title: Edge.wound scRNA

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

data_processing:
Cell demultiplexing, alignment, and filtering were performed using the 10X Genomics Cell Ranger package version 3.0.1, mapping to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: barcode, feature and matrix files

source_name: Skin tissue

growth_protocol: C57BL/6J mice were mainteined in the JHU animal facility and telogen mice (21-day old) were used for the experiment

extract_protocol:
Small pieces of tissue were incubated with 1 mL of 0.4 mg/mL Liberase TL (Roche, 05401020001) in DMEM with 100 units/mL of penicillin and 100 mg/mL of streptomycin, then washed with PBS and incubated with 0.05% TrypLE™ Select. The cell suspension was washed with 10% FBS in DMEM with 100 units/mL of penicillin and 100 mg/mL of streptomycin, then incubated with 100 units/mL of DNase I (New England BioLabs, M0303). The cell suspension was washed with 0.04% (w/v) BSA in PBS and filtered through a 40 µm strainer to prepare a single-cell suspension. To obtain a live single-cell suspension, Propidium Iodide (BioLegend, 421301) negative and Vybrant DyeCycle Violet (Invitrogen, V35003) positive single cells were sorted.
Library construction was performed using the 10x Chromium Single Cell v3 platform. Sequencing was conducted on the NovaSeq 6000 with v1.5 reagents. Basecalling and sample demultiplexing were carried out using Illumina’s BaseSpace software

treatment_protocol: A1 cm² section of skin was removed from the mouse's back

value: Skin tissue

value: Wound


title: Testes Wildtype Replicate 3

status: Public on Feb 10 2025

type: SRA

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description: Library name: WT_T_3

library_source: transcriptomic

data_processing:
16 totalRNA-Seq samples were pooled and sequenced on NovaSeq 6000 S1 using Illumina® Stranded Total RNA Prep. Ligation was done with Ribo-Zero Plus and paired-end sequencing
RNA-Seq FASTQ files were aligned to the reference genome using STAR using the 2-pass setting.
Raw counts were produced using RSEM.
Assembly: mm10 with the GENCODE_M21 GTF
Supplementary files format and content: Tab-delimited file containing RSEM raw counts for the Liver & Cerebellum samples used in this study.

molecule: total RNA

organism: Mus musculus

source_name: Testes

growth_protocol: Mice were housed at 25 ˚C in a 12 h light and 12 h dark cycle.

extract_protocol:
Mice were 6-12 weeks of age and of either sex, with age-matched littermates used as controls unless noted otherwise. Following euthanasia, tissues were isolated, flash-frozen in RNAlater using liquid nitrogen, and stored at −80 ˚C prior to Trizol extraction.
Total RNA from mouse tissues in which THUMPD1 gene has been knocked out (THUMPD1 KO) vs control (WT) were isolated by Trizol extraction and sequenced on NovaSeq 6000 S1 using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

tag: tissue

value: Testes

tag: genotype

value: Wildtype


title: Liver Knockout Replicate 7

description: Library name: KO_L_7

source_name: Liver

value: Liver

value: Knockout


title: Liver Knockout Replicate 8

description: Library name: KO_L_8


title: Testes Wildtype Replicate 2

description: Library name: WT_T_2


title: Testes Wildtype Replicate 1

description: Library name: WT_T_1


title: Liver Wildtype Replicate 4

description: Library name: WT_L_4


title: Liver Knockout Replicate 5

description: Library name: KO_L_5


title: SC398_1

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The raw data of scRNA-seq was processed by Cell Ranger v6.1.2.
Assembly: mm10
Supplementary files format and content: feature-barcode matrices generated by Cell Ranger in Market Exchange Format (MEX) (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-mex-matrices)

source_name: Prostate cancer tumor

extract_protocol:
Prostate tumors from castrated PSp and PCSp GEMM mice were dissected, minced, and digested into single-cell suspension using Collagenase A (Sigma, 11088793001) at 37°C for 45 min with continuously gentle shaking.  The dissociated tissues were centrifuged at 500g for 5 min, followed by further digestion with 0.25% Trypsin (Corning, 25053CI) at 37°C for 5 min. The samples were filtered using a 70uM strainer (Falcon, 352350) and centrifuged at 500g at 4°C for 5 min, followed by incubation in 1x RBC lysis buffer (Biolegend, 420302) at RT for 5 min. After washing with cold DMEM, the cells were collected and resuspended in cold PBS containing 0.04% BSA (Ambion, AM2616),  followed by measurement of cell number and viability.  Two PSp tumors and two PCSp tumors were submitted to the Single Cell Genomics Core facility at MD Anderson for library preparation and sequencing.
The scRNA-seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 30 V3 Reagent Kits (10X Genomics) according to the manufacturer’s recommendations.

value: Prostate cancer tumor

tag: cell line

value: Primary cells

tag: cell type

value: Epithelial, stromal, and immune cell populations

value: PB-Cre, PtenL/L, SpopF133V; mTmG

tag: treatment

value: Castration surgery


title: SC398_3

description: 10X Genomics

value: PB-Cre, PtenL/L, Chd1L/L, SpopF133V; mTmG


title: Liver Wildtype Replicate 2

description: Library name: WT_L_2


title: Wild type Piriform Cortex female 74-3

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description: FMQ 74-3

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: txt files include FPKM and Count values for each Sample

source_name: Piriform Cortex

extract_protocol:
Piriform cortex tissues were dissected from all mice at 12 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Piriform Cortex

tag: Sex

value: female

tag: age

value: 12 months

value: Wild type

tag: background

tag: plate

tag: well

tag: volume


title: Non-wounded scRNA


title: Liver Wildtype Replicate 1

description: Library name: WT_L_1


title: Center.wound scRNA


title: SC398_4

description: 10X Genomics


title: SC398_2

description: 10X Genomics


title: Wild type Piriform Cortex male 147-3

description: RFckQ 147-3

value: male


title: Wild type Piriform Cortex male 161-1

description: RFQ 161-1


title: Het (Q140) KI Piriform Cortex male 164-1

description: RFQ 164-1

value: Het (Q140) KI


title: Liver Knockout Replicate 6

description: Library name: KO_L_6


title: Het (Q140) KI Piriform Cortex female 150-2

description: RFckQ 150-2


title: Het (Q140) KI Piriform Cortex male 161-4

description: RFQ 161-4


title: Het (Q140) KI Piriform Cortex female 7205


title: Wild type Piriform Cortex female 150-1

description: RFckQ 150-1


title: Het (Q140) KI Piriform Cortex female 7214


title: Wild type Piriform Cortex female 148-1

description: RFckQ 148-1


title: Msh6-/- Striatum male 33-3

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq 6000 S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: txt files include FPKM and Count values for each Sample

source_name: Corpus Striatum

extract_protocol:
Brain cortical and striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Corpus Striatum

