering at 700g for 7 min.
Libraries were constructed according to 10x Genomics Single Cell Multiome ATAC + Gene Expression v1 chemistry, protocol CG000338 Revision E.

value: Testis


title: wt-control-1

description: Library name: wt-ve-579

value: WT


title: CBE3_2

description: Library name: CBE3_2


title: ko-control-1

description: Library name: ko-ve-553


title: Mouse motor cortex, TgTDP43, 15mth, rep2

description: Library name: TgTDP43_15mth_rep2


title: Testis, adult, 1 day old, ATAC, rep3


title: Mouse motor cortex, TgTDP43, 10mth, rep2

description: Library name: TgTDP43_10mth_rep2

value: 10 months


title: Testis, adult, 1 day old, ATAC, rep2


title: ko-treated-2

description: Library name: ko-86-556

value: long-acting glucagon


title: CBE3_1

description: Library name: CBE3_1


title: Testis, adult, 1 day old, GEX, rep2


title: CBE1_1

description: Library name: CBE1_1


title: CBE1_2

description: Library name: CBE1_2


title: Testis, adult, 1 day old, ATAC, rep1


title: Mouse motor cortex, TgTDP43, 10mth, rep3

description: Library name: TgTDP43_10mth_rep3


title: wt-treated-2

description: Library name: wt-86-565


title: ko-treated-1

description: Library name: ko-86-546

value: KO


title: EbKO_2

description: Library name: EbKO_2


title: Mouse motor cortex, TgTDP43, 10mth, rep1

description: Library name: TgTDP43_10mth_rep1


title: G2NA APOL1 risk allele, mouse kidney

first: Katalin

last: Susztak

state: Pennsylvania

address: 12-123 Smilow Translational Research Center, 3400 Civic Center Blvd

department: Renal, Electrolyte, and Hypertension Division, Department of Medicine

institute: University of Pennsylvania, Perelman School of Medicine

description:
Library name: G2NA43
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation of raw fastq files was performed using cellranger-6.0.1 (include introns = True).
Initial data processing and quality control was performed using Seurat 4.0.2. Cells were filtered based on mitochondrial genes (< 15%) and nCounts/nFeatures (> 300).
Doublets were identified using DoubletFinder 2.0.
Ambient RNA correction was performed using SoupX 1.5.0.
Final sample merging, integration, data cleaning, and cell type annotation was performed in Scanpy 1.9 using scVI 0.19.0 for integration in an iterative clustering approach (see our manuscript for more details).
Assembly: Mouse: mm10-3.0.0. Human: hg19-3.0.0
Supplementary files format and content:
Raw counts after final filtering in matrix format (.csv).
Human: Filtered matrix after Cell ranger (.h5)
Additional metadata including cell type annotation (.csv)

source_name: Kidney

extract_protocol:
Mouse: Nuclei were extracted using a lysis buffer composed of Tris-HCl, NaCl, MgCl2, 10% NP40, and an RNAse inhibitor (40 U/ul). Frozen mouse kidney was finely chopped into 1-2 mm segments using a razor blade in 500 µl of the lysis buffer. This minced tissue was then placed into a gentleMACS C tube and homogenized with 1 ml of lysis buffer in a gentleMACS homogenizer using the Multi_E_01 and Multi_E_02 programs for 30 seconds. The homogenate was then passed through a 40 µm strainer (08-771-1, Fisher Scientific) and the strainer was rinsed with 2 ml of wash buffer (PBS 1X + 10% BSA (50 mg/ml) + RNAse inhibitor (40 U/ul)). The nuclei were spun down at 500xg for 5 minutes at 4°C, and the resulting pellet was re-suspended in wash buffer and filtered again through a 40 µm Flowmi cell strainer (BAH136800040-50EA, Sigma Aldrich). The quality of the nuclei was assessed, and their number was counted. Following the manufacturer's instructions, 10,000 to 30,000 cells (varied per sample) were loaded into the Chromium Controller using a Chromium Next GEM chip G Single Cell Kit to create single-cell gel beads in an emulsion.
Human: Nuclei were extracted using a lysis buffer composed of Tris-HCl, NaCl, MgCl2, 10% NP40, and an RNAse inhibitor (40 U/ul). Frozen biopsy tissue weighing 1-3 mg was finely chopped into 1-2 mm segments using a razor blade in 500 µl of the lysis buffer. This minced tissue was then placed into a gentleMACS C tube and homogenized with 1 ml of lysis buffer in a gentleMACS homogenizer using the Multi_E_01 and Multi_E_02 programs for 30 seconds. The homogenate was then passed through a 40 µm strainer (08-771-1, Fisher Scientific) and the strainer was rinsed with 2 ml of wash buffer (PBS 1X + 10% BSA (50 mg/ml) + RNAse inhibitor (40 U/ul)). The nuclei were spun down at 500xg for 5 minutes at 4°C, and the resulting pellet was re-suspended in wash buffer and filtered again through a 40 µm Flowmi cell strainer (BAH136800040-50EA, Sigma Aldrich). The quality of the nuclei was assessed, and their number was counted. Following the manufacturer's instructions, 10,000 to 30,000 cells (varied per sample) were loaded into the Chromium Controller (10X Genomics, PN-120223) using a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to create single-cell gel beads in an emulsion.
Mouse: Library was generated following the manufacturer's instructions (Chromium Next GEM Single Cell 3′ GEM Kit v2) for synthesizing cDNA and preparing the library. The libraries underwent quality control with the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) prior to sequencing.
Human: The Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and the Single Index Kit T Set A (10X Genomics, PN-120262) were used as per the manufacturer's guidance for synthesizing cDNA and preparing the library. The libraries underwent quality control with the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) prior to sequencing.

value: Kidney

tag: Sex

value: male

value: 8-10 weeks

tag: model

value: G2NA APOL1 risk allele, podocyte


title: Testis, adult, 1 day old, GEX, rep1


title: wt-treated-1

description: Library name: wt-86-574


title: Folic acid model, mouse kidney, biol replicate 4

description:
Library name: GGT_eYFP
10X Genomics

value: 10-13 weeks

value: C57BL/6, GGT_eYFP

value: folic acid


title: Mouse motor cortex, Q331K, 6mth, rep3

description: Library name: Q331K_6mth_rep3

value: Motor cortex

value: 6 months


title: Mouse motor cortex, Q331K, 6mth, rep2

description: Library name: Q331K_6mth_rep2


title: Folic acid model, mouse kidney, biol replicate 3

description:
Library name: LYZ2_eYFP
10X Genomics

value: C57BL/6, LYZ2_eYFP


title: Ad-shJP2 rep3

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

description:
Library name: Ad-shJP2-3
AdshJP2-3 TPM

data_processing:
Raw files were uploaded as paired reads into Illumina's BaseSpace hub (basespace.illumina.com). Sequences from the same sample on each of four lanes were combined into a single "biosample".
Sequences were processed with the within the DRAGEN suite of apps within the BaseSpace platform using default settings unless otherwise noted.
Sequences were aligned to the mus musculus GRCm39 genome (uploaded from Ensembl) and gene counts produced using the DRAGEN RNA App (v4.3.7) and selecting soft polyA trimming.
Differentially expressed genes (DEGs) were determined by the DRAGEN Differential Expression app (v4.2.4) from DESeq2 and Salmon quantification data generated by the DRAGEN RNA app.
Assembly: GRCm39
Supplementary files format and content: comma separated file containing read counts (TPMs).

