title: MS03 - 0.1 micromolar BSJ-04-0146 - 24 hours - biological replicate 3

description: Library name: Sample 24

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome avaiable on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
The hit counts were summarized and reported using the geneID feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38
Supplementary files format and content: raw counts as comma separated values files "raw_counts.csv" where column header is "X1" for Sample 1 through "X24" for Sample 24

source_name: MS03 murine Nf2-/- Schwann cell line

growth_protocol: 10% FBS and 1% penicillin-streptomycin in DMEM, 37 degrees Celsius humidified incubator, 5% CO2

treatment_protocol: DMSO or indicated compound dissolved in DMSO for 24 hours, cells collected and washed in PBS, frozen cell pellets sent to Azenta/GeneWix for RNA sequencing.

value: MS03 murine Nf2-/- Schwann cell line


title: sc1_Experiment1_KO2

status: Public on Sep 17 2025

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
Library name: Sample 2
Experiment1_KO2

library_source: transcriptomic single cell

data_processing:
The raw sequence data were processed using Cell Ranger software (version: 4.0.0). The reads were aligned to mouse genome mm10 and gene counts matrix was summarized for each sample.
Assembly: mm10
Supplementary files format and content: HDF5 of the raw counts

molecule: total RNA

organism: Mus musculus

source_name: Breast

extract_protocol:
E0771.lmb tumors were grown  as previously described in wild-type and Shb ICKO (Shb flox/flox; Vav1-cre) mice. Mice were sacrificed on day 14-16 after tumor cell injection and CD45+ cells isolated by MACS microbeads.
Sequencing libraries were prepared from 10 000 cells after recovery using the Chromium Next GEM Single Cell 3’ Reagent kit v3.1 with dual-index (cat# 1000268/269/120/127/1000215, 10x Genomics) according to the manufacturer’ protocol (User guide CG000315, Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), 10x Genomics).

tag: tissue

value: Breast

tag: age

value: adult

tag: genotype

value: KO


title: sc1_Experiment1_KO1

description:
Library name: Sample 1
Experiment1_KO1


title: MS03 - 0.1 micromolar BSJ-04-0146 - 24 hours - biological replicate 2

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

country: USA

institute: Indiana University School of Medicine

description: Library name: Sample 23

library_source: transcriptomic

extract_protocol:
Performed by Azenta/GeneWiz: Qiagen Rneasy Plus Mini Kit with DNase treatment
NEBNext Ultra II RNA Library Prep with PolyA selection, 500ng input, 10 PCR amplification cycles

tag: cell line

tag: treatment


title: 22Rv1 cells, Active conditions, Biol rep 1

city: Tampa

first: Conor

last: Lynch

state: Florida

address: 12902 USF Magnolia Drive

institute: H.Lee MOFFITT Cancer Center

description:
Library name: 22RV1_D2_1
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt

data_processing:
The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the P3-200 cycle reagent kit to generate approximately 50M million 100-base read pairs per sample (Illumina, Inc., San Diego, CA). Paired-end sequencing reads were aligned to reference genome GRCh38 or mm10 using STAR v2.5.3a. Gene-level quantification was estimated by RSEM v1.3.0.
Assembly: Gene model GENCODE v30 and vM21 were used for quantification of human and mouse cell lines, respectively.
Supplementary files format and content: Tab delimited text files include raw counts for each species

organism: Homo sapiens

growth_protocol: RM1 cells were cultured routinely in 10% FBS-supplemented DMEM, while LAPC4 & 22Rv1 were cultured in 10% FBS-supplemented RPMI-1640.

extract_protocol:
RNA was extracted from (RM1, 22Rv1, and LAPC4) under different conditions using RNeasy purification kit (74104, Qiagen) with DNAse treatment (79254, Qiagen). 50 ng was used for library preparation.
The samples were then processed for RNA-sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (NuGEN Technologies, San Carlos, CA).  Briefly, 50 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.

treatment_protocol:
Dormancy induction was induced by seeding 91,000 cells / cm2 in regular tissue culture plates in serum free DMEM with high glucose (4.5 g/L) and 1% antibiotics for 48 hours.
Reawakening induction was induced by adding 10% FBS-supplemented DMEM to dormant cells for 24 hours.


title: sc2_Experiment1_KO1

description:
Library name: Sample 1
Experiment1_KO1

extract_protocol:
E0771.lmb tumors were grown after tamoxifen injection as previously described in wild-type and Cdh5-creERt2/Shb flox/flox mice. Mice were sacrificed on day 14-16 after tumor cell injection. The tumors were digested, CD45+-cells isolated by MACS microbeads (Miltenyi, Bergich Gladbach, Germany)
Sequencing libraries were prepared from 10 000 cells after recovery using the Chromium Next GEM Single Cell 3’ Reagent kit v3.1 with dual-index (cat# 1000268/269/120/127/1000215, 10x Genomics) according to the manufacturer’ protocol (User guide CG000315, Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), 10x Genomics).


title: Experiment4_WT3

description: Library name: Sample 21

data_processing:
Samples were analysed with the nf-core rnaseq pipeline release 3.3. In short, the pipeline  does the following: The workflow processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts and performs extensive quality-control on the results.
Assembly: GRCm38
Supplementary files format and content: Tab-seprated values files

extract_protocol:
E0771.lmb tumors were grown after tamoxifen injection as previously described in wild-type and Shb iECKO (Shb flox/flox; Cdh5-CreERt2) mice, alternatively Shb ICKO (Shb flox/flox; Vav1-cre) mice. Mice were sacrificed on day 14-16 after tumor cell injection. The tumors were digested, CD45+-cells isolated by MACS microbeads (Miltenyi, Bergich Gladbach, Germany)  and subsequently CD31+-cells isolated by fluorescence-activated cell sorting (FACS) after staining for CD31.
Libraries were prepared from 30ng total RNA using the Illumina Stranded Total RNA library preparation kit with Ribo-Zero Plus treatment (cat# 20040525/20040529, Illumina Inc.). Unique dual indexes (cat# 20040553/20040554, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (#1000000124514). Paired-end 150bp read length were sequenced.

value: WT


title: Experiment4_WT2

description: Library name: Sample 20


title: MS03 - 0.1 micromolar BSJ-04-0146 - 24 hours - biological replicate 1

description: Library name: Sample 22


title: Experiment4_WT1

description: Library name: Sample 19


title: Experiment4_KO3

description: Library name: Sample 18


title: Pt 'AML8', unenriched BMA, whole RNA 10x capture

city: Seattle

first: Sami

middle: B

last: Kanaan

address: 1100 FAIRVIEW AVE N

department: TST

institute: FRED HUTCHINSON CANCER CENTER

description:
Library name: AML8_BM
molecule: polyA RNA & protein
AML8_merged_Seurat_QCed_metadata.csv
AML8_merged_Seurat_QCed_barcodes.tsv.gz
AML8_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML8_merged_Seurat_QCed_RNA_features.tsv.gz

library_source: other

data_processing:
Illumina BCL conversion to FASTQ (`bcl2fastq` version 2.20.0)
FASTQ to generate BAM; H5, feature barcode TSV; etc... (`cellranger` version 6.0.2)
H5 feature barcode matrix file converted to Seurat object (`R` version 4.2.0; `Seurat` version 5.0.1)
Assembly: hg38
Supplementary files format and content: <…>_features.tsv.gz  A tab-separated file with feature (RNA or ADT) information, including gene IDs and names, or ADT names when applicable.
Supplementary files format and content: <…>_matrix.mtx.gz  A compressed Matrix Market file containing the assay data (expression matrix).
Supplementary files format and content: <…>_barcodes.tsv.gz  A tab-separated file with cell barcodes.
Supplementary files format and content: <…>_metadata.csv  A CSV file containing metadata from the Seurat object.

molecule: other

source_name: Bone marrow

extract_protocol:
Density-gradient collected bone marrow mononuclear cells were magnetically enriched for cells with CD34 cell surface markers (Miltenyi Biotec #130-097-047 or Stemcell #17856) or CD117 markers (Miltenyi Biotec #130-091-332). Both unsorted and enriched cells per each patient/timepoint were stained with BioLegend TotalSeq-C DNA-barcoded antibodies (for ADT expression). Single cell whole RNA capture and DNA-barcoded cell surface proteins capture (when applicable) were performed using either the 10x Genomics Next GEM Single Cell 3’ v3.1 with Feature Barcode chemistry or the 10x Genomics Next GEM Single Cell 5’ v2 with Feature Barcode chemistry according to manufacturer's protocols (10x Genomics User Guide document #CG000317_Rev_B for the 3’ chemistry; #CG000330_Rev_A for the 5’ chemistry).
scRNA-seq

value: Bone marrow

tag: cell type

value: mononuclear cells


title: Pt 'AML8', CD34-enriched BMA, whole RNA 10x capture

description:
Library name: AML8_34
molecule: polyA RNA & protein
AML8_merged_Seurat_QCed_metadata.csv
AML8_merged_Seurat_QCed_barcodes.tsv.gz
AML8_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML8_merged_Seurat_QCed_RNA_features.tsv.gz


title: 22Rv1 cells, Reawakened conditions, Biol rep 2

description:
Library name: R-22RV1_2
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt

value: Reawakening induction


title: Experiment4_KO2

description: Library name: Sample 17


title: Pt 'AML6', unenriched BMA, whole RNA and ADT 10x capture

description:
Library name: AML6_BM
molecule: polyA RNA & protein
AML6_merged_Seurat_QCed_metadata.csv
AML6_merged_Seurat_QCed_barcodes.tsv.gz
AML6_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML6_merged_Seurat_QCed_RNA_features.tsv.gz
AML6_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML6_merged_Seurat_QCed_ADT_features.tsv.gz


title: MS03 - 0.1 micromolar GSK215 - 24 hours - biological replicate 3

description: Library name: Sample 21


title: MS03 - 0.1 micromolar GSK215 - 24 hours - biological replicate 2

description: Library name: Sample 20


title: Experiment4_KO1

description: Library name: Sample 16


title: Experiment3_WT1

description: Library name: Sample 14


title: 22Rv1 cells, Active conditions, Biol rep 3

description:
Library name: 22RV1_D2_3
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Pt 'AML6', CD34-enriched BMA, whole RNA and ADT 10x capture

description:
Library name: AML6_34
molecule: polyA RNA & protein
AML6_merged_Seurat_QCed_metadata.csv
AML6_merged_Seurat_QCed_barcodes.tsv.gz
AML6_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML6_merged_Seurat_QCed_RNA_features.tsv.gz
AML6_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML6_merged_Seurat_QCed_ADT_features.tsv.gz


title: MS03 - 0.1 micromolar GSK215 - 24 hours - biological replicate 1

description: Library name: Sample 19


title: Experiment3_WT2

description: Library name: Sample 15


title: Experiment3_KO2

description: Library name: Sample 13


title: Experiment3_KO1

description: Library name: Sample 12


title: MS03 - 1 micromolar PROTAC FAK degrader 1 - 24 hours - biological replicate 3

description: Library name: Sample 18

value: PROTAC FAK degrader 1 (PROTAC-3)


title: Pt 'AML15', unenriched BMA, whole RNA and ADT 10x capture

description:
Library name: AML15_BM
molecule: polyA RNA & protein
AML15_merged_Seurat_QCed_metadata.csv
AML15_merged_Seurat_QCed_barcodes.tsv.gz
AML15_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML15_merged_Seurat_QCed_RNA_features.tsv.gz
AML15_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML15_merged_Seurat_QCed_ADT_features.tsv.gz


title: Experiment2_WT3

description: Library name: Sample 11


title: Pt 'AML15', CD117-enriched BMA, whole RNA and ADT 10x capture

description:
Library name: AML15_117
molecule: polyA RNA & protein
AML15_merged_Seurat_QCed_metadata.csv
AML15_merged_Seurat_QCed_barcodes.tsv.gz
AML15_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML15_merged_Seurat_QCed_RNA_features.tsv.gz
AML15_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML15_merged_Seurat_QCed_ADT_features.tsv.gz