value: 6 months


title: Het (Q140) KI X Msh6-/- Cortex female 38-1

source_name: Cerebral Cortex

value: Cerebral Cortex

value: Het (Q140) KI X Msh6-/-


title: Msh6-/- Cortex male 33-3


title: Het (Q140) KI X Msh6-/- Striatum female 32-4


title: Het (Q140) KI X Msh6-/- Cortex female 32-4


title: Msh6-/- Cortex female 32-1


title: Het (Q140) KI X Msh6-/- Striatum female 38-1


title: Msh6-/- Cortex male 29-2


title: Msh6-/- Striatum male 29-2


title: Msh6-/- Striatum female 32-1


title: Het (Q140) KI X Msh6-/- Striatum male 28-1


title: Het (Q140) KI Cortex male 29-3


title: Het (Q140) KI X Msh6-/- Striatum female 27-1


title: Het (Q140) KI Piriform Cortex male 161-2

description: RFQ 161-2


title: Het (Q140) KI X Msh6-/- Cortex female 27-1


title: Het (Q140) KI X Msh6+/- Striatum male 26-4

value: Het (Q140) KI X Msh6+/-


title: Msh6+/- Striatum male 26-3


title: Het (Q140) KI X Msh6+/- Cortex male 26-4


title: Msh6-/- Cortex male 26-2


title: Wild type Piriform Cortex male 147-1

description: RFckQ 147-1


title: Msh6-/- Striatum male 26-2


title: Msh6+/- Cortex male 26-3


title: Het (Q140) KI Striatum male 26-1


title: Het (Q140) KI Cortex male 26-1


title: Het (Q140) KI X Msh6-/- Cortex female 25-2


title: Het (Q140) KI X Msh6-/- Striatum female 25-2


title: Msh6+/- Cortex female 25-1


title: Msh6+/- Striatum female 25-1


title: Het (Q140) KI Striatum male 29-3


title: Msh6+/- Striatum male 24-4


title: Msh6-/- Striatum male 24-3


title: Msh6+/- Cortex male 24-4


title: Het (Q140) KI X Msh6-/- Cortex male 28-1


title: Het (Q140) KI X Msh6-/- Striatum male 24-2


title: Het (Q140) KI X Msh6-/- Cortex male 24-2


title: Msh6-/- Cortex male 24-3


title: Het (Q140) KI Cortex female 23-2


title: Msh6+/- Striatum female 23-1


title: Het (Q140) KI Striatum female 23-2


title: Het (Q140) KI Striatum male 24-1


title: Het (Q140) KI Cortex male 22-2


title: Msh6+/- Cortex female 23-1


title: Het (Q140) KI Striatum male 22-2


title: Msh6+/- Striatum male 22-1


title: Msh6+/- Cortex male 22-1


title: Het (Q140) KI X Msh6-/- Cortex male 21-3


title: Het (Q140) KI X Msh6+/- Cortex male 21-5


title: Het (Q140) KI X Msh6+/- Striatum male 21-5


title: Het (Q140) KI X Msh6-/- Striatum male 21-3


title: Het (Q140) KI X Msh6-/- Cortex male 21-4


title: Het (Q140) KI X Msh6-/- Striatum male 21-4


title: Wild type Cortex male 21-1


title: Msh6-/- Striatum female 20-1


title: Wild type Striatum female 20-2


title: Wild type Cortex female 20-2


title: Het (Q140) KI Cortex female 19-3


title: Msh6+/- Cortex female 19-2


title: Het (Q140) KI Striatum female 18-5


title: Het (Q140) KI Cortex male 24-1


title: Het (Q140) KI Striatum female 19-3


title: Msh6+/- Striatum female 19-2


title: Msh6+/- Cortex female 18-4


title: Wild type Cortex female 18-1


title: Het (Q140) KI Cortex female 18-5


title: Het (Q140) KI X Msh6+/- Striatum female 18-2


title: Wild type Striatum female 18-1


title: Het (Q140) KI X Msh6+/- Striatum female 16-4


title: Het (Q140) KI X Msh6+/- Striatum male 17-1


title: Het (Q140) KI X Msh6+/- Cortex female 18-2


title: Het (Q140) KI X Msh6+/- Cortex male 17-1


title: Het (Q140) KI X Msh6+/- Cortex female 16-4


title: Msh6-/- Striatum female 16-3


title: Msh6-/- Cortex female 16-3


title: Wild type Cortex female 16-2


title: Wild type Striatum female 16-2


title: Wild type Striatum male 15-2


title: Wild type Striatum female 16-1


title: Wild type Cortex female 16-1


title: Het (Q140) KI X Msh6+/- Cortex male 15-1


title: Het (Q140) KI X Msh6+/- Striatum male 15-1


title: Msh6-/- Cortex female 20-1


title: Msh6+/- Striatum female 18-4


title: Wild type Cortex male 15-2


title: Het (Q140) KI X Msh6+/- Striatum female 14-4


title: Het (Q140) KI X Msh6+/- Cortex female 14-4


title: Msh6-/- Striatum female 14-3


title: Msh6-/- Cortex female 14-3


title: Het (Q140) KI X Msh6+/- Cortex female 14-1


title: Msh6+/- Striatum male 13-3


title: Msh6+/- Cortex male 13-3


title: Het (Q140) KI Cortex female 14-2


title: Wild type Striatum male 13-2


title: Het (Q140) KI Striatum female 14-2


title: Wild type Striatum male 13-1


title: Wild type Cortex male 13-1


title: Wild type Cortex male 13-2


title: Tpi1_KD

city: ChengDu

first: Bi-Sen

last: Ding

address: Xinchuan Road

department: State Key Laboratory of Biotherapy

country: China

institute: Sichuan University

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: lung, isolated day7 after pneumonectomy, Tpi1EC KD mice

extract_protocol:
At indicated time points, mice were sacrificed and the lungs were perfused with cold 0.9% saline through the pulmonary artery, as previously described. The perfused lung tissues were minced and dissociated with HBSS (Gibco) containing dispase Ⅱ (Sigma), collagenase Ⅰ (Gibco), and DNase Ⅰ (Sigma) at 37 ℃ for 20 minutes. To remove connective tissue, the resulting cell suspension was filtered through a 40 μm filter to obtain single cell suspension.
Library was performed according to the manufacter's instruction(single cell 3' v3.1 protocol, 10x Genomics)

value: lung

value: whole cells

value: Tpi1EC KD

value: pneumonectomy


title: shNC

source_name: lung, isolated day7 after pneumonectomy, shNC mice

value: shNC


title: Tgm2_cko

source_name: lung, isolated day7 after pneumonectomy, Tgm2i∆EC/i∆EC mice


title: Tgm2_WT

source_name: lung, isolated day7 after pneumonectomy, Tgm2+/+ mice


title: PNX_Day24

source_name: lung, isolated day24 after pneumonectomy, wild type mice

value: WT


title: PNX_Day14

source_name: lung, isolated day14 after pneumonectomy, wild type mice


title: Sham

source_name: lung, sham operation, wild type mice

value: sham operation


title: PNX_Day7

source_name: lung, isolated day7 after pneumonectomy, wild type mice


title: PNX_Day3

source_name: lung, isolated day3 after pneumonectomy, wild type mice


title: PNX_Day0

source_name: lung, isolated day0 after pneumonectomy, wild type mice


title: BoTX_Ctrl

city: Basel

first: Alexander

middle: S

last: Ham

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: snRNAseq

data_processing:
Demultiplexing was done with bcl2fastq (version 2.20) and was performed by our local genomics facility (D-BSSE, ETH, Basel). FASTQ files were aligned to mouse reference mm10 (GENCODE vM23/Ensembl 98, from 2020) using cellranger count version 5.0 with the argument –include-introns.
Assembly: mm10 (GENCODE vM23/Ensembl 98, from 2020)
Supplementary files format and content: Filtered_feature_bc_matrix, output of cell ranger count (Tab-separated values and matrix files)

source_name: Tibialis Anterior

extract_protocol:
Nuclei were extracted from freshly dissected mouse muscle. The tissue was minced with scissors in nuclei lysis buffer (250 mM sucrose, 25 mM KCl, 4 mM MgCl2, 10 mM Tris-HCl pH 8 and 0.1% NP40 in nuclease RNase free H2O) and dounced with a dounce homogenizer. To separate nuclei from tissue pieces and cell debris, the slurry/lysate was filtered through cell strainers and centrifuged twice at 500g. For more details see methods section of publication.
To generate single nuclei libraries 10x Genomics Chromium Next GEM Single Cell 3’ kits (PN-1000121, PN-1000120, PN-1000213) and the corresponding protocol were used. We always aimed to get 10’000 nuclei libraries per sample which is the maximum recommended by the manufacturer. For more details see methods section of publication.

value: Tibialis Anterior

value: M

tag: age (months)

value: NaCl injected


title: MuskKO_Ctrl

description: snRNAseq

value: PBS injected


title: Den_TA_2

description: snRNAseq

value: Denervated


title: BoTX

description: snRNAseq

value: BoTX injected


title: MuskKO

description: snRNAseq

value: Musk-sgRNA injected


title: Den_TA_1

description: snRNAseq


title: Den_GAS_2

description: snRNAseq

source_name: Gastrocnemius

value: Gastrocnemius


title: Het (Q140) KI X Msh6+/- Striatum female 14-1

value: Corpus Striatum

value: female

value: 6 months


title: In_TA_1

description: snRNAseq

value: Control Innervated


title: In_TA_2

description: snRNAseq


title: In_GAS_2

description: snRNAseq


title: Den_GAS_1

description: snRNAseq


title: AAV_Pdzrn4_OE_4

description: bulk RNAseq

data_processing:
FASTQ files were aligned to the indexed mouse transcriptome mm10 using Salmon (version 1.1.0) with the flags validateMappings, seqBias and gcBias.
Assembly: mm10
Supplementary files format and content: Salmon output quant.sf file, contains plain-text, tab-separated

extract_protocol:
RNA was extracted from TA muscle using the RNeasy Fibrous Tissue Mini Kit (74704, Qiagen) according to the manufactures protocol (see methods section of publication for more details).
Libraries were prepared using the TruSeq stranded mRNA library kit (20020595, Illumina) starting from 200 ng of RNA.

value: Pdzrn4 overexpression


title: AAV_Pdzrn4_OE_3

description: bulk RNAseq


title: AAV_Pdzrn4_OE_2

description: bulk RNAseq


title: AAV_Pdzrn4_OE_1

description: bulk RNAseq


title: AAV_Lrtm1_OE_3

description: bulk RNAseq

value: Lrtm1 overexpression


title: AAV_Lrtm1_OE_2

description: bulk RNAseq


title: AAV_Lrtm1_OE_1

description: bulk RNAseq


title: AAV_Etv4_OE_3

description: bulk RNAseq

value: Etv4 overexpression


title: AAV_control_4

description: bulk RNAseq


title: AAV_Etv4_OE_1

description: bulk RNAseq


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into ectoderm (ECTO-RES), replicate 3

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Raw reads were processed using the GenPipes RNA sequencing pipeline v3.1.4. First, Trimmomatic v0.36 was used for quality trimming of raw reads and removal of sequencing adapters and STAR v2.5.3a was used for aligning reads to the mouse reference genome assembly GRCm38/mm10. Then, several functions from Picard v2.9.0 were employed: MergeSamFiles for merging read alignment files of each sample, SortSam for sorting files by coordinate and MarkDuplicates for identifying read duplicates. Next, the HTSeq_count function from HTSeq v0.7.2 was used with Python v2.7.13 for calculating raw counts and StringTie v1.3.5 was used for transcript assembly. Finally, DESeq2 v1.18.1 was used with R v3.4.3 for generating normalized counts and conducting differential gene expression analysis between experimental conditions, producing an adjusted p-value and log2 fold change for each gene.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig files containing genome-wide RPKM values (forward and reverse strands) for each experimental condition replicate.
Supplementary files format and content: BED file containing raw and normalized read counts as well as results from differential gene expression analysis (mESC: INV and RES vs CTL; Germ layer cell types: RES vs CTL). These data were obtained using the DESeq2 software.

source_name: R1 mESCs

growth_protocol: Dnmt1tet/tet mESCs were maintained on gelatin-coated plates, free of mouse embryonic fibroblast feeder cells, in mESC culture medium in humidified atmosphere with 5% CO2 at 37 °C. Cell culture plates were coated with 0.1% solution of gelatin (Sigma-Aldrich, G1890) in DPBS 1X (Corning, 21-031-CV), then placed in the incubator for 30 minutes after which excess gelatin was removed. Culture medium for mESCs consisted of DMEM (Corning, 10-013-CV) supplemented with 15% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D), 1% penicillin-streptomycin 100X (Corning, 30-002-CI) and 103 units/mL of recombinant mouse LIF protein (Sigma-Aldrich, ESG1107), which was stored at 4 °C for up to 1 week. Culture medium was changed every day and cell confluency was maintained below 80%. Trypsin-EDTA 0.25% (Thermo Fisher, 25200056) was used for passaging cell cultures, typically every other day. The day before beginning differentiation protocols, mESCs were passaged using TrypLE™ Express Enzyme 1X (Thermo Fisher, 12604021) supplemented with 10 μM ROCK Inhibitor Y-27632 (STEMCELL Technologies, 72302) for detachment, re-seeding them with a density of 30,000 cells/cm2 in mESC culture medium in dishes coated with laminin from mouse Engelbreth-Holm-Swarm sarcoma (Roche, 11243217001). For laminin coating, 2.5 μg/cm2 of laminin diluted in DMEM (Corning, 10-013-CV) was added to cell culture dishes in a minimal volume to coat entire dish surface, after which excess laminin was removed and dishes were air dried for 45 minutes inside sterile cell culture hood. The next day, mESC cultures were rinsed twice with differentiation medium prior to starting differentiation protocols. Differentiations were conducted in triplicates, maintaining cultures in humidified atmosphere with 5% CO2 at 37 °C without passaging. Differentiation cultures were rinsed twice daily with differentiation medium prior to adding freshly prepared differentiation treatments to remove dead cells as a fair amount of cell death was expected. On the last day of differentiation protocols, differentiation cultures were sorted based on lineage-specific cell surface and viability markers using fluorescence-activated cell sorting (FACS). Differentiation cultures were rinsed twice with FACS buffer consisting of DPBS 1X (Corning, 21-031-CV) supplemented with 1% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079). A minimal volume of FACS buffer was added to coat entire dish surface and cells were dissociated into single-cell suspension with a cell scraper and gentle pipetting and were transferred to conical tubes. Primary antibodies for cell surface markers were added to cell suspensions in the amount recommended by the manufacturer followed by an incubation of 45 minutes at 4°C, gently mixing every 10 mins. The primary antibodies used for endoderm, mesoderm and ectoderm were anti-CXCR4 (R&D Systems, MAB21651), anti-CDH2 (R&D Systems, AF6426) and anti-NCAM1 (R&D Systems, AF2408), respectively. Cell suspensions were then rinsed twice with FACS buffer and resuspended in FACS buffer containing the fluorophore-conjugated secondary antibody in the amount recommended by the manufacturer followed by an incubation of 45 minutes at 4°C, gently mixing every 10 mins. The secondary antibodies used for endoderm, mesoderm and ectoderm were APC-conjugated anti-Rat IgG (R&D Systems, F0113), APC-conjugated anti-Sheep IgG (R&D Systems, F0127) and Alexa Fluor™ 488-conjugated anti-Goat IgG (Thermo Fisher, A11055), respectively. Cell suspensions were rinsed twice with FACS buffer and resuspended in FACS buffer at a density of 2M cells/100 μL, transferring them to FACS tubes and adding 5 μL of propidium iodide 10 μg/mL (Thermo Fisher, P1304MP) per sample which was used for assessing viability. Cells were sorted with the BD FACSAria™ Fusion Flow Cytometer (BD Biosciences) and data was processed with the BD FACSDiva™ software v8.0.2. One unstained control sample per differentiation condition and one control sample of dead cells stained with propidium iodide were also sorted. The control sample of dead cells consisted of pooled differentiated cells heated at 65°C for 1 minute in a digital dry bath and then incubated on ice for 1 minute. After sorting, RNA was immediately extracted and stored at -80°C for subsequent mRNA sequencing.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104).
Libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, E7765) in conjunction with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490).

