title: T2WT_from_dot-13Tg_K79me2-vs-H3_rep2

description: Library name: T2WT_from_dot-13Tg_K79me2-vs-H3_rep2

extract_protocol:
Age synchronized worms at day-1 adulthood were used for sample preparation. Samples were fixed in 1% formaldehyde/PBS solution for 10 min. Crosslinking was quenched by adding glycine solution to a final concentration of 125 mM. Chromatin was fragmented by sonication at 4 °C. The ChIP-seq formulated antibodies were anti-histone H3 (CST #4620), H3K79me2 (CST #5427).
Sequencing libraries were constructed by NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads kit (NEB) according to manufacturer’s instructions. Liberaries were pooled together and sequenced on the Illumina NextSeq 2000 system.

treatment_protocol: The lipl-4 Tg and dot-1.3 Tg hermaphrodites were crossed with wild-type (WT) N2 males to generate F1 heterozygotes. These F1 heterozygotes were then self-crossed to yield F2 WT progeny. F3 WT descendants, designated as second transgenerational WT (T2 WT), were reproduced from F2 WT hermaphrodites via self-crossing and sampled for ChIP-seq analysis at day-1 adulthood. In parallel, WT N2 hermaphrodites were crossed with WT N2 males and F3 WT progeny were used as controls.

value: whole hermaphrodite_day-1 adult

value: wild type


title: CERT_ingAT_Ucp1ERCre_H3K4me1_1

status: Public on Jun 30 2025

type: SRA

city: Schwerzenbach

first: Laura

middle: Catharina

last: Hinte

address: Schorenstrasse 16

country: Switzerland

institute: ETH Zurich

library_source: genomic

data_processing:
*library strategy: Cut&Tag
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: Inguinal Adipose Tissue

extract_protocol:
Nuclei were isolated from snap frozen adipose tissue depots in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 10 mM sodium butyrate and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). All centrifugation steps were carried out in a to 4˚C cooled swinging bucket centrifuge with settings at 500 xg for 5 minutes. Nuclei were subsequently filtered through a 50µm cell strainer (Sysmex, #04-0042-2317) and washed two times in PBS-BSA (1% w/v) containing protease inhibitor and sodium butyrate. Nuclei were centrifuged and subsequently bound to pre-blocked Dynabeads MyOne Streptavidin C1 beads (ThermoFisher, #65002) for 30 minutes at 4˚C followed by 3 washes with PBS-BSA (1% w/v) on a magnetic stand. CUT&Tag was performed as previously described with minor adjustments36,37. All buffers were supplemented with 1 x cOmplete EDTA-free Protease inhibitor and 10mM sodium butyrate. Briefly, nuclei bound to beads were aliquoted into 96-well LoBind plates (Eppendorf, #0030129547) and incubated with primary antibodies – anti-H3K4me3 (abcam, #ab8580), anti-H3K27me3 (Cell Signaling Technology, #C36B11), anti-H3K27ac (abcam, #ab4729), anti-H3K4me1 (abcam, #ab8895), anti-H3K9me3 (abcam, #ab8898) – overnight at 4˚C. All antibodies were diluted 1:100. With the plate on a magnet the primary antibody solution was removed, the beads were resuspended in secondary antibody solution (guinea pig anti-rabbit IgG (antibodies-online gmbh, #ABIN101961); 1:200 dilution) and incubated at room temperature for 30 minutes while rocking. pA-Tn5 was bound to antibodies, transposition performed at 37 ˚C and stopped using TAPS-Wash solution. Nuclei were lysed and pA-Tn5 decrosslinked using SDS-release solution.
PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, X cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C. After 5 cycles the PCR was put on hold at 4˚C and 10% of the reaction was transferred into a 384 well plate and mixed with KAPA SYBR 2x (qPCR) and primers and qPCR was run for 20 cycles to determine the number of PCR cycles to be added38. Libraries were cleaned using SPRI beads using a 1.3 ratio, eluted in nuclease free water and pooled equimolecularily after library quantification using the KAPA library quantification kit (Roche Diagnostics, #079602).

treatment_protocol: control

tag: tissue

value: Inguinal Adipose Tissue

tag: cell type

value: Beige Adipocytes

tag: strain

value: Ucp1ERCre x NuTRAP on C57BL6 background

tag: histone

tag: replicate

value: biol rep 1

tag: treatment

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: Young D60, HTO

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: 10x Genomics

library_source: transcriptomic

data_processing:
Alignment of reads from the single cell RNA-seq library and unique molecular identifiers (UMIs) counting were performed with 10X Genomics Cell Ranger tool (v3.0.2).
Reads of oligonucleotides tags (HTOs) used for Cell Hashing were counted with CITE-seq-Count (v1.4.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: total RNA

source_name: Whole lung

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
After euthanasia, lung tissue was perfused with sterile saline through the heart and were inflated through the trachea with dissociation cocktail containing dispase (50 caseinolytic U/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 μg/ml). Lung were immediately removed, minced to small pieces ~1mm3), and transferred for mild enzymatic digestion for 20–30 min at 37 °C in 4 mL of the dissociation cocktail. Enzymatic activity was inhibited by adding 5 mL of PBS supplemented with 10% fetal calf serum (FCS). Single cells suspension were passed through a 40 micron mesh, and then harvest by centrifugation at 300 g for 5 min (4°C). Reb blood cell lysis was performed using RBC lysis buffer (Thermo fisher) for 2 minutes at 4°C and stopped using PBS 10% FCS. After another centrifugation at 300g for 5 min (4°C) cells were counted and critically assessed for single cell separation and overall cell viability using the Countess 3 FL(Fisher Scientific). Samples were then stained for multiplexing using cell hashing, using the Cell Hashing Total-Seq-ATM protocol (Biolegend) following the protocol provided by the supplier, using 6 distinct Hash Tag Oligonucleotides-conjugated mAbs (3 PBS and 3 Bleo). Samples were then adjusted to the same concentration and mixed in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/μl. Single-cell capture was performed using the 10X Genomics Chromium device (3′ V3). Single-cell libraries were sequenced on the Illumina NextSeq 500.

treatment_protocol: Seven-week (“young”) and 18-month (“old”)-old C57BL/6 male mice (Charles River) were divided randomly into two groups: (A) saline-only (PBS, n=3), or (B) bleomycin (Bleo, n=3). To induce fibrotic changes, 50-µl bleomycin (1 U/kg) or PBS was aerosolized in mouse lungs using a MicroSprayer Aerosolizer (Penn-Century, Inc.). Mice were sacrificed at designated time points (days 14, 28 and 60) after instillation.

value: All

value: Whole lung

tag: Stage

value: Young

tag: age

value: 7 weeks old

value: Bleomycin or PBS

tag: time


title: aging_study_Age_61_Surv_43_Rep2

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

description: Library name: aging_study_Age_61_Surv_43_Rep2

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing. Post deplexing, FASTQ files were quality inspected using the FastQC tool (available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the MultiQC tool (Ewels et al., 2016). For reference mapping (BDGP6), the nf-core RNA-Seq Seq pipeline was used (version 3.10.1; available at https://nf-co.re/rnaseq) in conjunction with select parameters (--outFilterMultimapNmax 500, --winAnchorMultimapNmax 500, --clip_r1 10, --clip_r2 10). To enumerate counts for known genes, the featureCounts tool was used (Liao et al., 2014). To enumerate counts for transposable elements (TEs), the TEcount tool was used (Jin et al., 2015). Enumerated counts across known genes and TEs were then row concatted by sample and saved as tab-delimited text files.
Assembly: BDGP6
Supplementary files format and content: Tab-delimited text files describing expression in counts for known genes and TEs.