title: Experiment2_WT2

description: Library name: Sample 10


title: MS03 - 1 micromolar PROTAC FAK degrader 1 - 24 hours - biological replicate 2

description: Library name: Sample 17


title: Experiment2_WT1

description: Library name: Sample 9


title: sc2_Experiment3_WT2

description:
Library name: Sample 12
Experiment3_WT2


title: Experiment2_KO2

description: Library name: Sample 7


title: Experiment1_WT3

description: Library name: Sample 5


title: Experiment2_KO3

description: Library name: Sample 8


title: MS03 - 1 micromolar PROTAC FAK degrader 1 - 24 hours - biological replicate 1

description: Library name: Sample 16


title: MS03 - 1 micromolar IN10018 - 24 hours - biological replicate 3

description: Library name: Sample 15


title: Pt 'AML4', unenriched BMA, whole RNA and ADT 10x capture, day 163 post-alloHCT

description:
Library name: AML4_d163_BM
molecule: polyA RNA & protein
AML4_d163_merged_Seurat_QCed_metadata.csv
AML4_d163_merged_Seurat_QCed_barcodes.tsv.gz
AML4_d163_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML4_d163_merged_Seurat_QCed_RNA_features.tsv.gz
AML4_d163_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML4_d163_merged_Seurat_QCed_ADT_features.tsv.gz


title: Pt 'AML4', unenriched BMA, whole RNA and ADT 10x capture, day 140 post-alloHCT

description:
Library name: AML4_d140_BM
molecule: polyA RNA & protein
AML4_d140_merged_Seurat_QCed_metadata.csv
AML4_d140_merged_Seurat_QCed_barcodes.tsv.gz
AML4_d140_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML4_d140_merged_Seurat_QCed_RNA_features.tsv.gz
AML4_d140_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML4_d140_merged_Seurat_QCed_ADT_features.tsv.gz


title: Experiment2_KO1

description: Library name: Sample 6


title: Pt 'AML4', CD34-enriched BMA, whole RNA and ADT 10x capture, day 163 post-alloHCT

description:
Library name: AML4_d163_34
molecule: polyA RNA & protein
AML4_d163_merged_Seurat_QCed_metadata.csv
AML4_d163_merged_Seurat_QCed_barcodes.tsv.gz
AML4_d163_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML4_d163_merged_Seurat_QCed_RNA_features.tsv.gz
AML4_d163_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML4_d163_merged_Seurat_QCed_ADT_features.tsv.gz


title: Pt 'AML4', CD34-enriched BMA, whole RNA and ADT 10x capture, day 140 post-alloHCT

description:
Library name: AML4_d140_34
molecule: polyA RNA & protein
AML4_d140_merged_Seurat_QCed_metadata.csv
AML4_d140_merged_Seurat_QCed_barcodes.tsv.gz
AML4_d140_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML4_d140_merged_Seurat_QCed_RNA_features.tsv.gz
AML4_d140_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML4_d140_merged_Seurat_QCed_ADT_features.tsv.gz


title: Experiment1_KO2

description: Library name: Sample 2


title: Experiment1_WT2

description: Library name: Sample 4


title: MS03 - 1 micromolar IN10018 - 24 hours - biological replicate 1

description: Library name: Sample 13


title: Pt 'AML4', unenriched BMA, whole RNA and ADT 10x capture, day 90 post-alloHCT

description:
Library name: AML4_d90_BM
molecule: polyA RNA & protein
AML4_d90_merged_Seurat_QCed_metadata.csv
AML4_d90_merged_Seurat_QCed_barcodes.tsv.gz
AML4_d90_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML4_d90_merged_Seurat_QCed_RNA_features.tsv.gz
AML4_d90_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML4_d90_merged_Seurat_QCed_ADT_features.tsv.gz


title: Experiment1_KO1

description: Library name: Sample 1


title: MS03 - 1 micromolar IN10018 - 24 hours - biological replicate 2

description: Library name: Sample 14


title: KC_treated3

city: Geneva

first: Roberto

last: Coppari

address: rue Michel servet 1

country: Switzerland

institute: University of Geneva

description:
Library name: SAMPLE 9
Column name in raw_counts: KC_treated3

data_processing:
The FastQ files were mapped to the Ensembl GRCm39 mouse reference with STAR v2.7.10b. The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR 1.38.4.
After normalization, the poorly detected genes were filtered out and out of 56’941 total genes, 17’175 genes with counts above 10 were kept for the analysis.
To visualize the network and perform functional enrichment analysis and transcription factor enrichment, Cytoscape was used together with ClueGO, CluePedia, and iRegulon apps.
Assembly: Ensembl GRCm39 mouse reference
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

molecule: nuclear RNA

source_name: Liver

extract_protocol:
Bead-bound nuclei isolated from KC-INTACT mice were resuspended in TRIzol. After further purification steps in chloroform and ethanol, samples were loaded onto RNeasy MicroColumn (QIAGEN, 74004). RNA quantification was performed with a Qubit fluorimeter (ThermoFisher Scientific) and RNA integrity was assessed with a Bioanalyzer (Agilent Technologies).
The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit was used for the library preparation with 1 to 5 ng of total RNA (depending on availability) as input. Library molarity and quality were assessed with the Qubit and Tapestation (DNA High sensitivity chip, Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads.

value: Liver

value: Kupffer cells

value: KC-INTACT

value: r-mS100A9 treated (DT + r-mS100A9


title: Pt 'AML4', CD34-enriched BMA, whole RNA and ADT 10x capture, day 90 post-alloHCT

description:
Library name: AML4_d90_34
molecule: polyA RNA & protein
AML4_d90_merged_Seurat_QCed_metadata.csv
AML4_d90_merged_Seurat_QCed_barcodes.tsv.gz
AML4_d90_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML4_d90_merged_Seurat_QCed_RNA_features.tsv.gz
AML4_d90_merged_Seurat_QCed_ADT_matrix.mtx.gz
AML4_d90_merged_Seurat_QCed_ADT_features.tsv.gz


title: MS03 - 1 micromolar GSK2256098 - 24 hours - biological replicate 3

description: Library name: Sample 12


title: MS03 - 1 micromolar GSK2256098 - 24 hours - biological replicate 2

description: Library name: Sample 11


title: KC_treated2

description:
Library name: SAMPLE 8
Column name in raw_counts: KC_treated2


title: KC_ID3

description:
Library name: SAMPLE 6
Column name in raw_counts: KC_ID3

value: diabetic (DT + saline treated)


title: KC_ID2

description:
Library name: SAMPLE 5
Column name in raw_counts: KC_ID2


title: Pt 'AML1', unenriched BMA, whole RNA 10x capture

description:
Library name: AML1_BM
molecule: polyA RNA & protein
AML1_merged_Seurat_QCed_metadata.csv
AML1_merged_Seurat_QCed_barcodes.tsv.gz
AML1_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML1_merged_Seurat_QCed_RNA_features.tsv.gz


title: KC_ID1

description:
Library name: SAMPLE 4
Column name in raw_counts: KC_ID1


title: KC_Healthy3

description:
Library name: SAMPLE 3
Column name in raw_counts: KC_Healthy3

value: No treatment


title: MS03 - 1 micromolar VS-4718 - 24 hours - biological replicate 3

description: Library name: Sample 9


title: Pt 'AML1', unenriched BMA, whole RNA 10x capture (3-prime)

description:
Library name: AML1_BM_3p
molecule: polyA RNA & protein
AML1_3p_merged_Seurat_QCed_metadata.csv
AML1_3p_merged_Seurat_QCed_barcodes.tsv.gz
AML1_3p_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML1_3p_merged_Seurat_QCed_RNA_features.tsv.gz


title: KC_Healthy2

description:
Library name: SAMPLE 2
Column name in raw_counts: KC_Healthy2


title: MS03 - 1 micromolar VS-4718 - 24 hours - biological replicate 2

description: Library name: Sample 8


title: KC_Healthy1

description:
Library name: SAMPLE 1
Column name in raw_counts: KC_Healthy1


title: Experiment1_WT1

description: Library name: Sample 3


title: Mus musculus,skeletal muscle,Ven,3-month-old,Biological Replicate 3

city: Chengdu

first: dongbin

last: zheng

state: 四川Sichuan

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural university

description: Library name: 3m_Ven_3

data_processing:
We constructed polyA-enriched RNA-seq libraries and sequenced them on the Illumina NovaSeq 6000 platform, generating an average of ~43 million 150-bp paired-end raw reads and ~41 million high-quality reads per library. Sequencing reads were aligned to the mouse reference genome (GRCm39) using STAR software (version 2.5.3a), and mRNA expression levels were quantified with Kallisto (version 0.44.0). A gene with TPM (Transcripts per million) > 0.5 in at least 1 sample is considered detectable in our dataset. Using such a criterion, we detected 16945 qualified genes across the examined tissues. DEG analysis was conducted with edgeR package in R, and DEGs were identified as the genes with |Log2FC|>1 and significance FDR < 0.05.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Ven

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen™) according to the manufacturer’s protocol.
We constructed polyA-enriched RNA-seq libraries and sequenced them on the Illumina NovaSeq 6000 platform, generating an average of ~43 million 150-bp paired-end raw reads and ~41 million high-quality reads per library.

value: skeletal muscle

value: Ven

tag: Sex

value: Female

tag: strain


title: Mus musculus,skeletal muscle,Ven,3-month-old,Biological Replicate 2

description: Library name: 3m_Ven_2


title: Mus musculus,skeletal muscle,Ven,3-month-old,Biological Replicate 1

description: Library name: 3m_Ven_1


title: U251 treated with DMSO, biological replicate 4

city: Besthesda

first: Charlotte

middle: M

last: Degorre

state: Maryland

address: 10 Center drive

department: NCI

institute: NIH

description: Library name: M_CTL_4

data_processing:
Basecalling software : RTA 3.9.25
Demultiplexing Software : Bcl2fastq v2.20
Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic before alignment with the reference genome (Human_hg38) and Reads were trimmed to a maximum of 27 bases to carry out miRNA analysis using miRDeep2 with the hg38 reference. miRDeep2 uses the Bowtie aligner for mapping,
Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility 2.18.26.
Assembly: hg38
Supplementary files format and content: miRseq_raw_read_counts.tsv

growth_protocol: U251 cell line was grown in DMEM supplemented with 10% FBS (Invitrogen)

extract_protocol:
RNA was extracted using the Rneasy mini kit from QIAGEN. DNA digestion was perfromed on column using DNase.
200 ng of RNA was used as input for mRNA capture with oligo-dT coated magnetic beads.  The mRNA was fragmented, followed by random-primed cDNA synthesis.  The resulting double-stranded cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification to generate a sequencing ready library

treatment_protocol: U251 cells were treated wither with DMSO before the extraction.