treatment_protocol: To inactivate Dnmt1, Dnmt1tet/tet mESCs were treated with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), a tetracycline derivative, which was added to the culture medium for 6 days. Then, doxycycline treatment was stopped, and cells were maintained for 21 days. Samples were collected prior to doxycycline treatment (Dnmt1 control, CTL), immediately following doxycycline treatment (Dnmt1 inactive, INV), and after the 21-day period of recovery from doxycycline treatment (Dnmt1 rescue, RES). For endoderm differentiation, the differentiation medium consisted of RPMI (Thermo Fisher, 11875093) supplemented with 10% KnockOut™ Serum Replacement (Thermo Fisher, 10828028), 2% B-27™ minus insulin 50X (Thermo Fisher, A1895601), 1.5% HEPES 1M (Thermo Fisher, 15630106), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D) and 1% penicillin-streptomycin 100X (Corning, 30-002-CI). Cells were treated with 3 μM CHIR99021 (Sigma-Aldrich, SML1046) and 50 ng/mL Activin A (R&D Systems, 338-AC) for 1 day followed by 50 ng/mL Activin A (R&D Systems, 338-AC) and 100 nM LDN193189 (STEMCELL Technologies, 72147) for 2 days. For mesoderm differentiation, the differentiation medium consisted of EMEM (Corning, 10009CV), 10% KnockOut™ Serum Replacement (Thermo Fisher, 10828028), 1% sodium pyruvate 100 mM (Thermo Fisher, 11360070), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D) and 1% penicillin-streptomycin 100X (Corning, 30-002-CI). Cells were treated with 5 μM CHIR99021 (Sigma-Aldrich, SML1046) and 21 ng/mL BMP-4 (R&D Systems, 5020-BP) for 3 days. For ectoderm differentiation, the differentiation medium was the same as the mESC culture medium but without recombinant mouse LIF protein. Cells were treated with 1 μM of retinoic acid (Sigma-Aldrich, R2625) for 3 days.

value: R1 mESCs

value: Embryonic stem cell

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into ectoderm


title: AAV_control_2

description: bulk RNAseq

value: Tibialis Anterior

value: M


title: AAV_control_3

description: bulk RNAseq

value: PBS injected


title: AAV_control_1

description: bulk RNAseq


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into ectoderm (ECTO-RES), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into mesoderm (MESO-RES), replicate 3

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into mesoderm


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into ectoderm (ECTO-CTL), replicate 1

value: Untreated mESCs differentiated into ectoderm


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into ectoderm (ECTO-CTL), replicate 3


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into mesoderm (MESO-RES), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into mesoderm (MESO-RES), replicate 1


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into ectoderm (ECTO-CTL), replicate 2


title: In_GAS_1

description: snRNAseq


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into ectoderm (ECTO-RES), replicate 1


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into mesoderm (MESO-CTL), replicate 1

value: Untreated mESCs differentiated into mesoderm


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated endoderm (ENDO-RES), replicate 1

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into endoderm


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into mesoderm (MESO-CTL), replicate 3


title: AAV_Etv4_OE_2

description: bulk RNAseq


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into endoderm (ENDO-CTL), replicate 3

value: Untreated mESCs differentiated into endoderm


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into endoderm (ENDO-CTL), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into endoderm (ENDO-CTL), replicate 1


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 3

value: Doxycycline (2 μg/mL) for 6 days, then recovery for 21 days


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 3

value: Doxycycline (2 μg/mL) for 6 days


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1

value: Untreated


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 3


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2, EM-seq

library_source: genomic

data_processing:
*library strategy: EM-seq
Raw reads were processed using the GenPipes methylation sequencing pipeline v3.6.0. Trimmomatic v0.36 was employed for quality trimming of raw reads and removal of sequencing adapters, Bismark v0.18.1 for read alignment to the mouse reference genome assembly GRCm38/mm10, Sambamba v0.7.0 for merging read set files of each sample, Picard v2.9.0 for removing duplicate reads and the methylation extractor function from Bismark v0.18.1 for obtaining the methylation level of single CpGs. Only CpGs that were sequenced in all samples with a coverage ≥ 10X were retained. Methylation levels of single CpGs were then averaged across triplicate samples for each experimental condition.
Assembly: GRCm38/mm10
Supplementary files format and content: map.input files containing CpG methylation and coverage data for each sample
Supplementary files format and content: BED file containing genomic coordinates of CpGs along with their methylation percentage and coverage values averaged among replicates for each experimental condition. Only CpGs that were sequenced in all samples with a coverage of at least 10X are included.

molecule: genomic DNA

growth_protocol: Dnmt1tet/tet mESCs were maintained on gelatin-coated plates, free of mouse embryonic fibroblast feeder cells, in mESC culture medium in humidified atmosphere with 5% CO2 at 37 °C. Cell culture plates were coated with 0.1% solution of gelatin (Sigma-Aldrich, G1890) in DPBS 1X (Corning, 21-031-CV), then placed in the incubator for 30 minutes after which excess gelatin was removed. Culture medium for mESCs consisted of DMEM (Corning, 10-013-CV) supplemented with 15% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D), 1% penicillin-streptomycin 100X (Corning, 30-002-CI) and 103 units/mL of recombinant mouse LIF protein (Sigma-Aldrich, ESG1107), which was stored at 4 °C for up to 1 week. Culture medium was changed every day and cell confluency was maintained below 80%. Trypsin-EDTA 0.25% (Thermo Fisher, 25200056) was used for passaging cell cultures, typically every other day.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini Kit (QIAGEN, 51304).
Libraries were prepared using the NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs, E7120L).

treatment_protocol: To inactivate Dnmt1, Dnmt1tet/tet mESCs were treated with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), a tetracycline derivative, which was added to the culture medium for 6 days. Then, doxycycline treatment was stopped, and cells were maintained for 21 days. Samples were collected prior to doxycycline treatment (Dnmt1 control, CTL), immediately following doxycycline treatment (Dnmt1 inactive, INV), and after the 21-day period of recovery from doxycycline treatment (Dnmt1 rescue, RES).


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 3, EM-seq


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1, EM-seq


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 3, EM-seq


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2, EM-seq


title: Dnmt1tet/tet mESCs, Dnmt1 control differentiated into mesoderm (MESO-CTL), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into endoderm (ENDO-RES), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 3, EM-seq


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1, EM-seq


title: NK_IL15C_N9

city: Innsbruck

first: Johannes

last: Woelk

address: Peter-Mayr-Str. 1a

department: Cell Genetics

country: Austria

institute: Medical University of Innsbruck

description:
readcount_IL15C_treated.txt
DESeq2_IL15C_treated.txt

data_processing:
Clean reads were obtained by filtering raw reads to remove those containing adapters, reads with more than 10% undetermined bases, and low-quality reads (quality value of over 50% bases of the read is <=5) using the fastp software. Paired-end clean reads were aligned to the mouse genome (mm10) using HISAT2 (V.2.0.5) (Mortazavi et al., 2008). Gene counts were derived based on the number of reads mapped to each gene using featureCounts (v1.5.0-p3). Differentially expression (DE) analysis was performed using the DESeq2 R package (1.20.0). The resulting p-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 were considered as differentially expressed.
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 file includes DESeq2 normalized values for each Sample

source_name: spleen

extract_protocol:
RNA from sorted cells was extracted using the RNeasy mini Kit as per manufacturer instructions. DNA was removed using DNA-removal columns (Quiagen). RNA quantity and integrity were determined by Agilent 5400, and only samples with > 100 ng RNA and RNA integrity number > 4 were used.
mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. The isolated mRNA was subjected to fragmentation, followed by the synthesis of first-strand cDNA employing random hexamer primers. Subsequently, second-strand cDNA synthesis was performed with dTTP to create a non-directional library. The prepared library underwent a series of steps, including end repair, poly-A enrichment, adapter ligation, size selection, amplification, and purification. The library quality and quantity were assessed using Quibit and real-time PCR for quantification and a bioanalyzer for size distribution analysis. Quantified libraries were pooled and subjected to next-generation Illumina sequencing, generating paired-end reads.