organism: Drosophila melanogaster

source_name: Whole Fly

growth_protocol: All experiments were performed on wild type adult male Drosophila melanogaster (Oregon R; y+ w+). Flies were maintained on Nutri-Fly Bloomington formulation food (Genesee Scientific, Raleigh/Durham NC) at 25°C and 50% humidity on a 12:12 hour light:dark cycle. For aging of flies, males and females were collected within 24 hours of eclosion by anesthetization with CO2 and transferred to fresh vials. After three days, males and females were separated on a CO2 pad and males only were placed into fresh vials, with 20 flies per vial. Any flies that died before separation of males and females were not included in either the aging or supine study. Aging male flies were flipped to fresh vials twice weekly, each time counting the number of dead and censored flies, until the population mortality reached ~20%. A fly was censored if it escaped, if it was stuck to the vial, if it was stuck to the food but still moving, or if it was removed for downstream analyses.   For the aging study, 3 flies (each from a separate vial) were gently removed each day without anaesthesia, using a mouth pipette once the population mortality reached ~20% (~day 50). Removed flies were frozen immediately in liquid nitrogen and stored at -80C for later RNA isolation. Daily removal of flies continued until the population mortality reached ~80 – 85 % (~day 70). After that, remaining flies were allowed to age until the entire population was dead. Additionally, when the population mortality reached ~50%, an additional 20 flies were collected, frozen in liquid nitrogen, and stored at -80C for later RNA isolation. The % mortality associated with the chronological age of each fly on its day of collection was interpolated from the survival curve of the entire population.  For the supine study, flies were checked three times daily for supine behavior once the population mortality reached ~20%. Supine behavior was defined as a fly remaining on its back for more than 10 seconds but still moving. Supine flies were gently removed from the vial using a mouth pipette. Half of these flies were immediately frozen in liquid nitrogen and stored at -80C for later RNA isolation. The other half of these flies were gently placed into a fresh vial for continued observation every few hours during the day, until they died. Note that there was a period of ~14 hours each night where no observations were made. Removal of supine flies continued daily until the population mortality reached ~80%, after which the remaining flies in the population were allowed to age until the entire population was dead. The % mortality associated with the chronological age of each fly on its day of collection was interpolated from the survival curve of the entire population.

extract_protocol:
Individual flies were homogenized in Lysis Binding Mix (from MagMAX mirVana Total RNA Isolation Kit; Thermo Fisher Scientific, Washington, DC; #A27828) using Navy Eppendorf RNA Lysis Kits (Next Advance, Troy, NY; #NAVYE5-RNA) and a Bullet Blender Storm 24 (Next Advance, Troy, NY; #4116-BBY24M). RNA was then isolated from these homogenates using the MagMAX mirVana Total RNA Isolation Kit as described in the manufacturer’s instructions, in conjunction with the KingFisher Apex Purification System with 96 Deep-Well head (Thermo Fisher Scientific, Washington, DC; #5400930).
RNA quality and quantity was first assessed by NanoDrop (Thermo Fisher Scientific, Washington, DC) and High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA). cDNA libraries were generated from 500 ng of total RNAusing NEBNext Ultra II Directional Poly-A RNA Library Prep Kit for Illumina (New EnglandBiolabs, Ipswich, MA; #E7760). cDNA library quality and quantity were assessed byTapeStation 2200 and Qubit (Thermo Fisher Scientific, Washington, DC). cDNA librarieswere sequenced on a NextSeq 2000 machine using NextSeq 2000 P3 reagents (Illumina,San Diego, CA).

value: Whole Fly

value: Oregon R; y+ w+

tag: study

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

tag: Sex

value: Male

tag: supine death_phenotype


title: TN_ingAT_AdipoCre_H3K4me1_4

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: biol rep 4

value: 9 week old at death, born and kept at 30 degrees during whole life


title: TN_ingAT_AdipoCre_H3K4me1_2

value: Inguinal Adipose Tissue

value: biol rep 2


title: T2WT_from_lipl-4Tg_K79me2-vs-H3_rep1

city: Houston

first: Qinghao

last: Zhang

email: qinghaoz@bcm.edu, qhzhang87@gmail.com

state: Texas

address: BCM N820, One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

description: Library name: T2WT_from_lipl-4Tg_K79me2-vs-H3_rep1

data_processing:
Illumina NextSeq 2000 system was used for base-calling.
Raw reads of ChIP-seq were filtered using Trim Galore (version 0.4.5).
Reads were aligned to the C. elegans reference genome by Bowtie2 (version 2.1.0).
Samtools (version 1.7) was used to converse sequence alignment/map (sam) format to binary alignment/map (bam).
MACS2 algorithm (version 2.1.0) was used to call peaks for H3K79me2 or histone H3 by arguments "-t -c --broad -g --broad-cutoff 0.1 -B --keep-dup auto --nomodel --extsize", where histone H3 ChIP-seq reads from the same sample were employed as controls to normalize the data and offset differences in nucleosome occupancy.
Assembly: Ce11
Supplementary files format and content: bigWig, broadpeak.

organism: Caenorhabditis elegans

source_name: whole hermaphrodite_day-1 adult

growth_protocol: Worms were grown on standard nematode growth medium (NGM) agar plates seeded with a pre-cultured common laboratory bacterial strain E. coli OP50 (straptomycin-resistant) at 20 °C

value: whole hermaphrodite_day-1 adult

tag: genotype

value: wild type


title: T2WT_from_lipl-4Tg_K79me2-vs-H3_rep2

description: Library name: T2WT_from_lipl-4Tg_K79me2-vs-H3_rep2


title: aging_study_Age_60_Surv_47_Rep1

description: Library name: aging_study_Age_60_Surv_47_Rep1


title: CERT_ingAT_Ucp1ERCre_H3K27ac_1

value: Beige Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 1

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: Old D28, HTO

description: 10x Genomics

value: All

value: Whole lung

value: Old

value: 18 months old

value: Bleomycin or PBS


title: Young D60, scRNAseq

description: 10x Genomics

value: Young

value: 7 weeks old


title: aging_study_Age_60_Surv_47_Rep2

description: Library name: aging_study_Age_60_Surv_47_Rep2

value: Whole Fly

value: Oregon R; y+ w+

value: aging

value: Male


title: aging_study_Age_59_Surv_51_Rep14

description: Library name: aging_study_Age_59_Surv_51_Rep14


title: TN_ingAT_AdipoCre_H3K27ac_4

value: Inguinal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: biol rep 4

value: 9 week old at death, born and kept at 30 degrees during whole life


title: T2WT_from_N2_K79me2-vs-H3_rep1

description: Library name: T2WT_from_N2_K79me2-vs-H3_rep1

value: whole hermaphrodite_day-1 adult

value: wild type


title: T2WT_from_N2_K79me2-vs-H3_rep2

description: Library name: T2WT_from_N2_K79me2-vs-H3_rep2


title: T2WT_from_dot-13Tg_K79me2-vs-H3_rep1

description: Library name: T2WT_from_dot-13Tg_K79me2-vs-H3_rep1


title: Young D28, HTO

description: 10x Genomics

value: All

value: Whole lung


title: aging_study_Age_61_Surv_43_Rep3

description: Library name: aging_study_Age_61_Surv_43_Rep3


title: TN_ingAT_AdipoCre_H3K27ac_2

value: biol rep 2


title: Young D28, scRNAseq

description: 10x Genomics

value: Bleomycin or PBS


title: CERT_ingAT_Ucp1ERCre_H3K27me3_1

value: Beige Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 1

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: aging_study_Age_59_Surv_51_Rep12