source_name: heart

growth_protocol: Cardiac fibroblasts were isolated from Langendorff perfused and enzymatically digested adult C57BL6/N male mouse hearts. Cardiomyocytes were removed through two rounds of gravity settling. The remaining cell suspension was centrifuged at 1000xg for 5 min at 4C before resuspension in DMEM/F-12 medium supplemented with 1% penicillin-streptomycin and 10% fetal bovine serum and filtering with a 40 micron cell strainer. After allowing to attach in 10 cm dishes for 30 minutes, cells were washed and maintained in DMEM-F-12 medium at 37C.

extract_protocol:
Fibroblasts were washed in PBS and homozenized in Trizol reagent. RNA was precipitated from the aqueous phase with isopropanol and centrifugation at 4C, washed with 75% ethanol, and resuspended in DEPC-treated water. Genomic DNA was removed with an RNeasy Plus Mini Kit (QIAGEN)
PolyA RNA was enriched and stranded libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA sample preparation kit.

treatment_protocol: After fibroblasts reached 70-80% confluency, cells were infected with adenoviruses (1x10E6 pfu/ml) in serum free DMEM for two hrs. Media was then replaced with DMEM with 1% penicillin/streptomycin and 10% fetal bovine serum and incubated for a total of 72 hrs.

value: heart

tag: strain

value: cardiac fibroblast

value: wildtype

value: JP2 shRNA adenovirus


title: Ad-shJP2 rep1

description:
Library name: Ad-shJP2-1
AdshJP2-1 TPM


title: Rett patient 5602 MECP2 mutant neurons

city: Oxnard

first: Abril

last: Morales

address: 1300 East Pleasant Valley Road, Spc 119

institute: University of California, Los Angeles

description:
Library name: 5602_Mminus_Nplus
10X Genomics

data_processing:
A Chromium Single Cell 3’ Gene Expression library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The 10X Barcode and 12 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sample index sequences are incorporated as the sample index read. TruSeq Read 1 and TruSeq Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. These libraries were sequenced using Illumina's NovaSeq X+ platform in paired end configuration. Data quality check was done on Illumina SAV, and data de-multiplexing was performed with 10X CellRanger mkfastq software. Data analysis was performed using 10X CellRanger count software pipeline under default parameters.
Assembly: hg38
Supplementary files format and content: Tab-seperated values and matrix files

source_name: brain

extract_protocol:
Brain tissue was cut on ice using a scalpel and homogenized in a glass dounce. The homogenate was then filtered through a 40-um cell strainer and centrifuged at 1000g for 8 min at 4ºC. The pellet was resuspended in a homogenization buffer and mixed with equal amounts of iodixanol. This mixture was then gently placed in a new tube over 29% iodixanol. The nuclei were centrifuged at 13500g for 20 min at 4ºC. The pellet was resuspended in the immunostaining buffer and incubated for 15 min at 4ºC. Next, primary antibody was added to the nuclei pellet and incubated on a rotator at 4ºC for 40 min. The following primary antibodies were used: rabbit MECP2 (Diagenode C15410052, 1:250), chicken NeuN (Millipore Sigma MAB377 1:250). Nuclei were centrifuged at 400 g for 5 min at 4ºC and washed with PBS/BSA twice. Secondary antibodies conjugated with Alexa 488 and 594 (1:500, Life Technologies A-21203, A21202) were added, accompanied by DAPI (Invitrogen 1:500), the nuclei were incubated on a rotator at 4ºC for 30 min. Immunostained nuclei were subjected to FACS.
Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: brain

value: neurons


title: Folic acid model, mouse kidney, biol replicate 2

description:
Library name: PDGFR-eYFP
10X Genomics

value: C57BL/6, PDGFR_eYFP


title: Mouse motor cortex, Q331K, 6mth, rep1

description: Library name: Q331K_6mth_rep1

data_processing:
Adapter sequences were removed with Cutadapt v4.4
Sequences were aligned to the mm39 genome using STAR v2.7.10b
Expression was quantified using Tetranscripts v2.2.3 with Refseq (Apr 2023) and RepeatMasker annotaitons
Differential analysis were performed using DESeq2
Variance stabilizing transformation was performed to allow subsequent visualization with heatmaps using the NMF package.
Assembly: mm39
Supplementary files format and content: Count tables with gene or TE feature, along with the counts for each feature


title: Mouse motor cortex, Q331K, 3mth, rep3

description: Library name: Q331K_3mth_rep3

value: 3 months


title: Ad-shJP2 rep2

description:
Library name: Ad-shJP2-2
AdshJP2-2 TPM

value: male


title: Folic acid model, mouse kidney, biol replicate 1

description:
Library name: FA3
10X Genomics

value: Kidney


title: Rett patient 4516 MECP2 mutant neurons

description:
Library name: 4516_Mminus_Nplus
10X Genomics


title: Ad-JP2 rep2

description:
Library name: Ad-JP2-2
AdJP2-2 TPM

value: JP2 adenovirus


title: Rett patient 3575 MECP2 mutant neurons

description:
Library name: 3575_Mminus_Nplus
10X Genomics


title: Mouse motor cortex, Q331K, 3mth, rep2

description: Library name: Q331K_3mth_rep2


title: Ad-JP2 rep3

description:
Library name: Ad-JP2-3
AdJP2-3 TPM


title: Rett patient 5602 MECP2 wildtype neurons

description:
Library name: 5602_Mplus_Nplus
10X Genomics


title: Mouse motor cortex, Q331K, 1pt5mth, rep4

description: Library name: Q331K_1pt5mth_rep4

value: 1.5 months


title: Healthy control, mouse kidney

description:
Library name: CNU
10X Genomics

value: 4 weeks

value: control


title: Rett patient 1815 MECP2 wildtype neurons

description:
Library name: 1815_Mplus_Nplus
10X Genomics


title: Ad-GFP rep3

description:
Library name: Ad-GFP-3
AdGFP-3 TPM

value: GFP adenovirus


title: Rett patient 3575 MECP2 wildtype neurons

description:
Library name: 3575_Mplus_Nplus
10X Genomics


title: Ad-JP2 rep1

description:
Library name: Ad-JP2-1
AdJP2-1 TPM


title: TMD8 shIRF4 2 ATAC

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

description: Library name: TMD8_siIRF4_2

data_processing:
Raw reads were aligned against hg38 human genome and peaks were called using MAC2 software.
Assembly: hg38
Supplementary files format and content: Text file with peaks and their associated read counts

extract_protocol:
Intact nuclei were extracted from each cell line and treated with a transposase mutant.
The tagmented DNA was indexed and amplified. Amplified product was sequenced on HiSeq4000.