value: spleen

value: NK cells


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1, EM-seq


title: NK_IL15C_N8


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2


title: Dnmt1tet/tet mESCs, Dnmt1 rescue differentiated into endoderm (ENDO-RES), replicate 3


title: NK_IL15C_N6


title: NK_IL15C_N7


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1


title: NK_IL15C_WT4

value: wild-type


title: NK_UN_N8

description:
readcount_untreated.txt
DESeq2_untreated.txt


title: NK_IL15C_WT3


title: NK_IL15C_WT2


title: NK_UN_N10


title: NK_UN_WT5


title: NK_UN_WT3


title: NK_UN_WT4


title: G3

city: Leuven

first: Elizabeth

last: Jones

address: Herestraat 49

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

description: 10x Genomics

data_processing:
Sequencing files werepre-processed using Cell Ranger and aligned to the GRCm38 mm10 genome
Data integration, normalisation, clustering, and differential expression analysis were performedusing standard Seurat pipelinein R
Assembly: GRCm38 mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: heart

extract_protocol:
The mouse hearts were flushed with saline, minced up and enzyme digested (2.5mg/ml collagenase I).Next, cells were passed over a 40µm cell strainer, cell debris was removed using a cell debris removal kit and cells were resuspended in red blood cell lysis buffer.  The, cells were filtered through a 30µm and 20µm filter to remove cardiomyocytes. Next, CD45+ cells were depleted using anti-CD45 anti-mouse microbeads (Miltenyi, 130-052-301) and magnetic associated cell sorting (MACS). Finally, cells were resuspended in PBS + 0.04% filtered BSA and counted using an automated cell counter (Luna FL). Samples were further diluted to achieve approx. 1x106 cells/ml (~1000 cells/µl) before loading into 10x Chromium.
Cells were loaded into 10X Chromium followed by library preparation targeting an average of 10 000 cells per library. All libraries were dual index and prepared using 10X 3’kitv3.1.

value: heart

value: cardiomyocyte-depleted and CD45+ depleted cells

value: db/+


title: 18790X8 miR-155 fl/fl CD4Cre+/- (PBS) Female

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

data_processing:
The refdata-gex-mm10-2020-A mouse reference was downloaded from 10X genomics
The Fastq files were aligned to the refdata-gex-mm10-2020-A mouse reference dataset from 10X genomics using CellRanger count version 5.0.0, and feature-barcode matrices were generated. All subsequent analyses were performed using Seurat R package (v4.2.0). Data were preprocessed to remove low-quality cells based on the following criteria: cells with less than 300 features (considered low-quality), or more than 6000 features (potentially representing duplicates), or more than 5% mitochondrial gene fraction (indicative of stressed or dying cells) were excluded from further analysis. After removing unwanted cells from the dataset, the Seurat’s sctransform method was used to normalize and integrate data sets Hafemeister, Genome Biology 20, 296 (2019)). After integration, dimensionality reduction was performed through Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) with 12 principal components. Single cells were clustered based on nearest-neighbor graph construction via FindNeighbors and FindClusters Seurat functions, and 14 clusters were identified at the resolution level of 0.6. Marker genes defining each cluster were determined using Seurat’s FindAllMarkers function with default parameters. The output of this function (i.e. differentially expressed gene information) was used to name clusters using log fold-change dot product method of CIPR with the ImmGen database as the reference ((Heng TS, Nat Immunol. 2008;9(10):1091-4), (Ekiz HA, BMC Bioinformatics. 2020;21(1):191)). Additionally, annotations of T cell clusters were verified against T cell reference datasets using ProjectTil package (v3.3) (Andreatta M, Nature Communications. 2021;12(1):2965.).
Assembly: mm10
Supplementary files format and content: Fitlered gene barcode matrices in MEX format

source_name: Syngeneic MC38 CRC Implanted Ectopic Tumors

growth_protocol: Mice were challenged with MC38 tumors that were allowed to grow 14 days.

extract_protocol:
Tumors were excised and disaggregated in medium on ice, and live tumor resident CD45+ immune cells were FACS isolated from and into PBS with 0.4% BSA by the University of utah Flow Cytometry Core.
The Chromium Next GEM Single Cell 5’ Reagent kits v1 (PN-1000006) was used to barcode individual cells with oligonucleotides containing (i) an Illumina R1 sequence, (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a 13 nt template switch oligo (TSO) according to the manufacturer. The following protocol based on 10x Genomics user guide (CG000086) was performed by High-Throughput Genomics Shared Resource at Huntsman Cancer Institute, University of Utah. Briefly, isolated CD45+ single cells suspended in PBS/0.04% BSA were filtered through 40 micron cell strainer.  Viability and cell count were assessed on Cellometer K2 (Nexcelom Bioscience) by dual fluorescence staining of Acridine Orange and Propidium Iodide (AO/PI). Nano-droplets were generated by loading samples sufficient for targeted recovery of 6,000 cells, along with 10x Gel Beads and reverse transcription reagents to the Chromium Single Cell Chip A (PN-1000009) to form Gel-Bead-In EMulsions (GEMs). Within individual GEMs, barcoded cDNA generated from captured poly-adenylated mRNA was synthesized by reverse transcription (RT) with a master mix containing reverse transcription reagents and poly d(T) RT primer at the setting of 53°C for 45 min followed by 85°C for 5 min.  Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with i7 Multiplex Kit (PN-120262) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 2200 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumina Platforms (KK4842).  Multiple libraries were then normalized, pooled and sequenced on NovaSeq 6000 with 150x150 paired-end mode.

treatment_protocol: Tumor transplanted mice were treated with anti-PD-1 antibodies or vehicle on days 7 and 10.

tag: strain

value: miR-155 fl/fl CD4Cre+/-

value: CD45+ Immune Cells

value: female

value: PBS


title: 18790X7 miR-155 fl/fl CD4Cre+/- (anti-PD-1) Female

value: Syngeneic MC38 CRC Implanted Ectopic Tumors


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2, EM-seq

value: R1 mESCs

value: Embryonic stem cell


title: 18790X3 miR-155 fl/fl CD4Cre+/- (anti-PD-1) Male

value: male


title: 18790X6 miR-155 fl/fl (PBS) Female

value: miR-155 fl/fl


title: 18790X2 miR-155 fl/fl (PBS) Male


title: HOs co-cultured with LiECs, P8, Day 10_3

city: Suwon-si

first: Jongsu

last: Kim

address: 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea (16419)

country: South Korea

institute: Sungkyunkwan university

data_processing:
Ilumina NovaSeq 6000 reads were trimmed in Trimmomatic v0.38.
Quality check was performed though FastQC v0.11.7.
High throughput sequencing data mapped to GRCh37 genomic reference using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1.
FPKM and TPM were calculated using StringTie version 2.1.3b.
Assembly: mm10
Supplementary files format and content: Tab file includes FPKMs and TPMs for each sample

source_name: Liver

growth_protocol: Hepatobiliary organoids were maintained in advanced DMEM supplemented with 25mM HEPES, 100μg/ml heparin, GlutaMAX, 5% Knock-out serum replacement, 10mM Nicotinamide, 100μg/ml Primocin, 50U/ml penicillin, 50μg/ml streptomycin, 100μg/ml ECGS, 10μg/ml Y-27632, and 50ng/ml EGF

extract_protocol:
RNA was isolated using  Arcturus picopure RNA isolation kit (ThermoFisher) following manufacturer's instructions
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded totalRNA ribo-zero kit

treatment_protocol: Hepatobiliary organoids were co-cultured with or without liver endothelial cells for 10 days

value: Liver

value: Primary cell

value: Liver stem/progenitor cells

value: Wild-type

value: co-cultured with LiECs


title: HOs alone, P1, Day 10_2


title: HOs co-cultured with LiECs, P8, Day 10_2


title: HOs co-cultured with LiECs, P8, Day 10_1


title: 18790X4 miR-155 fl/fl CD4Cre+/- (PBS) Male


title: NK_UN_N7

value: spleen

value: NK cells


title: OIR1

city: Shanghai

first: Miao

middle: miao

last: Liu

address: Kongjiang Road

institute: liumiaobiotech

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house per scripts.In this step.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ftp://ftp.ensembl.org/pub/release-80/fasta/anas_platyrhynchos/dna/
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: retina at P17

extract_protocol:
eighteen polyA mRNA-seq libraries, including nine from Gaoyou duck PM and nine fom Jingding duck PM, RNA was harvested using Trizol reagent. Illlumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the Construction of Sequencing.
RNA lilbraries were prepared for sequencing using standard illumina protocol.

value: retina at P17

value: WT

value: C57BL/6J puppies were exposed to 75% oxygen fromthe 7-day postnatal (P7) to P12, and returned to room air (RA) from  P12 to P17.


title: OIR2


title: OIR3


title: NK_IL15C_WT1

value: wild-type


title: Control-2

value: C57BL/6J puppies were maintained in room air (RA) from  P7 to P17.


title: SD, replicate 4, snRNA-seq

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description:
10X Genomics
sleepseq_matrix.mtx.gz
sleepseq_barcodes.tsv.gz
sleepseq_features.tsv.gz
sleepseq_meta.tsv.gz

data_processing:
CellRanger mkfastq, CellRanger count
FastQC
CellBender
DoubletFinder
Seurat
Assembly: mm10 (GRCm38p6)
Supplementary files format and content: sleepseq_matrix.mtx.gz' has raw counts for all samples.
Supplementary files format and content: sleepseq_barcodes.tsv.gz' has list of barcodes for all samples matching with raw counts.
Supplementary files format and content: sleepseq_features.tsv.gz' has list of genes matching to raw counts.
Supplementary files format and content: sleepseq_meta.tsv.gz' has all meta information including assigned celltypes.

molecule: nuclear RNA

source_name: Brain, Cortex

extract_protocol:
Nuclei for snRNA-seq were isolated from mice, 8-10 weeks old.
Droplet-based snRNA-seq libraries were prepared using Chromium Single Cell 3ʹ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol42. Libraries were sequenced using an Illumina NovaSeq 6000.

treatment_protocol: All mice were accommodated for 1-2 weeks to a cage and treadmill, consis7ng of a bofomless plexiglass enclosure suspended over the treadmill with ad lib access to food and water. For sleep depriva7on (SD) the slow-moving treadmill (0.1KM/hour) was engaged from ZT 0-6 hours and for recovery sleep (RS) from ZT 0-4. There was no treadmill engagement for RS from ZT 4-6 hours and for control sleep (CS), no treadmill engagement for the en7re ZT 0-6 hours period. All animals were sacrificed at ZT=6 hours and 7ssue rapidly prepared for either electrophysiological (exVivo brain slices) or transcriptomic analysis

value: Brain, Cortex

value: SD


title: G4

description: 10x Genomics

value: heart

value: cardiomyocyte-depleted and CD45+ depleted cells

value: db/db

value: 1percent salt


title: SD, replicate 3, snRNA-seq


title: HOs alone, P1, Day 10_1

value: Liver

value: Primary cell


title: SD, replicate 1, snRNA-seq


title: CS, replicate 4, snRNA-seq

value: CS


title: CS, replicate 3, snRNA-seq


title: CS, replicate 2, snRNA-seq


title: 18790X1 miR-155 fl/fl (anti-PD-1) Male

value: Syngeneic MC38 CRC Implanted Ectopic Tumors

value: miR-155 fl/fl

value: CD45+ Immune Cells

value: male


title: 18790X5 miR-155 fl/fl (anti-PD-1) Female

value: female


title: WT Striatum female snRNA rep2 [Msh3 snRNA-seq]

description:
72-4
Single-cell RNA sequencing

data_processing:
Samples were sequenced on NovaSeq S4 platform at UCLA Technology Center for Genomics and Bioinformatics.
Cellranger-6.1.2 from 10x Genomics was used for alignment and quantification.
Assembly: mm10-2020-A
Supplementary files format and content: Tar archives include barcodes, features, and count matrix, in the forms of tab-separated and market exchange format, respectively.