description: Library name: aging_study_Age_59_Surv_51_Rep12

value: Whole Fly

value: Oregon R; y+ w+

value: aging


title: TN_ingAT_AdipoCre_H3K27me3_4

value: Inguinal Adipose Tissue

value: Adipocytes


title: Mycn-nGEMM-low tumor and CD45 cells, biol rep 1

city: San Francisco

first: Hiroyuki

last: Yoda

state: CA

address: 1450 3rd street

institute: UCSF

description:
Library name: Sample 1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data from a single tumor sample was aligned to the GRCm39-2024-A mouse reference genome using Cell Ranger (v8.0.0). The resulting output was processed using Seurat (v5).
Assembly: Mouse mm39
Supplementary files format and content: values files and matrix files

source_name: Tumor

extract_protocol:
Mycn-nGEMM tumors were harvested and were dissociated into single cells. Tumor cells were digested with collagenase I, collagenase IV and deoxyribonuclease I at 37C under agitation for 30min. Cell suspensions were strained through a 70um mesh cell strainer and washed with PBS. ACK lysing buffer were added to lyse erythrocytes for 5min at room temperature. Reactions were quenched with PBS. Cells were stained by LIVE/DEAD cell stain kit for 30min and by anti-mouse CD45 antibody for 30min. Finally, live tumor and CD45+ cells were isolated by FACS for scRNA-seq.
Library was performed according to the manufacter's instructions (single cell 3' Gene Expression v3.1 protocol, 10X Genomics) by MedGenome.

value: Tumor


title: Old D14, HTO

description: 10x Genomics

value: Old

value: 18 months old


title: aging_study_Age_59_Surv_51_Rep9

description: Library name: aging_study_Age_59_Surv_51_Rep9

value: Male


title: Old D14, scRNAseq

description: 10x Genomics

value: All


title: KRT20-cKO, IR, 24h-3

city: Changsha

first: Lijun

last: Yin

address: No. 139 Renmin Middle Road

country: China

institute: The Second Xiangya Hospital of Central South University

data_processing:
Illumina Casava2.19 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low complexity or low quality sequence, then mapped to mm8 whole genome using Hisat2 v2.2.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapne 11
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: kideny

extract_protocol:
Retinas were removed,flash frozen on dry ice, and RNA was hanvested using Trizol reagent lumina TruSeg RNA Sample Prep Kit (Cat#FC-122-10)
RNA libraries were prepared for sequencing using standard lllumina protocols

treatment_protocol: Ischemia/reperfusion-induced AKI (IR-AKI) mouse model was established with routine protocols. Briefly, male mice (8-12 weeks old) were injected intraperitoneally with pentobarbital (50 mg/kg) for anesthesia, and their body temperature was maintained at 36.5±0.3°C with a Homeothermic Blanket Control Unit (Harvard Apparatus Ltd, U.K.). Bilateral renal pedicles were exposed through flank incisions and clamped for 30 minutes to induce ischemia. The clamps were removed to restore renal blood supply, and the mice were sacrificed 24 hours after reperfusion. The mice in sham group underwent the similar procedures without clamping the renal pedicles.

value: kideny

value: Krt20 cKO


title: aging_study_Age_59_Surv_51_Rep13

description: Library name: aging_study_Age_59_Surv_51_Rep13


title: Mycn-nGEMM-low tumor and CD45 cells, biol rep 3

description:
Library name: Sample 3
10X Genomics


title: Old D28, scRNAseq

description: 10x Genomics

value: Whole lung

value: Bleomycin or PBS


title: Wnt1Cre - TdTomato

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing was performed on Illumina NovaSeq 6000.
Data analysis was performed using Cellranger and Seurat.
Assembly: mm10
Supplementary files format and content: Expression matrices

source_name: Aortic Arch from the aortic root to just pass the left subclavian artery from 1 Male/1 Female Mice

extract_protocol:
30 minutes following SQ injection of 400 i.u of heparin 4 male and 4 female C57BL/6J mice were sacrificed and perfused with 10mL of Versene. Following perfusion, the carotid arteries and the aorta (from the aortic root to the iliac bifurcation) were harvested from the mouse and further dissected under a microscope to remove the adventitial layer. Subsequently the three vascular fragments: carotid arteries (right and left common not their branches), aortic arch (from the root to the subclavian branch), the thoracic aorta (below the subclavian up to the infra-renal branches, but excluding all branches) and the abdominal aorta (from the infra-renal branches to iliac birfucation, excluding all branches) were obtained, minced into small fragments and incubated under agitation into 500μL digestion buffer containing freshly prepared liberase solution (2.5% Liberase TH from frozen stock [Sigma Aldrich], 5 Kunitz Unit/mL DNase1, 1M HEPES IN 1X HBSS). All preparations were done at temperature except for the digestion, which was done at 37oC for approximately 20min. The suspension was neutralized with DMEM + 10%FBS and ran through a 40uM filter and then centrifuged for 5 min at 10,000 x g. Following centrifugation, the cell pellet was resuspended in in 0.4% BSA-PBS and assessed for viability prior to library preparation using trypan blue staining with the TC20 cell counter (BioRad). Only samples with more than 85% viability were used in the generation of libraries.
Libraries were prepared using 10X Genomics Chromium™ Single Cell 3' Library & Gel Bead Kit v3, as per manufacturer’s protocol. For the generation of single-cell gel beads in emulsion, cells were loaded on a Chromium single cell instrument (10x Genomics) with an estimated targeted cell recovery of ~5,000 to 10,000 cells, per library.

value: Male/Female

tag: animal number

value: Wnt1Cre(+)/Rtom(fl/fl) - F, Wnt1Cre(+)Rtom(fl/wt) - M

value: 16 weeks


title: Young D14, scRNAseq

description: 10x Genomics

tag: tissue

value: Young

value: 7 weeks old


title: Wnt1 Control

source_name: Aortic Arch from the aortic root to just pass the left subclavian artery from 1 male Mice


title: KRT20-cKO, IR, 24h-1


title: aging_study_Age_59_Surv_51_Rep6

description: Library name: aging_study_Age_59_Surv_51_Rep6

value: Whole Fly

value: Oregon R; y+ w+

value: aging


title: KRT20-cKO, sham-3

value: sham


title: Mef2cCre - EGFP

source_name: Aortic Arch from the aortic root to just pass the left subclavian artery from 3 male Mice


title: Mef2c - Control

value: Aortic Arch from the aortic root to just pass the left subclavian artery from 3 male Mice


title: aging_study_Age_59_Surv_51_Rep5

description: Library name: aging_study_Age_59_Surv_51_Rep5


title: aging_study_Age_59_Surv_51_Rep11

description: Library name: aging_study_Age_59_Surv_51_Rep11


title: Descending-Male

source_name: Thoracic Aorta from left subclavian artery to diaphram from 4 Male mice

value: 12 weeks


title: aging_study_Age_59_Surv_51_Rep4

description: Library name: aging_study_Age_59_Surv_51_Rep4

value: Male


title: Mycn-nGEMM-low tumor and CD45 cells, biol rep 2

description:
Library name: Sample 2
10X Genomics

value: Tumor


title: SRAKO2365

city: Nanjing

first: Wen

address: No. 101 Longmian Avenue, Jiangning District, Nanjing, China

institute: Nanjing Medical University

description: Library name: SAMPLE4

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text file includes  FPKM values for each Sample

source_name: heart

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: heart


title: SRAKO2371

description: Library name: SAMPLE5


title: SRAKO2372

description: Library name: SAMPLE6


title: KRT20-cKO, sham-1

value: kideny

value: Krt20 cKO


title: KRT20-cKO, sham-2


title: aging_study_Age_59_Surv_51_Rep8

description: Library name: aging_study_Age_59_Surv_51_Rep8


title: KRT20-cKO, IR, 24h-2


title: aging_study_Age_59_Surv_51_Rep7

description: Library name: aging_study_Age_59_Surv_51_Rep7


title: WT2378

description: Library name: SAMPLE3


title: aging_study_Age_59_Surv_51_Rep3

description: Library name: aging_study_Age_59_Surv_51_Rep3


title: E18.5,RNAseq,Aortic smooth muscle,WT3

city: Shanghai

first: Chunxiao

last: Wang

address: Siping road

institute: Tongji university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and nepalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Aortic smooth muscle