value: ABC


title: TMD8 shIRF4 1 ATAC

description: Library name: TMD8_siIRF4_1


title: Mouse motor cortex, Q331K, 3mth, rep1

description: Library name: Q331K_3mth_rep1

extract_protocol:
Animals were perfused with ice-cold PBS on ice. The MC was dissected on ice and flash-frozen in 100% ethanol and dry ice. The tissue samples were stored at -80 degrees for a few days. Samples were shipped to Azenta, and total RNA were extracted according to Azenta's sample preparation protocols
Strand-specific library preparation with rRNA deplettion was performed according to Azenta's library preparation protocol to be compatible with Illumina sequencing

value: Motor cortex


title: Rett patient 1815 MECP2 mutant neurons

description:
Library name: 1815_Mminus_Nplus
10X Genomics


title: Mouse motor cortex, Q331K, 1pt5mth, rep3

description: Library name: Q331K_1pt5mth_rep3


title: STAMP_91

type: other

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

hyb_protocol: The Imaging based platforms used in this study are the CosMX SMI (Nanostring) and the Xenium Analyzer (10X Genomics) with all specifications required for this study outlined in the CosMX SMI was used for both RNA and protein assays. All sections were also stained after data acquisition on their respective imaging platform. The specifics for each assay is outlined in the proceeding sections and found in STSOP. All methods were used across the three institutions: site #1 (UoA), site #2 (St. Jude Children’s Research Hospital), and site #3 (Weill-Cornell Medicine).  CosMx RNA Slide Preparation: Samples were processed following the guidelines outlined in the CosMx slide preparation manual MAN-10159-02 for prostate cancer processed in Adelaide and MAN-10184-01-1 for all other tissues. In summary, 5-μm sections were placed onto the 15 mm x 22 mm scannable area of a Superfrost Plus Micro Slide (VWR, 48311-703) and dried in an oven at 37°C for 2 hours then kept at room temperature with desiccant overnight before storage at 4°C. The slides were then incubated overnight at 60°C for 17–18 hours and then brought to room temperature for 3–5 minutes. This was followed by two xylene washes for 5 minutes each, and two washes in 100% ethanol for 2 minutes each. For normal tissues, CitroSolv workflow was used in place of xylene. The slides were then dried in an oven at 60°C for 5 minutes. The slides were immersed in pre-heated 1X Target Retrieval solution (CosMx FFPE slide preparation kit, RNA) in a pressure cooker (or steamer) at 100°C for 15 minutes, timing started once the retrieval solution reached 100°C. The slides were immediately transferred to water for 15 seconds, then washed in 100% ethanol for 3 minutes, and air-dried at room temperature for 30 minutes to 1 hour. Incubation frames were attached to each slide, and a pre-warmed digestion buffer containing 3 ug/mL Proteinase K (CosMx FFPE slide preparation kit, RNA) and 1X PBS (AM9922, AM9625 was applied and incubated in a hybridization chamber for 30 minutes. The slides were then rinsed twice in water, and fiducials were applied at 0.001%, followed by a 5-minute incubation at room temperature, shielded from light. The slides underwent a 1X PBS wash for 1 minute, were fixed in 10% NBF for 1 minute, immediately followed by two washes in NBF stop buffer for 5 minutes each, and then a 5-minute wash in 1X PBS. A 100 mM NHS-acetate solution was applied to the tissue for 15 minutes at room temperature, followed by two washes in 2X SSC for 5 minutes each. The CosMx Human Universal Cell Characterization RNA Panel (CMX-H-USCP-1KP-R) targeting 950 human genes and a 50-target add-on panel set, were denatured at 95°C for 2 minutes and then cooled on ice for 1 minute. A probe mix containing RNase inhibitor, buffer R, and nuclease free water was applied to the slide and incubated for 17 hours in the hybridization chamber at 37°C. Post-incubation, the slides were washed twice in a final concentration of 50% deionized formamide and 2X SSC mix for 25 minutes each, followed by two washes in 2X SSC for 2 minutes each. DAPI stock was diluted to 1:40 and applied to the slides for 15 minutes at room temperature, protected from light. The slides were then washed in 1X PBS for 5 minutes and stained for 1 hour with a cocktail of CD298/B2M, PanCK, CD45, and CD68 antibodies (Item # 121500020, 121500021, 121500022). Colon, HCC TMA, pancreas, and prostate cancer samples were stained with 4 uL of the CD298/B2M antibody, following the guidelines in MAN-10184-01-1. In contrast, appendix, ileum, and prostate cancer samples received a staining of 8 uL of the CD298/B2M antibody, as specified in MAN-10159-01-1.The slides were washed three times in 1X PBS for 5 minutes each and then stored in 2X SSC. The pre-bleaching profile followed configuration C, while the cell segmentation profile adhered to configuration A, except for the HCC TMA, which used configuration E. These procedures were consistently applied across all sites: St. Jude Children's Research Hospital, Weill Cornell Medical Center, and the University of Adelaide, with FOVs remaining uniform across all three locations.  CosMx Protein Slide Preparation: Samples were processed according to the guidelines provided in the CosMx SMI slide preparation manual MAN-10185-01-1 (NanoString). In summary, 5-μm FFPE sections were placed onto the 15 mm x 22 mm scannable area of a Superfrost Plus Micro Slide and dried in an oven at 37°C for 12 hours, sealed with desiccant and dried for a further 12 hours at room temperature before storage at 4°C. The slides were baked at 65°C for 2 hours and then equilibrated to room temperature for 3–5 minutes, and then washed twice in xylene (or CitriSolv) for 5 minutes each at room temperature. The slides were then washed twice in 100% ethanol for 10 minutes each, twice in 95% ethanol for 5 minutes each, and once in 70% ethanol for 5 minutes, followed by two washes in 1X PBS for 5 minutes each. The slides were immersed in pre-heated 1X Target Retrieval solution and heated in a pressure cooker at 100°C with the valve closed for 15 minutes, then allowed to equilibrate to room temperature in the same solution. Afterward, the slides were washed three times in 1X PBS for 5 minutes each, and incubation frames were attached. Tissue sections were then covered with Buffer W and incubated at room temperature for 1 hour in the dark. The NanoString 64-plex human protein antibody panel was combined with CD298/B2M and PanCK/CD45 segmentation markers in Buffer W. Samples from the appendix, ileum, and pancreas were also incubated with the CD68 segmentation marker. The primary antibody mix was incubated at 4°C for 17 hours, followed by three washes with 1X TBS-T buffer for 10 minutes each and once with 1X PBS for 2 minutes. Fiducials, prepared at the recommended concentration of 0.00005%, were applied to the slides at room temperature for 5 minutes, protected from light. Slides were then washed once with 1X PBS for 5 minutes and fixed with 4% PFA for 15 minutes. This was followed by three washes in 1X PBS for 5 minutes each. Sections were stained with nuclei stain for 10 minutes, washed twice with 1X PBS for 5 minutes, and incubated with 100 mM NHS acetate for 5 minutes, before a final wash in 1X PBS for 5 minutes. The selected pre-bleaching profile was configuration C, and the cell segmentation profile was configuration A. These procedures were uniformly followed at St. Jude Children's Research Hospital, Weill Cornell Medical Center, and the UoA, ensuring consistency in the FOVs across all three locations. Breast cancer, normal appendix, and normal ileum samples processed as part of the NanoString’s Technology Access Program followed the methods previously described (He et al,. Nat Biotechnol, 2022).  