source_name: Corpus Striatum

extract_protocol:
Brain striatal tissues were dissected and snap-frozen on dry ice. Nuclei were isolated using the ‘Frankenstein’ protocol by Luciano Martelotto (10x Genomics Customer Developed Protocol). With FACS, 16,500 DAPI+ nuclei were collected for each sample and loaded onto the 10X chromium device.
The library preparation and sequencing were performed following 10X Genomics Chromium protocols.

value: Corpus Striatum

value: Wild type

tag: strain/background

value: 12 months


title: CS, replicate 1, snRNA-seq

value: Brain, Cortex

value: wild-type


title: Control-3

value: retina at P17

value: WT

value: C57BL/6J puppies were maintained in room air (RA) from  P7 to P17.


title: WT Striatum female snRNA rep1 [Msh3 snRNA-seq]

description:
71-4
Single-cell RNA sequencing


title: Control-1


title: Msh3+/- Striatum male snRNA rep2 [Msh3 snRNA-seq]

description:
33-1
Single-cell RNA sequencing


title: Msh3+/- Striatum female snRNA rep2 [Msh3 snRNA-seq]

description:
19-4
Single-cell RNA sequencing


title: WT Striatum male snRNA rep1 [Msh3 snRNA-seq]

description:
17-4
Single-cell RNA sequencing


title: Msh3+/- Striatum female snRNA rep1 [Msh3 snRNA-seq]

description:
21-3
Single-cell RNA sequencing


title: Msh3-/- Striatum female snRNA rep2 [Msh3 snRNA-seq]

description:
26-1
Single-cell RNA sequencing


title: Msh3-/- Striatum male snRNA rep2 [Msh3 snRNA-seq]

description:
20-1
Single-cell RNA sequencing


title: Msh3-/- Striatum male snRNA rep1 [Msh3 snRNA-seq]

description:
5-5
Single-cell RNA sequencing


title: Het (Q140) KI X Msh3+/- Striatum male snRNA rep2 [Msh3 snRNA-seq]

description:
31-1
Single-cell RNA sequencing

value: Het (Q140) KI X Msh3+/-


title: Msh3+/- Striatum male snRNA rep1 [Msh3 snRNA-seq]

description:
22-2
Single-cell RNA sequencing


title: SD, replicate 2, snRNA-seq

value: SD


title: Het (Q140) KI X Msh3+/- Striatum male snRNA rep1 [Msh3 snRNA-seq]

description:
17-5
Single-cell RNA sequencing


title: Het (Q140) KI X Msh3+/- Striatum female snRNA rep2 [Msh3 snRNA-seq]

description:
21-4
Single-cell RNA sequencing


title: Het (Q140) KI X Msh3-/- Striatum female snRNA rep2 [Msh3 snRNA-seq]

description:
30-1
Single-cell RNA sequencing

value: Het (Q140) KI X Msh3-/-


title: Het (Q140) KI X Msh3-/- Striatum male snRNA rep2 [Msh3 snRNA-seq]

description:
47-1
Single-cell RNA sequencing


title: Msh3-/- Striatum female snRNA rep1 [Msh3 snRNA-seq]

description:
18-3
Single-cell RNA sequencing


title: Het (Q140) KI X Msh3-/- Striatum female snRNA rep1 [Msh3 snRNA-seq]

description:
39-2
Single-cell RNA sequencing


title: Het (Q140) KI Striatum male snRNA rep2 [Msh3 snRNA-seq]

description:
20-2
Single-cell RNA sequencing

value: Het (Q140) KI


title: WT Striatum male mRNA rep4 [Ccdc82]

description:
Ccdc82_STR36_2
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse390_FPKM_Ccdc82_STR_6m.csv: Comma-separated text file includes FPKM values.
Supplementary files format and content: hdgse390_metaReadCount_Ccdc82_STR_6m.csv: Comma-separated text file includes count values.

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: 6 months

tag: well address


title: Het (Q140) KI Striatum male snRNA rep1 [Msh3 snRNA-seq]

description:
40-5
Single-cell RNA sequencing


title: WT Striatum male snRNA rep2 [Msh3 snRNA-seq]

description:
22-3
Single-cell RNA sequencing


title: Het (Q140) KI Striatum female snRNA rep1 [Msh3 snRNA-seq]

description:
18-5
Single-cell RNA sequencing


title: Het (Q140) KI X Msh3-/- Striatum male snRNA rep1 [Msh3 snRNA-seq]

description:
36-5
Single-cell RNA sequencing


title: WT Striatum male mRNA rep3 [Ccdc82]

description:
Ccdc82_STR34_1
mRNA


title: WT Striatum female mRNA rep4 [Ccdc82]

description:
Ccdc82_STR33_2
mRNA


title: WT Striatum female mRNA rep3 [Ccdc82]

description:
Ccdc82_STR31_1
mRNA


title: Wild type Striatum male 21-1


title: Het (Q140) KI X Ccdc82+/- Striatum male mRNA rep4 [Ccdc82]

description:
Ccdc82_STR32_3
mRNA

value: Het (Q140) KI X Ccdc82+/-


title: WT Striatum female mRNA rep2 [Ccdc82]

description:
Ccdc82_STR21_2
mRNA


title: WT Striatum female mRNA rep1 [Ccdc82]

description:
Ccdc82_STR18_3
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum male mRNA rep2 [Ccdc82]

description:
Ccdc82_STR19_4
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum male mRNA rep3 [Ccdc82]

description:
Ccdc82_STR25_2
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum female mRNA rep4 [Ccdc82]

description:
Ccdc82_STR33_5
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum female mRNA rep2 [Ccdc82]

description:
Ccdc82_STR16_3
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum male mRNA rep1 [Ccdc82]

description:
Ccdc82_STR19_2
mRNA


title: WT Striatum male mRNA rep1 [Ccdc82]

description:
Ccdc82_STR17_1
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum female mRNA rep3 [Ccdc82]

description:
Ccdc82_STR31_2
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female snRNA rep1 [Msh3 snRNA-seq]

description:
18-2
Single-cell RNA sequencing


title: Het (Q140) KI X Ccdc82-/- Striatum male mRNA rep4 [Ccdc82]

description:
Ccdc82_STR41_1
mRNA

value: Het (Q140) KI X Ccdc82-/-


title: Het (Q140) KI X Ccdc82-/- Striatum male mRNA rep3 [Ccdc82]

description:
Ccdc82_STR32_2
mRNA

value: male


title: Het (Q140) KI X Ccdc82-/- Striatum male mRNA rep2 [Ccdc82]

description:
Ccdc82_STR32_1
mRNA


title: Het (Q140) KI X Ccdc82+/- Striatum female mRNA rep1 [Ccdc82]

description:
Ccdc82_STR16_2
mRNA

value: female


title: Het (Q140) KI Striatum female snRNA rep2 [Msh3 snRNA-seq]

description:
71-2
Single-cell RNA sequencing

value: Corpus Striatum


title: Het (Q140) KI X Ccdc82-/- Striatum male mRNA rep1 [Ccdc82]

description:
Ccdc82_STR27_5
mRNA


title: Het (Q140) KI X Ccdc82-/- Striatum female mRNA rep3 [Ccdc82]

description:
Ccdc82_STR40_4
mRNA


title: Het (Q140) KI X Ccdc82-/- Striatum female mRNA rep2 [Ccdc82]

description:
Ccdc82_STR21_1
mRNA


title: Het (Q140) KI X Ccdc82-/- Striatum female mRNA rep1 [Ccdc82]

description:
Ccdc82_STR18_4
mRNA


title: WT Striatum male mRNA rep2 [Ccdc82]

description:
Ccdc82_STR27_4
mRNA

value: Wild type


title: Het (Q140) KI Striatum male mRNA rep1 [Ccdc82]

description:
Ccdc82_STR25_4
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Ccdc82]

description:
Ccdc82_STR29_1
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Ccdc82]

description:
Ccdc82_STR27_1
mRNA


title: Het (Q140) KI Striatum male mRNA rep4 [Ccdc82]

description:
Ccdc82_STR29_5
mRNA


title: Het (Q140) KI Striatum female mRNA rep3 [Ccdc82]

description:
Ccdc82_STR26_1
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Ccdc82]

description:
Ccdc82_STR21_3
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Ccdc82]

description:
Ccdc82_STR22_4
mRNA


title: Ccdc82+/- Striatum male mRNA rep2 [Ccdc82]

description:
Ccdc82_STR19_3
mRNA


title: Ccdc82+/- Striatum male mRNA rep3 [Ccdc82]

description:
Ccdc82_STR29_2
mRNA


title: Ccdc82+/- Striatum male mRNA rep4 [Ccdc82]

description:
Ccdc82_STR29_3
mRNA


title: Ccdc82+/- Striatum female mRNA rep3 [Ccdc82]

description:
Ccdc82_STR28_3
mRNA


title: Ccdc82+/- Striatum female mRNA rep4 [Ccdc82]

description:
Ccdc82_STR33_3
mRNA


title: Ccdc82+/- Striatum female mRNA rep2 [Ccdc82]

description:
Ccdc82_STR26_3
mRNA


title: Ccdc82-/- Striatum male mRNA rep4 [Ccdc82]

description:
Ccdc82_STR41_3
mRNA


title: Ccdc82-/- Striatum male mRNA rep2 [Ccdc82]

description:
Ccdc82_STR25_1
mRNA


title: Ccdc82+/- Striatum female mRNA rep1 [Ccdc82]

description:
Ccdc82_STR22_3
mRNA


title: Ccdc82-/- Striatum male mRNA rep1 [Ccdc82]

description:
Ccdc82_STR19_5
mRNA


title: Ccdc82-/- Striatum female mRNA rep4 [Ccdc82]

description:
Ccdc82_STR37_3
mRNA


title: Ccdc82-/- Striatum male mRNA rep3 [Ccdc82]

description:
Ccdc82_STR36_3
mRNA


title: Ccdc82-/- Striatum female mRNA rep3 [Ccdc82]

description:
Ccdc82_STR31_3
mRNA


title: WT Cortex male mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX36_2
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse389_FPKM_Ccdc82_CTX_6m.csv: Comma-separated text file includes FPKM values.
Supplementary files format and content: hdgse389_metaReadCount_Ccdc82_CTX_6m.csv: Comma-separated text file includes count values.