value: Vehicle


title: KC_treated1

description:
Library name: SAMPLE 7
Column name in raw_counts: KC_treated1


title: Mus musculus,skeletal muscle,TA,3-month-old,Biological Replicate 4

description: Library name: 3m_TA_4

source_name: TA

value: TA


title: Mus musculus,skeletal muscle,TA,3-month-old,Biological Replicate 3

description: Library name: 3m_TA_3


title: MS03 - 1 micromolar defactinib - 24 hours - biological replicate 2

description: Library name: Sample 5

value: MS03 murine Nf2-/- Schwann cell line

value: defactinib


title: MS03 - 1 micromolar GSK2256098 - 24 hours - biological replicate 1

description: Library name: Sample 10


title: U251 treated with DMSO, biological replicate 3

description: Library name: M_CTL_3

value: WT


title: Mus musculus,skeletal muscle,Ven,3-month-old,Biological Replicate 4

description: Library name: 3m_Ven_4


title: U251 treated with DMSO, biological replicate 2

description: Library name: M_CTL_2


title: U251 treated with DMSO, biological replicate 1

description: Library name: M_CTL_1


title: Mus musculus,skeletal muscle,TA,3-month-old,Biological Replicate 1

description: Library name: 3m_TA_1


title: Mus musculus,skeletal muscle,ST,3-month-old,Biological Replicate 4

description: Library name: 3m_ST_4

source_name: ST

value: ST


title: MS03 - 1 micromolar VS-4718 - 24 hours - biological replicate 1

description: Library name: Sample 7


title: Mus musculus,skeletal muscle,ST,3-month-old,Biological Replicate 3

description: Library name: 3m_ST_3


title: MS03 - DMSO - 24 hours - biological replicate 3

description: Library name: Sample 3

value: DMSO


title: Pt 'AML1', CD34-enriched BMA, whole RNA 10x capture

description:
Library name: AML1_34
molecule: polyA RNA & protein
AML1_merged_Seurat_QCed_metadata.csv
AML1_merged_Seurat_QCed_barcodes.tsv.gz
AML1_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML1_merged_Seurat_QCed_RNA_features.tsv.gz

value: Bone marrow

value: mononuclear cells


title: MS03 - 1 micromolar defactinib - 24 hours - biological replicate 1

description: Library name: Sample 4


title: Mus musculus,skeletal muscle,ST,3-month-old,Biological Replicate 2

description: Library name: 3m_ST_2


title: MS03 - 1 micromolar defactinib - 24 hours - biological replicate 3

description: Library name: Sample 6


title: Pt 'AML1', CD34-enriched BMA, whole RNA 10x capture (3-prime)

description:
Library name: AML1_34_3p
molecule: polyA RNA & protein
AML1_3p_merged_Seurat_QCed_metadata.csv
AML1_3p_merged_Seurat_QCed_barcodes.tsv.gz
AML1_3p_merged_Seurat_QCed_RNA_matrix.mtx.gz
AML1_3p_merged_Seurat_QCed_RNA_features.tsv.gz


title: R4_c93plus_INPUT

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq (v2.20.0.422)
Reads underwent filtering for adapters and low quality using cutadapt (version 1.18).
Reads were aligned to a hybrid mouse (hg38) and fly (dm6) genome using bowtie2 (version 2.4.2).
Duplicate reads were then removed with Picard: Version 2.26.10. Only reads with a mapping quality above 20 were retained for subsequent downstream analyses.
bigwig files were generated using genomecov from bedtools and bedGraphToBigWig from UCSC
Assembly: hg38 and dm6
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: U2OS cells were grown under standard conditions at 37 °C and 5% CO2 in DMEM (Thermo) supplemented with 10% FBS (v/v) and Penicillin-Streptomycin (Thermo). Drosophila S2-DRSC cells were cultivated in suspension in spinners using M3+BPYE media, 10% heat-inactivated FBS , and 1X penicillin/streptomycin . Cells were incubated at 25°C.

extract_protocol:
U2OS/shUb/HA-Ub(WT) and U2OS/shUb/HA-Ub(K29R) cells and S2-DRSC cells were fixed with 1% formaldehyde for 10 min. Then, glycine was added to quench the reaction and cells were subsequently lysed. Sonication was performed on isolated nuclei using a Covaris E220 Evolution. For each ChIP reaction, 30 μg of U2OS chromatin was mixed with 0.5% sonicated Drosophila S2 chromatin and then immunoprecipitated with the corresponding antibody.
Libraries were costructed using the KAPA Hyperprep kit and Illumina-compatible indexed adapters (IDT, 10005903) following manufacturer’s instruction. For the amplification step, 6-7 PCR cycles were used. Subsequently, the DNA underwent size selection using Agencourt AMPure XP beads (Beckman Coulter, A63881) to obtain fragments between 200-700 bp. Libraries were validated using D5000 DNA ScreenTape on a TapeStation 4200.

treatment_protocol: U2OS/shUb/HA-Ub(WT) and U2OS/shUb/HA-Ub(K29R) cells were seeded in a 15 cm plate (3 plates per cell line). Cells were treated or not with DOX for 72 h.

value: human osteosarcoma

value: plus DOX


title: MS03 - DMSO - 24 hours - biological replicate 2

description: Library name: Sample 2


title: R4_c93_INPUT

value: minus DOX


title: Mus musculus,skeletal muscle,SOL,3-month-old,Biological Replicate 4

description: Library name: 3m_SOL_4

source_name: SOL

value: SOL


title: Mus musculus,skeletal muscle,ST,3-month-old,Biological Replicate 1

description: Library name: 3m_ST_1


title: Mus musculus,skeletal muscle,SOL,3-month-old,Biological Replicate 3

description: Library name: 3m_SOL_3


title: Mus musculus,skeletal muscle,SOL,3-month-old,Biological Replicate 1

description: Library name: 3m_SOL_1


title: Mus musculus,skeletal muscle,SOL,3-month-old,Biological Replicate 2

description: Library name: 3m_SOL_2


title: R4_WTplus_INPUT


title: Mus musculus,skeletal muscle,TA,3-month-old,Biological Replicate 2

description: Library name: 3m_TA_2


title: R4_WT_INPUT


title: Mus musculus,skeletal muscle,Qua,3-month-old,Biological Replicate 4

description: Library name: 3m_Qua_4

source_name: Qua

value: Qua


title: Hypomorph_female3

city: Omaha

first: Brian

last: North

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University School of Medicine

data_processing:
Quality control of the raw sequencing data was performed using FastQC. The fastq reads were aligned to the mouse reference genome GRCm38/mm10 using HiSat2 and quantified with StringTie. Subsequent analysis was performed in RStudio (version 4.4.0) using Bioconductor and the DESeq2 package. Differential gene expression analysis identified significantly expressed genes, which were visualized with heatmaps and volcano plots using the ‘pheatmap’ and ‘EnhancedVolcano’ packages, respectively. Gene abundance values were calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: tab delimited text file (csv) which contains the significantly dysregulated genes , log2fold change, p-value, and adjusted p-values

source_name: Heart (Ventricles)

extract_protocol:
Total RNA was extracted with the the qiagen fibrous tissue RNA extraction kit.
Extracted RNA was sent to LC sciences for library preparation and sequencing.

value: Heart (Ventricles)

value: BubR1 Hypomorphic


title: R3_c93plus_INPUT


title: Mus musculus,skeletal muscle,Qua,3-month-old,Biological Replicate 2

description: Library name: 3m_Qua_2

value: skeletal muscle

value: Female


title: Mus musculus,skeletal muscle,Qua,3-month-old,Biological Replicate 1

description: Library name: 3m_Qua_1


title: Mus musculus,skeletal muscle,PMM,3-month-old,Biological Replicate 4

description: Library name: 3m_PMM_4

source_name: PMM

value: PMM


title: R3_c93_INPUT


title: Mus musculus,skeletal muscle,PMM,3-month-old,Biological Replicate 3

description: Library name: 3m_PMM_3


title: Hypomorph_female1


title: Mus musculus,skeletal muscle,PMM,3-month-old,Biological Replicate 1

description: Library name: 3m_PMM_1


title: Wildtype_female2

value: wildtype


title: Mus musculus,skeletal muscle,Mas,3-month-old,Biological Replicate 3

description: Library name: 3m_Mas_4

source_name: Mas

value: Mas


title: Mus musculus,skeletal muscle,Qua,3-month-old,Biological Replicate 3

description: Library name: 3m_Qua_3


title: R3_WT_INPUT

value: WT


title: Mus musculus,skeletal muscle,Mas,3-month-old,Biological Replicate 2

description: Library name: 3m_Mas_3


title: Wildtype_female1


title: Mus musculus,skeletal muscle,Mas,3-month-old,Biological Replicate 1

description: Library name: 3m_Mas_2


title: Mus musculus,skeletal muscle,LDM,3-month-old,Biological Replicate 4

description: Library name: 3m_LDM_4

source_name: LDM

value: LDM


title: R2_c93plus_INPUT


title: Hypomorph_female2


title: Hypomorph_male3


title: MS03 - DMSO - 24 hours - biological replicate 1

description: Library name: Sample 1

value: MS03 murine Nf2-/- Schwann cell line

value: DMSO


title: Mus musculus,skeletal muscle,LDM,3-month-old,Biological Replicate 3

description: Library name: 3m_LDM_3


title: Mus musculus,skeletal muscle,LDM,3-month-old,Biological Replicate 2

description: Library name: 3m_LDM_2


title: Hypomorph_male2


title: Mus musculus,skeletal muscle,LDM,3-month-old,Biological Replicate 1

description: Library name: 3m_LDM_1


title: Mus musculus,skeletal muscle,Gas,3-month-old,Biological Replicate 4

description: Library name: 3m_Gas_4

source_name: Gas

value: Gas


title: R2_WTplus_INPUT

value: human osteosarcoma


title: Mus musculus,skeletal muscle,PMM,3-month-old,Biological Replicate 2

description: Library name: 3m_PMM_2


title: Mus musculus,skeletal muscle,Gas,3-month-old,Biological Replicate 2

description: Library name: 3m_Gas_2


title: R2_WT_INPUT


title: Wildtype_female3


title: Wildtype_male3


title: Mus musculus,skeletal muscle,Gas,3-month-old,Biological Replicate 3

description: Library name: 3m_Gas_3


title: R1_c93plus_INPUT

value: plus DOX


title: Mus musculus,skeletal muscle,EDL,3-month-old,Biological Replicate 4

description: Library name: 3m_EDL_4

source_name: EDL

value: EDL


title: Wildtype_male2


title: Mus musculus,skeletal muscle,EDL,3-month-old,Biological Replicate 3

description: Library name: 3m_EDL_3


title: R1_c93_INPUT

value: minus DOX


title: Mus musculus,skeletal muscle,EDL,3-month-old,Biological Replicate 1

description: Library name: 3m_EDL_1


title: Mus musculus,skeletal muscle,EDL,3-month-old,Biological Replicate 2

description: Library name: 3m_EDL_2


title: R1_WTplus_INPUT


title: Mus musculus,skeletal muscle,Dia,3-month-old,Biological Replicate 4

description: Library name: 3m_Dia_4

source_name: Dia

value: Dia


title: mESC, INPUT (H3K9me3), UHRF1KO

city: Boston

first: Harleen

last: Saini

state: MA

address: 240 Longwood Avenue

institute: Harvard Medical School

data_processing:
Single-end 150-bp raw reads were demultiplexed using the FASTX-Toolkit (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/). Reads were aligned to the reference mouse genome (GRCm38/mm10, downloaded on January 4, 2020 from https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/) (Lander et al., 2001) using Bowtie2 (version 2.3.4.3) (Langmead and Salzberg, 2012) in local alignment mode with default parameters. To analyze H3K9me3 signal on the reporter gene, mm10 genome assembly was edited to include 2762 nt of the reporter sequence at its integration site on chromosome 2 (Chr2: 13574347). Chromosomal coordinates in the genome annotation (downloaded on January 13, 2021 from http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/mm10.ncbiRefSeq.gtf.gz) were edited accordingly to incorporate the reporter. The edited genome sequence is provided at GSE212155 as 'mm10_genome_with_reporterCHR2.fasta.gz' and a corresponding annotation as 'mm10_ncbiRefSeq_with_reporterCHR2.gtf'.
For H3K9me3 analysis at the reporter gene, duplicate reads were removed using Picard (version 2.8.0) (http://broadinstitute.github.io/picard/). For data visualization, aligned reads were normalized to counts per million using deepTools bamCoverage (version 3.0.2) (Ramirez et al., 2014) and coverage values in bigwig files were computed using 10 bp bins.
For genome-wide H3K9me3 enrichment analysis, epic2 (version 0.0.51) (Stovner and Saetrom, 2019) was used to call peaks with default parameters without removing duplicate reads (-kd) using input for background normalization.
Assembly: GRCm38/mm10
Supplementary files format and content: Bigwig files of alignments to the mouse genome (tagged as 'mm10') are provided. H3K9me3 peaks called by epic2 (version 0.0.51, Stovner and Saetrom, 2019) are also provided as a tab-separated table.