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: Aortic smooth muscle

value: WT


title: Descending-Female

source_name: Thoracic Aorta from left subclavian artery to diaphram from 4 Female Mice

value: Female


title: aging_study_Age_59_Surv_51_Rep2

description: Library name: aging_study_Age_59_Surv_51_Rep2


title: WT2379

description: Library name: SAMPLE2


title: WT, IR,24h-3


title: Carotids-Male

source_name: Left and Right Carotid Arteries from 4 Male Mice


title: WT, IR,24h-2


title: WT2368

description: Library name: SAMPLE1


title: aging_study_Age_59_Surv_51_Rep1

description: Library name: aging_study_Age_59_Surv_51_Rep1


title: Carotids-Female

source_name: Left and Right Carotid Arteries from 4 Female Mice


title: WT, IR,24h-1


title: aging_study_Age_58_Surv_55_Rep12

description: Library name: aging_study_Age_58_Surv_55_Rep12


title: WT, sham-3


title: 22-RNA-W1

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
FastQC used for triming reads. It can binning reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
DEseq2 used to analyze the difference expression of mRNA
Supplementary files format and content: tab-delimited text files include the number of reads relative RPKM values, and P-values for control and experimental group Sample.

source_name: Female germ line stem cells

growth_protocol: FGSCs were cultured in Minimum Essential Medium-alpha (MEM-alpha; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 1mM non-essential amino acids (Invitrogen Life Sciences,CA, USA), 1mMsodium pyruvate (Amresco), 0.1mg/mL penicillin (Amresco, Lardner, PA, USA), 2mM L-glutamine (Amresco), 100μM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA), 10ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 10ng/mL mouse glial cell line-derived neurotrophic factor (R&D Systems, Minneapolis, MN, USA), 10ng/mL mouse basic fibroblast growth factor (BD Biosciences, Franklin Lakes, NJ, USA), and 20ng/mL mouse epidermal growth factor (PeproTech, NJ, USA).

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbard, CA, USA). RNA quantity and quality were determined with 2100 Bioanalyzer (Agilent Technologies).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: ovary

value: FGSCs

tag: developmental stage

value: Female mice


title: Arch-Root-Male

source_name: Aortic Arch from the aortic root to just pass the left subclavian artery from 4 Male Mice


title: aging_study_Age_58_Surv_55_Rep11

description: Library name: aging_study_Age_58_Surv_55_Rep11

value: Whole Fly

tag: strain


title: 21-RNA-W1


title: Arch-Root-Female

source_name: Aortic Arch from the aortic root to just pass the left subclavian artery from 4 Female Mice


title: WT, sham-2


title: 02-RNA-W1


title: aging_study_Age_58_Surv_55_Rep10

description: Library name: aging_study_Age_58_Surv_55_Rep10

value: Oregon R; y+ w+


title: 01-RNA-W1


title: aging_study_Age_58_Surv_55_Rep9

description: Library name: aging_study_Age_58_Surv_55_Rep9

value: aging


title: WT, sham-1

value: sham


title: STAMP_113

type: RNA

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.

source_name: Isolated brain/heart/kidney/liver/ling mixed nuclei

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

tag: sample source

value: Robertson Lab (The University of Adelaide)

tag: sample processed

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

tag: sample type

value: Fixed nuclei

tag: technology

value: Xenium

tag: panel size

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001

tag: panel size custom


title: STAMP_112

source_name: Isolated lung nuclei

value: Lung nuclei

tag: replicate


title: aging_study_Age_58_Surv_55_Rep8

description: Library name: aging_study_Age_58_Surv_55_Rep8

source_name: Whole Fly

tag: study

tag: replicate sample

tag: chronological age_(days)

value: Male


title: Heart, Trem1 KO Recruited

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 425 S Euclid Ave

department: Department of Surgery

institute: Washington University School of Medicine

data_processing:
Alignment: Cell Ranger V3, aligned to mm10 transcriptome
QC and Filtering: Seurat V4
Unsupervised Clustering: Seurat V4
Assembly: mm10
Supplementary files format and content: Clustered and annotated data in R objects (.rds)

source_name: Heart

extract_protocol:
Transplanted hearts were collected, perfused, and enzymatically digested to a single cell supsension. Monocytes and macrophages were sorted via FACS.
Chromium Single Cell 3′ Library & Gel Bead Kit from 10X Genomics

tag: group

value: Recruited

value: Heart

value: Trem1 KO

tag: treatment

value: syngeneic heart transplant


title: Heart, Trem1 KO Donor

value: Donor

tag: genotype


title: aging_study_Age_58_Surv_55_Rep7

description: Library name: aging_study_Age_58_Surv_55_Rep7

tag: tissue

tag: percent population_survival

tag: Sex

tag: supine death_phenotype


title: STAMP_111

source_name: Isolated liver nuclei

tag: tissue type

value: Liver nuclei

tag: sample source


title: Heart, Control Recruited

value: Trem1 WT


title: aging_study_Age_58_Surv_55_Rep6

description: Library name: aging_study_Age_58_Surv_55_Rep6

value: Whole Fly

tag: strain

value: Oregon R; y+ w+


title: STAMP_110

source_name: Isolated kidney nuclei

value: Kidney nuclei

tag: sample processed

tag: sample type

tag: technology


title: Colon resident CD8+ T cells, ART, Rep8

city: CAMBRIDGE

first: Qiming

state: MA

address: 88 Ames Street

institute: Koch institute

description: Library name: ART8

data_processing:
The reads were used to quantify transcripts from the mm9 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 and gene level summaries were prepared using tximport version 1.16.1
Assembly: mm9
Supplementary files format and content: Tab-delimited csv file includes raw counts for each sample

organism: Homo sapiens

source_name: Colon

extract_protocol:
RNA was extracted from organoids using TRIzol and Ambion PureLink RNA Mini Kit (Thermo Fisher Scientific, 12-183-018 A) according to the manufacturer’s instructions.
For RNA-seq library preparation, NEBNext Ultra II Directional RNA preparation with poly(A) selection is used to selectively capture mRNA from total RNA and barcoded libraries were generated. 2 ×40 paired-end sequencing was performed on an Illumina NextSeq 500.

value: Colon

tag: cell type

value: CD8+ T cells

value: ART


title: Colon resident CD8+ T cells, ART, Rep9

description: Library name: ART9


title: Colon resident CD8+ T cells, ART, Rep10

description: Library name: ART10


title: aging_study_Age_58_Surv_55_Rep5

description: Library name: aging_study_Age_58_Surv_55_Rep5

tag: study

value: aging


title: Heart, Control Donor


title: STAMP_109

source_name: Isolated heart nuclei

value: Heart nuclei

value: Robertson Lab (The University of Adelaide)

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

value: Fixed nuclei

tag: replicate

value: Xenium

tag: panel size

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001

tag: panel size custom


title: Colon resident CD8+ T cells, ART, Rep7

description: Library name: ART7


title: Abdominal-Male

source_name: Abdominal Aorta from 4 Male Mice

value: Abdominal Aorta from 4 Male Mice

value: Male

tag: animal number

tag: age

value: 12 weeks


title: Colon resident CD8+ T cells, ART, Rep6

description: Library name: ART6

tag: tissue

tag: genotype


title: aging_study_Age_58_Surv_55_Rep2

description: Library name: aging_study_Age_58_Surv_55_Rep2

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

tag: Sex


title: 21dpi_cKO

first: Nathan

middle: A

last: Ewing-Crystal

address: 513 Parnassus Ave, HSW12 Room 1201A

department: Laboratory Medicine

institute: University of California, San Francisco

description: 10x Genomics snRNASeq

data_processing:
Sequencing data were aligned to mouse genome mm10 with CellRanger version 7.1.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.tsv.gz: gene expression count data in Matrix Market Exchange Format