Xenium Slide Preparation: Sections for Xenium were prepared according to the Xenium In Situ for FFPE-Tissue Preparation Guide (CG000578 Rev C, 10X Genomics) protocol. Briefly, 5-μm sections were cut, floated in an RNAse-free water bath, and carefully placed onto the 10.45 mm x 22.45 mm sample area of Xenium slides (PN-3000941, 10X Genomics). The slides were then placed on a drying rack at room temperature for 30 minutes to remove excess water. This was followed by a 3-hour incubation at 42 ̊C on a Xenium Thermocycler Adapter plate, positioned atop the 96-well block of a C1000 Touch Thermal Cycler (BioRad) with the lid open. Subsequently, the slides were stored overnight at room temperature with a desiccant to facilitate further drying. The slides were then processed following the Xenium In Situ for FFPE Deparaffinization and Decrosslinking protocol (CG000580 Rev C, 10X Genomics). The slides were placed again on a Xenium Thermocycler Adapter plate atop the 96-well block of a thermocycler with the lid open and incubated at 60 ̊C for 2 hours. They were then equilibrated to room temperature for 7 minutes, deparaffinized, and rehydrated by immersion twice in xylene for 10 minutes each, twice in 100% ethanol for 3 minutes each, twice in 96% ethanol for 3 minutes each, once in 70% ethanol for 3 minutes, and once in water for 20 seconds. Subsequently, the Xenium slides were assembled into Xenium cassettes and hydrated with 1X PBS. The tissue sections were reverse crosslinked using a decrosslinking buffer containing tissue enhancer, urea, and perm enzyme B, at 80 ̊C for 30 minutes, followed by three washes with PBS-T. Slides were then immediately processed following the Xenium In Situ Gene Expression user guide (CG000582 Rev E, 10X Genomics) for the remaining slide preparation steps. Briefly, the pre-designed gene expression probe set, Xenium Human Multi-Tissue and Cancer Panel (10X-1000626, 10X Genomics) targeting 377 human genes, was utilized for prostate cancer, ileum, appendix, pancreas, and colon samples. For breast cancer samples, the Xenium Human Breast Panel (10X-1000463, 10X Genomics) targeting 380 human genes was used. Panels were denatured at 95 ̊C for 2 minutes, crash-cooled on ice for 1 minute, and then equilibrated to room temperature before being added to the probe hybridization buffer and TE buffer to make the probe hybridization mix. The slides were incubated with the hybridization mix at 50 ̊C for 17 hours. Slides were washed three times with PBS-T for 1 minute each then incubated with a post-hybridisation wash buffer for 30 minutes at 37 ̊C. Slides were washed three times with PBS-T for 1 minute each and incubated with ligation mix for 2 hours at 37 ̊C. Three 1-minute PBS-T washes were followed by a 2-hour incubation at 30 ̊C with an amplification mix. Slides were then washed three times with TE buffer then three washes with 1X PBS for 1 minute each followed by incubation with reducing agent B for 10 minutes, washed once in 70% ethanol for 1 minute, twice in 100% ethanol then treated with autofluorescence solution for 10 minutes in the dark. Slides were washed three times with 100% ethanol for 2 minutes each then dried for 5 minutes at 37 ̊C before rehydrating with 1X PBS then PBS-T for 2 minutes. Slides were stained with a nuclei staining buffer for 1 minute at room temperature followed by three washes with PBS-T for 1 minute each in the dark. The slides were then assembled into Xenium Cassettes and loaded into the Xenium Analyzer for imaging and decoding. These procedures were uniformly followed at St. Jude Children's Research Hospital, Weill Cornell Medical Center, 10x Genomics, and the UoA, ensuring consistency in theFOVs across all four locations. Breast cancer samples processed as part of the 10x Genomics’ Catalyst Program followed the methods previously described (19); these experiments were carried out at 10X Genomics headquarters (Pleasanton, CA, USA). Sections from the prostate cancer samples were also subjected to Xenium Multimodal segmentation through an early access program and processed at the 10X Genomics headquarters (Pleasanton, CA). In brief, the procedure for in situ gene expression with cell segmentation staining was conducted following the Demonstrated Protocol for Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578 Rev C, 10X Genomics), the Xenium In Situ Gene Expression User Guide (CG000582 Rev F, 10X Genomics), and the Xenium In Situ Gene Expression Cell Segmentation User Guide (CG000749 Rev A, 10X Genomics). The combined protocol utilized the Xenium Human Multi-Tissue and Cancer Panel for in situ gene expression and the Xenium Cell Segmentation Staining Reagents add-on (PN-1000661, 10X Genomics) for segmentation staining. This add-on kit contains a single cocktail of Xenium Multi-Tissue Stain Mix (PN-2000991, 10X Genomics), which contains a cocktail of antibodies labeling the membranes (anti-ATP1A1/CD45/E-cadherin), antibodies labeling the cell interior (anti-alphaSMA/Vimentin) and a universal interior label against Ribosomal RNA (18S rRNA). Stain was then enhanced by the addition of Xenium Staining Enhancer reagent, followed by treatment of the sections with Xenium Autofluorescence Mix (PN-2000753, 10X Genomics) to diminish unwanted autofluorescence and enhance the signal-to-noise ratio in the tissue sections. Subsequently, Xenium Nuclei Staining Buffer (PN-2000762, 10x Genomics) was used to help the identification of tissues or regions of interest during the instrument's overview scan.  Xenium RNA to CosMx Protein slide preparation: Following completion of the Xenium RNA run, slides were removed from the instrument and stored in the Xenium cassette with PBS-T at 4C. After storage for up to 3 days, slides were washed three times in PBS-T for 1 minute each as recommended in Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709 Rev A, 10X Genomics), removed from the Xenium cassette and placed into a wash jar of 1X PBS for 5 minutes as described in CosMx SMI Manual Slide Preparation for Protein Assays (MAN-10185-01-1, NanoString), incubation frames were attached to the Xenium slide and tissue sections were covered with Buffer W and incubated at room temperature for 1 hour in the dark. Afterwards, MAN-10185-01-1 and MAN-10161-03-2 were followed as previously described in CosMx Protein slide preparation and CosMx SMI setup and data acquisition.