growth_protocol: E14TG2a mES cells (ATCC, #CRL-1821) were cultured on 0.1% gelatin-coated (Sigma, #G1890) plates in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS) (Gibco, #10437), 1% MEM non-essential amino acid (Gibco, #11140), 2 mM Glutamine (Gibco, #25030081), 100 μM β-mercaptoethanol (Sigma, #63689), 10 U/ml penicillin/streptomycin (Gibco, #15140), 1,000 U/ml LIF (Stemcell, #78056) at 37 °C with 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched by the addition of glycine to a final concentration of 125 mM for 5 min. Hypotonic lysis buffer and dounce homogenization was used to lyse cells. Nuclei were pelleted by centrifugation and sonicated to shear chromatin using Covaris E220 Focused-Ultrasonicator (140 watt peak incident, 5% duty factor, 200 cycles/burst, 330 secs sonication time) to a fragment distribution of 200 – 500 bp. Chromatin samples were incubated with specific antibodies overnight at 4°C. For H3K9me3 ChIP, 3 μg of anti-H3K9me3 (Abcam 8898) was used.
For ChIP-seq, reverse crosslinked DNA was treated with RNase A and proteinase K. DNA was purified using phenol/chloroform/isoamyl alcohol and ethanol precipitated with 20 μg glycogen carrier. 10 ng of DNA was used to prepare libraries from two biological replicates per sample.

value: Embryonic stem cells

value: UHRF1 knockout

tag: chip antibody


title: Mus musculus,skeletal muscle,Dia,3-month-old,Biological Replicate 3

description: Library name: 3m_Dia_3

value: skeletal muscle


title: R1_WT_INPUT


title: Mus musculus,skeletal muscle,Dia,3-month-old,Biological Replicate 2

description: Library name: 3m_Dia_2

value: Female


title: Mus musculus,skeletal muscle,Dia,3-month-old,Biological Replicate 1

description: Library name: 3m_Dia_1


title: mESC, H3K9me3, UHRF1KO, rep2

value: H3K9me3 (Abcam 8898)


title: R2_c93_INPUT


title: R4_c93plus_ChIP_H3K9me3


title: Hypomorph_male1

value: Heart (Ventricles)

value: BubR1 Hypomorphic


title: Mus musculus,skeletal muscle,Ven,24-month-old,Biological Replicate 4

description: Library name: 24m_Ven_O_4

value: Ven


title: mESC, H3K9me3, UHRF1KO, rep1


title: Mus musculus,skeletal muscle,Ven,24-month-old,Biological Replicate 3

description: Library name: 24m_Ven_O_3


title: Mus musculus,skeletal muscle,Gas,3-month-old,Biological Replicate 1

description: Library name: 3m_Gas_1


title: Mus musculus,skeletal muscle,Ven,24-month-old,Biological Replicate 1

description: Library name: 24m_Ven_O_1


title: R4_c93_ChIP_H3K9me3


title: mESC, H3K9me3, maintenance, UHRF1KO

data_processing:
Single-end 150-bp raw reads were demultiplexed using the FASTX-Toolkit (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/). Reads were aligned to the reference mouse genome (GRCm38/mm10, downloaded on January 4, 2020 from https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/) (Lander et al., 2001) using Bowtie2 (version 2.3.4.3) (Langmead and Salzberg, 2012) in local alignment mode with default parameters. To analyze H3K9me3 signal on the reporter gene, mm10 genome assembly was edited to include 2762 nt of the reporter sequence at its integration site on chromosome 2 (Chr2: 13574347). Chromosomal coordinates in the genome annotation (downloaded on January 13, 2021 from http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/mm10.ncbiRefSeq.gtf.gz) were edited accordingly to incorporate the reporter. The edited genome sequence is provided as 'mm10_genome_with_reporterCHR2.fasta.gz' and a corresponding annotation as 'mm10_ncbiRefSeq_with_reporterCHR2.gtf'.
For H3K9me3 analysis at the reporter gene, duplicate reads were removed using Picard (version 2.8.0) (http://broadinstitute.github.io/picard/). For data visualization, aligned reads were normalized to counts per million using deepTools bamCoverage (version 3.0.2) (Ramirez et al., 2014) and coverage values in bigwig files were computed using 10 bp bins.
For genome-wide H3K9me3 enrichment analysis, sequencing depth was first equalized across libraries by subsampling aligned reads using SAMtools (version >1.10) (Li et al., 2009) to get ~61 million reads per library. H3K9me3 peaks/regions were identified using epic2 (version 0.0.51) (Stovner and Saetrom, 2019) for each library with default parameters without removing duplicate reads (-kd) and with wild-type input for background normalization.
Assembly: GRCm38/mm10
Supplementary files format and content: Bigwig files of alignments to the mouse genome (tagged as 'mm10') and the edited mouse genome with reporter (tagged as 'mm10reporter') are provided. To visualize read alignments to the reporter gene, an edited mouse genome sequence with the 2762 bp reporter incorporated at position Chr2: 13574347 is included alongwith its annotation in gtf format. The reporter is called 'AT_reporter' in the annotation file. H3K9me3 peaks identified by  epic2 (version 0.0.51, Stovner and Saetrom, 2019) are also provided as a tab-separated table.

extract_protocol: 10 ng of DNA was used to prepare libraries for each sample as described previously (Wong et al., 2013). Libraries were pooled and sequenced on Illumina HiSeq platform.


title: Mus musculus,skeletal muscle,TA,24-month-old,Biological Replicate 4

description: Library name: 24m_TA_O_4

value: TA


title: Wildtype_male1

value: wildtype


title: R4_WT_ChIP_H3K9me3

value: WT


title: Mus musculus,skeletal muscle,TA,24-month-old,Biological Replicate 2

description: Library name: 24m_TA_O_2


title: Mus musculus,skeletal muscle,ST,24-month-old,Biological Replicate 4

description: Library name: 24m_ST_O_4

value: ST


title: mESC, H3K9me3, maintenance, WT, rep2


title: Mus musculus,skeletal muscle,ST,24-month-old,Biological Replicate 3

description: Library name: 24m_ST_O_3


title: R3_c93_ChIP_H3K9me3

value: human osteosarcoma


title: R3_c93plus_ChIP_H3K9me3

value: plus DOX


title: R3_WTplus_INPUT


title: Mus musculus,skeletal muscle,ST,24-month-old,Biological Replicate 2

description: Library name: 24m_ST_O_2


title: Mus musculus,skeletal muscle,ST,24-month-old,Biological Replicate 1

description: Library name: 24m_ST_O_1


title: Mus musculus,skeletal muscle,SOL,24-month-old,Biological Replicate 4

description: Library name: 24m_SOL_O_4

value: SOL


title: mESC, H3K9me3, maintenance, WT, rep1


title: R3_WTplus_ChIP_H3K9me3


title: mESC, H3K9me3, established before maintenance, UHRF1KO


title: Mus musculus,skeletal muscle,SOL,24-month-old,Biological Replicate 2

description: Library name: 24m_SOL_O_2


title: Mus musculus,skeletal muscle,SOL,24-month-old,Biological Replicate 3

description: Library name: 24m_SOL_O_3


title: R3_WT_ChIP_H3K9me3

value: minus DOX


title: Mus musculus,skeletal muscle,Ven,24-month-old,Biological Replicate 2

description: Library name: 24m_Ven_O_2


title: mESC, H3K9me3, established before maintenance, DHX9KO


title: Mus musculus,skeletal muscle,SOL,24-month-old,Biological Replicate 1

description: Library name: 24m_SOL_O_1


title: mESC, H3K9me3, maintenance, DHX9KO, rep2


title: Mus musculus,skeletal muscle,TA,24-month-old,Biological Replicate 3

description: Library name: 24m_TA_O_3


title: R2_c93plus_ChIP_H3K9me3


title: Mus musculus,skeletal muscle,Qua,24-month-old,Biological Replicate 4

description: Library name: 24m_Qua_O_4

value: Qua


title: Mus musculus,skeletal muscle,Qua,24-month-old,Biological Replicate 3

description: Library name: 24m_Qua_O_3


title: R4_WTplus_ChIP_H3K9me3


title: R2_c93_ChIP_H3K9me3


title: mESC, H3K9me3, established before maintenance, WT

value: Embryonic stem cells


title: mESC, H3K9me3, maintenance, DHX9KO, rep1


title: mESC, H3K9me3, before establishment, WT


title: Mus musculus,skeletal muscle,Qua,24-month-old,Biological Replicate 2

description: Library name: 24m_Qua_O_2_B1


title: Mus musculus,skeletal muscle,TA,24-month-old,Biological Replicate 1

description: Library name: 24m_TA_O_1


title: Mus musculus,skeletal muscle,Qua,24-month-old,Biological Replicate 1

description: Library name: 24m_Qua_O_1


title: Mus musculus,skeletal muscle,PMM,24-month-old,Biological Replicate 4

description: Library name: 24m_PMM_O_4

value: PMM


title: Mus musculus,skeletal muscle,PMM,24-month-old,Biological Replicate 3

description: Library name: 24m_PMM_O_3

value: skeletal muscle


title: R2_WT_ChIP_H3K9me3


title: mESC, INPUT (H3K9me3), DHX9KO

value: input


title: Mus musculus,skeletal muscle,PMM,24-month-old,Biological Replicate 2

description: Library name: 24m_PMM_O_2

value: Female


title: R2_WTplus_ChIP_H3K9me3


title: mESC, INPUT (H3K9me3), WT


title: R1_c93plus_ChIP_H3K9me3


title: mESC, H3K9me3, DHX9KO, rep2

value: H3K9me3 (Abcam 8898)


title: Mus musculus,skeletal muscle,Mas,24-month-old,Biological Replicate 2

description: Library name: 24m_Mas_O_2_B1

value: Mas


title: Mus musculus,skeletal muscle,Mas,24-month-old,Biological Replicate 1

description: Library name: 24m_Mas_O_1


title: R1_c93_ChIP_H3K9me3


title: Mus musculus,skeletal muscle,PMM,24-month-old,Biological Replicate 1

description: Library name: 24m_PMM_O_1


title: R1_WTplus_ChIP_H3K9me3


title: mESC, H3K9me3, DHX9KO, rep1


title: Mus musculus,skeletal muscle,LDM,24-month-old,Biological Replicate 4

description: Library name: 24m_LDM_O_4

value: LDM


title: Mus musculus,skeletal muscle,LDM,24-month-old,Biological Replicate 3

description: Library name: 24m_LDM_O_3


title: Mus musculus,skeletal muscle,Mas,24-month-old,Biological Replicate 3

description: Library name: 24m_Mas_O_3


title: R1_WT_ChIP_H3K9me3


title: mESC, H3K9me3, WT, rep1


title: mESC, H3K9me3, WT, rep2


title: Mus musculus,skeletal muscle,LDM,24-month-old,Biological Replicate 1

description: Library name: 24m_LDM_O_1


title: RM1 cells, Reawakened conditions, Biol rep 3

description:
Library name: R.RM1_3
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt

value: Reawakening induction


title: Mus musculus,skeletal muscle,Gas,24-month-old,Biological Replicate 4

description: Library name: 24m_Gas_O_4

value: Gas


title: Mus musculus,skeletal muscle,Gas,24-month-old,Biological Replicate 3

description: Library name: 24m_Gas_O_3


title: RM1 cells, Reawakened conditions, Biol rep 2

description:
Library name: R.RM1_2
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: Mus musculus,skeletal muscle,Gas,24-month-old,Biological Replicate 2

description: Library name: 24m_Gas_O_2


title: Mus musculus,skeletal muscle,Gas,24-month-old,Biological Replicate 1

description: Library name: 24m_Gas_O_1_B1


title: RM1 cells, Reawakened conditions, Biol rep 1

description:
Library name: R.RM1_1
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: Mus musculus,skeletal muscle,EDL,24-month-old,Biological Replicate 4