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Immediately following euthanasia, mice were transcardially perfused (10mL DPBS), and skullcaps with lesions were removed and placed in iMED+ (15mM HEPES and 0.6% glucose in HBSS with phenol red). Lesions were dissected; tissue from male and female mice within experimental conditions were combined. Tissue was minced for 10 minutes in 100mL of TST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, and 0.01% BSA in nuclease-free water), followed by filtration (40mm), and washing with TST and ST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, and 21 mM MgCl2). Samples were centrifuged (500g 10 minutes), resuspended (PBS/1% BSA/0.2UmL Protector RNAse inhibitor), filtered (35mm), re-centrifuged (500g 5 minutes), and resuspended in FANS buffer with 0.2U/mL RNase inhibitor and 2mg/mL DAPI. Nuclei were subsequently sorted (FSC/SSC/DAPI). All samples were centrifuged (500g 15 minutes) and resuspended to a maximum of 16,500 nuclei in 45uL.
Up to 1.6 x 10^4 nuclei were loaded onto the Chromium Controller (10X Genomics). Chromium Single Cell 3’ v3.1 reagents were used for library preparation according to the manufacturer’s protocol.

value: Brain

tag: microanatomical region

value: PT lesion

tag: condition

value: PT injury

value: Col1a2(creER); Tgfbr2(flox)

tag: treatment

tag: timepoint


title: STAMP_108

source_name: Isolated brain nuclei

tag: tissue type

value: Brain nuclei

tag: sample source

tag: sample processed

tag: sample type

tag: technology


title: aging_study_Age_58_Surv_55_Rep1

description: Library name: aging_study_Age_58_Surv_55_Rep1

value: Whole Fly

tag: strain

value: Oregon R; y+ w+

tag: study

tag: supine death_phenotype


title: Abdominal-Female

source_name: Abdominal Aorta from 4 Female Mice

tag: tissue

value: Abdominal Aorta from 4 Female Mice

value: Female

tag: animal number

tag: genotype

tag: age


title: STAMP_107

source_name: Dissociated brain/heart/kidney/liver/ling mixed cells

value: Robertson Lab (The University of Adelaide)

value: Fixed cells

tag: replicate

tag: panel size

tag: panel size custom


title: aging_study_Age_57_Surv_59_Rep4

description: Library name: aging_study_Age_57_Surv_59_Rep4

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

tag: Sex


title: Colon resident CD8+ T cells, ART, Rep4

description: Library name: ART4

value: Colon

tag: cell type

value: CD8+ T cells

value: ART


title: aging_study_Age_66_Surv_25_Rep1

description: Library name: aging_study_Age_66_Surv_25_Rep1

value: Male


title: Colon resident CD8+ T cells, ART, Rep5

description: Library name: ART5


title: 21dpi_Ctrl

description: 10x Genomics snRNASeq

tag: microanatomical region

tag: condition

value: WT

tag: treatment

tag: timepoint


title: aging_study_Age_57_Surv_59_Rep3

description: Library name: aging_study_Age_57_Surv_59_Rep3

tag: strain

tag: study

tag: supine death_phenotype


title: STAMP_106

source_name: Dissociated lung cells

tag: tissue type

value: Lung cells

tag: sample source

tag: sample processed

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

tag: sample type

tag: technology

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: 21dpi_ADWA11

description: 10x Genomics snRNASeq

tag: tissue

value: Brain

value: PT lesion

value: PT injury

tag: genotype


title: aging_study_Age_57_Surv_59_Rep2

description: Library name: aging_study_Age_57_Surv_59_Rep2

value: Whole Fly

value: Oregon R; y+ w+

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival


title: Colon resident CD8+ T cells, ART, Rep2

description: Library name: ART2

tag: cell type


title: aging_study_Age_57_Surv_59_Rep1

description: Library name: aging_study_Age_57_Surv_59_Rep1

tag: Sex


title: 7dpi_Ctrl

description: 10x Genomics snRNASeq

tag: microanatomical region

tag: condition

tag: treatment


title: 7dpi_ADWA11

description: 10x Genomics snRNASeq

tag: timepoint


title: Colon resident CD8+ T cells, ART, Rep3

description: Library name: ART3


title: STAMP_102

source_name: Dissociated brain cells

value: Brain cells

value: Robertson Lab (The University of Adelaide)

tag: replicate

tag: panel size

tag: panel size custom


title: 21dpi_cKO_CMO

description:
10x Genomics snRNASeq (Cell Multiplexing Oligonucleotides)
processed data are linked to GEX sample

data_processing:
Sequencing data were aligned to mouse genome mm10 with CellRanger version 7.1.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: features.tsv.gz: list of gene IDs (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: matrix.tsv.gz: gene expression count data in Matrix Market Exchange Format (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: feature_reference.csv: Reference table linking barcodes (CMO) with subsamples (microanatomical regions) (provided for each region)

extract_protocol:
Immediately following euthanasia, mice were transcardially perfused (10mL DPBS), and brains were removed and placed in iMED+ (15mM HEPES and 0.6% glucose in HBSS with phenol red). Dura, lesion, and perilesional cortex were dissected and processed separately. Tissue from male and female mice within experimental conditions were combined. Tissue was minced for 10 minutes in 100mL of TST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, and 0.01% BSA in nuclease-free water), followed by filtration (40mm), and washing with TST and ST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, and 21 mM MgCl2). Samples were centrifuged (500g 10 minutes), resuspended (PBS/1% BSA/0.2UmL Protector RNAse inhibitor), filtered (35mm), and counted. A maximum of 2x10^6 nuclei were multiplexed and washed (CellPlex, 10X Genomics), per manufacturer’s instructions.  Immediately before sorting, multiplexed microanatomical regions (lesion, parenchyma, and dural meninges) from individual mice were combined at desired ratios (75% lesion, 25% parenchyma; for resting samples, pooling was not performed until after sorting). Nuclei were subsequently sorted (FSC/SSC/DAPI). Dura was enriched for fibroblasts using Col1a2creER; Rosa26Sun1GFP fluorescence. All samples were centrifuged (500g 15 minutes) and resuspended to a maximum of 16,500 nuclei in 45uL.
Up to 1.6 x 10^4 nuclei were loaded onto the Chromium Controller (10X Genomics). Chromium Single Cell 3’ v3.1 reagents were used for library preparation according to the manufacturer’s protocol.