scan_protocol: CosMx SMI Setup and Data Acquisition: The setup and scan acquisition for the CosMx SMI instrument were carried out as detailed in the CosMx SMI Instrument User Manual   (MAN-10161-02-1 or MAN-10161-03-2, Software Version 1.1, NanoString). A new acquisition process was initiated through the CosMx SMI Control Center web interface. Prior to insertion into the CosMx Flow Cell Assembly Tool, the slides were carefully dried in the areas surrounding the imaging region. The process involved lowering the tailgate, placing the slide, and then securing it by raising the tailgate. After removing the adhesive backing, a new flow cell coverslip was precisely aligned above the slide's imaging area. The Assembly Tool's lid was closed securely to affix the coverslip to the slide, thus creating a functional CosMx flow cell. Following the assembly, 2X SSC was gently introduced through one of the flow cell ports to hydrate the tissue section. Subsequent steps included entering the flow cell configuration data into the Control Center interface, which comprised the flow cell's barcode and the slide's ID number. The prostate sections underwent scanning with Configuration C for the pre-bleaching profile and Configuration A for the cell segmentation profile. Further details regarding the probe panel, cell segmentation, and supplemental markers were entered into the flow cell configuration data for each section. Assembled flow cells/slides, along with Buffer Bottles 1–4, were then loaded into the instrument. Before positioning Bottle 4, catalase and pyranose oxidase enzymes were added. The Control Center configuration was verified and following a period of equilibration to room temperature and the addition of an RNase inhibitor to a designated well in the CosMx imaging tray, the tray was placed in the instrument. A pre-run check and a tissue find scan for each tissue section were performed by the instrument. After the completion of tissue find scans, rectangular scan areas were delineated around each tissue section for the preview scan. The preview scan images facilitated the selection of a contiguous region of FOVs using the grid FOV placement tool, thoroughly covering the tissue areas on each slide. FOV selections for each slide were confirmed before initiating the cycling process. CosMx scan data were automatically uploaded to NanoString’s cloud-based AtoMx Spatial Analysis Platform during the run, as detailed in the CosMx Data Analysis manual (MAN-10162-02, Software Version 1.1, NanoString). Briefly, upon the completion of the run and the full upload of scan data to AtoMx, a study was created for each CosMx scan. Within AtoMx, pipelines were executed for each study, facilitating the export of data in various formats, such as TileDB arrays and Seurat objects, for in-house analysis.     Xenium Analyzer Setup and Data Acquisition: Xenium slides, assembled within Xenium cassettes, were imaged using the Xenium Analyzer, in accordance with the guidelines specified in the Xenium Analyzer User Guide (CG000584 Rev D and Rev E for Multi-modal Segmentation-stained slides, 10X Genomics). The Xenium Decoding Consumables Kit, (PN-1000487, 10X Genomics) was used for instrument loading. Briefly, Xenium slide ID numbers and information on pre-designed gene expression probes—were input into the Analyzer. The necessary consumables and reagents were loaded into the instrument: reagent module B, thawed at 4 ̊C overnight and equilibrated to room temp for 30 minutes prior to loading into the instrument, reagent module A, stored at 4 ̊C until loading in the instrument, instrument wash buffer (100% Milli-Q water), sample wash buffer A (1X PBS, 0.05% Tween-20), sample wash buffer B (100% Milli-Q water), and probe removal buffer (50% DMSO, 50 mM KCl, 0.1% Tween-20) were mixed prior to loading into the instrument with buffer caps along with, pipette tip rack, extraction tip, objective wetting consumable. After loading, the sample was scanned to generate images of the fluorescently labeled nuclei in each section which was used for FOV selection prior scanning. For the prostate cancer sample, the entire section was included in the full scan as 4 regions were selected for the appendix. After the run, the instrument was cleared of consumables, and the Xenium slides were carefully removed. Fresh PBS-T was applied to each slide/cassette, which were then   covered and stored in the dark at 4°C until post-run H&E staining. All procedures were standardized across three sites. The data were then acquired using the Xenium In Situ software suite (v1.9, 10X Genomics), which is a set of software applications for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer. For prostate samples stained with Multi-Modal Cell Segmentation reagents (10X Genomics Headquarters), both in situ gene expression and segmentation data were simultaneously collected and processed using v2.0 of the Xenium In Situ software suite.

data_processing:
To ensure a fair comparison, cells without detected transcripts were excluded from the analysis following the Xenium Onboard Analysis or the AtoMx processing workflow. Subsequent analyses, including cell type annotation, were conducted using raw transcript counts
Processed data: Transcript counts derived from intensity values within the boundaries of segmented cells.

molecule: other

source_name: PBMC, MCF-7, SK-BR-3

label_protocol: CosMx and Xenium barcoded probes for RNA and protein assays.