description: Library name: 24m_EDL_O_4

value: EDL


title: Mus musculus,skeletal muscle,EDL,24-month-old,Biological Replicate 3

description: Library name: 24m_EDL_O_3


title: Mus musculus,skeletal muscle,Mas,24-month-old,Biological Replicate 4

description: Library name: 24m_Mas_O_4


title: RM1 cells, Dormant conditions, Biol rep 3

description:
Library name: D.RM1_3
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt

value: Dormancy induction


title: Mus musculus,skeletal muscle,EDL,24-month-old,Biological Replicate 2

description: Library name: 24m_EDL_O_2


title: RM1 cells, Dormant conditions, Biol rep 1

description:
Library name: D.RM1_1
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: Mus musculus,skeletal muscle,EDL,24-month-old,Biological Replicate 1

description: Library name: 24m_EDL_O_1


title: RM1 cells, Dormant conditions, Biol rep 2

description:
Library name: D.RM1_2
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: RM1 cells, Active conditions, Biol rep 3

description:
Library name: RM1_3
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: Mus musculus,skeletal muscle,LDM,24-month-old,Biological Replicate 2

description: Library name: 24m_LDM_O_2


title: MF, aged, stroked, BEX, biol rep 1

city: Houston

first: Shun-Ming

last: Ting

state: TX

address: 6431 Fannin

department: Neurology

institute: The University of Texas Health Science Center at Houston

description: Library name: S16

data_processing:
Sequencing reads were trimmed using Trimmomatic v0.40 with the adapters file TrueSeq3-PE-2. (parameters: leading:3, trailing:3, slidingwindow:4:15, minilen:36)
Trimmed reads were aligned to GRCm39 genome using Star v2.7.10a using default parameters.
Aligned reads were recalibrated using GATK BaseRecalibrator v4.2.6.1.
Read count extraction and differential expression analysis were performed using R v4.4.2.
Gene set enrichment analysis was performed using GSEA v4.3.3 (parameters: set_min:15, set_max:500, nperm:1000, norm:meandiv)
Assembly: GRCm39
Supplementary files format and content: csv file contains raw count for each sample
Supplementary files format and content: csv file contains significant DEGs

source_name: brain

extract_protocol:
The mice brains were physically and enzymatically dissociated using gentleMACS C tubes (Miltenyi) and enzyme mix papain (20 Units/ml) and DNase I (100 ug/ml). The enzyme mix was pre-warmed at 37oC for 30 minutes. The brains were cut into 2 mm x 2 mm pieces and transferred into the pre-warmed enzyme mix in C tubes. The C tubes were then placed on gentleMACS Dissociator and run brain tissue program 1 to 3. After each program finished, the C tubes were incubated at 37oC for 5 minutes. After the final incubation, the dissociated brain cells were passed through a 100 mm strainer and washed with DMEM.  The washed cells were then reconstituted in 10 ml of 30% Percoll and centrifuged 1000 x g for 10 minutes, with a full break. The cell pellet was reconstituted in staining buffer with Ly6G microbeads and incubated for 10 minutes at 4oC before being sorted with MS Column (Miltenyi). The flow-through was collected (Ly6G negative selection) and washed with staining buffer (PBS with 10% FBS). The cell pellet was reconstituted in staining buffer with CD11b microbeads (1:200) and incubated for 15 minutes at 4oC before being sorted with MS Column (CD11b positive selection).
RNA was extracted using RNeasy micro kits (Qiagen) following the manufacturer’s protocol.
Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions.

treatment_protocol: Bexarotene (BEX, Sigma) dissolved in 3% DMSO was administered i.p. at 5 mg/kg, first 24 hours after surgery and then once a day for two days. DMSO (3%) in saline was used for vehicle control.

value: WT

value: 18-20 months old

value: male

value: brain

value: microglia/macrophages

tag: disease state

value: ischemic stroke

value: bexarotene

tag: time


title: MF, aged, stroked, BEX, biol rep 3

description: Library name: S18


title: Mus musculus,skeletal muscle,Dia,24-month-old,Biological Replicate 2

description: Library name: 24m_Dia_O_3

value: skeletal muscle

value: Dia


title: MF, aged, stroked, BEX, biol rep 2

description: Library name: S17


title: Mus musculus,skeletal muscle,Dia,24-month-old,Biological Replicate 1

description: Library name: 24m_Dia_O_1_B1

value: Female


title: Mus musculus,skeletal muscle,Dia,24-month-old,Biological Replicate 3

description: Library name: 24m_Dia_O_4


title: MF, aged, stroked, vehicle, biol rep 3

description: Library name: S15

value: vehicle


title: MF, aged, stroked, vehicle, biol rep 2

description: Library name: S14


title: RM1 cells, Active conditions, Biol rep 2

description:
Library name: RM1_2
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: MF, aged, stroked, vehicle, biol rep 1

description: Library name: S13


title: MF, aged, BEX, biol rep 3

description: Library name: S12


title: RM1 cells, Active conditions, Biol rep 1

description:
Library name: RM1_1
Lynch_RM1_mouse_RNAseq_rsem_raw_count.txt


title: Female_mice_F591_Trem2_T96K_p

city: Charlestown

first: Ana

last: Griciuc

address: 114 16th Street

institute: Massachusetts General Hospital

description: Library name: F591_HLc20

data_processing:
Sequencing reads (FASTQ files) were de-multiplexed, aligned, and mapped in a splice-aware fashion to the mouse reference genome (GRCm38/mm10 assembly) using the STAR aligner tool as implemented in CellRanger 7.0.
Expression levels were quantified as both raw counts and transcripts per million (TPM) using the RNA-Seq by Expectation-Maximization (RSEM) software package (Li and Dewey, 2011).
Assembly: GRCm38/mm10 assembly
Supplementary files format and content: Seurat RDS files

molecule: polyA RNA

extract_protocol:
Microglial cells (CD11b+CD45Low-to-Intermediate) were collected into PBS (pH 7.4) containing 1mM EDTA based on FACS sorting using the FACSAria Fusion machine (BD Biosciences).
Library preparation was performed following the manufacturer’s instructions (#PN-120237, 10× Genomics). Briefly, the single-cell suspension and ChromiumTM Single Cell 3’ v2 Master Mix were loaded into ChromiumTM Single Cell A chip to collect individual cells encapsulated by gel bead-in-emulsion (GEMs) using the 10× ChromiumTM Controller apparatus. Quality control of the cDNA library was examined with the High Sensitivity DNA Kit (#5067-4626, Agilent Technology) on the Bioanalyzer 2100. Library sequencing was performed in paired-end mode on Illumina NextSeq 2000 instrument to the depth of approximately 100 million reads per library at MGH Next-Generation Sequencing Core.

value: microglia

value: female

value: 8 months old


title: MF, aged, BEX, biol rep 2

description: Library name: S11


title: lol_male_head_2

type: RNA

city: Sapporo

first: Masanao

last: Sato

state: Hokkaido

address: Kita 9 jo Nishi 9 chome, Kita-ku, Sappro

country: Japan

institute: Hokkaido University

description: This sample is of Drosophila melanogaster lol (mutant flies) male head samples. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled samples were hybridized to the Nimblegen 12 plex slide arrays per manufactures instructions. Hybridization took place in a Maui Mixer maintained at 42 degrees C for 18 hours.

scan_protocol: Scanning was performed using microarray scanner G2565CA (Agilent Technologies).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Drosophila melanogaster

source_name: Drosophila melanogaster lol male head 2

label_protocol: Labeling were performed according to manufacture’s instructions (NimbleGen One-Color DNA Labeling Kit, Roche) and the technical note “Roche cDNA Synthesis System for use with NimbleGen Gene Expression Microarray”.

growth_protocol: lol mutant and w[1118] were reared with standard cornmeal/yeast/glucose/agar media supplemented with rice bran (3% w/v) at 23 ℃.

extract_protocol: Total RNA was isolated from whole body and adult heads  of w[1118] and lol flies using Isogen (Nippon Gene).  One hundred whole bodies and heads were used as starting materials for each extraction.

treatment_protocol: Day 2 adult flies after ecolusion were collected and were frozen in liquid nitrogen. In the case of heads, the frozen samples were separated from body carcasses with sieve.

value: lol

value: head


title: MF, aged, vehicle, biol rep 3

description: Library name: S9


title: MF, aged, BEX, biol rep 1

description: Library name: S10


title: lol_male_head_1

description: This sample is of Drosophila melanogaster lol (mutant flies) male head samples. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol male head 1


title: lol_male_head_3

description: This sample is of Drosophila melanogaster lol (mutant flies) male head samples. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol male head 3


title: MF, aged, vehicle, biol rep 2

description: Library name: S8


title: Female_mice_F584_Trem2_p_p

description: Library name: F584_HLc19


title: lol_female_head_3

description: This sample is of Drosophila melanogaster lol (mutant flies) female head samples. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol female head 3


title: lol_female_head_1

description: This sample is of Drosophila melanogaster lol (mutant flies) female head samples. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol female head 1


title: w[1118]_male_head_3

description: This sample is of Drosophila melanogaster w[1118] (control flies) male head samples. It is the third of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] male head 3


title: w[1118]_male_head_1

description: This sample is of Drosophila melanogaster w[1118] (control flies) male head samples. It is the first of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] male head 1


title: w[1118]_male_head_2

description: This sample is of Drosophila melanogaster w[1118] (control flies) male head samples. It is the second of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] male head 2


title: w[1118]_female_head_3

description: This sample is of Drosophila melanogaster w[1118] (control flies) female head samples. It is the third of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] female head 3


title: MF, aged, vehicle, biol rep 1

description: Library name: S7


title: lol_female_head_2

description: This sample is of Drosophila melanogaster lol (mutant flies) female head samples. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol female head 2


title: Female_mice_F614_5XFAD_Trem2_T96K_T96K

description: Library name: F614_HLc29


title: MF, young, BEX, biol rep 1

description: Library name: S4

value: 2-4 months old


title: Female_mice_F595_5XFAD_Trem2_T96K_T96K

description: Library name: F595_HLc25


title: MF, young, BEX, biol rep 3

description: Library name: S6

value: WT


title: Female_mice_F613_5XFAD_Trem2_T96K_T96K

description: Library name: F613_HLc28


title: MF, young, BEX, biol rep 2

description: Library name: S5


title: MF, young, vehicle, biol rep 2

description: Library name: S2


title: MF, young, vehicle, biol rep 1

description: Library name: S1


title: lol_male_whole_body_3

description: This sample is of Drosophila melanogaster lol (mutant flies) male whole body samples. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol male whole body 3

value: whole body


title: w[1118]_female_head_2

description: This sample is of Drosophila melanogaster w[1118] (control flies) female head samples. It is the second of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] female head 2


title: w[1118]_female_head_1

description: This sample is of Drosophila melanogaster w[1118] (control flies) female head samples. It is the first of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] female head 1


title: lol_male_whole_body_2

description: This sample is of Drosophila melanogaster lol (mutant flies) male whole body samples. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol male whole body 2

value: male


title: DN1_ATAC_ER_TcfLefKO_r1

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

description: Library name: DN1_ATAC_ER_TcfLefKO_r1

data_processing:
Paired end sequenced reads were trimmed for 30bp from both ends to remove the low quality base. RNA-seq reads were then mapped to mm10 genome with hisat2 and only reads with MAPQ>30 were considered in following analysis. Expression index (RPKM) is generated by Stringtie.
ATAC-seq reads were trimmed to 36bp from 3'end and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 unique loci) using macs2 (with -q 0.01 and --keep-dup all --nomodel --extsize 146 --llocal 7500 parameters ).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files (generated by Stringtie) include RPKM and TPM of genes for each RNA-seq Sample.
Supplementary files format and content: Macs2 detected peak file for each ATAC-seq sample.