value: Cortex and PT Lesion

value: Col1a2(creER) or Cdh5(creER); Tgfbr2(flox)


title: Colon resident CD8+ T cells, HIV-Negative, Rep10

description: Library name: NEG10

value: Colon

value: CD8+ T cells

value: HIV-ve


title: Colon resident CD8+ T cells, HIV-Negative, Rep9

description: Library name: NEG9


title: 7dpi_cKO_CMO


title: STAMP_155

source_name: MD3 HDF

tag: tissue type

value: induced Pluripotent Stem Cells

tag: sample source

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

tag: sample processed

value: Fixed cells

value: r1, r2:Replicate slide 2/2


title: aging_study_Age_55_Surv_66_Rep4

description: Library name: aging_study_Age_55_Surv_66_Rep4

tag: tissue

tag: strain

tag: study

value: aging

value: Male

tag: supine death_phenotype


title: Colon resident CD8+ T cells, HIV-Negative, Rep8

description: Library name: NEG8

tag: genotype


title: 21dpi_Ctrl_CMO

value: Brain

value: WT


title: Colon resident CD8+ T cells, HIV-Negative, Rep7

description: Library name: NEG7

tag: cell type


title: aging_study_Age_55_Surv_66_Rep3

description: Library name: aging_study_Age_55_Surv_66_Rep3

value: Whole Fly

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

tag: Sex


title: STAMP_154

source_name: MD3 iTSC

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

tag: sample type

tag: technology

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: STAMP_105

source_name: Dissociated liver cells

value: Liver cells

value: Robertson Lab (The University of Adelaide)

tag: replicate

tag: panel size


title: 7dpi_cKO

description: 10x Genomics snRNASeq

tag: microanatomical region

value: PT lesion

tag: condition

value: PT injury

value: Col1a2(creER); Tgfbr2(flox)

tag: treatment

tag: timepoint


title: STAMP_153

source_name: MD3 iPSC

tag: tissue type

value: induced Pluripotent Stem Cells

tag: sample source

tag: sample processed

tag: panel size custom


title: Colon resident CD8+ T cells, ART, Rep1

description: Library name: ART1

tag: tissue

value: Colon

tag: cell type

value: CD8+ T cells

tag: genotype

value: ART


title: STAMP_104

source_name: Dissociated kidney cells

value: Kidney cells

value: Fixed cells


title: aging_study_Age_55_Surv_66_Rep2

description: Library name: aging_study_Age_55_Surv_66_Rep2

source_name: Whole Fly

tag: strain

value: Oregon R; y+ w+

tag: study

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

value: Male

tag: supine death_phenotype


title: STAMP_103

source_name: Dissociated heart cells

value: Heart cells

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

tag: sample type

tag: replicate

tag: technology

tag: panel size


title: aging_study_Age_56_Surv_62_Rep2

description: Library name: aging_study_Age_56_Surv_62_Rep2

value: Whole Fly

tag: Sex


title: Colon resident CD8+ T cells, HIV-Negative, Rep6

description: Library name: NEG6

value: HIV-ve


title: STAMP_152

source_name: KELLY

tag: tissue type

value: Human neuroblastoma cell line

tag: sample source

value: Goodall Lab (University of South Australia)

value: r1, r2:Replicate slide 2/2

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: aging_study_Age_55_Surv_66_Rep1

description: Library name: aging_study_Age_55_Surv_66_Rep1


title: aging_study_Age_56_Surv_62_Rep1

description: Library name: aging_study_Age_56_Surv_62_Rep1


title: Rest_Ctrl_CMO

value: Brain

tag: microanatomical region

value: Cortex and Dura

tag: condition

value: Rest

value: WT

tag: timepoint


title: STAMP_151

source_name: SK-N-DZ

tag: sample processed

value: Fixed cells

tag: panel size custom


title: Colon resident CD8+ T cells, HIV-Negative, Rep4

description: Library name: NEG4

source_name: Colon

tag: tissue

value: Colon

tag: cell type

value: CD8+ T cells

tag: genotype


title: Colon resident CD8+ T cells, HIV-Negative, Rep5

description: Library name: NEG5


title: 21dpi_cKO_GEX

description: 10x Genomics snRNASeq (Gene Expression)

value: Cortex and PT Lesion

value: PT injury

value: Col1a2(creER) or Cdh5(creER); Tgfbr2(flox)


title: STAMP_150

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

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)


title: aging_study_Age_53_Surv_72_Rep4

description: Library name: aging_study_Age_53_Surv_72_Rep4

value: Whole Fly

tag: strain

value: Oregon R; y+ w+

tag: study

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

value: Male


title: 7dpi_Ctrl_CMO

value: Brain


title: Colon resident CD8+ T cells, HIV-Negative, Rep3

description: Library name: NEG3

value: HIV-ve


title: aging_study_Age_53_Surv_72_Rep3

description: Library name: aging_study_Age_53_Surv_72_Rep3

tag: supine death_phenotype


title: Colon resident CD8+ T cells, HIV-Negative, Rep2

description: Library name: NEG2


title: STAMP_148

source_name: LNCaP, SK-BR-3, MCF-7, KELLY

value: Mixed cells

tag: sample type

tag: replicate

value: r1, r2:Replicate slide 2/2

tag: technology

value: Xenium

tag: panel size

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: 2dpi_Ctrl_CMO

source_name: Brain

tag: microanatomical region

tag: condition

value: WT


title: 21dpi_Ctrl_GEX

description: 10x Genomics snRNASeq (Gene Expression)

value: Cortex and PT Lesion

tag: timepoint


title: aging_study_Age_53_Surv_72_Rep2

description: Library name: aging_study_Age_53_Surv_72_Rep2

tag: Sex


title: Tunicamycin treatment, unsorted population, rep 4

city: Ottawa

first: Truc

last: Losier

state: ON

address: 451 Smyth Road

department: CMM

country: Canada

institute: University of Ottawa

description: Library name: Sample 48

library_source: other

data_processing:
Sequencing was done on an Illumina Nextseq500 150 cycle high output kit, 150 bp single end reads with 8 bp dual indexes were performed.
Basecalling was performed by Illumina Real-Time Analysis (RTA v2)
FastQ generation was performed with Illumina bcl2fastq v2.20+
NGS results were analysed using CRISPRBetaBinomial.
Supplementary files format and content: csv files incude various metrics about the data quality (total read counts, mapped read counts, mappability, and coverage) and provide sgRNA- and gene-level summary statistics of the screens.
Library strategy: CRISPR Screen

molecule: other

growth_protocol: HEK293A expressing DsRed-IRES-GFP-p62 reporter line were cultured in DMEM supplemented with 10% bovine calf serum (VWR Life Science Seradigm).

extract_protocol:
Genomic DNA of the sorted and unsorted fixed cells were then extracted using the protocol described previously. The sgRNA library was amplified by a two-step PCR protocol for NGS. All gDNA of sorted samples were used to maximize the representations. For the unsorted/bulk samples, 22890 ng of gDNA, which is relevant to 1250 x representation, was used for PCR1. PCR1 and PCR2 products were purified using AMPure XP Bead-Based Reagent (Beckman Coulter, A63881) according to manufacturer's instructions.
The CRISPR knockout pooled library was purchased from Addgene (Cat#1000000083) and amplified using the protocol provided by Addgene.

treatment_protocol: Media was changed 24 h before experiments. Amino acid starvation media was prepared based on Gibco standard recipe omitting all amino acids and supplemented as above without addition of non-essential amino acids and substitution with dialysed FBS (Invitrogen). Tunicamycin (10 µg/mL) or clofibrate (1 mM) was added to the cells for 6 hours. The untreated and treated cells were fixed with 2% PFA for 10 min at room temperature, followed by 15 min incubation with Tris (pH 8, direct addition to 2% PFA to create a final concentration of 1 M). Following aspiration of media, the cells were collected using scrapers, stored in ice-cold flow buffer (1% BSA and 2 mM EDTA in PBS), and filtered using cell strainers (70 µM, Falcon). The samples were then sorted into high and low GFP populations. These populations were then pelleted by centrifugation (4000 rpm for 10 min at 40C) and stored at -80C freezer for downstream analysis.