extract_protocol: To confirm the RNA quality of all the samples included in this study three consecutive 10-μm scrolls for the isolation and purification of total RNA using the Norgen Biotek FFPE RNA Purification Kit (Product ID 25300). RNA material (5 ng) was analyzed using a 5200 Fragment Analyzer with the High Sensitivity RNA Assay kit (DNF-472, Agilent Technologies). DV200 values across all samples ranged between 50%–70%. Single Nucleus RNA sequencing was performed following the snPATHO-Seq protocol (Wang et al. BioRxiv, 2023). Briefly, two 30- to 50-μm-thick scrolls from each sample, adjacent to sections for CosMx, Xenium, and H&E staining, were cut and placed into 1.5-mL Eppendorf tubes and stored at 4°C inside Ziplock bags with desiccants to control moisture. Scrolls were stored for up to 1 week. For the preparation of nuclei suspensions, scrolls sections underwent a triple wash in 1 mL of xylene (214736, Millipore Sigma) for 10 minutes each to dewax, followed by rehydration through sequential ethanol (E7023, Millipore Sigma) immersions of decreasing concentrations (100% twice, then 70%, 50%, and 30% once each), each for a duration of 1 minute. Of note, the initial xylene wash was performed at 55°C for 10 minutes to enhance paraffin removal. Subsequent to rehydration, a single wash was performed using 1 mL of wash RPMI 1640 media (11875093, Gibco). After removing the RPMI1640 wash, 50–100 uL of digestion mix [RPMI1640 supplemented with 1 mg/mL of Liberase TH (5401151001, Millipore-Sigma), along with 1 U/uL RNAse Inhibitor (RiboLock RNase Inhibitor, EO0382, Thermo Fisher Scientific)] was added to the tissue scrolls breaking them to smaller pieces with a 1.5-mL pellet pestle before topping up to 1 mL with the same digestion media. Digestion was carried out in a Thermomixer at 800 rpm. After digestion, 400 uL of Ez Lysis Buffer (NUC-101, Sigma-Aldrich) was added, mixed by inversion five times, and centrifuged at 850xRCF for 5 minutes at 4°C. The pellet, consisting of released nuclei and undigested tissue, was resuspended in 250 uL of Ez Lysis buffer with 2% BSA (130-091-376,  MACS BSA Stock Solution, Miltenyi) and 1 U/uL RNAse Inhibitor, followed by homogenization using a 1.5-mL pellet pestle. This was supplemented with an additional 750 uL of the same lysis mix, with further disaggregation achieved through pipetting. The sample was then filtered through a 70-μm strainer (pluriStrainer Mini 70um, 43-10070-50, pluriSelect) and centrifuged, with the flow-through washed again with 800 uL of the lysis mix. Nuclei pellet was washed three times in 1x PBS (70011044, Gibco) with 1% BSA, followed by two washes in 0.5x PBS (70011044, Gibco) with 0.02% BSA. Nuclei was finally resuspended in a volume of 500-1000 uL of the same buffer, dependent on pellet size, and filtered through a 40-μm strainer (pluriStrainer Mini 40um, 43-10040-50, pluriSelect. Nuclei were counted using a Luna-FX7 using Acridine Orange/Propidium Iodide Stain (Logos). For immediate analysis, the suspension was kept on wet ice until processing using the Chromium X controller and the Chromium Fixed RNA Profiling Reagent Kits for multiplexed samples (Chromium Fixed RNA Kit, Human Transcriptome, PN1000475; Chromium Next GEM Chip Q Single Cell Kit, PN-1000418; Dual Index Kit TS Set A, PN-1000251, 10x Genomics) and the User guide CG000527, Rev E. For storage, the pre- or post-hybridized nuclei suspensions were supplemented with 10% Glycerol and 0.1X Enhancer (PN-2000482, 10x Genomics), rested on ice for 10 minutes, and then cryopreserved at −80°C. For the hybridization step, between 500,000 and 1.5 million nuclei were used; hybridization was conducted for 20 hours at 42°C across all samples. BC1-4 were used in all samples used in this study. Post-hybridization washes were carried out in a pool-wash setting as per User guide, with an additional wash included. Approximately 10,000 nuclei/sample were aimed for capture. An extra cycle was introduced for the Pre-Amplification PCR step. Indexing PCR conditions were tailored to attain the target library concentration of 50–200 nM. Libraries were checked for quality control and quantified using a Fragment Analyzer 5200 (Agilent) and a Qbit Flex Fluorometer (Thermo Fisher Scientific), respectively. The indexed libraries were sequenced using the Illumina NovaSeq 6000 system. The read configuration was Read 1: 28, i7: 10, i5: 10, and Read 2: 90. Libraries were sequenced to aim for 20,000–30,000 read pairs/nuclei.

treatment_protocol: Normal and cencerous samples used for RNA and/or protein profiling (Xenium and CosMx platforms) as well as for tissue staining (Hematoxylin and Eosin, H&E) and single nuclei RNA-seq (snPATHO-Seq, using Chromium platform) were fixed in 10% neutral buffered formalin (NBF) and parafin embedeed (FFPE). To confirm the RNA quality of all the samples included in this study three consecutive 10-μm scrolls for the isolation and purification of total RNA (DV200 was used as measure of RNA intgrity post BioAnalyzer, TapeStation or Fragment Analyzer run). for snRNA-Seq from FFPE (snPATHO-Seq).

tag: tissue type

value: Blood and spiked-in MCF-7 and SK-BR-3 cancer cells

tag: sample source

value: STEMCELL Technologies (PBMC), Swarbrick Lab (MCF-7/SK-BR-3, The Garvan Institute)

tag: sample processed

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

tag: sample type

value: FFPE isolated nuclei

tag: replicate

tag: technology

value: Single Molecule Imager

tag: panel size

value: Human Immuno-Oncology Protein Panel:64


title: Mouse motor cortex, Q331K, 15mth, rep3

first: Oliver

last: Tam

address: 435 E 30th St

institute: NYU Grossman School of Medicine

description: Library name: Q331K_15mth_rep3

tag: tissue

tag: age

value: 15 months


title: Rett patient 4516 MECP2 wildtype neurons

description:
Library name: 4516_Mplus_Nplus
10X Genomics

value: brain

tag: cell type

value: neurons


title: Ad-GFP rep2

description:
Library name: Ad-GFP-2
AdGFP-2 TPM

value: heart

value: male

value: cardiac fibroblast

tag: genotype

value: wildtype

tag: treatment


title: TMD8 Control 1 ATAC

description: Library name: TMD8_Ctr_1

tag: cell line


title: STAMP_92

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)


title: Mouse motor cortex, Q331K, 1pt5mth, rep1

description: Library name: Q331K_1pt5mth_rep1

value: 1.5 months


title: STAMP_90


title: Ad-GFP rep1

description:
Library name: Ad-GFP-1
AdGFP-1 TPM

value: GFP adenovirus


title: TMD8 IRF4 shRNA Rep6

description: Library name: TMD8_IRF4_2_2_S11

data_processing:
Sequencing data were mapped to hg38 using STAR aligner and gene-wise counts were extracted for each sample using HTSeq configured to use Ensemble 78 transcriptome.
Assembly: hg38
Supplementary files format and content: Text file containing counts

extract_protocol:
mRNA was extracted and library was constructed using TruSeq kit.
Cell pellets were collected at 24 hours and immediately stored at −80°C pending RNA extraction. Following extraction of total RNA, mRNA libraries were constructed (Illumina, TruSeq Technology, San Diego, CA, USA) using TruSeq stranded RNA kit following the manufacturer's recommended protocol. Prepared libraries were sequenced using 100 base-pair paired-end sequencing method on an Illumina HiSeq instrument.

value: cell line

value: ABC lymphoma


title: TMD8 IRF4 shRNA Rep5

description: Library name: TMD8_IRF4_2_3_S13


title: 10x-scRNA-seq_R188QCreKI_rep2

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: Library name: 10x-scRNA-seq_R188QCreKI_rep2