source_name: BM-derived DN1 cells

growth_protocol: BM LSK cells were sorted from CreER+ WT or  CreER+ Tcf7-floxed, Lef1-floxed mice and seeded on OP9-DL1 monolayers for culture. The cells were treated with 4-OH tamoxifen during days 3-5 culture and Lin-CD8-CD4-CD44hiCD25- ckit+ cells were sorted on day 7 of culture for bulk RNA-seq and ATAC-seq analysis.

extract_protocol:
RNA-seq and ATAC-seq were performed on the sort-purified Lin-CD8-CD4-CD44hiCD25- ckit+ cells. The cells were used for total RNA extraction using standard Qiagen RNeasy columns, or treated with TN5 transposase to generate tagged DNA fragments.
RNA libraries were prepared for sequencing using stardard Illumina protocol. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries.

treatment_protocol: Sorted cells were used directly for downstream analyses without further treatment.

value: BM-derived DN1 cells

value: Lin-CD8-CD4-CD44hiCD25- ckit+

value: Tcf1Lef1KO DN1 cells


title: lol_male_whole_body_1

description: This sample is of Drosophila melanogaster lol (mutant flies) male whole body samples. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol male whole body 1


title: DN1_ATAC_ER_WT_r2

description: Library name: DN1_ATAC_ER_WT_r2

value: WT DN1 cells


title: DN1_ATAC_ER_WT_r1

description: Library name: DN1_ATAC_ER_WT_r1


title: Female_mice_F592_5XFAD_Trem2_T96K_p

description: Library name: F592_HLc21

source_name: brain

value: brain


title: Female_mice_F585_5XFAD_Trem2_T96K_p

description: Library name: F585_HLc16


title: DN1_RNA_ER_TcfLefKO_r2

description: Library name: DN1_RNA_ER_TcfLefKO_r2


title: DN1_RNA_ER_WT_r2

description: Library name: DN1_RNA_ER_WT_r2


title: DN1_RNA_ER_TcfLefKO_r1

description: Library name: DN1_RNA_ER_TcfLefKO_r1


title: MF, young, vehicle, biol rep 3

description: Library name: S3

value: microglia/macrophages


title: lol_female_whole_body_3

description: This sample is of Drosophila melanogaster lol (mutant flies) female whole body samples. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol female whole body 3


title: Trim66_KO_homo_ATAC_seq_rep_1 (2)

city: Shanghai

first: Yalei

last: Kong

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University

data_processing:
Reads were mapped to the mouse reference genome (mm10) using Bowtie 2 (version 2.5.1) with the “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700” parameters. The olfactory enhancer peaks were visualized in a multi-region track using the UCSC genome browser and deeptools (version 3.5.5).
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Main Olfactory Epithelium (MOE)

extract_protocol:
The MOE from Olfr1507-ires-tdTomato; Trim66 -/- or Olfr1507-ires-tdTomato; Trim66 +/- mice was dissected and dissociated. Then more than 10,000 tdTomato-positive cells were sorted by flow cytometry
Libraries were prepared with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).

value: Main Olfactory Epithelium (MOE)


title: Female_mice_F600_5XFAD_Trem2_T96K_p

description: Library name: F600_HLc10


title: Trim66_KO_homo_ATAC_seq_rep_2 (2)

description: merge bw file of Homo 1 and 2


title: Female_mice_F605_5XFAD_Trem2_p_p

description: Library name: F605_HLc27


title: DN1_RNA_ER_WT_r1

description: Library name: DN1_RNA_ER_WT_r1


title: Female_mice_F579_5XFAD_Trem2_T96K_p

description: Library name: F579_HLc14


title: Trim66_KO_het_ATAC_seq_rep_2 (2)

description: merge bw file of Het 1 and 2


title: Female_mice_F586_5XFAD_Trem2_T96K_T96K

description: Library name: F586_HLc17


title: DN1_ATAC_ER_TcfLefKO_r2

description: Library name: DN1_ATAC_ER_TcfLefKO_r2


title: Trim66_KO_homo_Olfr1507_OSN_H3K27me3_CUT&Tag_rep_2

data_processing:
Reads were mapped to the mouse reference genome (mm10) using Bowtie 2 (version 2.5.1) with the “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700” parameters. The olfactory enhancer peaks were visualized in a multi-region track using the UCSC genome browser and deeptools (version 3.5.5).
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag


title: Female_mice_F581_5XFAD_Trem2_T96K_T96K

description: Library name: F581_HLc15


title: Female_mice_F604_5XFAD_Trem2_p_p

description: Library name: F604_HLc26


title: lol_female_whole_body_2

description: This sample is of Drosophila melanogaster lol (mutant flies) female whole body samples. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol female whole body 2


title: lol_female_whole_body_1

description: This sample is of Drosophila melanogaster lol (mutant flies) female whole body samples. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster lol female whole body 1


title: Trim66_KO_homo_Olfr1507_OSN_H3K27me3_CUT&Tag_rep_1


title: w[1118]_male_whole_body_1

description: This sample is of Drosophila melanogaster w[1118] (control flies) male whole body samples. It is the first of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] male whole body 1


title: Trim66_KO_het_Olfr1507_OSN_H3K27me3_CUT&Tag_rep_2


title: w[1118]_male_whole_body_3

description: This sample is of Drosophila melanogaster w[1118] (control flies) male whole body samples. It is the third of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] male whole body 3


title: Female_mice_F593_5XFAD_Trem2_p_p

description: Library name: F593_HLc24


title: Trim66_KO_het_Olfr1507_OSN_H3K27me3_CUT&Tag_rep_1


title: Trim66_KO_homo_Olfr1507_OSN_H3K27ac_CUT&Tag_rep_2


title: w[1118]_male_whole_body_2

description: This sample is of Drosophila melanogaster w[1118] (control flies) male whole body samples. It is the second of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] male whole body 2


title: Female_mice_F601_5XFAD_Trem2_p_p

description: Library name: F601_HLc11


title: w[1118]_female_whole_body_3

description: This sample is of Drosophila melanogaster w[1118] (control flies) female whole body samples. It is the third of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] female whole body 3


title: Trim66_KO_het_ATAC_seq_rep_1 (2)


title: Male_mice_M24_5XFAD_Trem2_T96K_T96K

description:
Library name: M24_5XFAD_Trem2_T96K_T96K
Samples_Mutant_Males_RPKM_Table.xlsx

data_processing:
Sequencing reads (FASTQ files) were mapped in a splice-aware fashion to the mouse reference genome (GRCm37/mm9  assembly) using the STAR aligner tools (Dobin et al., 2013).
Read counts over transcripts were calculated using the HTSeq program (Anders et al., 2015) based on the Ensembl annotation for GRCm37/mm9.
Differential expression analysis of genes was performed using the R package edgeR (Robinson et al., 2010) based on at least 2-fold change cutoffs.
Assembly: GRCm37/mm9
Supplementary files format and content: xlsx files include RPKM values for each sample

extract_protocol:
Cell lysates were carefully collected to isolate RNA using the RNeasy Plus Micro Kit (#74034, Qiagen) following the manufacturer’s instructions. cDNA was generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (#634890, Takara) following manufacturer’s instructions.
The PCR-amplified cDNA was purified using the Agencourt AMPure XP beads (#A63880, Beckman Coulter), and cDNA concentrations were measured using the Qubit dsDNA High Sensitivity Assay Kit (#Q32851, Thermo Fisher Scientific) on the Qubit Fluorometer 3.0. Libraries were prepared using Nextera XT DNA Sample Prep Kit (#FC-131-1024, Illumina) and Nextera XT 24 Indexes (#FC-131-1001, Illumina) following manufacturer’s instructions.


title: Trim66_KO_het_Olfr1507_OSN_H3K27ac_CUT&Tag_rep_2


title: mRNAseq_N2_30h_Rep2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: 2917F17

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR package in R with splicedAlignement = TRUE, using the aligner HISAT2including an exon-exon junction database. Gene expression levels were quantified using the qCount() function. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
We performed cosine curve fitting separately for every gene using a linear model. In addition to the two oscillatory predictors cos(φ) and sin(φ), we also included a graded term calculated as the average expression of "rising genes" as defined in (PMID: 24440504). For φ we directly used the inferred unwrapped pseudo times (in radians) obtained from the RNA-seq experiments. This allowed us to compensate for slight differences in the timing between the two replicates, to combine the two replicates in one single cosine curve fitting procedure and to obtain calibrated phases (molt-sync).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts
Supplementary files format and content: tab-delimited text file with amplitudes and phases obtained by a cosine fit. Also included is the graded coefficient (captures graded expreesion trends) as well as the sum of squares error
Supplementary files format and content: tab-delimited text file with calibrated pseudo time estimates (larval stage pseudo time, multiply by 2*pi to obtain radians)
Supplementary files format and content: bed file with gene body coordinates for expressed genes colored by amplitude and phase (hsv space)

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Synchronized L1 animals were seeded on 10 cm plates coated with OP50 bacteria, and grown at 25oC. Animals were subsequently collected hourly from 14 hours to 30 hours (17 samples total / time course), washed 3 times with M9 and then resuspended in Trizol and then flash frozen in liquid N2. Samples were stored at -80 until further processing.

extract_protocol:
For RNA extraction, samples were submitted to 4 rounds of freeze-thawing, and then RNA was purified using the Direct-zol RNA microcprep kit (R2062, Zymo Research) according to manufacturers instructions.
Libraries were prepared using the TruSeq Illumina mRNA-seq (stranded - high input) protocol.

value: Whole animal


title: Trim66_KO_het_Olfr1507_OSN_H3K27ac_CUT&Tag_rep_1


title: KO Lung, 30 μg papain in 25 μl PBS every day for 3 days,ATAC-seq, replicate2

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: ILC2mem KO2

data_processing:
Raw sequence reads were initially processed by “fastp” for quality control, and then adapter sequences and poor-quality reads were removed. Mapping, peak calling and differential analysis was performed using the Galaxy web platform public server (https://usegalaxy.org). Quality filtered reads were mapped to mouse genome (mm10) using “Bowtie2” (Galaxy Version 2.5.3), and only uniquely mapped reads were kept. Duplicates reads were removed with “MarkDuplicates” (Galaxy Version 3.1.1.0). Peak calling was done using “MACS2 callpeak” (Galaxy Version 2.2.9.1) with p value of 0.01 as cutoff. Identified peaks were merged with “bedtools intersect intervals”, “bedtools Multiple Intersect” (Galaxy Version 2.31.1) and “bedtools MergeBED” (Galaxy Version 2.31.1) sequentially. Peak annotation was performed with “ChIPseeker” (Galaxy Version 1.28.3). Bigwig files were generated using “bamcoverage” (Galaxy Version 3.5.4) function normalized to 1× depth (reads per genome coverage). Raw counts based on BED file of merged peaks were analyzed using “bedtools MultiCovBed” (Galaxy Version 2.31.1). Differentially expressed peaks were analyzed using “EdgeR” (Galaxy Version 3.34.0).
Assembly: mm10
Supplementary files format and content: Excel, peaks start and end, raw counts

source_name: lung

extract_protocol:
Female mice were used for library construction unless otherwise stated. Lung ILC2s were purified from Il5Cre/+Smarca4+/+  and Il5Cre/+Smarca4f/f  mice challenged with papain (intranasal administration, 30 μg per day) for 3 days and rested for 2 months.Each biological repeat was pooled about 5×104cells from 2-4 mice.
Library was constructed by TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme (Nanjing, China). 1.2×Agencourt AMPure XP beads (Beckman Coulter) were used to purify the libraries.