tag: cell line

value: human embryonic kidney cells


title: aging_study_Age_53_Surv_72_Rep1

description: Library name: aging_study_Age_53_Surv_72_Rep1

tag: tissue


title: Colon resident CD8+ T cells, HIV-Negative, Rep1

description: Library name: NEG1

value: Colon

tag: cell type

value: CD8+ T cells

tag: genotype


title: 7dpi_Ctrl_GEX

description: 10x Genomics snRNASeq (Gene Expression)

value: PT injury


title: aging_study_Age_54_Surv_69_Rep2

description: Library name: aging_study_Age_54_Surv_69_Rep2

tag: strain

tag: study


title: 2dpi_Ctrl_GEX

description: 10x Genomics snRNASeq (Gene Expression)


title: STAMP_147

tag: tissue type

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

tag: sample source

value: Goodall Lab (University of South Australia)

tag: sample processed

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

value: Fixed cells

tag: panel size custom


title: aging_study_Age_52_Surv_75_Rep2

description: Library name: aging_study_Age_52_Surv_75_Rep2

value: Whole Fly

value: Oregon R; y+ w+

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

value: Male

tag: supine death_phenotype


title: Tunicamycin treatment, unsorted population, rep 3

description: Library name: Sample 47


title: STAMP_146

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

value: Human squamous cell carcinoma cell line

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

tag: sample type

tag: replicate

value: r1, r2:Replicate slide 2/2

tag: technology

tag: panel size


title: STAMP_145

source_name: Tongue cancer CAFs

value: Cancer-associated fibroblasts (CAFs) isolated from tongue squamous cell carcinoma

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: Rest_Ctrl_GEX

description: 10x Genomics snRNASeq (Gene Expression)

tag: tissue

value: Brain

tag: microanatomical region

value: Cortex and Dura

tag: condition

value: Rest

value: WT

tag: timepoint


title: Tunicamycin treatment, unsorted population, rep 2

description: Library name: Sample 46

tag: cell line

tag: cell type

value: human embryonic kidney cells


title: Cortex_21dpi_Deleter

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Sequencing data were aligned to mouse genome mm10 with SpaceRanger version 2.0.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: features.tsv.gz: list of gene IDs (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: matrix.tsv.gz: gene expression count data in Matrix Market Exchange Format (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: aligned_fiducials.jpg.: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

extract_protocol:
Following mouse euthanasia, brains were snap frozen in O.C.T., and 10mm slices were prepared via cryostat and directly mounted onto Spatial Gene Expression slides (10X Genomics). Tissue was processed as per manufacturer’s recommendations, with a permeabilization time of 12 minutes.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions.

tag: genotype

value: Cthrc1(creER); R26(DTA)

value: PT injury


title: aging_study_Age_51_Surv_78_Rep4

description: Library name: aging_study_Age_51_Surv_78_Rep4

value: Whole Fly

tag: strain

tag: study

tag: Sex


title: Tunicamycin treatment, unsorted population, rep 1

description: Library name: Sample 45


title: 7dpi_cKO_GEX

description: 10x Genomics snRNASeq (Gene Expression)

value: Cortex and PT Lesion

value: Col1a2(creER) or Cdh5(creER); Tgfbr2(flox)


title: STAMP_149

tag: tissue type

value: Human neuroblastoma cell line

tag: sample source

value: Goodall Lab (University of South Australia)

tag: sample processed

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

value: Fixed cells

tag: panel size custom


title: STAMP_143

value: Human erythroleukemia cell line

value: Dr. Winnie Kan (University of South Australia)

tag: sample type

tag: replicate

value: r1, r2:Replicate slide 2/2


title: Tunicamycin treatment, low GFP population, rep 4

description: Library name: Sample 44


title: aging_study_Age_51_Surv_78_Rep3

description: Library name: aging_study_Age_51_Surv_78_Rep3

value: Oregon R; y+ w+

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

value: Male

tag: supine death_phenotype


title: Cortex_21dpi

tag: tissue

value: Brain

value: WT

tag: condition

tag: timepoint


title: STAMP_142

value: Immortalized human mammary epithelial cell line

value: Sweeney Lab (South Australian immunoGENomics Cancer Institute, The University of Adelaide)

tag: technology

value: Xenium

tag: panel size

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: Cortex_7dpi

tag: genotype

value: PT injury


title: Tunicamycin treatment, low GFP population, rep 3

description: Library name: Sample 43

tag: cell line

tag: cell type

value: human embryonic kidney cells


title: STAMP_141

tag: tissue type

value: Immortalized human pancreatic beta cell line

tag: sample source

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


title: STAMP_140

source_name: hESC H1

value: human Embryonic Stem Cells

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

tag: sample processed

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

value: Fixed cells

tag: panel size custom


title: aging_study_Age_51_Surv_78_Rep1

description: Library name: aging_study_Age_51_Surv_78_Rep1

value: Whole Fly

tag: strain

value: Oregon R; y+ w+

tag: study

tag: Sex


title: LG333_178

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in mouse thalamus

data_processing:
Gene counts were obtained by aligning reads to human genome (hg38) mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than three cells, cells with a unique gene count over 9000 or less than 300, cells with UMI over 50000 and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
Seurat v3.0.182 R package used for analysis
Assembly: hg38 and mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

source_name: thalamus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: thalamus

value: Female

tag: age

value: PGRN KO:-/-; Axl KO:-/-


title: Tunicamycin treatment, low GFP population, rep 2

description: Library name: Sample 42


title: Tunicamycin treatment, low GFP population, rep 1

description: Library name: Sample 41


title: Cortex_Rest_2dpi

value: Brain

value: WT

value: Rest and PT injury

value: 0 and 2dpi


title: LG333_174

description: mRNA expression in mouse thalamus

value: Male


title: Tunicamycin treatment, high GFP population, rep 4

description: Library name: Sample 40

value: human embryonic kidney cells


title: LG333_173

description: mRNA expression in mouse thalamus


title: aging_study_Age_52_Surv_75_Rep1

description: Library name: aging_study_Age_52_Surv_75_Rep1

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

tag: supine death_phenotype


title: Tunicamycin treatment, high GFP population, rep 3

description: Library name: Sample 39


title: STAMP_138

source_name: LNCaP

value: Prostate cancer cell line

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

tag: sample type

tag: replicate

value: r1, r2:Replicate slide 2/2

tag: technology

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: STAMP_144

value: Human glioblastoma-astrocytoma cell line

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

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

value: Fixed cells

tag: panel size


title: LG333_167

description: mRNA expression in mouse thalamus

tag: tissue

value: thalamus

value: Female

tag: genotype

value: PGRN KO:-/-; Axl KO:-/-


title: STAMP_137

tag: tissue type

value: Breast cancer cell line

tag: sample source

value: Swarbrick Lab (The Garvan Institute)


title: Axl_4

description: mRNA expression in mouse thalamus

value: Male

value: Axl KO:-/-


title: STAMP_135

source_name: PBMC

value: Blood

value: STEMCELL Technologies

tag: sample processed

tag: panel size custom


title: Tunicamycin treatment, high GFP population, rep 2

description: Library name: Sample 38

tag: cell line

tag: cell type

value: human embryonic kidney cells


title: STAMP_136

value: r1, r2:Replicate slide 2/2


title: aging_study_Age_51_Surv_78_Rep2

description: Library name: aging_study_Age_51_Surv_78_Rep2

value: Whole Fly

tag: strain

value: Oregon R; y+ w+

tag: study

value: aging

tag: Sex


title: Clofibrate treatment, unsorted population, rep 4

description: Library name: Sample 36


title: Axl_2

description: mRNA expression in mouse thalamus

tag: age


title: STAMP_134

source_name: MD3 HDF

value: induced Pluripotent Stem Cells

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

value: r1, r2:Replicate slide 1/2

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: STAMP_139

source_name: iPSC 32F

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

value: Fixed cells


title: Clofibrate treatment, unsorted population, rep 3

description: Library name: Sample 35


title: STAMP_133

source_name: MD3 iTSC


title: Clofibrate treatment, unsorted population, rep 2

description: Library name: Sample 34


title: Axl_1

description: mRNA expression in mouse thalamus

value: thalamus


title: STAMP_132

source_name: MD3 iPSC


title: LG332_266

description: mRNA expression in mouse thalamus

value: Male

value: PGRN KO:-/-; MerTK KO:-/-


title: LG332_255

description: mRNA expression in mouse thalamus

value: Female


title: Clofibrate treatment, low GFP population, rep 4

description: Library name: Sample 32


title: Clofibrate treatment, unsorted population, rep 1

description: Library name: Sample 33


title: Young D14, HTO

description: 10x Genomics

data_processing:
Alignment of reads from the single cell RNA-seq library and unique molecular identifiers (UMIs) counting were performed with 10X Genomics Cell Ranger tool (v3.0.2).
Reads of oligonucleotides tags (HTOs) used for Cell Hashing were counted with CITE-seq-Count (v1.4.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