data_processing:
For ChIC-seq: Paired-end raw reads were mapped to mouse genome mm10 by Bowtie2 (v2.3.5)57 and converted into bigwig files with reads per million (RPM) signals for aggregation analysis and visualization in WashU Genome Browser.  For RNA-seq: Raw reads were mapped to mouse genome mm10 with STAR (v2.5.1b)53. The gene expression levels were quantified and normalized by cuffnorm from cufflinks (v2.2.1)54 package into an FPKM matrix. Genes were filtered off if their expression levels < 1 FPKM in all samples. The expression matrix was further log2-transformed. The differentially expressed genes (DEGs) were called with cuffdiff (v2.2.1),55 requiring q-value <0.01, absolute fold change between the two conditions >=2, the sum of mean expression level between the two conditions >=1 and genes in the filtered expression matrix. The enriched GO terms were identified by findGO.pl from HOMER package (v4.10.4)56, requiring at least 5 genes in the target biological process term, fewer than 500 total genes in the term,  and a p-value < 1e-5. Ingenuity Pathway Analysis (Ingenuity Systems) was performed to identify upstream regulators of the DEGs; For scRNA-seq: Reads were pre-processed with cellranger count (v7.2.0) (10x Genomics). Cells were retained for subsequent analysis if they expressed at least 500 genes, had fewer than 5% of reads mapping to mitochondrial genes, and had more than 5% of reads mapping to ribosomal genes. These cells were then normalized and integrated with our previous study data using Seurat (v4.2.1). All cells UMAP visualization and marker genes for the four populations were also obtained with Seurat. Cells classified as the AMP populations were extracted, and their normalized expression matrix was used to obtain the first two component values for each cell with the PCA implemented in scikit-learn package (https://scikit-learn.org/stable/). The first two components were then fed to UMAP (https://umap-learn.readthedocs.io/en/latest/) with key parameters: n=100, init='pca', metric='euclidean', min_dist=0.0, n_epochs=1000, andom_state =123. The AMP UMAP results were clustered using HDBSCAN (v0.8.33) (https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html) with key parameters: min_samples=1000,min_cluster_size=100. Differentially expressed genes within the AMP cells between clusters were identified using a two-sided Wilcoxon rank-sum test implemented in the Scipy package (v1.11.3)61 (scipy.stats.ranksums), with criteria of p-value < 1e-10, absolute fold change >=2, and expression in more than 20% of cells in at least one condition.
Assembly: mm10
Supplementary files format and content: ChIP-seq: BigWig files containing normalized reads per million (RPM) signals. RNA-seq: Text files containing gene expression matrices quantified using RPKM (Reads Per Kilobase of transcript per Million reads). 10x scRNA-seq: H5 files generated by the Cell Ranger pipeline.

source_name: Mice AMP cells

extract_protocol:
Total RNA were extracted with AllPrep DNA/RNA/Protein Mini Kit (QIAGEN)
ChIC-seq libraries were constructed as previously described (Ku, W.L., et al., Nature Methods, 16, 323-325). RNA-seq libraries were prepared using poly(A) enrichment and  the Illumina TruSeq Stranded mRNA Sample Prep Kits according to manufacturer’s instructions. 10x scRNA-seq libraries were generated following the manufacturer’s instructions.

treatment_protocol: For ChIC-seq, wildtype (WT), Mx1-CreCbfb+/56M(dHABD), Mx1-CreCbfb+/56M-ΔHABD (dHABD) and Mx1-CreCbfb+/56M-mDE (mDE) mice were injected with pIpC and 2-3 weeks later, the LK population in the bone marrow cells of these mice were sorted out. For RNA-seq, (1) wildtype (WT), Mx1-CreCbfb+/56M(dHABD), Mx1-CreCbfb+/56M-ΔHABD (dHABD) and Mx1-CreCbfb+/56M-mDE (mDE) mice were injected with pIpC and 2-3 weeks later, the LK population in the bone marrow cells of these mice were sorted out; (2) Mx1-CreCbfb+/56M (Mx1CreKI) and Runx1+/R188QMx1-CreCbfb+/56M (R188QCreKI) mice were injected with pIpC and 83 weeks later, the LK population in the bone marrow cells of these mice were sorted out.

value: Mice AMP cells

value: pIpC


title: TMD8 IRF4 shRNA Rep4

description: Library name: TMD8_IRF4_2_1_S2


title: TMD8 IRF4 shRNA Rep3

description: Library name: TMD8_IRF4_1_3_S15


title: STAMP_89

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

value: FFPE isolated nuclei

value: Single Molecule Imager


title: Mouse motor cortex, Q331K, 15mth, rep2

description: Library name: Q331K_15mth_rep2

value: Motor cortex

value: 15 months


title: 10x-scRNA-seq_R188QCreKI_rep1

description: Library name: 10x-scRNA-seq_R188QCreKI_rep1


title: Mouse motor cortex, Q331K, 15mth, rep1

description: Library name: Q331K_15mth_rep1


title: TMD8 Control 2 ATAC

description: Library name: TMD8_Ctr_2

value: ABC


title: Mouse motor cortex, Q331K, 1pt5mth, rep2

description: Library name: Q331K_1pt5mth_rep2


title: STAMP_88

value: Blood and spiked-in MCF-7 and SK-BR-3 cancer cells

value: STEMCELL Technologies (PBMC), Swarbrick Lab (MCF-7/SK-BR-3, The Garvan Institute)

value: Human Immuno-Oncology Protein Panel:64


title: 10x-scRNA-seq_Mx1CreKI_rep1

description: Library name: 10x-scRNA-seq_Mx1CreKI_rep1


title: Mouse motor cortex, Q331K, 10mth, rep2

description: Library name: Q331K_10mth_rep2

value: 10 months


title: 10x-scRNA-seq_Mx1CreKI_rep2

description: Library name: 10x-scRNA-seq_Mx1CreKI_rep2


title: RNA-seq_R188QCreKI_rep3

description: Library name: RNA-seq_R188QCreKI_rep3


title: Mouse motor cortex, Q331K, 10mth, rep3

description: Library name: Q331K_10mth_rep3


title: STAMP_87

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)


title: TMD8 IRF4 shRNA Rep1

description: Library name: TMD8_IRF4_1_1_S5


title: STAMP_86

type: RNA

source_name: 31568F (snPATHO nucs)

value: Prostate cancer FFPE block

value: Butler lab (South Australian Health and Medical Research Institute)

value: CosMx Human 6K Discovery Panel:6000


title: TMD8 Control Rep6

description: Library name: TMD8_Ctr_2_3_S20

value: cell line

value: ABC lymphoma


title: RNA-seq_R188QCreKI_rep2

description: Library name: RNA-seq_R188QCreKI_rep2

value: Mice AMP cells

value: pIpC


title: Mouse motor cortex, Q331K, 10mth, rep1

description: Library name: Q331K_10mth_rep1

source_name: Motor cortex


title: STAMP_85

source_name: 31944 1N (snPATHO nucs)

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

value: FFPE isolated nuclei

value: Single Molecule Imager


title: RNA-seq_R188QCreKI_rep1

description: Library name: RNA-seq_R188QCreKI_rep1


title: D(froR) uninduced rep3 (SK11)

city: Irvine

first: Albert

last: Siryaporn

address: 4129 Reines Hall

institute: University of California Irvine

description: Library name: Sample21

data_processing:
Adapters were trimmed in Trimmomatic version 0.39
Reads were aligned using aligner Bowtie2 version 2.5.4
Processed count table was generated using FeatureCounts in Subread version 2.0.8
Assembly: NC_008463.1
Supplementary files format and content: raw counts and normalized counts of transcript on CDS (coding sequence) and sRNA (non coding region)

organism: Pseudomonas aeruginosa

source_name: bacterial culture

growth_protocol: 18 hours in a roller drum spinning at 200 rpm at 37 °C MinA minimal medium, which contains per 1 L of water: 4.5 g KH2PO4, 10.5 g K2HPO4, 1 g (NH4)2SO4, 1 mM MgSO4 and 0.2 % (w/v) sodium citrate

extract_protocol:
RNA was harvested using Macherey-Nagel NucleoSpin RNA purification kit.
Library construction was performed by UCI Genomics High-Throughput Facility (GHTF) using Nextera DNA library prep kit.

treatment_protocol: 1:1000 dilution of the overnight culture, 2.5 hour outgrowth, and stimulated with NaOCl, H2O2, or untreated for 0.5 hour.

value: bacterial culture

value: D(froR)


title: STAMP_84

source_name: MD3 HDF

value: induced Pluripotent Stem Cells

value: Polo Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)

value: Fixed cells

value: r1, r2:Replicate slide 2/2


title: D(froR) uninduced rep2 (SK10)

description: Library name: Sample20


title: TMD8 Control Rep4

description: Library name: TMD8_Ctr_2_1_S7

source_name: cell line


title: RNA-seq_Mx1CreKI_rep3

description: Library name: RNA-seq_Mx1CreKI_rep3


title: RNA-seq_Mx1CreKI_rep2

description: Library name: RNA-seq_Mx1CreKI_rep2


title: D(froR) 4 uM H2O2 rep3 (SK9)

description: Library name: Sample19


title: TMD8 IRF4 shRNA Rep2

description: Library name: TMD8_IRF4_1_2_S14


title: STAMP_83

source_name: MD3 iTSC


title: TMD8 Control Rep3

description: Library name: TMD8_Ctr_1_3_S10


title: STAMP_82

source_name: MD3 iPSC


title: TMD8 Control Rep2

description: Library name: TMD8_Ctr_1_2_S21


title: RNA-seq_Mx1CreKI_rep1

description: Library name: RNA-seq_Mx1CreKI_rep1


title: STAMP_80

value: Human neuroblastoma cell line

value: Goodall Lab (University of South Australia)


title: D(froR) 1 uM NaOCl rep3 (SK7)

description: Library name: Sample17

value: NaOCl


title: RNA-seq_Cbfb-MYH11-KI_rep3

description: Library name: RNA-seq_Cbfb-MYH11-KI_rep3

source_name: Mice LSK cells

value: Mice LSK cells


title: STAMP_81

source_name: KELLY

value: CosMx Human 6K Discovery Panel:6000


title: RNA-seq_Cbfb-MYH11-KI_rep2

description: Library name: RNA-seq_Cbfb-MYH11-KI_rep2


title: TMD8 Control Rep1

description: Library name: TMD8_Ctr_1_1_S6

value: cell line

value: ABC lymphoma


title: STAMP_79

source_name: SK-N-SH


title: D(froR) 1 uM NaOCl rep2 (SK6)

description: Library name: Sample16


title: WT8H

city: Barcelona

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

country: Spain

institute: Sequientia Biotech

data_processing:
RNA-seq read quality control (QC) analyses and filtering of high-quality reads were executed using FastQC and BBDuk (Bushnell et al. 2017) by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were aligned to the mouse genome reference (GrCm38p6/mm10) with STAR 2.7.3a (Dobin et al. 2012), while FeatureCounts 1.6.3 package (Liao et al. 2014) was used to assign reads to genes.
Genes with low, constant levels of raw counts across one or more experimental conditions were filtered out using HTSFilter 1.30.1 (Rau et al. 2013). Filtered gene data was further processed with the EdgeR package (Robinson et al. 2009) to normalize the raw counts.
Assembly: GRCz11
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with fpkm normalized gene counts for every gene and every sample

organism: Danio rerio

source_name: Intestine

extract_protocol:
Trizol
TruSeq Stranded mRNA LT Sample Prep Kit was used. The Poly-A containing mRNA molecules are purified using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was done using DNA Polymerase I and RNase H, followed by 5' and 3' adapter ligation. Adapter-ligated fragments were then PCR amplified and gel purified.

value: Intestine

value: Tubingen


title: TMD8 Control Rep5

description: Library name: TMD8_Ctr_2_2_S16


title: RNA-seq_Cbfb-MYH11-KI_rep1

description: Library name: RNA-seq_Cbfb-MYH11-KI_rep1

value: pIpC


title: STAMP_78

source_name: SK-N-DZ

value: Dr. Jason Gummow (Functional Genomics South Australia and Gene Silencing and Expression Laboratory, The University of Adelaide)

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

value: Single Molecule Imager


title: RNA-seq_Cbfb-MYH11-dHABD_rep3

description: Library name: RNA-seq_Cbfb-MYH11-dHABD_rep3


title: AL143 1 uM NaOCl rep4 (SK3)

description: Library name: Sample13

value: bacterial culture

value: WT


title: STAMP_77

value: Derivative of the human embryonic kidney 293 (HEK293) cell line, modified to express the SV40 large T antigen

value: Fixed cells


title: WT6H


title: WT7H


title: RNA-seq_Cbfb-MYH11-dHABD_rep2

description: Library name: RNA-seq_Cbfb-MYH11-dHABD_rep2


title: AL143 4 uM H2O2 rep4 (SK4)

description: Library name: Sample14


title: STAMP_76

value: Human neuroblastoma cell line

value: Butler, Swarbrick Lab, Goodall Labs (South Australian Health and Medical Research Institute, The Garvan Institute, University of South Australia)

value: r1, r2:Replicate slide 2/2


title: RNA-seq_Cbfb-MYH11-dHABD_rep1

description: Library name: RNA-seq_Cbfb-MYH11-dHABD_rep1

value: Mice LSK cells


title: D(froR) 4 uM H2O2 rep2 (SK8)

description: Library name: Sample18

value: D(froR)


title: WT4M


title: STAMP_75

value: Castration-resistant prostate cancer cell line derived from LNCaP cells

value: Goodall Lab (University of South Australia)

value: CosMx Human 6K Discovery Panel:6000


title: AL143 1 uM NaOCl rep3 (SK2)

description: Library name: Sample12

value: NaOCl


title: WT3M

value: Intestine

value: Tubingen


title: AL143 uninduced rep3 (SK1)

description: Library name: Sample11


title: RNA-seq_Cbfb-MYH11-mDE_rep3

description: Library name: RNA-seq_Cbfb-MYH11-mDE_rep3

value: pIpC


title: D(froR) uninduced rep1 (AS10)

description: Library name: Sample10


title: RNA-seq_Cbfb-MYH11-mDE_rep2

description: Library name: RNA-seq_Cbfb-MYH11-mDE_rep2


title: AL143 4 uM H2O2 rep5 (SK5)

description: Library name: Sample15


title: WT2M


title: STAMP_74

source_name: Oral cancer cell line (UM-SCC-1)

value: Human squamous cell carcinoma cell line

value: Dr. Marina Kochetkova (University of South Australia)

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

value: Single Molecule Imager