value: lung

value: Lin-CD45+RFP+ cells

value: 30 μg papain in 25 μl PBS every day for 3 days, and waiting for 2 months


title: KO Lung, 30 μg papain in 25 μl PBS every day for 3 days, ATAC-seq, replicate1

description: ILC2mem KO1


title: Male_mice_M15_5XFAD_Trem2_T96K_T96K

description:
Library name: M15_5XFAD_Trem2_T96K_T96K
Samples_Mutant_Males_RPKM_Table.xlsx

value: microglia

value: 8 months old


title: mRNAseq_N2_29h_Rep2

description: Library name: 2917F16


title: Male_mice_M11_5XFAD_Trem2_T96K_T96K

description:
Library name: M11_5XFAD_Trem2_T96K_T96K
Samples_Mutant_Males_RPKM_Table.xlsx


title: WT Lung, 30 μg papain in 25 μl PBS every day for 3 days, ATAC-seq, replicate1

description: ILC2mem WT1


title: w[1118]_female_whole_body_2

description: This sample is of Drosophila melanogaster w[1118] (control flies) female whole body samples. It is the second of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] female whole body 2

value: female


title: KO male Lung, IL-33, 4 days,  ATAC-seq, replicate3

description:
ILC2eff male KO3
process data ATAC-seq on WT and KO ILC2eff male and female.xlsx

extract_protocol:
Female mice were used for library construction unless otherwise stated. Lung ILC2s were purified from IL-33-treated Il5Cre/+Smarca4+/+(Ctrl) and Il5Cre/+Smarca4f/f (KO) mice. Mice were intraperitoneally injected with 500 ng recombinant mouse rmIL-33 (BioLegend) in 100 μl PBS for 4 consecutive days. On day 5, lungs were harvested. Each biological repeat was pooled about 5×104cells from 2-4 mice.
Library was constructed by TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme (Nanjing, China). 1.2×Agencourt AMPure XP beads (Beckman Coulter) were used to purify the libraries.

value: 500ng IL-33, i.p, 4 days


title: WT Lung, 30 μg papain in 25 μl PBS every day for 3 days, ATAC-seq, replicate2

description: ILC2mem WT2


title: Male_mice_M10_5XFAD_Trem2_T96K_T96K

description:
Library name: M10_5XFAD_Trem2_T96K_T96K
Samples_Mutant_Males_RPKM_Table.xlsx


title: w[1118]_female_whole_body_1

description: This sample is of Drosophila melanogaster w[1118] (control flies) female whole body samples. It is the first of three control biological replicates used in this experiment, each from separate cultures.

source_name: Drosophila melanogaster w[1118] female whole body 1

value: whole body


title: KO female Lung, IL-33, 4 days,  ATAC-seq, replicate2

description:
ILC2eff female KO2
process data ATAC-seq on WT and KO ILC2eff female only.xlsx
process data ATAC-seq on WT and KO ILC2eff male and female.xlsx


title: Male_mice_M6_5XFAD_Trem2_T96K_T96K

description:
Library name: M6_5XFAD_Trem2_T96K_T96K
Samples_Mutant_Males_RPKM_Table.xlsx

value: male


title: KO female Lung, IL-33, 4 days,  ATAC-seq, replicate1

description:
ILC2eff female KO1
process data ATAC-seq on WT and KO ILC2eff female only.xlsx
process data ATAC-seq on WT and KO ILC2eff male and female.xlsx


title: mRNAseq_N2_27h_Rep2

description: Library name: 2917F14


title: mRNAseq_N2_26h_Rep2

description: Library name: 2917F13


title: WT male Lung, IL-33, 4 days,  ATAC-seq, replicate3

description:
ILC2eff male WT3
process data ATAC-seq on WT and KO ILC2eff male and female.xlsx


title: Trim66_KO_homo_Olfr1507_OSN_H3K27ac_CUT&Tag_rep_1


title: Male_mice_M5_5XFAD_Trem2_T96K_T96K

description:
Library name: M5_5XFAD_Trem2_T96K_T96K
Samples_Mutant_Males_RPKM_Table.xlsx


title: mRNAseq_N2_25h_Rep2

description: Library name: 2917F12


title: WT female Lung, IL-33, 4 days,  ATAC-seq, replicate1

description:
ILC2eff female WT1
process data ATAC-seq on WT and KO ILC2eff female only.xlsx
process data ATAC-seq on WT and KO ILC2eff male and female.xlsx


title: KO lung, 500ng IL-33, 4 days, Input, replicate2

description: ILC2eff KO2

data_processing:
Raw sequence reads were initially processed by “fastp” for quality control, and then adapter sequences and poor-quality reads were removed. Mapping, peak calling and differential analysis was performed using the Galaxy web platform public server (https://usegalaxy.org). Quality filtered reads were mapped to mouse genome (mm10) using “Bowtie2” (Galaxy Version 2.5.3), and only uniquely mapped reads were kept. Duplicates reads were removed with “MarkDuplicates” (Galaxy Version 3.1.1.0). Peak calling was done using “MACS2 callpeak” (Galaxy Version 2.2.9.1) with p value of 0.01 as cutoff. Identified peaks were merged with “bedtools intersect intervals”, “bedtools Multiple Intersect” (Galaxy Version 2.31.1) and “bedtools MergeBED” (Galaxy Version 2.31.1) sequentially. Peak annotation was performed with “ChIPseeker” (Galaxy Version 1.28.3). Bigwig files were generated using “bamcoverage” (Galaxy Version 3.5.4) function normalized to 1× depth (reads per genome coverage). Raw counts based on BED file of merged peaks were analyzed using “bedtools MultiCovBed” (Galaxy Version 2.31.1). Differentially expressed peaks were analyzed using “EdgeR” (Galaxy Version 3.34.0).
Assembly: mm10
Supplementary files format and content: Excel, library name, peaks start and end, raw counts
Library strategy: CUT&Tag

extract_protocol:
Female mice were used for library construction. Lung ILC2s were sorted from naïve mice, IL-33-treated wild-type mice and IL-33-treated Il5Cre/+Smarca4f/f mice. Each biological repeat was 5×104cells pooled from 2-6 mice.
CUT&Tag library preparation was performed by Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vanzyme, TD901) according to the manufacturer’s instructions.

value: 500ng IL-33, 4 days


title: Male_mice_M22_5XFAD_Trem2_T96K_p

description:
Library name: M22_5XFAD_Trem2_T96K_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: lung, 500ng IL-33, 4 days, Cut&Tag, replicate2

value: Lin-CD25+ST2+ cells

value: wild type


title: KO lung, 500ng IL-33, 4 days, Input, replicate1

description: ILC2eff KO1


title: lung, 500ng IL-33, 4 days, Cut&Tag, replicate1


title: mRNAseq_N2_24h_Rep2

description: Library name: 2917F11


title: Male_mice_M14_5XFAD_Trem2_T96K_p

description:
Library name: M14_5XFAD_Trem2_T96K_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: mRNAseq_N2_28h_Rep2

description: Library name: 2917F15


title: Male_mice_M9_5XFAD_Trem2_T96K_p

description:
Library name: M9_5XFAD_Trem2_T96K_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: memory Lung ILC2, 30ug papain, 3 days and waiting for 2 months, ATAC-seq, replicate2

data_processing:
raw sequence reads were initially processed by “fastp” for quality control, and then adapter sequences and poor-quality reads were removed. Mapping, peak calling and differential analysis was performed using the Galaxy web platform public server (https://usegalaxy.org).Quality filtered reads were mapped to mouse genome (mm10) using “Bowtie2” (Galaxy Version 2.5.3), and only uniquely mapped reads were kept. Duplicates reads were removed with “MarkDuplicates” (Galaxy Version 3.1.1.0). Peak calling was done using “MACS2 callpeak” (Galaxy Version 2.2.9.1) with p value of 0.01 as cutoff. Identified peaks were merged with “bedtools intersect intervals”, “bedtools Multiple Intersect” (Galaxy Version 2.31.1) and “bedtools MergeBED” (Galaxy Version 2.31.1) sequentially. Peak annotation was performed with “ChIPseeker” (Galaxy Version 1.28.3). Bigwig files were generated using “bamcoverage” (Galaxy Version 3.5.4) function normalized to 1× depth (reads per genome coverage). Raw counts based on BED file of merged peaks were analyzed using “bedtools MultiCovBed” (Galaxy Version 2.31.1). Differentially expressed peaks were analyzed using “EdgeR” (Galaxy Version 3.34.0).
Assembly: mm10
Supplementary files format and content: Excel, library name, peaks start and end, raw counts

extract_protocol:
Female wild-type mice were used for library construction unless otherwise stated. Lung ILC2s (Lin-CD25+ST2+ cells) were sorted by flow cytometry (Beckman Coulter) respectively from naïve (as ILC2nav) or papain-treated (30 μg/day for 3 days) mice (as ILC2eff). ILC2mem were isolated from the lungs of wild-type mice challenged with papain (intranasal administration, 30 μg per day) for 3 days and rested for 2 months.Each biological repeat was pooled about 5×104cells from 2-4 mice.
Library was constructed by TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme (Nanjing, China). 1.2×Agencourt AMPure XP beads (Beckman Coulter) were used to purify the libraries.

value: wild-type

value: 30ug papain, 3 days and witing for 2 months


title: mRNAseq_N2_22h_Rep2

description: Library name: 2917F9


title: mRNAseq_N2_23h_Rep2

description: Library name: 2917F10


title: lung, PBS, 4 days, Cut&Tag, replicate2

value: PBS, 4 days


title: Male_mice_M8_5XFAD_Trem2_T96K_p

description:
Library name: M8_5XFAD_Trem2_T96K_p
Samples_Mutant_Males_RPKM_Table.xlsx

value: brain


title: mRNAseq_N2_21h_Rep2

description: Library name: 2917F8

value: Whole animal


title: memory Lung ILC2, 30ug papain, 3 days and waiting for 2 months, ATAC-seq, replicate1

value: lung


title: lung, PBS, 4 days, Cut&Tag, replicate1


title: effector Lung ILC2, 30ug papain, 3 days, ATAC-seq, replicate2

value: 30ug papain, 3 days


title: Male_mice_M4_5XFAD_Trem2_T96K_p

description:
Library name: M4_5XFAD_Trem2_T96K_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: effector Lung ILC2, 30ug papain, 3 days, ATAC-seq, replicate1


title: mRNAseq_N2_20h_Rep2

description: Library name: 2917F7


title: WT female Lung, IL-33, 4 days,  ATAC-seq, replicate2

description:
ILC2eff female WT2
process data ATAC-seq on WT and KO ILC2eff female only.xlsx
process data ATAC-seq on WT and KO ILC2eff male and female.xlsx

value: Lin-CD45+RFP+ cells


title: naïve Lung ILC2,PBS, 3days, ATAC-seq, replicate2

value: PBS, 3 days


title: mRNAseq_N2_19h_Rep2

description: Library name: 2917F6


title: naïve Lung ILC2,PBS, 3days, ATAC-seq, replicate1


title: Male_mice_M21_5XFAD_Trem2_p_p

description:
Library name: M21_5XFAD_Trem2_p_p
Samples_Mutant_Males_RPKM_Table.xlsx

value: microglia

value: 8 months old


title: Ezh2b, wild type, IgG

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
CUT&TAG data processing was conducted based on the online tutorial provided by the Henikoff Lab (https://yezhengstat.github.io/CUTTag_tutorial/index.html).
After trimming with Trim-galore (version 0.6.10), the raw paired-end reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (version 2.5.4) with specific options. Then, PCR duplicates were removed by the ‘MarkDuplicates’ command in Picard tools (version 3.1.1).
After validating reproducibility (Pearson correlation coefficient > 0.85), biological replicates were pooled for visualization and other analyses. BigWig tracks for genome browser visualization were generated using deepTools (version 3.5.5) with bamCoverage and specific options.
Peak calling was performed using MACS3 (version 3.0.1) in narrow-peak mode, and differential enrichment analysis was carried out using the bdgdiff module of MACS3. Heatmaps and profile plots of peaks were generated using computeMatrix and plotHeatmap (or plotProfile) from deepTools.
Peak annotation was carried out using the R packages ChIPseeker and ChIPpeakAnno. GO and KEGG enrichment analysis of overlapping genes was conducted through over-representation analysis using a biological process database (WebGestalt) and visualized using ggplot2.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

source_name: MEF

growth_protocol: The embryonic fibroblasts were cultured in  DMEM high-glucose medium. DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Utilizing the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (TD903), we performed CUT&Tag experiments as follows: MEFs were harvested at room temperature and incubated with ConA Beads for 10 minutes. They were then incubated with anti-EZH2 (CST, 5246),  anti-H3K27me3 (CST, #9733) antibodies overnight at 4°C. On the next day, the samples were incubated with a secondary antibody at room temperature for 1h, followed by incubation with pA/G-Tnp for 1h.  After DNA purification with the MinElute kit, and the PCR was performed to amplify the library for 12 cycles and libraries were purified with the MinElute kit. Amplified  libraries were sequenced on the Illumina Novaseq 6000 platform.
Amplified ChIP-seq libraries were sequenced on the Illumina Novaseq 6000 platform.