source_name: Cerebral Cortex

extract_protocol:
Cerebral cortex tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Cerebral Cortex


title: Ccdc82-/- Striatum female mRNA rep2 [Ccdc82]

description:
Ccdc82_STR28_2
mRNA


title: WT Cortex male mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX34_1
mRNA


title: Ccdc82-/- Striatum female mRNA rep1 [Ccdc82]

description:
Ccdc82_STR22_2
mRNA


title: WT Cortex male mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX27_4
mRNA


title: WT Cortex male mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX17_1
mRNA


title: WT Cortex female mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX33_2
mRNA


title: WT Cortex female mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX31_1
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Ccdc82]

description:
Ccdc82_STR26_2
mRNA


title: WT Cortex female mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX18_3
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex male mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX25_2
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex male mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX32_3
mRNA


title: Ccdc82+/- Striatum male mRNA rep1 [Ccdc82]

description:
Ccdc82_STR19_1
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex male mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX19_4
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex female mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX33_5
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex female mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX31_2
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex male mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX19_2
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex female mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX16_3
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex male mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX32_2
mRNA


title: Het (Q140) KI X Ccdc82+/- Cortex female mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX16_2
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex male mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX41_1
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex male mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX32_1
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex female mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX21_1
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX29_5
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex female mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX40_4
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX25_4
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX26_2
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex female mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX18_4
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX29_1
mRNA


title: Het (Q140) KI X Ccdc82-/- Cortex male mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX27_5
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX22_4
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX21_3
mRNA


title: Ccdc82+/- Cortex male mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX29_3
mRNA


title: WT Cortex female mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX21_2
mRNA


title: Ccdc82+/- Cortex male mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX19_3
mRNA


title: Ccdc82+/- Cortex male mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX19_1
mRNA


title: Ccdc82+/- Cortex female mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX26_3
mRNA


title: Ccdc82+/- Cortex female mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX33_3
mRNA


title: Ccdc82+/- Cortex female mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX22_3
mRNA


title: Ccdc82-/- Cortex male mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX36_3
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX27_1
mRNA


title: Ccdc82-/- Cortex female mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX37_3
mRNA


title: Ccdc82-/- Cortex male mRNA rep4 [Ccdc82]

description:
Ccdc82_CTX41_3
mRNA


title: Ccdc82-/- Cortex male mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX19_5
mRNA


title: Ccdc82-/- Cortex male mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX25_1
mRNA


title: Ccdc82-/- Cortex female mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX31_3
mRNA


title: Ccdc82-/- Cortex female mRNA rep2 [Ccdc82]

description:
Ccdc82_CTX28_2
mRNA


title: WT Striatum male mRNA rep5 [Pms2_striatum]

description:
PQ55_1_STR
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse323_Pms2_Striatum_FPKM.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: hdgse323_Pms2_Striatum_metaReadCount.txt: Tab-delimited text file includes count values.

value: C57BL/6 x 129S2/SvPas


title: WT Striatum male mRNA rep6 [Pms2_striatum]

description:
PQ55_3_STR
mRNA


title: WT Striatum male mRNA rep4 [Pms2_striatum]

description:
PQ40_3_STR
mRNA


title: WT Striatum male mRNA rep3 [Pms2_striatum]

description:
PQ37_2_STR
mRNA


title: WT Striatum male mRNA rep1 [Pms2_striatum]

description:
PQ20_1_STR
mRNA


title: WT Striatum male mRNA rep2 [Pms2_striatum]

description:
PQ36_5_STR
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX26_1
mRNA


title: Ccdc82+/- Cortex male mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX29_2
mRNA


title: WT Striatum female mRNA rep2 [Pms2_striatum]

description:
PQ50_2_STR
mRNA


title: WT Striatum female mRNA rep1 [Pms2_striatum]

description:
PQ36_1_STR
mRNA


title: Pms2+/- Striatum female mRNA rep3 [Pms2_striatum]

description:
PQ42_1_STR
mRNA


title: Ccdc82+/- Cortex female mRNA rep3 [Ccdc82]

description:
Ccdc82_CTX28_3
mRNA


title: Pms2+/- Striatum male mRNA rep2 [Pms2_striatum]

description:
PQ44_5_STR
mRNA


title: Pms2+/- Striatum female mRNA rep1 [Pms2_striatum]

description:
PQ23_1_STR
mRNA


title: Pms2+/- Striatum female mRNA rep2 [Pms2_striatum]

description:
PQ23_3_STR
mRNA


title: Pms2-/- Striatum male mRNA rep4 [Pms2_striatum]

description:
PQ82_1_STR
mRNA


title: Pms2-/- Striatum male mRNA rep3 [Pms2_striatum]

description:
PQ46_3_STR
mRNA


title: Pms2-/- Striatum male mRNA rep2 [Pms2_striatum]

description:
PQ40_2_STR
mRNA


title: Pms2-/- Striatum female mRNA rep2 [Pms2_striatum]

description:
PQ42_3_STR
mRNA


title: Het (Q140) KI X Pms2+/- Striatum male mRNA rep3 [Pms2_striatum]

description:
PQ40_4_STR
mRNA

value: Het (Q140) KI X Pms2+/-


title: Het (Q140) KI X Pms2+/- Striatum male mRNA rep4 [Pms2_striatum]

description:
PQ40_5_STR
mRNA


title: Pms2-/- Striatum female mRNA rep1 [Pms2_striatum]

description:
PQ23_2_STR
mRNA


title: Het (Q140) KI X Pms2+/- Striatum male mRNA rep1 [Pms2_striatum]

description:
PQ20_2_STR
mRNA


title: Het (Q140) KI X Pms2+/- Striatum male mRNA rep2 [Pms2_striatum]

description:
PQ20_5_STR
mRNA


title: Ccdc82-/- Cortex female mRNA rep1 [Ccdc82]

description:
Ccdc82_CTX22_2
mRNA


title: Het (Q140) KI X Pms2+/- Striatum female mRNA rep3 [Pms2_striatum]

description:
PQ41_4_STR
mRNA


title: Het (Q140) KI X Pms2+/- Striatum female mRNA rep2 [Pms2_striatum]

description:
PQ23_4_STR
mRNA


title: Het (Q140) KI X Pms2+/- Striatum female mRNA rep1 [Pms2_striatum]

description:
PQ21_2_STR
mRNA


title: Pms2-/- Striatum male mRNA rep1 [Pms2_striatum]

description:
PQ34_4_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum male mRNA rep5 [Pms2_striatum]

description:
PQ58_3_STR
mRNA

value: Het (Q140) KI X Pms2-/-


title: Het (Q140) KI X Pms2-/- Striatum male mRNA rep3 [Pms2_striatum]

description:
PQ37_5_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum male mRNA rep4 [Pms2_striatum]

description:
PQ51_5_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum male mRNA rep2 [Pms2_striatum]

description:
PQ37_4_STR
mRNA


title: Het (Q140) KI X Pms2+/- Striatum female mRNA rep4 [Pms2_striatum]

description:
PQ43_2_STR
mRNA


title: Pms2+/- Striatum female mRNA rep4 [Pms2_striatum]

description:
PQ43_1_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum female mRNA rep6 [Pms2_striatum]

description:
PQ77_5_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum female mRNA rep5 [Pms2_striatum]

description:
PQ50_5_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum female mRNA rep4 [Pms2_striatum]

description:
PQ41_5_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum female mRNA rep3 [Pms2_striatum]

description:
PQ39_2_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum female mRNA rep2 [Pms2_striatum]

description:
PQ36_2_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep5 [Pms2_striatum]

description:
PQ49_3_STR
mRNA


title: Het (Q140) KI X Pms2-/- Striatum female mRNA rep1 [Pms2_striatum]

description:
PQ21_3_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep4 [Pms2_striatum]

description:
PQ46_1_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Pms2_striatum]

description:
PQ35_1_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Pms2_striatum]

description:
PQ39_1_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep1 [Pms2_striatum]

description:
PQ34_2_STR
mRNA


title: WT Cortex male mRNA rep3 [Pms2]

description:
PQ55_1_CTX
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse322_Pms2_Cortex_FPKM.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: hdgse322_Pms2_Cortex_metaReadCount.txt: Tab-delimited text file includes count values.


title: WT Cortex male mRNA rep2 [Pms2]

description:
PQ40_3_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Striatum male mRNA rep6 [Pms2_striatum]

description:
PQ60_1_STR
mRNA


title: WT Cortex male mRNA rep1 [Pms2]

description:
PQ34_2_CTX
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Pms2_striatum]

description:
PQ21_1_STR
mRNA


title: WT Cortex female mRNA rep4 [Pms2]

description:
PQ50_2_CTX
mRNA


title: WT Cortex female mRNA rep3 [Pms2]

description:
PQ39_1_CTX
mRNA


title: Pms2+/- Striatum male mRNA rep1 [Pms2_striatum]

description:
PQ33_1BC_STR
mRNA


title: Pms2+/- Cortex male mRNA rep4 [Pms2]

description:
PQ44_5_CTX
mRNA


title: WT Cortex female mRNA rep2 [Pms2]

description:
PQ33_1BC_CTX
mRNA


title: Pms2+/- Cortex male mRNA rep1 [Pms2]

description:
PQ36_1_CTX
mRNA


title: Pms2+/- Cortex male mRNA rep2 [Pms2]

description:
PQ36_5_CTX
mRNA


title: Pms2+/- Cortex male mRNA rep3 [Pms2]

description:
PQ40_2_CTX
mRNA


title: Pms2+/- Cortex female mRNA rep4 [Pms2]

description:
PQ43_1_CTX
mRNA


title: Pms2+/- Cortex female mRNA rep3 [Pms2]

description:
PQ42_1_CTX
mRNA


title: Pms2-/- Cortex male mRNA rep4 [Pms2]

description:
PQ82_1_CTX
mRNA


title: Pms2+/- Cortex female mRNA rep1 [Pms2]

description:
PQ35_1_CTX
mRNA


title: Pms2-/- Cortex male mRNA rep2 [Pms2]

description:
PQ36_2_CTX
mRNA


title: Pms2-/- Cortex male mRNA rep3 [Pms2]

description:
PQ46_3_CTX
mRNA


title: Pms2-/- Cortex male mRNA rep1 [Pms2]

description:
PQ20_1_CTX
mRNA


title: WT Cortex male mRNA rep4 [Pms2]

description:
PQ55_3_CTX
mRNA


title: Pms2+/- Cortex female mRNA rep2 [Pms2]

description:
PQ39_2_CTX
mRNA


title: Pms2-/- Cortex female mRNA rep3 [Pms2]

description:
PQ37_2_CTX
mRNA


title: Pms2-/- Cortex female mRNA rep2 [Pms2]

description:
PQ23_4_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Striatum male mRNA rep1 [Pms2_striatum]

description:
PQ36_3_STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Pms2_striatum]

description:
PQ41_3_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep6 [Pms2_striatum]

description:
PQ67_1_STR
mRNA


title: Pms2-/- Cortex female mRNA rep1 [Pms2]

description:
PQ23_1_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex male mRNA rep4 [Pms2]

description:
PQ40_5_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex male mRNA rep2 [Pms2]

description:
PQ34_4_CTX
mRNA


title: Pms2-/- Cortex female mRNA rep4 [Pms2]

description:
PQ42_3_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex female mRNA rep4 [Pms2]

description:
PQ43_2_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex male mRNA rep1 [Pms2]

description:
PQ20_2_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex female mRNA rep3 [Pms2]

description:
PQ41_4_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex female mRNA rep1 [Pms2]

description:
PQ23_2_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex female mRNA rep2 [Pms2]

description:
PQ37_5_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex male mRNA rep2 [Pms2]

description:
PQ51_5_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex male mRNA rep3 [Pms2]

description:
PQ58_3_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex female mRNA rep4 [Pms2]

description:
PQ77_5_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex male mRNA rep1 [Pms2]

description:
PQ36_3_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex female mRNA rep2 [Pms2]

description:
PQ41_5_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex female mRNA rep3 [Pms2]

description:
PQ50_5_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex male mRNA rep4 [Pms2]

description:
PQ60_1_CTX
mRNA


title: Het (Q140) KI X Pms2-/- Cortex female mRNA rep1 [Pms2]

description:
PQ21_1_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Pms2]

description:
PQ46_1_CTX
mRNA


title: Het (Q140) KI X Pms2+/- Cortex male mRNA rep3 [Pms2]

description:
PQ40_4_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Pms2]

description:
PQ37_4_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Pms2]

description:
PQ67_1_CTX
mRNA


title: WT Striatum male mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_MhCQ16_4
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse321_Msh3_striatum_6month_FPKM.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: hdgse321_Msh3_striatum_6month_metaReadCount.txt: Tab-delimited text file includes count values.


title: Het (Q140) KI Cortex male mRNA rep3 [Pms2]

description:
PQ49_3_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Pms2]

description:
PQ20_5_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Pms2]

description:
PQ23_3_CTX
mRNA


title: WT Striatum male mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q38_1
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Pms2]

description:
PQ41_3_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Pms2]

description:
PQ21_2_CTX
mRNA


title: WT Striatum male mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Msh3Q8_3
mRNA


title: WT Striatum female mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q39_4
mRNA


title: WT Striatum male mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_MMQC17_3
mRNA


title: WT Cortex female mRNA rep1 [Pms2]

description:
PQ21_3_CTX
mRNA


title: Msh3+/- Striatum male mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q11_4
mRNA


title: WT Striatum female mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q42_5
mRNA


title: Msh3+/- Striatum female mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q40_3
mRNA


title: Msh3+/- Striatum male mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q51_4
mRNA


title: Msh3+/- Striatum male mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q44_3
mRNA


title: Msh3+/- Striatum female mRNA rep5 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Msh3Q9_5
mRNA


title: WT Striatum female mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q66_5
mRNA


title: Msh3+/- Striatum female mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_MMQC24_3
mRNA


title: Msh3+/- Striatum female mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q48_3
mRNA


title: Msh3+/- Striatum female mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q45_3
mRNA


title: Msh3-/- Striatum male mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q51_3
mRNA


title: Msh3-/- Striatum male mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Msh3Q8_1
mRNA


title: Msh3-/- Striatum male mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q56_3
mRNA


title: Msh3-/- Striatum male mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q47_5
mRNA


title: Msh3-/- Striatum female mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q40_4
mRNA


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q47_4
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q39_5
mRNA


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Msh3Q8_5
mRNA


title: Msh3+/- Striatum male mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q11_5
mRNA


title: Msh3-/- Striatum female mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q48_5
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q42_4
mRNA


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q56_5
mRNA


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q53_5
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Msh3Q9_2
mRNA


title: Msh3-/- Striatum female mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q48_4
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q45_1
mRNA


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q65_2
mRNA


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q52_2
mRNA


title: Msh3-/- Striatum female mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q40_1
mRNA


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q71_3
mRNA


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q61_1
mRNA


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q48_2
mRNA


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q58_1
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q41_4
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Msh3Q9_3
mRNA


title: Het (Q140) KI Striatum female mRNA rep3 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q66_1
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q34_2
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q34_1
mRNA


title: Het (Q140) KI Striatum male mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q33_5
mRNA


title: WT Cortex male mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Msh3Q8_3
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse320_Msh3_cortex_6month_FPKM.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: hdgse320_Msh3_cortex_6month_metaReadCount.txt: Tab-delimited text file includes count values.


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep1 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q44_1
mRNA


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q56_1
mRNA


title: WT Cortex male mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_MhCQ16_4
mRNA


title: WT Cortex female mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q42_5
mRNA


title: WT Cortex female mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q66_5
mRNA


title: WT Cortex male mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q38_1
mRNA


title: Msh3+/- Cortex male mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q11_5
mRNA


title: Msh3+/- Cortex female mRNA rep5 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Msh3Q9_5
mRNA


title: Msh3+/- Cortex male mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q44_3
mRNA


title: Msh3+/- Cortex female mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q45_3
mRNA


title: Msh3+/- Cortex female mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q48_3
mRNA


title: Het (Q140) KI Striatum male mRNA rep4 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q65_1
mRNA


title: Msh3+/- Cortex female mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_MMQC24_3
mRNA


title: Msh3-/- Cortex male mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q51_3
mRNA


title: Msh3-/- Cortex male mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q47_5
mRNA


title: Msh3-/- Cortex male mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Msh3Q8_1
mRNA


title: Msh3-/- Cortex female mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q48_5
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Msh3_striatum_6m]

description:
Mh3Q6mSTR_Mh3Q35_1
mRNA


title: Msh3-/- Cortex male mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q56_3
mRNA


title: WT Cortex female mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q39_4
mRNA


title: Msh3-/- Cortex female mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q40_4
mRNA


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q65_2
mRNA


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q47_4
mRNA


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q44_1
mRNA


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q53_5
mRNA


title: WT Cortex male mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_MMQC17_3
mRNA


title: Msh3-/- Cortex female mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q40_1
mRNA


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q42_4
mRNA


title: Msh3+/- Cortex male mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q11_4
mRNA


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Msh3Q9_2
mRNA


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q39_5
mRNA


title: Het (Q140) KI X Msh3-/- Cortex male mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q56_5
mRNA


title: Het (Q140) KI X Msh3-/- Cortex male mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Msh3Q8_5
mRNA


title: Msh3+/- Cortex female mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q40_3
mRNA


title: Het (Q140) KI X Msh3-/- Cortex male mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q52_2
mRNA


title: Het (Q140) KI X Msh3-/- Cortex female mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q71_3
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q65_1
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q35_1
mRNA


title: Het (Q140) KI X Msh3-/- Cortex female mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q61_1
mRNA


title: Het (Q140) KI X Msh3-/- Cortex male mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q56_1
mRNA


title: Msh3-/- Cortex female mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q48_4
mRNA


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q45_1
mRNA


title: Het (Q140) KI X Msh3-/- Cortex female mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q48_2
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q66_1
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q34_1
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Msh3Q9_3
mRNA


title: Het (Q140) KI X Msh3-/- Cortex female mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q58_1
mRNA


title: WT Striatum male mRNA rep4 [Mlh1_4m]

description:
MLQ4m_59_1
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse318_Mlh1_striatum_4month_FPKM.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: hdgse318_Mlh1_striatum_4month_metaReadCount.txt: Tab-delimited text file includes count values.

extract_protocol:
Brain striatal tissues were dissected from all mice at 4 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: 4 months


title: WT Striatum male mRNA rep2 [Mlh1_4m]

description:
MLQ4m_45_2
mRNA


title: WT Striatum female mRNA rep4 [Mlh1_4m]

description:
MLQ4m_54_4
mRNA


title: WT Striatum male mRNA rep1 [Mlh1_4m]

description:
MLQ4m_45_1
mRNA


title: WT Striatum female mRNA rep3 [Mlh1_4m]

description:
MLQ4m_48_2
mRNA


title: WT Striatum female mRNA rep2 [Mlh1_4m]

description:
MLQ4m_40_1BC
mRNA


title: WT Striatum female mRNA rep1 [Mlh1_4m]

description:
MLQ4m_39_1
mRNA


title: Mlh1+/- Striatum male mRNA rep4 [Mlh1_4m]

description:
MLQ4m_59_2
mRNA


title: Msh3+/- Cortex male mRNA rep4 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q51_4
mRNA


title: Mlh1+/- Striatum male mRNA rep2 [Mlh1_4m]

description:
MLQ4m_47_2
mRNA


title: Mlh1+/- Striatum female mRNA rep5 [Mlh1_4m]

description:
MLQ4m_74_3
mRNA


title: Mlh1+/- Striatum male mRNA rep1 [Mlh1_4m]

description:
MLQ4m_43_1
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q41_4
mRNA


title: Mlh1+/- Striatum female mRNA rep3 [Mlh1_4m]

description:
MLQ4m_46_5
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q33_5
mRNA


title: Mlh1+/- Striatum female mRNA rep4 [Mlh1_4m]

description:
MLQ4m_48_1
mRNA


title: Mlh1-/- Striatum male mRNA rep2 [Mlh1_4m]

description:
MLQ4m_47_3
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Msh3_cortex_6m]

description:
Mh3Q6mCTX_Mh3Q34_2
mRNA


title: Mlh1+/- Striatum female mRNA rep1 [Mlh1_4m]

description:
MLQ4m_39_2
mRNA


title: Mlh1-/- Striatum male mRNA rep4 [Mlh1_4m]

description:
MLQ4m_67_1
mRNA


title: Mlh1-/- Striatum female mRNA rep3 [Mlh1_4m]

description:
MLQ4m_72_2
mRNA


title: Mlh1-/- Striatum male mRNA rep1 [Mlh1_4m]

description:
MLQ4m_43_2
mRNA


title: Mlh1-/- Striatum male mRNA rep3 [Mlh1_4m]

description:
MLQ4m_65_2
mRNA


title: WT Striatum male mRNA rep3 [Mlh1_4m]

description:
MLQ4m_53_3
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep4 [Mlh1_4m]

description:
MLQ4m_45_3
mRNA

value: Het (Q140) KI X Mlh1+/-


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep5 [Mlh1_4m]

description:
MLQ4m_73_3
mRNA


title: Mlh1-/- Striatum female mRNA rep2 [Mlh1_4m]

description:
MLQ4m_54_1
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep3 [Mlh1_4m]

description:
MLQ4m_43_3
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep2 [Mlh1_4m]

description:
MLQ4m_41_4
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep3 [Mlh1_4m]

description:
MLQ4m_71_1
mRNA


title: Mlh1+/- Striatum male mRNA rep3 [Mlh1_4m]

description:
MLQ4m_53_4
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep1 [Mlh1_4m]

description:
MLQ4m_39_5
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum male mRNA rep3 [Mlh1_4m]

description:
MLQ4m_59_3
mRNA

value: Het (Q140) KI X Mlh1-/-


title: Het (Q140) KI X Mlh1-/- Striatum male mRNA rep1 [Mlh1_4m]

description:
MLQ4m_47_1
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum female mRNA rep5 [Mlh1_4m]

description:
MLQ4m_66_3
mRNA


title: Mlh1+/- Striatum female mRNA rep2 [Mlh1_4m]

description:
MLQ4m_44_3
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum male mRNA rep4 [Mlh1_4m]

description:
MLQ4m_70_3
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum female mRNA rep4 [Mlh1_4m]

description:
MLQ4m_54_3
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Mlh1_4m]

description:
MLQ4m_61_3
mRNA


title: Mlh1-/- Striatum female mRNA rep1 [Mlh1_4m]

description:
MLQ4m_39_3
mRNA


title: Het (Q140) KI Striatum male mRNA rep1 [Mlh1_4m]

description:
MLQ4m_45_4
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Mlh1_4m]

description:
MLQ4m_55_3
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Mlh1_4m]

description:
MLQ4m_42_4
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Mlh1_4m]

description:
MLQ4m_63_5
mRNA


title: WT Cortex male mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX59_1
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: hdgse317_Mlh1_Cortex_4month_FPKM.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: hdgse317_Mlh1_Cortex_4month_metaReadCount.txt: Tab-delimited text file includes count values.

extract_protocol:
Cerebral cortex tissues were dissected from all mice at 4 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).


title: Het (Q140) KI X Mlh1-/- Striatum female mRNA rep1 [Mlh1_4m]

description:
MLQ4m_44_1
mRNA


title: Het (Q140) KI Striatum female mRNA rep3 [Mlh1_4m]

description:
MLQ4m_44_4
mRNA


title: WT Cortex male mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX53_3
mRNA


title: WT Cortex female mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX54_4
mRNA


title: WT Cortex male mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX45_1
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum female mRNA rep3 [Mlh1_4m]

description:
MLQ4m_46_4
mRNA


title: WT Cortex male mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX45_2
mRNA


title: WT Cortex female mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX48_2
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep1 [Mlh1_4m]

description:
MLQ4m_38_1
mRNA


title: WT Cortex female mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX40_1BC
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep2 [Mlh1_4m]

description:
MLQ4m_44_5
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum male mRNA rep2 [Mlh1_4m]

description:
MLQ4m_53_2
mRNA


title: WT Cortex female mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX39_1
mRNA


title: Mlh1+/- Cortex male mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX59_2
mRNA


title: Mlh1+/- Cortex male mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX53_4
mRNA


title: Mlh1+/- Cortex male mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX47_2
mRNA


title: Het (Q140) KI X Mlh1-/- Striatum female mRNA rep2 [Mlh1_4m]

description:
MLQ4m_44_2
mRNA


title: Mlh1+/- Cortex female mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX48_1
mRNA


title: Mlh1+/- Cortex female mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX46_5
mRNA


title: Mlh1+/- Cortex female mRNA rep5 [Mlh1_4m]

description:
MLQ4mCTX74_3
mRNA


title: Mlh1+/- Cortex female mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX44_3
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Mlh1_4m]

description:
MLQ4m_39_4
mRNA


title: Mlh1-/- Cortex male mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX67_1
mRNA


title: Mlh1+/- Cortex female mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX39_2
mRNA


title: Mlh1-/- Cortex male mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX65_2
mRNA


title: Mlh1-/- Cortex female mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX72_2
mRNA


title: Mlh1-/- Cortex male mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX43_2
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX45_3
mRNA


title: Mlh1-/- Cortex male mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX47_3
mRNA


title: Mlh1-/- Cortex female mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX54_1
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX38_1
mRNA


title: Mlh1-/- Cortex female mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX39_3
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX71_1
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX44_5
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX43_3
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX41_4
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex male mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX70_3
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep5 [Mlh1_4m]

description:
MLQ4mCTX73_3
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex male mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX53_2
mRNA


title: Mlh1+/- Cortex male mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX43_1
mRNA


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX39_5
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex female mRNA rep5 [Mlh1_4m]

description:
MLQ4mCTX66_3
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex female mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX54_3
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex male mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX59_3
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex female mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX46_4
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex female mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX44_1
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX61_3
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX63_5
mRNA


title: Het (Q140) KI X Mlh1-/- Cortex female mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX44_2
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Mlh1_4m]

description:
MLQ4mCTX55_3
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX45_4
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Mlh1_4m]

description:
MLQ4mCTX44_4
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Mlh1_4m]

description:
MLQ4mCTX42_4
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX39_4
mRNA


title: WT Striatum Male rep3 [Msh3]

data_processing:
Libraries for ATAC-seq were sequenced using an Illumina Novaseq S4.
Burrows-Wheeler Aligner (BWA) was used for alignment with default parameters to mouse genome GRCm38,
Samtools and Picard were used for marking and removing duplicates,
MACS2 was used to identify peaks with parameter nomodel,
and featureCounts was used to quantify the reads.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Msh3_striatum_12month_combined.narrowPeak_counts_annot.txt: Tab-delimited text file includes the count matrix.

source_name: Striatum

extract_protocol:
Brain tissues were dissected from mice at 12 months of age. Nuclei were dissociated from frozen striatal tissues and labeled with Alexa 488-conjugated anti-NeuN antibody. Neuronal nuclei were then harvested by flow cytometric sorting. 50,000 nuclei for each sample were used for transposition reactions and library prep.
The transposition reactions and ATAC-seq library preparation generally followed the steps set out in the original ATAC-seq paper using Nextera DNA Library Preparation Kit.

value: Striatum

value: 12 months

value: Male


title: WT Striatum Male rep2 [Msh3]


title: WT Striatum Female rep2 [Msh3]

value: Female


title: WT Striatum Male rep1 [Msh3]


title: Msh3-/- X Het (Q140) KI Striatum Male rep2 [Msh3]

value: Msh3-/- X Het (Q140) KI


title: Msh3-/- X Het (Q140) KI Striatum Male rep3 [Msh3]


title: WT Striatum Female rep3 [Msh3]


title: WT Striatum Female rep1 [Msh3]


title: Msh3-/- X Het (Q140) KI Striatum Male rep1 [Msh3]


title: Msh3-/- X Het (Q140) KI Striatum Female rep2 [Msh3]


title: Msh3-/- X Het (Q140) KI Striatum Female rep1 [Msh3]


title: Msh3-/- Striatum Male rep1 [Msh3]


title: Msh3-/- Striatum Male rep3 [Msh3]


title: Msh3-/- Striatum Male rep2 [Msh3]


title: Msh3-/- Striatum Female rep1 [Msh3]


title: Msh3-/- Striatum Female rep3 [Msh3]


title: Het (Q140) KI Striatum Male rep2 [Msh3]

value: Het (Q140) KI


title: Msh3-/- Striatum Female rep2 [Msh3]


title: Het (Q140) KI Striatum Female rep3 [Msh3]


title: Het (Q140) KI Striatum Male rep1 [Msh3]


title: Het (Q140) KI Striatum Female rep1 [Msh3]


title: Het (Q140) KI Striatum Female rep2 [Msh3]


title: DMA-H-2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: mm10
Supplementary files format and content: Raw gene count matrix (rawCounts.tsv)

source_name: Bone marrow

growth_protocol: BM HSPCs were FACS sorted from indicated mice using conventional cell surface markers (Lin-Sca-1+cKit+).

extract_protocol:
RNA was extracted using the Qiagen RNAeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either water (H2O) or ADP-heptose for 90mins in vitro

value: Bone marrow

value: Primary cells

value: LSK


title: DMA-A-2

value: ADP-heptose


title: DMA-H-3


title: DMA-A-1


title: DMA-A-3


title: DM-A-3


title: Msh3-/- X Het (Q140) KI Striatum Female rep3 [Msh3]


title: DMA-H-1


title: DM-A-2


title: DM-H-2


title: DM-A-1


title: DM-H-3


title: DM-H-1


title: WT-A-3


title: Het (Q140) KI X Mlh1-/- Cortex male mRNA rep1 [Mlh1_4m]

description:
MLQ4mCTX47_1
mRNA

value: Cerebral Cortex

value: male


title: WT-A-1


title: WT-H-2


title: WT-H-3


title: WT Striatum male mRNA rep3 [Tcerg1]

description:
Tcerg10_1STR
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Semicolon-delimited csv files include FPKM and Count values for each Sample.

value: Corpus Striatum

value: Wild type

value: 6 months


title: WT Striatum male mRNA rep4 [Tcerg1]

description:
Tcerg18_4STR
mRNA


title: WT Striatum male mRNA rep2 [Tcerg1]

description:
Tcerg7_4STR
mRNA


title: WT Striatum female mRNA rep4 [Tcerg1]

description:
Tcerg22_3STR
mRNA

value: female


title: WT Striatum female mRNA rep1 [Tcerg1]

description:
Tcerg12_2STR
mRNA


title: WT Striatum female mRNA rep3 [Tcerg1]

description:
Tcerg15_2STR
mRNA


title: WT Striatum female mRNA rep2 [Tcerg1]

description:
Tcerg15_1STR
mRNA


title: WT Cortex male mRNA rep4 [Tcerg1]

description:
Tcerg18_4CTX
mRNA


title: WT Striatum male mRNA rep1 [Tcerg1]

description:
Tcerg7_1STR
mRNA