source_name: Whole lung

value: All

value: Whole lung

tag: Stage

value: Young

value: 7 weeks old

tag: treatment

value: Bleomycin or PBS

tag: time


title: Clofibrate treatment, low GFP population, rep 3

description: Library name: Sample 31

value: human embryonic kidney cells


title: LG332_254

description: mRNA expression in mouse thalamus


title: STAMP_130

value: Human neuroblastoma cell line

value: Goodall Lab (University of South Australia)

tag: sample type

tag: replicate

tag: technology


title: STAMP_129

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

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

value: r1, r2:Replicate slide 1/2

tag: panel size


title: LG324_20

description: mRNA expression in mouse thalamus

tag: tissue

tag: genotype

value: MerTK KO:-/-


title: STAMP_128

tag: tissue type

tag: sample source

tag: sample processed

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

value: Fixed cells

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: LG332_115

description: mRNA expression in mouse thalamus

value: thalamus

value: Male

value: PGRN KO:-/-; MerTK KO:-/-


title: Clofibrate treatment, low GFP population, rep 2

description: Library name: Sample 30

tag: cell line

tag: cell type


title: TN_ingAT_AdipoCre_H3K27me3_2

data_processing:
*library strategy: Cut&Tag
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions for each sample

source_name: Inguinal Adipose Tissue

extract_protocol:
Nuclei were isolated from snap frozen adipose tissue depots in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 10 mM sodium butyrate and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). All centrifugation steps were carried out in a to 4˚C cooled swinging bucket centrifuge with settings at 500 xg for 5 minutes. Nuclei were subsequently filtered through a 50µm cell strainer (Sysmex, #04-0042-2317) and washed two times in PBS-BSA (1% w/v) containing protease inhibitor and sodium butyrate. Nuclei were centrifuged and subsequently bound to pre-blocked Dynabeads MyOne Streptavidin C1 beads (ThermoFisher, #65002) for 30 minutes at 4˚C followed by 3 washes with PBS-BSA (1% w/v) on a magnetic stand. CUT&Tag was performed as previously described with minor adjustments36,37. All buffers were supplemented with 1 x cOmplete EDTA-free Protease inhibitor and 10mM sodium butyrate. Briefly, nuclei bound to beads were aliquoted into 96-well LoBind plates (Eppendorf, #0030129547) and incubated with primary antibodies – anti-H3K4me3 (abcam, #ab8580), anti-H3K27me3 (Cell Signaling Technology, #C36B11), anti-H3K27ac (abcam, #ab4729), anti-H3K4me1 (abcam, #ab8895), anti-H3K9me3 (abcam, #ab8898) – overnight at 4˚C. All antibodies were diluted 1:100. With the plate on a magnet the primary antibody solution was removed, the beads were resuspended in secondary antibody solution (guinea pig anti-rabbit IgG (antibodies-online gmbh, #ABIN101961); 1:200 dilution) and incubated at room temperature for 30 minutes while rocking. pA-Tn5 was bound to antibodies, transposition performed at 37 ˚C and stopped using TAPS-Wash solution. Nuclei were lysed and pA-Tn5 decrosslinked using SDS-release solution.
PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, X cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C. After 5 cycles the PCR was put on hold at 4˚C and 10% of the reaction was transferred into a 384 well plate and mixed with KAPA SYBR 2x (qPCR) and primers and qPCR was run for 20 cycles to determine the number of PCR cycles to be added38. Libraries were cleaned using SPRI beads using a 1.3 ratio, eluted in nuclease free water and pooled equimolecularily after library quantification using the KAPA library quantification kit (Roche Diagnostics, #079602).

value: Inguinal Adipose Tissue

value: Adipocytes

tag: strain

value: AdipoCre x NuTRAP on C57BL6 background

tag: histone

value: biol rep 2

value: 9 week old at death, born and kept at 30 degrees during whole life


title: LG324_18

description: mRNA expression in mouse thalamus

tag: Sex

value: Female

tag: age


title: Clofibrate treatment, low GFP population, rep 1

description: Library name: Sample 29

value: human embryonic kidney cells


title: STAMP_127

value: Mixed cells

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

tag: panel size custom


title: Clofibrate treatment, high GFP population, rep 4

description: Library name: Sample 28


title: LG324_17

description: mRNA expression in mouse thalamus

value: MerTK KO:-/-


title: STAMP_126

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

value: Goodall Lab (University of South Australia)

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

value: r1, r2:Replicate slide 1/2


title: Clofibrate treatment, high GFP population, rep 3

description: Library name: Sample 27


title: STAMP_125

value: Human squamous cell carcinoma cell line

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

value: Fixed cells

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: Clofibrate treatment, high GFP population, rep 2

description: Library name: Sample 26


title: LG332_239

description: mRNA expression in mouse thalamus

value: thalamus

value: MerTK KO:+/+;PGRN KO:-/-


title: STAMP_131

source_name: KELLY

value: Human neuroblastoma cell line


title: LG324_16

description: mRNA expression in mouse thalamus

value: Male


title: STAMP_124

value: Cancer-associated fibroblasts (CAFs) isolated from tongue squamous cell carcinoma


title: Clofibrate treatment, high GFP population, rep 1

description: Library name: Sample 25

value: human embryonic kidney cells


title: STAMP_123

value: Human glioblastoma-astrocytoma cell line


title: LG332_228

description: mRNA expression in mouse thalamus


title: STAMP_122

value: Human erythroleukemia cell line

value: Dr. Winnie Kan (University of South Australia)


title: Starvation, unsorted population, rep 4

description: Library name: Sample 24


title: Starvation, unsorted population, rep 3

description: Library name: Sample 23


title: LG332_174

description: mRNA expression in mouse thalamus


title: STAMP_120

value: Immortalized human pancreatic beta cell line

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


title: STAMP_121

value: Immortalized human mammary epithelial cell line

value: Sweeney Lab (South Australian immunoGENomics Cancer Institute, The University of Adelaide)

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

value: r1, r2:Replicate slide 1/2


title: Starvation, unsorted population, rep 2

description: Library name: Sample 22


title: LG180_1655

description: mRNA expression in mouse thalamus

value: Female


title: STAMP_119

value: human Embryonic Stem Cells

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

value: Fixed cells

value: Xenium

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001


title: LG180_1653

description: mRNA expression in mouse thalamus

value: thalamus


title: Starvation, low GFP population, rep 4

description: Library name: Sample 20

value: human embryonic kidney cells


title: Starvation, unsorted population, rep 1

description: Library name: Sample 21


title: Starvation, low GFP population, rep 3

description: Library name: Sample 19


title: STAMP_118

value: induced Pluripotent Stem Cells

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


title: LG180_1601

description: mRNA expression in mouse thalamus

value: Male


title: STAMP_117

value: Prostate cancer cell line

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


title: STAMP_116

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)


title: Starvation, low GFP population, rep 1

description: Library name: Sample 17