value: MEF

value: Ezh2b, wild type

tag: antibody

value: IgG


title: Ezh2b, wild type, EZH2, rep2


title: mRNAseq_N2_18h_Rep2

description: Library name: 2917F5


title: Ezh2b, wild type, EZH2, rep1


title: Male_mice_M13_5XFAD_Trem2_p_p

description:
Library name: M13_5XFAD_Trem2_p_p
Samples_Mutant_Males_RPKM_Table.xlsx

value: male


title: mRNAseq_N2_17h_Rep2

description: Library name: 2917F4


title: Ezh2b, wild type, H3K27me3, rep2


title: Ezh2b, wild type, H3K27me3, rep1


title: Ezh2b, mutation, IgG

value: Ezh2b, mutation


title: Male_mice_M7_5XFAD_Trem2_p_p

description:
Library name: M7_5XFAD_Trem2_p_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: Male_mice_M2_5XFAD_Trem2_p_p

description:
Library name: M2_5XFAD_Trem2_p_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: mRNAseq_N2_16h_Rep2

description: Library name: 2917F3


title: mRNAseq_N2_15h_Rep2

description: Library name: 2917F2


title: Male_mice_M3_5XFAD_Trem2_T96K_p

description:
Library name: M3_5XFAD_Trem2_T96K_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: Male_mice_M1_5XFAD_Trem2_p_p

description:
Library name: M1_5XFAD_Trem2_p_p
Samples_Mutant_Males_RPKM_Table.xlsx


title: Ezh2b, mutation, H3K27me3, rep2


title: Ezh2a, wild type, IgG

value: Ezh2a, wild type


title: Ezh2a, wild type, EZH2, rep2


title: Ezh2b, mutation, EZH2, rep1


title: mRNAseq_N2_14h_Rep2

description: Library name: 2917F1


title: Ezh2a, wild type, EZH2, rep1


title: Ezh2b, mutation, H3K27me3, rep1


title: mRNAseq_N2_30h_Rep1

description: Library name: 2772F17


title: Female_mice_F27_5XFAD_Trem2_T96K_T96K

description:
Library name: F27_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx

value: female


title: Female_mice_F21_5XFAD_Trem2_T96K_T96K

description:
Library name: F21_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Ezh2a, wild type, H3K27me3, rep1


title: mRNAseq_N2_28h_Rep1

description: Library name: 2772F15


title: Ezh2a, mutation, IgG

value: Ezh2a, mutation


title: mRNAseq_N2_29h_Rep1

description: Library name: 2772F16


title: Ezh2a, mutation, EZH2, rep2


title: Female_mice_F20_5XFAD_Trem2_T96K_T96K

description:
Library name: F20_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Ezh2a, mutation, EZH2, rep1


title: Ezh2b, mutation, EZH2, rep2


title: mRNAseq_N2_27h_Rep1

description: Library name: 2772F14


title: Ezh2a, mutation, H3K27me3, rep2


title: Ezh2a, mutation, H3K27me3, rep1


title: Female_mice_F15_5XFAD_Trem2_T96K_T96K

description:
Library name: F15_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Female_mice_F9_5XFAD_Trem2_T96K_T96K

description:
Library name: F9_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: SRC1 KO 03

first: Jonathan

middle: Carter

last: Bean

address: 1100 Bates Ave

institute: Baylor College of Medicine

data_processing:
alignment with STAR v2.7.10a
count data summarized with featureCounts v2.0.3
Assembly: GRCm39
Supplementary files format and content: .txt; counts

source_name: Brain/Hypothalamus

extract_protocol:
Rneasy
Illumina TruSeq

value: Brain/Hypothalamus

value: SRC1 KO


title: Female_mice_F34_5XFAD_Trem2_T96K_T96K

description:
Library name: F34_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx

value: brain


title: SRC1 KO 02


title: SRC1 KO 01


title: WT 03

value: Wild-type


title: mRNAseq_N2_25h_Rep1

description: Library name: 2772F12

value: Whole animal


title: Female_mice_F3_5XFAD_Trem2_T96K_T96K

description:
Library name: F3_5XFAD_Trem2_T96K_T96K
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: scRNAseq_HW3125_24h_PoolC

description: Library name: 2837F12

data_processing:
Pre-Processing of scRNAseq data: scRNA-seq data was mapped to the C. elegans genome (WBce11) and quantified (WormBase WS270 gene annotation) using CellRanger version 6.1.2 with default parameters. From a total of 107.7k we retained 96.6k cells with a coverage of at least 750 reads.We further only considered 14,344 genes that were expressed in at least 0.05% of cells.We scaled the expression profile of every cell to the average library size (4623.85), log2transformed and added a pseudocount of 1. We selected the top 2000 variable genes using the getTopHVGs() function from the scran package. For 2D embedding we performed PCA (2000 top variable genes) using 30 components and calculated a UMAP using the function runUMAP() from the scater package. To obtain single cell clusters, we segmented the UMAP as follows: We calculated a 2D density estimate using the function bkde2d() from the KernSmooth package (bandwidth=0.15 on a 800x800 grid) and segmented the resulting 2D density into disconnected territories using the function bwlabel() from the EBImage package. After removing all clusters with less than 100 cells, we obtained a total of 22 clusters. Within this set we detected and removed four doublet clusters, resulting in a total of 18clusters.UMAP cluster annotations: To identify the cell types corresponding to our clusters, we compared pseudobulk expression profiles of our clusters to annotated pseudo-bulk expression profiles from public data (Cao 2017). For most clusters, we identified a unique corresponding cell type, except for cluster 10 which we could not map and cluster 22 which mapped well to Pharyngeal muscle as well as to Pharyngeal epithelia. Considering the latter, using gene markers from the published pseudobulk expression data, we managed to split our cluster 22 into two components (Pharyngeal muscle: Cluster 22 and Pharyngeal epithelia: Cluster 30), resulting in a total of 19 annotated clusters.
Detection of cell clusters with circular expression: To identify cell types with potential rhythmic gene regulation we performed PCA on individual single cell clusters as follows: For each cluster we first normalized each cell to the average library size (considering only the cells of a particular cluster). Then we removed outlier cells with too many detected genes (1.5 fold) or too few detected genes (1.5 fold). We next determined the variable genes within each cluster of cells and performed PCA. Finally, we recovered all the cells that were removed in the last step by projecting them back into PC space.
Pseudotiming: For each cell cluster that showed a ring-like structure in PC1 vs. PC2 space (Clusters 3,4,8,11,12,22,30), we determined its center by calculating the mean of the 5% and 95% quantiles for x and y separately. We then calculated the angle (from 0 to 360 degrees) of each cell with respect to the center using the atan2 function and used that angle as a measure of relative pseudotime. We specifically refer to the word “relative” because at this point, pseudotime is not synchronized among the ring-like structures in principal component space. The developmental time of e.g., 20h in C.elegans development might be located at 30 degrees in one cluster but at a completely different angle in another cluster. Furthermore, the directions of the time progression are also not synchronized. In one cluster developmental time might progress clockwise while in another cluster it could be counterclockwise.
Inference of cell type-specific relative pseudotime gene expression profiles: We inferred relative pseudotime expression profiles for oscillating cell types (clusters 3,4,8,11,12,22,30) as follows: One gene at a time, we selected all the cells in a given cell cluster fitted a cubic smoothing spline in the pseudotime (x-axis) vs. single cell expression (y-axis) scatter. For this, the R function smooth.spline() was used with the smoothing parameter spar set to 0.9. To ensure continuity across the 0 and 360 degree boundary in the resulting expression profiles, we duplicated and shifted the data on both sides of the scatter plot, once shifted by 360 degrees on the x-axis and once shifted by -360 degrees. Finally, we resampled the resulting interpolation line at a fixed grid from 0 to 350 degrees in increments of 10 degrees (36 pseudo time points). We refer to the result as a relative pseudo-time gene expression profiles for individual cell types.
Synchronization of cell-type specific pseudotime expression profiles: To obtain time-and tissue resolved expression profiles in absolute time, rather than relative, we synchronized the expression profiles using an external bulk RNA-seq time course experiment as a common reference. We speculated that for each oscillating tissue, there should be an optimal starting point and an optimal direction in the PC1 vs. PC2 space such that the correlation to the bulk RNA-seq would reach a maximum. To achieve that, we first selected the genes that showed oscillatory gene expression in bulk and that were detected in our relative-time expression profiles from the single cell data. We then normalized the latter by dividing the expression levels for each gene (in linear space) by its maximum level in any cell type (resulting in a maximum expression of 1 for every gene). To create a comparable dataset from the bulk RNA-seq experiment, we used the previously determined phase information for every gene (from 0 to 360°) to synthesize expression profiles (using normal distributions) that peak at the experimentally determined phase (also normalized to a maximum of 1). To determine the optimal starting point and an optimal direction in the PC1 vs. PC2 space for every cell type, we created multiple versions of the expression profiles (which are in relative time), each starting at a different time point and each of those in both clockwise and counterclockwise directions. This resulted in a total of 2*36=72 versions which we correlated to the bulk. We quantified the similarity using the Pearson correlation coefficient and selected the expression profile version with the greatest correlation as the absolute pseudotime gene expression profile for any given cell type.
Assembly: ce11
Supplementary files format and content: R data file with the scRNA count table as well as additional meta data
Supplementary files format and content: tab-delimited text file with pseudo bulk expression levels (RPM) for all tissues
Supplementary files format and content: tab-delimited text file with time resolved expression levels for 7 oscillating tissues (RPM)
Supplementary files format and content: tab-delimited text file with time resolved expression levels for 7 oscillating tissues (reads per cell)
Supplementary files format and content: tab-delimited text file with time resolved expression levels for 7 oscillating tissues, considering only genes that oscillate in bulk. Gene expression is in absolute space and each gene is normalized to a maximum expression of 1. The order of the genes is determined by 1D tSNE of the full data matrix.
Supplementary files format and content: tab-delimited text file with cosine fits for each gene in each oscillating tissue (x=a*cos(phi),y=a*sin(phi))

growth_protocol: Synchronized L1 animals were seeded on peptone-rich XL plates coated with 10x concentrated OP50 bacteria, and grown at 25oC. Animals were subsequently collected at timepoints 18, 20, 22 and 24 hours later, washed at least 3 times with M9 and then processed for cell isolation and FACS sorting.

extract_protocol:
To dissociate single cells, we followed the protocol of Cao et al., 2017, Science) with minor adjustments. To remove animal debry, cells were then sorted on a BD FACSAria using the GFP and mCherry markers.
10x Genomics protocol with the Chromium Controller (10x 3'RNAv3)


title: WT 02


title: Ezh2a, wild type, H3K27me3, rep2


title: scRNAseq_HW3125_24h_PoolB

description: Library name: 2837F11


title: Female_mice_F33_5XFAD_Trem2_T96K_p

description:
Library name: F33_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: mRNAseq_N2_23h_Rep1

description: Library name: 2772F10


title: mRNAseq_N2_24h_Rep1

description: Library name: 2772F11


title: mRNAseq_N2_22h_Rep1

description: Library name: 2772F9


title: Female_mice_F26_5XFAD_Trem2_T96K_p

description:
Library name: F26_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx