title: Donor2_PMA/Ionomycin_10X GEX

data_processing:
The cellranger mutli pipeline (v7.1.0) was deployed to process gene expression and immune profiling data generated from the 10X Genomics Chromium platform. Intronic mapped reads were also included in gene expression quantification. The reference index refdata-gex-GRCh38-2020-A, provided within the cellranger package, was used for read alignment and quantification of the 10X data.
Seurat (v5.0.0) was used for quality control and downstream analysis of gene expression data
Assembly: GRCh38
Supplementary files format and content: RDS file includes Seurat object for all cells
Supplementary files format and content: CSV file includes TCR clonotypes for each sample
Supplementary files format and content: CSV file includes filtered contig annotations for each sample

extract_protocol:
PBMCs from healthy donors were isolated by SepMateTM tubes (STEMCELL Technologies, Catalog#85450), following manufacturer’s instruction, and resuspended in RPMI 1640 medium (Gibco, Catalog#11875093) containing 5% human serum (Sigma, Catalog# H3667-100ML) and 1% penicillin-streptomycin and cultured in 6-well plates (3 mL/well). After overnight culture, the PBMC was resuspended and cultured at 5 × 106 cells/ml in 48-well plate and treated immediately with DMSO or phorbol-12-myristate-13-acetate (PMA) plus ionomycin (PMA/Ionomycin) cocktail (Cell stimulation cocktail, eBioscience, Catalog#00-4970) for 3 h. Then, PBMC was stained with APC mouse anti-human CD4 (SK3, BD Biosciences, Catalog#340443) and Alexa Fluor 488 mouse anti-human CD3 (UCHT1, BioLegend, Catalog#300454) before sorting. The dead cells were gated out after staining with viability dye eFluor 780 (Invitrogen, Catalog#65-0865-14). The CD4+ T-cells were sorted into 15-ml centrifuge tubes with collection buffer (PBS with 1% BSA).
We stained cells with acridine orange and propidium iodide (AO/PI, Catalog# CS2-0106-5ML, Thermo Fisher Scientific) to assess viability, and then performed scRNA-seq and scTCR-seq library preparations by loading 12,000 cells for the targeted cell recovery of approximately 8000 cells, according to the Chromium Single-cell 5’ Library and V(D)J library version 2 user guide.

value: PMA/Ionomycin

tag: assay

value: 10X Genomics Chromium Next GEM Single Cell 5' Kit v2

value: GEX


title: Donor2_DMSO_HT SS3_Plate3_1364

status: Public on Jul 02 2024

type: SRA

city: Foster City

first: Ruidong

last: Li

state: CA

address: 324 Lakeside Drive

department: Research Data Sciences

country: USA

institute: Gilead Sciences, Inc.

description:
Seurat_Object_HT_SS3.rds
TraCeR_filtered_cell_data_HT_SS3.csv
TraCeR_filtered_recombinants_HT_SS3.txt

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files for cells on each plate were first merged using the merge_demultiplexed_fastq.R script provided in the zUMIs tool (v2.9.7). Then, the zUMIs.sh script was used to execute a series of steps - filtering, mapping, counting, and summarizing - to generate the gene expression count matrices and summary statistics.
The source code in the runfeatureCountFun.R script within zUMIs was modified to exclude multi-mappers (countMultiMappingReads=FALSE) and fragments that were not successfully mapped to both ends (requireBothEndsMapped=TRUE) from quantification. The read count matrix for both exonic and intronic mapping was used for downstream analysis.
To ensure consistency for benchmarking, the same genome reference sequence (genome.fa) and gene annotation information (genes.gtf) provided in cellranger reference index refdata-gex-GRCh38-2020-A was used for Smart-seq3 data analysis
Seurat (v5.0.0) was used for quality control and downstream analysis of gene expression data
To reconstruct TCR sequences from HT Smart-seq3 RNA sequencing data, we utilized the Docker image of the TraCeR tool (v0.6.0) in Docker Hub. The assemble module within TraCeR was first used to reconstruct TCR sequences for each individual cell, and the summarise module was subsequently used to generate the summary statistics and detailed information for all cells
Assembly: GRCh38
Supplementary files format and content: RDS file includes Seurat object for all cells
Supplementary files format and content: CSV file includes cell data output from TraCeR summarise analysis for all cells
Supplementary files format and content: tab-delimited TXT file includes recombinants output from TraCeR summarise analysis for all cells

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs from healthy donors were isolated by SepMateTM tubes (STEMCELL Technologies, Catalog#85450), following manufacturer’s instruction, and resuspended in RPMI 1640 medium (Gibco, Catalog#11875093) containing 5% human serum (Sigma, Catalog# H3667-100ML) and 1% penicillin-streptomycin and cultured in 6-well plates (3 mL/well). After overnight culture, the PBMC was resuspended and cultured at 5 × 106 cells/ml in 48-well plate and treated immediately with DMSO or phorbol-12-myristate-13-acetate (PMA) plus ionomycin (PMA/Ionomycin) cocktail (Cell stimulation cocktail, eBioscience, Catalog#00-4970) for 3 h. Then, PBMC was stained with APC mouse anti-human CD4 (SK3, BD Biosciences, Catalog#340443) and Alexa Fluor 488 mouse anti-human CD3 (UCHT1, BioLegend, Catalog#300454) before sorting. The dead cells were gated out after staining with viability dye eFluor 780 (Invitrogen, Catalog#65-0865-14). The live and single CD4+ T-cells were sorted into 96-well plates containing lysis buffer using SH800S cell sorter (Sony Biotechnology Inc, San Jose, CA) with a 100-μm nozzle.
The Smart-seq3 library preparations were performed as previously described [Hagemann-Jensen et al., Nat Biotechnol, 2020, 38:708-714] with some modifications. In addition, we developed and optimized an automated sample handling process for most steps of the Smart-seq3 protocol, including single-cell lysis, reverse transcription, and library construction by using Integra Biosciences VIAFLO 96 electronic pipetting system and Mantis liquid handler (Formulatrix, Bedford, MA, USA).

tag: tissue

value: PBMC

tag: cell type

value: CD4+ T cells

tag: donor id

value: Donor 2

tag: plate

value: Plate 3

tag: disease

value: Healthy

tag: treatment

value: DMSO


title: Donor2_PMA/Ionomycin_10X TCR

tag: library type

value: TCR


title: Donor2_DMSO_HT SS3_Plate3_1354


title: Heart, Exercise Trained, Muscle-Specific Bmal1KO_2

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

description: HeartCPM.xlsx

library_source: transcriptomic

data_processing:
Partek Flow
Quality score trimmed for Phred <20, 3-prime right end, min-read length 25,
Trimmed sequence reads were mapped to mm10, GRCm39. Annotated to genomes. Star alignment 2.7.8a
CPM values used in processed data file.
Assembly: mm10 (GRCm39)
Supplementary files format and content: tab-delimited text files include CPM values for each sample. Each tissue has its own file containing the data from all 4 groups.

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
Trizol with Qiagen, RNEasy Kit
Illumina library kit.

value: Heart

tag: genotype

value: Cre+:iMSBmal1 fl/fl

value: iMSBMal1KO + Exercise Training

tag: time

value: 48-hours post


title: Donor2_DMSO_10X GEX


title: Donor2_DMSO_HT SS3_Plate3_1352


title: Donor2_DMSO_HT SS3_Plate3_1351


title: Heart, Exercise Trained, Muscle-Specific Bmal1KO_1

description: HeartCPM.xlsx


title: Heart, Exercise Trained, Muscle-Specific Bmal1KO_3

description: HeartCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1353


title: Donor2_DMSO_10X TCR


title: Donor2_DMSO_HT SS3_Plate3_1349


title: Donor2_DMSO_HT SS3_Plate3_1348


title: Donor1_PMA/Ionomycin_10X TCR

value: Donor 1


title: Heart, Exercise Trained_5

description: HeartCPM.xlsx

value: Vehicle + Exercise Training


title: Donor1_PMA/Ionomycin_10X GEX


title: Donor2_DMSO_HT SS3_Plate3_1345


title: Donor2_DMSO_HT SS3_Plate3_1347


title: Heart, Exercise Trained_4

description: HeartCPM.xlsx


title: Donor1_DMSO_10X TCR


title: Cetuximab-resistant LIM1215-R2 – biol rep 3 [S54]

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fa file.
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: Excel file with the matrix of raw counts.

growth_protocol: DiFi cells were cultured in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12; #11330032, Thermo Fisher Scientific) while LIM1215 cells were grown in RPMI-1640 medium + GlutaMAX (#61870-010, Thermo Fisher Scientific). Media were supplemented with 10% heat-inactivated fetal bovine serum (FBS; F7524, Sigma-Aldrich), and 1% penicillin-streptomycin (#15140163, Thermo Fisher Scientific), and cells were maintained in exponential growth in 5% CO2/95% air in a humidified incubator at 37°C. All cell lines were tested for mycoplasma contamination with the PCR-based MycoplasmaCheck service from Eurofins Genomics.

extract_protocol:
Total RNA was extracted from frozen cell pellets with the Monarch Total RNA Miniprep kit (New England Biolabs) by following manufacturer’s protocol. Total RNA (300 ng/sample) was ribodepleted by using the NEBNEXT rRNA Depeletion kit (New England Biolabs) according to manufacturer’s instructions.
Ribodepleted RNA was then used for the library preparation with the NEBNext Ultra II Directional RNA library prep kit for Illumina (New England Biolabs) according to manufacturer’s instructions.
Libraries were paired-end sequenced (2*100 base pairs) on a NextSeq2000 device (Illumina), with a minimal depth of 10 million reads.

treatment_protocol: Cetuximab-resistant DiFi and LIM1215 cancer cells were cultured under continuous treatment with 25 µg/mL cetuximab (Erbitux 5 mg/mL; Merck #L01XC06).

tag: cell line

value: colon cancer cells

tag: genotype/phenotype

value: cetuximab-resistant


title: Donor1_DMSO_10X GEX

value: 10X Genomics Chromium Next GEM Single Cell 5' Kit v2


title: Heart, Exercise Trained_3

description: HeartCPM.xlsx


title: Cetuximab-resistant LIM1215-R2 – biol rep 2 [S53]


title: Cetuximab-resistant LIM1215-R2 – biol rep 1 [S52]


title: Cetuximab-resistant LIM1215-R1 – biol rep 3 [S51]


title: Heart, Exercise Trained_2

description: HeartCPM.xlsx


title: Cetuximab-resistant LIM1215-R1 – biol rep 2 [S50]


title: Heart, Exercise Trained_1

description: HeartCPM.xlsx


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1384

value: PMA/Ionomycin


title: Cetuximab-sensitive LIM1215-S – biol rep 2 [S47]

value: cetuximab-sensitive


title: Cetuximab-resistant LIM1215-R1 – biol rep 1 [S49]


title: Heart, Sedentary, Muscle-Specific Bmal1KO_5

description: HeartCPM.xlsx

value: iMSBmal1KO + No Exercise


title: Cetuximab-sensitive LIM1215-S – biol rep 3 [S48]


title: SZ4, shGTSF1, 3

city: Montreal

first: Amelia

last: Martinez Villarreal

state: Quebec

address: 1001 Boulevard Decarie

country: Canada

institute: McGill University

data_processing:
Base calling was performed with RTA (Version 3)
Bcl2fastq2 (Version 2.20) was used to demultiplex samples and generate FASTQ reads.
Reads were trimmed using Trimmomatic (Version 0.39 )
Quality of the reads was assessed using FastQC
Kallisto (Version 0.48.0) was used to align the reads to the transcriptome and to quantify the transcripts.
The transcriptome of the human genome GRCh38 was created using gffread (cufflinks Version 2.2.1) with the Ensembl annotation and genome files (Version 105).
Transcript abundance was combined to obtain the gene level quantification.
The tximport package (Version 1.22.0) was used to summarize kallisto count estimates at the gene level.
DESeq2 (Version 1.34) was subsequently used to identify DEGs between SCR control and shGTSF1 knockdown conditions, using the default Benjamini and Hochberg correction method.
Assembly: The transcriptome of the human genome GRCh38 was created using gffread (cufflinks Version 2.2.1) with the Ensembl annotation and genome files (Version 105).
Supplementary files format and content: tab separated values file includes TPM info for each sample
Supplementary files format and content: tab separated values file includes estimated counts for each sample

growth_protocol: Cells were grown in RPMI-1640 containing 10% Fetal Bovine Serum and 1% penicillin-streptomycin. In addition, SZ4 was supplemented with IL-2 and IL-4. After transdcution, cells were sorted based on GFP expression.

extract_protocol:
RNA was isolated with a RNeasy Mini Kit (Qiagen)
RNA integrity was assessed using 5K/RNA/Charge Variant Assay LabChip and RNA Assay Reagent Kit (Perkin Elmer). Libraries were generated from 250 ng of total RNA as follows: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the KAPA Library Quantification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX II (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.02N NaOH and neutralized using HT1 buffer. The pool was loaded at 200pM on an Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.

value: GTSF1 knockdown


title: SZ4, shGTSF1, 1


title: SZ4, shGTSF1, 2


title: Donor2_DMSO_HT SS3_Plate3_1346

value: PBMC

value: CD4+ T cells

value: Donor 2

value: Plate 3


title: Heart, Sedentary, Muscle-Specific Bmal1KO_4

description: HeartCPM.xlsx

value: Heart


title: Cetuximab-resistant DiFi-R2 – biol rep 3 [S45]

source_name: DiFi

value: DiFi


title: Cetuximab-resistant DiFi-R2 – biol rep 1 [S43]


title: Heart, Sedentary, Muscle-Specific Bmal1KO_3

description: HeartCPM.xlsx

value: Cre+:iMSBmal1 fl/fl


title: SZ4, SCR, 2

value: SCR


title: Cetuximab-resistant DiFi-R1 – biol rep 1 [S40]


title: Cetuximab-resistant DiFi-R1 – biol rep 2 [S41]


title: SZ4, SCR, 1


title: Heart, Sedentary, Muscle-Specific Bmal1KO_1

description: HeartCPM.xlsx

value: 48-hours post


title: Cetuximab-sensitive DiFi-S – biol rep 3 [S39]


title: Cetuximab-sensitive DiFi-S – biol rep 2 [S38]


title: MyLa, shGTSF1, 3

source_name: MyLa 2000

value: MyLa 2000


title: Cetuximab-sensitive LIM1215-S – biol rep 1 [S46]

value: colon cancer cells


title: Cetuximab-sensitive DiFi-S – biol rep 1 [S37]


title: MyLa, shGTSF1, 1


title: SZ4, SCR, 3


title: Cetuximab-resistant DiFi-R2 – biol rep 2 [S44]

value: cetuximab-resistant


title: SK-N-BE Neuroblastoma cell line, Differentiation Day 1.5, CyCoNP PullDown, Replicate1

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

data_processing:
Following the sequencing run, basecalling was performed on the FAST5 data using Guppy v. 6.4.6 (available at https://community.nanoporetech.com) with the following parameters: --enable_trim_barcodes, --trim_adapters, --trim_primers, --recursive, --min_qscore 9, –compress_fastq, -x "cuda:0", --num_callers 14, --gpu_runners_per_device 8, --chunks_per_runner 768, --chunk_size 500; only the reads flagged as “pass” (average quality higher than or equal to 9) were kept for downstream analyses. The quality of the reads was assessed using PycoQC v2.5.2 (Leger and Leonardi 2019). Nanofilt v2.8.0 (De Coster et al. 2018) was used to remove reads shorter than 100 nucleotides. The resulting reads were then aligned to the Homo sapiens GRCh38 reference genome (Schneider et al. 2017) using Minimap2 v2.24-r1122 (Li 2018)with the parameter -ax splice, which allows spliced alignments. Transcript quantification was performed using Bambu v1.1.2 (Chen et al. 2023)without the discovery of new isoforms (discovery = FALSE), utilizing the Ensembl 99 annotation(Yates et al. 2020) as a reference
Assembly: GRCh38
Supplementary files format and content: gene_CPM_table.tsv contains gene level CPM

source_name: SK-N-BE

growth_protocol: SK-N-BE cells were cultured in growth medium with RPMI-1640 , 10% fetal bovine serum (FBS), 1% GlutaMAX , 1% Pen/Strep,  1% Sodium Piruvate. Differentiation was induced by adding differentiation medium: RPMI-1640, 2.5% heat-inactivated FBS , 1% GlutaMAX , 1% Pen/Strep, 1% Sodium Piruvate  and 10 μM retinoic acid

extract_protocol:
Total RNA from cells was extracted with the Direct-zol RNA Purification Kit (Zymo Research)
Libraries were prepared from total RNA according to protocols provided by Oxford Nanopore (Oxford Nanopore Technologies) for PCR-cDNA barcoding (SQK-PCB109)
Total RNA, single end

treatment_protocol: 1.5 days differentiated SK-N-BE treated with biotinylated probes against CyCoNP or LacZ

value: SK-N-BE

value: Neuroblastoma


title: SK-N-BE Neuroblastoma cell line, Differentiation Day 1.5, LacZ PullDown, Replicate2


title: MyLa, shGTSF1, 2


title: Heart, Sedentary_4

description: HeartCPM.xlsx

value: Vehicle + No Exercise


title: SK-N-BE Neuroblastoma cell line, Differentiation Day 1.5, LacZ PullDown, Replicate1


title: Cetuximab-resistant DiFi-R1 – biol rep 3 [S42]


title: Heart, Sedentary_5

description: HeartCPM.xlsx


title: MyLa, SCR, 3


title: Heart, Sedentary_2

description: HeartCPM.xlsx


title: Heart, Sedentary_3

description: HeartCPM.xlsx


title: SK-N-BE Neuroblastoma cell line, Differentiation Day 1.5, INPUT, Replicate1


title: Donor2_DMSO_HT SS3_Plate3_1447

value: Healthy

value: DMSO


title: SK-N-BE Neuroblastoma cell line, Differentiation Day 1.5, CyCoNP PullDown, Replicate2


title: Heart, Sedentary, Muscle-Specific Bmal1KO_2

description: HeartCPM.xlsx

value: iMSBmal1KO + No Exercise


title: MyLa, SCR, 1


title: Heart, Sedentary_1

description: HeartCPM.xlsx


title: SK-N-BE Neuroblastoma cell line, Differentiation Day 1.5, INPUT, Replicate2


title: MyLa, SCR, 2


title: Liver, Exercise Trained, Muscle-Specific Bmal1KO_5

description: LiverCPM.xlsx

source_name: Liver

value: Liver

value: iMSBMal1KO + Exercise Training


title: Mac2A, shGTSF1, 3

value: GTSF1 knockdown


title: Phoxinus brain, Salt, biol rep 3

city: Cologne

first: Camilo

last: Escobar Sierra

state: NRW

address: Zülpicher Strasse 47b

department: Institute of Zoology

country: Germany

institute: University of Cologne

data_processing:
Quality improvement via an adaptor and low-quality reads filtering using TRIMMOMATIC, with a threshold of phred + 33 quality score of at least 25 for all bases, and a minimum length of 50 bp for all reads kept for downstream analyses
TRINITY v2.9.1 was used to create a de novo assembly using the nine pairs of clean sequences.
The reads of the raw nine paired sequences were aligned to the de novo transcriptome using SALMON
BUSCO v5.2.2 was used to assess transcriptome assembly completeness by searching against the actinopterygii_odb10 (Creation date: 2021-02-19) dataset.
The expression matrix was generated and the low expressions transcripts (minimum expression of 1.0) were filtered using TRINITY v2.9.1, the expression levels were normalized as transcripts per million transcripts (TPM). Identification of likely protein-coding regions in transcripts was performed with TRANSDECODER v5.5.0.
The filtered transcriptome sequencing reads were aligned to protein, signal peptides, and transmembrane domains using the tools, DIAMOND v2.0.8 [49], SIGNALP 6.0 [50], TMHMM v2.0 [51], and, HMMER v3.3.2 [52]. The de novo transcriptome was then functionally annotated using the tool TRINOTATE v3.2.2 [45].
Before the differential gene expression analysis, the SALMON tool was used to align the clean reads of the three sites to the filtered transcriptome and the mapping rate was calculated. The mapping tables were merged according to the stations and using TMM [53] normalization. Differential expression analysis with three biological replicates of the two stations with higher chloride (A and C) were compared to the reference condition (Station B) using the DESeq2 [54] package, the fold change cut-off was set at >2, and the FDR≤0.05.
Assembly: de novo (trinity)
Supplementary files format and content: tab-delimited text file with annotated TMM counts for each sample output of deseq2

organism: Phoxinus septimaniae

source_name: invasive minnow (Phoxinus septimaniae x P. dragarum)

extract_protocol:
RNA was extracted using an RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
Illumina Tru-Seq™ RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) was applied in generating sequencing libraries following the manufacturer’s protocol

value: brain

value: Salt


title: Phoxinus gills, Salt, biol rep 1

value: gills


title: Phoxinus liver, Reference, biol rep 3

value: liver

value: Reference


title: Phoxinus liver, Salt, biol rep 3


title: Liver, Exercise Trained, Muscle-Specific Bmal1KO_4

description: LiverCPM.xlsx

value: Cre+:iMSBmal1 fl/fl

value: 48-hours post


title: Liver, Exercise Trained, Muscle-Specific Bmal1KO_3

description: LiverCPM.xlsx


title: Mac2A, shGTSF1, 2


title: Phoxinus brain, Reference, biol rep 3


title: Phoxinus liver, Salt, biol rep 2


title: Mac2A, shGTSF1, 1


title: Liver, Exercise Trained, Muscle-Specific Bmal1KO_2

description: LiverCPM.xlsx


title: Phoxinus brain, Salt, biol rep 2


title: Phoxinus liver, Reference, biol rep 2


title: Liver, Exercise Trained, Muscle-Specific Bmal1KO_1

description: LiverCPM.xlsx


title: Mac2A, SCR, 2

value: SCR


title: Phoxinus brain, Reference, biol rep 2


title: Phoxinus liver, Reference, biol rep 1


title: Phoxinus gills, Reference, biol rep 1


title: Liver, Exercise Trained_5

description: LiverCPM.xlsx

value: Vehicle + Exercise Training


title: Phoxinus brain, Reference, biol rep 1


title: Mac2A, SCR, 1


title: Phoxinus liver, Salt, biol rep 1


title: IgG_rep2

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

library_source: genomic

data_processing:
CUT&RUN-seq data were preprocessed and analyzed using cutRunTools pipeline.
This pipeline automated the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data was further utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalized by subtracting the treatment file to the corresponding control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: narrowPeak files
Supplementary files format and content: bigWig files

molecule: genomic DNA

growth_protocol: MOLT-4 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the Cut&Run-seq samples and sequencing of paired-end-150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end Cut&Run-Seq sequencing

treatment_protocol: The cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina Novaseq at GENEWIZ Azenta Life Sciences Co. Ltd.


title: Phoxinus gills, Salt, biol rep 3


title: IgG_rep1


title: Phoxinus brain, Salt, biol rep 1


title: Liver, Exercise Trained_2

description: LiverCPM.xlsx


title: Phoxinus gills, Reference, biol rep 3


title: Liver, Exercise Trained_4

description: LiverCPM.xlsx


title: Replicate4, Fib-Del

city: Erlangen

first: Harald

last: Schuhwerk

address: Glückstrasse 6

description:
cell type: Various, see "Metadata_Merge.tsv"
SortSeq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were aligned to the ensemble transcriptome using BWA (Li and Durbin, 2010). The corresponding transcript count table was generated using a custom-written script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon tumor

extract_protocol:
Primary colon tumors of mice with fibroblast-specific deletion of Zeb1 or of Zeb1-proficient control mice were dissected and dissociated into single cells. After erythrocyte lysis in ACK buffer, cells were incubated with Fc Block, anti-CD45-PE/Cy7, anti-CD31-PE, anti-Epcam-eFluor450, a-CD140a-APC and eFluor780 in PBS/2 % FCS/2 mM EDTA. Single viable cells (eFluor-) were sequentially gated asto 'Fibroblast' (all negative), 'Epithelial' cells (Epcam-positive but CD31- and CD45-negative) and 'Immune' cells (Epcam- and CD31-negative but CD45-positive), sorted into 384-well capture plates containing 50 µL lysis buffer and barcoded primers covered by 10 µL of mineral oil  by flow cytometry using a BD FACSAria Fusion fluorescence activated cell sorter (BD biosciences) and capture plates were sent for paired-end sequencing at Single Cell Discoveries in Utrecht (Illumina Nextseq™ 500). Empty wells were included as 'Control' as well. The plate and well setup with 'Fibroblast', 'Epithelial', 'Immune' cells as well as the empty 'Control'  wells is provided in the "Metadata_Merge.tsv" file. Information on the genotype of the respective mice is provided in the file 'PlateInformation.txt'
Library preparation according to the CEL-Seq2 protocol was performed by SCD. Briefly, after heat-lysis of the cells at 65° C, sequential barcoding, amplification and in vitro transcription was performed to generate a final cDNA library containing TruSeq small RNA primers (Illumina) for sequencing. Pleaase also see https://www.scdiscoveries.com/support/materials-methods/

value: Colon tumor

tag: genetic modification

value: Col1a1Cre-ERT2 transgene positive

value: Tamoxifen diet


title: Mac2A, SCR, 3


title: Replicate3, Fib-Del


title: Phoxinus gills, Salt, biol rep 2


title: Replicate2, FibCtrl

value: Col1a1Cre-ERT2 transgene negative


title: GLTSCR_rep2


title: Replicate4, FibCtrl


title: Liver, Sedentary, Muscle-Specific Bmal1KO_5

description: LiverCPM.xlsx

value: iMSBmal1KO + No Exercise


title: GLTSCR_rep1


title: Replicate3, FibCtrl


title: Liver, Exercise Trained_1

description: LiverCPM.xlsx

value: Liver


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1381

value: PBMC

value: CD4+ T cells

value: Donor 2

value: Plate 3

value: Healthy

value: PMA/Ionomycin


title: Replicate2, Fib-Del


title: Replicate1, FibCtrl


title: DPF2_rep2


title: Liver, Sedentary, Muscle-Specific Bmal1KO_4

description: LiverCPM.xlsx


title: Replicate1, Fib-Del


title: DPF2_rep1


title: FAU-MS-006 [FAU-MS-006]

description: SortSeq

extract_protocol:
Primary colon tumors of mice with fibroblast-specific deletion of Zeb1 or of Zeb1-proficient control mice were dissected and dissociated into single cells. After erythrocyte lysis in ACK buffer, cells were incubated with Fc Block, anti-CD45-PE/Cy7, anti-CD31-PE, anti-Epcam-eFluor450, a-CD140a-APC and eFluor780 in PBS/2 % FCS/2 mM EDTA. Single viable cells (eFluor-) were sequentially gated for Epcam-,CD45- and CD31 negative cells. These were index-sorted into 384-well capture plates containing 50 µL lysis buffer and barcoded primers covered by 10 µL of mineral oil  by flow cytometry using a BD FACSAria Fusion fluorescence activated cell sorter (BD biosciences) and capture plates were sent for paired-end sequencing at Single Cell Discoveries in Utrecht (Illumina Nextseq™ 500).
Library preparation according to the CEL-Seq2 protocol was performed by SCD. Briefly, after heat-lysis of the cells at 65° C, sequential barcoding, amplification and in vitro transcription was performed to generate a final cDNA library containing TruSeq small RNA primers (Illumina) for sequencing. Pleaase also see https://www.scdiscoveries.com/support/materials-methods/

value: CAFs

value: Col6a1Cre transgene positive


title: Liver, Sedentary, Muscle-Specific Bmal1KO_3

description: LiverCPM.xlsx

value: Cre+:iMSBmal1 fl/fl

value: 48-hours post


title: FAU-MS-005 [FAU-MS-005]

description: SortSeq


title: Liver, Exercise Trained_3

description: LiverCPM.xlsx

value: Vehicle + Exercise Training


title: FAU-MS-004 [FAU-MS-004]

description: SortSeq

value: Colon tumor

value: Col6a1Cre transgene negative


title: Liver, Sedentary, Muscle-Specific Bmal1KO_2

description: LiverCPM.xlsx


title: FAU-MS-003 [FAU-MS-003]

description: SortSeq


title: BRD9-P_rep1


title: Liver, Sedentary, Muscle-Specific Bmal1KO_1

description: LiverCPM.xlsx


title: FAU-MS-002 [FAU-MS-002]

description: SortSeq


title: FAU-MS-001 [FAU-MS-001]

description: SortSeq


title: BRD9-C_rep2


title: Tcell_CoCulture_KO_3

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: CXCR6_coculture_expected_count.csv column "Tcell_CoCulture_KO_2"

data_processing:
Bulk RNA-Seq data was processed using nextflow-based RNA-Seq pipeline with STAR and RSEM for alignment and transcript quantification ('--aligner star_rsem'), nf-core/tools v2.3.2 (https://github.com/nf-core/tools), bioconda, and nextflow v22.04.0 (https://github.com/nextflow-io/nextflow).
Counts and transcripts per million (TPM) values were computed per sample.
Assembly: mm10
Supplementary files format and content: expected count expression matrix for all samples in CSV (comma-separated-values) format

source_name: CD8+ T cell

growth_protocol: CD8+ T cells were isolated from the spleens and lymph nodes using CD8a microbeads (Miltenyi). 5x105 cells per well were plated in the presence of murine IL-12 (10ng/mL) in 24-well plates that were previously coated with 1ug/mL anti-CD3/anti-CD28. After 48 hours, media was changed to contain IL-2 (6ng/mL) and cells were moved to uncoated plates. Cells were cultured in the presence of IL-2 for an additional 3 days before use in co-culture assay

extract_protocol:
After 24 hours, cells were stained with antibodies against CD45.2 and CD45.1 along with 7AAD for dead cell removal. 5000 CD45.2+ cells were isolated by cell sorting into tubes containing 10uL TCL buffer (Qiagen) with 1% 2-mercaptoethanol.
Smart Seq 2 for populations

treatment_protocol: Bone marrow-derived DCs (BM-DCs) from CD45.1 mice activated overnight with 2ug/mL of the sting agonist DMXAA (Invitrogen, tlrl-dmx). The following morning DCs were pulsed with 1nM of OVA257-264 peptide (GenScript) for 3 hours at 37°C. 5x105 ova-pulsed DCs and 5x105 T cells were cultured together in 48 well plates.

value: CD8+ T cell

value: CXCR6 KO OTI (Jax stock 005693 crossed with OTI)

value: Co-culture with ova-pulsed BM-DC

tag: timepoint

value: 24 hours


title: Tcell_CoCulture_KO_2


title: Liver, Sedentary_5

description: LiverCPM.xlsx

value: Liver

value: Vehicle + No Exercise


title: Tcell_CoCulture_WT_3

description: CXCR6_coculture_expected_count.csv column "Tcell_CoCulture_WT_3"

value: Wildtype OTI


title: BRD9-C_rep1


title: BRD7_rep2


title: Liver, Sedentary_4

description: LiverCPM.xlsx


title: Tcell_CoCulture_WT_2

description: CXCR6_coculture_expected_count.csv column "Tcell_CoCulture_WT_2"


title: Liver, Sedentary_3

description: LiverCPM.xlsx


title: Tcell_CoCulture_WT_1

description: CXCR6_coculture_expected_count.csv column "Tcell_CoCulture_WT_1"


title: BRD7_rep1


title: Liver, Sedentary_2

description: LiverCPM.xlsx


title: WT_Mouse5_TP24

description: aggregated_tpm column "32_S32_TPM"

data_processing:
RNA-seq reads were aligned using STAR to mouse genome version mm10
Expression levels were calculated using RSEM using annotated transcripts (mm10)
Further processing using the Bioconductor package DESeq2 in R
Data was normalized using TPM normalization
Assembly: mm10
Supplementary files format and content: TPM expression matrix in TSV (tab-separated-values) format

growth_protocol: CD8+ T cells were isolated from the spleens and lymph nodes of mice using CD8 microbeads (Miltenyi)

extract_protocol:
For each timepoint, 1,000 cells were sorted into 5uL of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol
Smart Seq 2 for populations

treatment_protocol: After taking a timepoint 0 sample, cells were plated on plates previously coated with 1 ug/mL anti-CD3/anti-CD28 in the presence of murine IL2 (6ng/mL)


title: Microdissected stroma from FFPE tissue, sclerosing BCC 3

city: Schlieren

first: Gaetana

last: Restivo

address: Wagistrasse 18

department: Department of Dermatology

country: Switzerland

institute: University Hospital Zurich

data_processing:
Transcript abundances were estimated using Salmon v1.5.0 in selective alignment mode, with a k-mer length of 31, GC-bias correction, sequence strand bias correction, and mapping validation enabled. Raw reads were mapped to a pre-indexed human genome reference database (index v5) created from the GRCh38_no_alt_analysis_set from NCBI.
Assembly: hg38
Supplementary files format and content: Salmon quantification files. Plain-text, tab-separated files with a single header line (which names all of the columns).

source_name: Skin

extract_protocol:
RNA was isolated from FFPE tissue cuts captured by LCM using the truXTRAC FFPE microtube RNA Kit (Covaris).
For library construction, the SMARTer® Stranded Total RNA-Seq Kit v2 Pico Input Mammalian (A Takara Bio Company) was used. The libraries were normalized to 10nM.

value: Skin

tag: tissue type

value: sclerosing


title: BRD9-P_rep2


title: cKO_Mouse3_TP24

description: aggregated_tpm column "30_S30_TPM"

value: Tcf7 cKO OTI


title: WT_Mouse4_TP24

description: aggregated_tpm column "31_S31_TPM"


title: Liver, Sedentary_1

description: LiverCPM.xlsx


title: Microdissected stroma from FFPE tissue, sclerosing BCC 2


title: cKO_Mouse2_TP24

description: aggregated_tpm column "29_S29_TPM"


title: Fib-KO2_rep2

first: Marc

middle: P.

last: Stemmler

address: Glückstr. 6

department: Experimental Medicine 1

institute: Friedrich-Alexander University of Erlangen-Nürnberg

data_processing:
Salmon quantified reads from STAR mapped raw reads
Assembly: GRCm38
Supplementary files format and content: salmon counts

source_name: colon

extract_protocol:
Qiagen Rneasy Mini Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: colon

value: fibroblast

value: Zeb1 del/del


title: Microdissected stroma from FFPE tissue, sclerosing BCC 1


title: Fib-Ctrl2_rep2

value: Zeb1 flox/flox


title: WT_Mouse6_TP8

description: aggregated_tpm column "24_S24_TPM"

value: 8 hours


title: Tcell_CoCulture_KO_1

description: CXCR6_coculture_expected_count.csv column "Tcell_CoCulture_KO_1"


title: Microdissected stroma from FFPE tissue, superficial BCC 3

value: superficial


title: cKO_Mouse3_TP8

description: aggregated_tpm column "21_S21_TPM"


title: WT_Mouse4_TP8

description: aggregated_tpm column "22_S22_TPM"


title: cKO_Mouse2_TP8

description: aggregated_tpm column "20_S20_TPM"


title: Fib-Ctrl1_rep2


title: cKO_Mouse1_TP8

description: aggregated_tpm column "19_S19_TPM"


title: cKO_Mouse1_TP24

description: aggregated_tpm column "28_S28_TPM"


title: Microdissected stroma from FFPE tissue, superficial BCC 2


title: WT_Mouse6_TP24

description: aggregated_tpm column "33_S33_TPM"


title: Microdissected stroma from FFPE tissue, superficial BCC 1


title: WT_Mouse6_TP4

description: aggregated_tpm column "15_S15_TPM"

value: 4 hours


title: Microdissected stroma from FFPE tissue, nodular BCC 3

value: nodular


title: Fib-KO2_rep1


title: Fib-Ctrl2_rep1


title: Microdissected stroma from FFPE tissue, nodular BCC 2


title: cKO_Mouse1_TP4

description: aggregated_tpm column "10_S10_TPM"

value: CD8+ T cell


title: cKO_Mouse2_TP4

description: aggregated_tpm column "11_S11_TPM"


title: Microdissected stroma from FFPE tissue, nodular BCC 1


title: cKO_Mouse3_TP4

description: aggregated_tpm column "12_S12_TPM"


title: WT_Mouse5_TP8

description: aggregated_tpm column "23_S23_TPM"


title: WT_Mouse6_TP0

description: aggregated_tpm column "6_TP0_S6_TPM"

value: 0 hours


title: WT_Mouse4_TP4

description: aggregated_tpm column "13_S13_TPM"


title: Fib-Ctrl1_rep1


title: WT_Mouse5_TP4

description: aggregated_tpm column "14_S14_TPM"


title: Microdissected stroma from FFPE tissue, micronodular BCC 2

value: micronodular


title: Microdissected stroma from FFPE tissue, healthy skin 6

value: healthy skin


title: Fib-KO1_rep2


title: WT_rep3

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

data_processing:
Libraries were mapped against the GRCh38 human genome using hisat2 v2.1.0 with options --no-unal --no-softclip --new-summary --no-mixed --no-discordant
Read counts were generated in SeqMonk v1.48.0 using the Ensembl v102 gene build with annotated lncRNAs removed.  Quantitation was done in non-directional mode
Assembly: Ensembl v102 GRCh38
Supplementary files format and content: Tab delimited file of raw read counts

organism:
Homo sapiens
Mus musculus

source_name: Human tumors Xenografted into mouse

growth_protocol: Xenograft

extract_protocol:
Snap frozen tumor material, ground to a powder and RNA extracted using Qiagen RNAEasy plus kit.
Poly A enrichment

treatment_protocol: Doxycycline in drinkng water

value: Human tumors Xenografted into mouse

value: Colorectal cancer

value: Wildtype

value: Doxycycline


title: Microdissected stroma from FFPE tissue, micronodular BCC 3

value: Skin


title: WT_Mouse5_TP0

description: aggregated_tpm column "5_TP0_S5_TPM"

value: Wildtype OTI


title: engrafted_KAPP_rep1_snRNA

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

description: single-nuclei

data_processing:
Cell Ranger v3.0.1 (10x Genomics) and Cell Ranger v6.1.1 (for engrafted_KAPP_rep1_snRNA) was used using the count function with default parameters for read alignment, demultiplexing, and quantification of gene counts per cell. Data was aligned to a custom mm10 reference integrating the different vectors added to the mouse genome. Five custom chromosomes were added to the mm10 genome, the first one containing the piggybac transferase; the second one containing Akaluc and the GFP sequences; the third one containing the human H3F3A gene with HA tag; the fourth one containing the p53 guide RNA and the last one containing the shATRX sequence.
Reads mapping to these sequences were counted using a custom GTF file supplied to Cell Ranger.
Assembly: mm10
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes), barcodes and expression matrices generated by Cell Ranger.

source_name: Hindbrain

extract_protocol:
Tumor-bearing C57BL/6J mice were euthanized by CO2 exposure. Brains were rapidly dissected in ice-cold dissociation medium (DM) containing: 20 mM glucose, 81.8 mM Na2SO4, 30 mM K2SO4, 5.8 mM MgCl2, 250 µM CaCl2, 1 mM HEPES, 160 µM NaOH, 0.8 mM kynurenic acid, 50 µM D-APV, 100 U/mL penicillin, 100 µg/mL streptomycin, 5 µg/ml plasmocin and 100 µg/ml primocin. Coronal sections were cut using a brain matrix and GFP+ (tumor) and GFP- regions (stroma) were microdissected under an epifluorescence stereomicroscope (Leica M205, Leica Biosystems).
Microdissected tissue was then enzymatically digested into a single-cell suspension using the Papain Dissociation System according to the manufacturer’s instructions (Worthington Biochemicals). The samples were sequenced using the 10X Chromium single-cell 3' protocol.

treatment_protocol: Engrafted KAPP tumors were obtained using intracranial stereotaxic injection. For this, 150-350,000 single cell resuspended in cold HBSS were injected into the pons of 5- to 6-week-old female NSG NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ or C57BL/6J (BL6) mice, Jackson Laboratory. For tumor serial transplantation experiments, GFP+ tumors were dissected from brains once mice showed tumor burden symptoms, mechanically disaggregated and followed by enzymatic digestion using DNase and Liberase T (Roche Cat# 05401020001). Briefly, tissue was incubated at 37°C for 10-20min and reaction was inhibited by adding PBS containing 75U DNase and 1% FBS. Cells were spined and resuspended in neurobasal media. For in vivo treatment, anti-CSF1R (CD115, BioXCell Cat # BP0213) and anti-PD-1 4H2 (kindly provided by Bristol-Meyer Squibb) antibodies were administered by intraperitoneal (IP) injection. Animals were randomly assigned. Mice received 200 or 300µg of anti-CSF1R three times for one week and 200µg of anti-PD-1 twice a week during four weeks, 3 days post cell injection.

value: Hindbrain

value: brain tumor

tag: strain

value: H3.3K27M, ATRX LOF, P53 LOF, PDGFRA WT overexpression

tag: Sex

value: female


title: WT_Mouse4_TP0

description: aggregated_tpm column "4_TP0_S4_TPM"


title: cKO_Mouse2_TP0

description: aggregated_tpm column "2_TP0_S2_TPM"

value: Tcf7 cKO OTI


title: Microdissected stroma from FFPE tissue, micronodular BCC 1


title: cKO_Mouse3_TP0

description: aggregated_tpm column "3_TP0_S3_TPM"


title: engrafted_KAPP_rep2_snRNA

description: single-nuclei


title: WT_rep4


title: Glud1KO_fusedMyotubes_4

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

data_processing:
bcl2Fastq v2.20 software used for demultiplexing + basecalling
fastp 0.20.0 used for trimming
Kallisto v0.46.1 used for gene quantification
edgeR v3.36 used for count normalization and differential expression analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited raw count matrix of each sample

source_name: primary myoblasts

extract_protocol:
RNeasy plus micro kit Qiagen
Illumina TRUseq mRNA

value: primary myoblasts

tag: replicate

value: biol rep 4

tag: condition

value: fused myotubes

tag: time point


title: Microdissected stroma from FFPE tissue, healthy skin 5

tag: tissue


title: Fib-KO1_rep1

value: colon

value: fibroblast

value: Zeb1 del/del


title: WT_rep1

value: Human tumors Xenografted into mouse

tag: cell type


title: RQ_rep2

value: Colorectal cancer

value: PTPRK KO + PTPRK.R1095Q


title: cKO_Mouse1_TP0

description: aggregated_tpm column "1_TP0_S1_TPM"

value: CD8+ T cell

value: 0 hours


title: RQ_rep4

value: Doxycycline


title: Glud1KO_fusedMyotubes_1

value: biol rep 1


title: Microdissected stroma from FFPE tissue, healthy skin 4

value: Skin

value: healthy skin


title: RQ_rep3


title: RQ_rep1


title: WT_rep5

value: Wildtype


title: Glud1KO_fusedMyotubes_3

value: biol rep 3


title: WT_rep2


title: Glud1KO_diffMyotubes_2

value: primary myoblasts

value: biol rep 2

value: differentiated myotubes


title: Rescue_rep6

value: PTPRK KO + PTPRK


title: Rescue_rep5


title: Rescue_rep4


title: Microdissected stroma from FFPE tissue, healthy skin 2


title: Microdissected stroma from FFPE tissue, healthy skin 1


title: Rescue_rep3


title: Glud1KO_fusedMyotubes_2

value: fused myotubes


title: Glud1KO_myoblasts_2

value: proliferating myoblasts


title: Rescue_rep1

value: Human tumors Xenografted into mouse


title: Glud1KO_diffMyotubes_1


title: Microdissected stroma from FFPE tissue, basosquamous BCC 3

value: basosquamous


title: Microdissected stroma from FFPE tissue, healthy skin 3


title: Microdissected stroma from FFPE tissue, basosquamous BCC 2


title: Glud1KO_myoblasts_3


title: KO_rep5

value: Colorectal cancer

value: PTPRK KO + tGFP


title: KO_rep4


title: Glud1KO_myoblasts_1


title: KO_rep3


title: KO_rep1


title: Microdissected stroma from FFPE tissue, basosquamous BCC 1


title: KO_rep2


title: WT_fusedMyotubes_4

value: biol rep 4

value: WT


title: Macrophage, resting, hypoxia, 24hr, noS4U [S27]

city: Boulder

first: Edward

last: Courvan

address: 3415 Colorado Ave

institute: University of Colorado

data_processing:
Unique sequences filtered with FastUniq v1.1
Adaptor trimming with Cutadapt v2.3
Alignment with HISAT-3N
Mapped read counting with Htseq v0.9.1
TimeLapse Mutations scored with bam2bakR
Assembly: GRCh39: GCA_000001405.29
Supplementary files format and content: cB_TimeLapse_S10toS18.csv: cB file used for input in bakR to quantify transcript mutation rates and decay rates. Each row is indexed by the sample and is annotated for the number of reads matching the exact characteristics of the other columns. See bam2bakR documentation for column details.
Supplementary files format and content: cB_TimeLapse_S01andS19.csv: cB file used for input in bakR to quantify transcript mutation rates and decay rates. Each row is indexed by the sample and is annotated for the number of reads matching the exact characteristics of the other columns. See bam2bakR documentation for column details.
Supplementary files format and content: RawCounts_S10toS18.csv: gene level counts for main experimental samples

source_name: macrophage

growth_protocol: Macrophages were grown in StemCell Technologies SF Immunocult Macrophage Medium at 37C in a humidified incubator

extract_protocol:
Cells were scraped from dishes and extracted in trizol
Total RNA was subjected to the TimeLapse-seq oxidation protocol before constructing libraries using Takara biosiences SMARTer seq Pico V3 Kit
nucleoside recoding RNA-seq (TimeLapse)

value: macrophage

tag: s4u feed

value: female

tag: activation state

value: resting

value: hypoxia (1% sea level O2)


title: CS_rep5

value: PTPRK KO + PTPRK. C1089S

tag: treatment

value: Doxycycline


title: WT_fusedMyotubes_3

value: primary myoblasts

value: biol rep 3

tag: genotype


title: CS_rep4


title: Macrophage, resting, normoxia, 24hr, noS4U [S26]

value: normoxia (17% sea level O2)


title: Rescue_rep2

value: PTPRK KO + PTPRK


title: CS_rep2


title: WT_fusedMyotubes_2

value: biol rep 2

value: fused myotubes


title: CS_rep1

value: Human tumors Xenografted into mouse


title: Macrophage, resting, hypoxia, 24hr, rep2 [S24]


title: Macrophage, resting, hypoxia, 24hr, rep3 [S25]


title: Macrophage, resting, normoxia, 24hr, rep3 [S22]


title: KO

description: 10X single cell sequencing

data_processing:
Aligned reads to the mm10 genome using CellRanger software (v1.3 10 3 Genomics)
Assembly: mm10
Supplementary files format and content: Files (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz) generated after cellranger converts the data from fastq files to files used for input in R

source_name: B16Ova tumor

growth_protocol: Wildtype (WT, E8i-cre-, Tcf7 FL/FL) and Tcf7 cKO (KO, E8i-cre+, Tcf7 FL/FL) mice were injected with 2.5x10^5 B16Ova cells subcutaneously in their flanks. On day 13, tumors were harvested (n=3 per group) and dissociated to single cell suspensions prior to FACS

extract_protocol:
2000 cells from each category (A,B,C,D) were sorted from each tumor and then mixed equally before loading 7000 cells per 10X channel.  A = CD8+Tcrb+CD45+, B = CD4+Tcrb+CD45+, C = CD4-CD8-Tcrb-CD45+CD64-B220-NK1.1-LY6G- CD11c+ MHCII+ CD24+/low, D = CD4-CD8-Tcrb-CD45+CD64+B220+Ly6G+NK1.1+CD11c-MHCII-CD24- and CD4-CD8-Tcrb-CD45+CD64-B220-Ly6G-NK1.1-CD11c-MHCII-CD24+
10X single cell sequencing

value: B16Ova tumor

tag: time

value: day 13 post tumor injection

value: Intratumoral immune cells

value: Tcf7 cKO (KO, E8i-cre+, Tcf7 FL/FL)


title: Blood3GFP

city: Baltimore

first: Ines

last: Godet

state: MD

address: 1650 Orleans Street, CRB1, room 128

department: Oncology

institute: Johns Hopkins University

data_processing:
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files using default parameters.
rsem-1.3.0 was used for running the alignments as well as generating gene and transcript expression levels
Assembly: The data was aligned to “hg38” reference genome
Supplementary files format and content: Comma delimited text file containing gene-level counts

source_name: human cell line MDA-MB-231

growth_protocol: MDA-MB-231 cells obtained directly from the ATCC. The hypoxia fate-mapping system was developed as reported in Godet et. al, Nat Comm, 2019.

extract_protocol:
RNA was extracted using the Direct-zol microRNA kit (Zymo) and samples with RIN>8 were submitted for low input RNA sequencing.
Library preparation was conducted using an Ovation RNA-Seq System V2 kit and samples were sequenced in a HiSeqX, 150x150 paired-end.

treatment_protocol: Whole blood was harvested from NSG female mice bearing MDA-MB-231 hypoxia fate-mapping orthotopic tumors. After ACK lysis, 7,000 to 25,000 CTCs were DsRed+ or GFP+ sorted directly into TRI-reagent (Zymo).

tag: mouse #

value: Mouse #3

tag: cell population

value: GFP+


title: Blood2DsRed

value: Mouse #2

value: DsRed+


title: WT_fusedMyotubes_1

tag: cell line

value: biol rep 1

value: WT


title: WT_diffMyotubes_3

value: primary myoblasts

value: differentiated myotubes


title: Blood3DsRed


title: Blood2GFP


title: WT

description: 10X single cell sequencing

value: wildtype (WT, E8i-cre-, Tcf7 FL/FL)

value: female


title: Macrophage, resting, hypoxia, 24hr, rep1 [S23]

value: macrophage

value: resting

value: hypoxia (1% sea level O2)


title: WT_myoblasts_3

value: biol rep 3

value: proliferating myoblasts


title: Macrophage, resting, normoxia, 24hr, rep1 [S20]

value: normoxia (17% sea level O2)


title: CS_rep3

value: Human tumors Xenografted into mouse

value: Colorectal cancer

value: PTPRK KO + PTPRK. C1089S

value: Doxycycline


title: WT_diffMyotubes_1


title: Hom 3-1 l

first: Matthew

middle: D

last: Shoulders

address: 77 Massachusetts Avenue

department: Chemistry

institute: Massachusetts Institute of Technology

description:
p.Gly1170Ser homozygous substitution in COL2A22
Hom_3-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

data_processing:
Base calling was performed using the Illumina Offline Base Caller, Illumina RTA v. 2.11.3.
Forward reads containing barcode information (Read 1) were extracted and split into well barcode and unique molecular identifier (UMI) sequences and added to the header of the corresponding reverse read (Read 2), which was then treated as a single-end read.
Reads were aligned against hg19 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
For mapping and quantitation, reads were scored against GRCh38/ENSEMBL 101 annotation using Salmon v.1.3 with flags quant -p 8 -l ISR –validateMappings. The resulting quant.sf files were imported into the R statistical environment using the tximport library (tximport function, option “salmon”), and gene-level counts and transcript per-milllion (TPM) estimates were calculated for all genes.
Assembly: GRCh38/ENSEMBL 101
Supplementary files format and content: Raw counts per sample (merged salmon quant.sf output).
Supplementary files format and content: log2Tpm values per sample (merged salmon quant.sf output).

source_name: iPSC-derived cartilage

growth_protocol: iPSCs were grown on Matrigel (Corning) coated plates in Essential 8 medium. Differentiation to chondrocytes was carried out as descirbed by Lamandé et al. (PNAS, 2023)

extract_protocol:
Individual chondronoids were snap frozen and pulverized. Each of the three independent differentiations was considered a biological replicate. Chondronoids from the same differentiation are indicated as such (-1,-2 etc.). The pulverized tissue was resuspended in TRIzol, and extracted by chloroform according to manufacturer's protocol. The aqueous phase was collected and RNA was purified using Direct-zol RNA Microprep kit (Zymo Research) according to manufacturer's protocol.
High throughput three prime digital gene expression (HT-3'DGE) was adapted from the Soumillon et al. protocol (Soumillon et al. BioRxiv https://www.biorxiv.org/content/10.1101/003236v1) to perform reverse-transcription reactions using a dedicated RT primer containing sample and unique molecular identifier (UMI) sequences, to generate four subpools of 24 samples each. After second strand synthesis, Illumina adapters were added using the Nextera Flex tagmentation protocol substituting the normal P500 primer with an ad-hoc primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500 in high-output paired-end mode (20/57 nt reads).

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte

value: Gly1170Ser homozygote

value: LATE (day 44)

tag: technical replicate

tag: biological replicate

tag: included


title: Macrophage, resting, normoxia, 24hr, rep2 [S21]

tag: Sex


title: ds.P

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

description: RNA were extracted with Nucleospin RNA Mini kit - Macherey-Nagel. We performed Illumina RNA sequencing (30M single reads 50 bases)

data_processing:
Raw single end reads were trimmed using trimmomatic version 0.39  with parameters LEADING:30 TRAILING:30 MINLEN:36
Cleaned reads were aligned using STAR version 2.7.5a on human GENCODE reference genome version GRCh38 Release 37.
Gene counts were estimated using RSEM version 1.3.2.
Assembly: Genome Reference Consortium Human Build 38 Release 37
Supplementary files format and content: tab delimited text file including RSEM estimated raw counts combining all samples
Supplementary files format and content: tab delimited text file including RSEM estimated raw counts, FPKM and TPM for each sample

growth_protocol: HCC364 are cultured in standard DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1% penicillin-streptomycin

extract_protocol:
RNA were extracted with Nucleospin RNA Mini kit - Macherey-Nagel
Total RNA samples (500ng) were converted into sequencing libraries with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760), as recommended by the manufacturer.

treatment_protocol: HCC364-DTP and DTEP were generated by treating HCC364 cells with 250 nM dabrafenib and 5 nM trametinib for 3 and 40 weeks, respectively.

value: Lung adenocarcinoma

value: control


title: ds.L

value: 40 weeks

value: dabrafenib + trametinib


title: Hom 2-4 l

description:
p.Gly1170Ser homozygous substitution in COL2A21
Hom_2-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: female

tag: replicate


title: PBMC_P2_P7_P9_Raw_TCR-2-1

city: New York

first: Alexander

last: Tsankov

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomics

institute: Icahn School of Medicine at Mount SInai

description:
T cell receptor
10x Genomics

data_processing:
Raw features by cells matrices were generated with CellRanger > v3.1
Assembly: GRCh38
Supplementary files format and content: seurat objects including raw count matrices
Supplementary files format and content: contig files of TCR-seq

source_name: pleural mesothelioma

extract_protocol:
Tumor samples were transported in MACS® Tissue Storage Solution stored at 4°C, rinsed with PBS, minced and incubated in a rotation shaker for 40 minutes at 37°C in Collagenase IV 0.25mg/ml, Collagenase D 200U/ml and DNAse I 0.1mg.ml (all Sigma). Cell suspensions were then aspirated through a 18G needle ten times and strained through a 70-micron mesh prior to RBC lysis. Dead cells were removed using an EasySep Dead Cell Removal (Annexin V) Kit. Cell suspensions were sorted into CD45+ and CD45- cells using the EasySepTM Human CD45 Depletion Kit per kit instructions.
Single-cell RNA-seq (scRNA-seq) was performed on tumor samples using the Chromium platform (10x Genomics, Pleasanton, CA) utilizing both the 3′ and 5’ gene expression kits. Approximately 6000 CD45+ and CD45- cells were loaded into each channel of the 10x Chromium controller, following the manufacturer-supplied protocol. For 5’ gene expression samples, BCR and TCR CDR3 sequences were enriched using the human V(D)J B/T cell enrichment. 10x libraries were constructed using the 10x supplied protocol and sequenced at the Mount Sinai Genomics Core Facility. Gel-bead in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and then sequenced in paired-end mode on a HiSeq 2500 instrument (Illumina, San Diego, CA).
scRNA-seq CITE-seq TCR-seq

value: pleural mesothelioma


title: ds.3w

value: 3 weeks


title: Hom 3-4 l

description:
p.Gly1170Ser homozygous substitution in COL2A25
Hom_3-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: PBMC_P2_P7_P9_Raw_CITE-2-2

description:
surface protein
10x Genomics


title: engrafted_KAPP_rep2_scRNA

description: single-cell

data_processing:
Cell Ranger v3.0.1 (10x Genomics) was used using the count function with default parameters for read alignment, demultiplexing, and quantification of gene counts per cell. Data was aligned to a custom mm10 reference integrating the different vectors added to the mouse genome. Five custom chromosomes were added to the mm10 genome, the first one containing the piggybac transferase; the second one containing Akaluc and the GFP sequences; the third one containing the human H3F3A gene with HA tag; the fourth one containing the p53 guide RNA and the last one containing the shATRX sequence.
Reads mapping to these sequences were counted using a custom GTF file supplied to Cell Ranger.
Assembly: mm10
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes and peaks), barcodes and expression matrices generated by Cell Ranger.

extract_protocol:
Tumor-bearing C57BL/6J mice were euthanized by CO2 exposure. Brains were rapidly dissected in ice-cold dissociation medium (DM) containing: 20 mM glucose, 81.8 mM Na2SO4, 30 mM K2SO4, 5.8 mM MgCl2, 250 µM CaCl2, 1 mM HEPES, 160 µM NaOH, 0.8 mM kynurenic acid, 50 µM D-APV, 100 U/mL penicillin, 100 µg/mL streptomycin, 5 µg/ml plasmocin and 100 µg/ml primocin. Coronal sections were cut using a brain matrix and GFP+ (tumor) and GFP- regions (stroma) were microdissected under an epifluorescence stereomicroscope (Leica M205, Leica Biosystems).
Microdissected tissue was then enzymatically digested into a single-cell suspension using the Papain Dissociation System according to the manufacturer’s instructions (Worthington Biochemicals). The samples were sequenced using the 10X Chromium single-cell 3' protocol.
single-cell RNA-seq and single-nuclei RNA-seq

value: Hindbrain

value: brain tumor

tag: strain

value: H3.3K27M, ATRX LOF, P53 LOF, PDGFRA WT overexpression


title: WT_myoblasts_2

value: primary myoblasts

value: biol rep 2

tag: condition

value: proliferating myoblasts

tag: time point

value: WT


title: Hom 1-3 l

description:
p.Gly1170Ser homozygous substitution in COL2A16
Hom_1-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: tissue

value: iPSC-derived cartilage

tag: cell type

value: iPSC-derived chondrocyte


title: Hom 3-3 l

description:
p.Gly1170Ser homozygous substitution in COL2A24
Hom_3-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: Gly1170Ser homozygote

value: LATE (day 44)


title: PBMC_P2_P7_P9_Raw_TCR-2-2

description:
T cell receptor
10x Genomics


title: de_novo_KAPP_rep1_snRNA

description: single-nuclei


title: Hom 3-2 l

description:
p.Gly1170Ser homozygous substitution in COL2A23
Hom_3-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: WT_myoblasts_1

value: biol rep 1


title: WT_diffMyotubes_2

value: differentiated myotubes


title: Hom 2-3 l

description:
p.Gly1170Ser homozygous substitution in COL2A20
Hom_2-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Hom 2-2 l

description:
p.Gly1170Ser homozygous substitution in COL2A19
Hom_2-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Het 3-3 l

description:
p.Gly1170Ser heterozygous substitution in COL2A11
Het_3-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: Gly1170Ser heterozygote


title: engrafted_KAPP_rep1_scRNA

description: single-cell

value: female


title: Hom 2-1 l

description:
p.Gly1170Ser homozygous substitution in COL2A18
Hom_2-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: PBMC_P2_P7_P9_Raw_CITE-2-1

description:
surface protein
10x Genomics

value: pleural mesothelioma


title: Tumor_raw_TCR_P13

description:
T cell receptor
10x Genomics


title: Het 3-2 l

description:
p.Gly1170Ser heterozygous substitution in COL2A10
Het_3-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: de_novo_KAPP_rep2_snRNA

description: single-nuclei


title: Hom 1-2 l

description:
p.Gly1170Ser homozygous substitution in COL2A15
Hom_1-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Hom 1-4 l

description:
p.Gly1170Ser homozygous substitution in COL2A17
Hom_1-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: PBMC_P2_P7_P9_Raw_GEX-2-2

description:
mRNA
10x Genomics


title: Tumor_raw_TCR_P7

description:
T cell receptor
10x Genomics
P7_filtered_contig_annotations.csv

data_processing:
Raw features by cells matrices were generated with CellRanger > v3.1
Assembly: GRCh38
Supplementary files format and content: contig files of TCR-seq
Library strategy: scTCR-seq

extract_protocol:
Tumor samples were transported in MACS® Tissue Storage Solution stored at 4°C, rinsed with PBS, minced and incubated in a rotation shaker for 40 minutes at 37°C in Collagenase IV 0.25mg/ml, Collagenase D 200U/ml and DNAse I 0.1mg.ml (all Sigma). Cell suspensions were then aspirated through a 18G needle ten times and strained through a 70-micron mesh prior to RBC lysis. Dead cells were removed using an EasySep Dead Cell Removal (Annexin V) Kit. Cell suspensions were sorted into CD45+ and CD45- cells using the EasySepTM Human CD45 Depletion Kit per kit instructions.
Single-cell RNA-seq (scRNA-seq) was performed on tumor samples using the Chromium platform (10x Genomics, Pleasanton, CA) utilizing both the 3′ and 5’ gene expression kits. Approximately 6000 CD45+ and CD45- cells were loaded into each channel of the 10x Chromium controller, following the manufacturer-supplied protocol. For 5’ gene expression samples, BCR and TCR CDR3 sequences were enriched using the human V(D)J B/T cell enrichment. 10x libraries were constructed using the 10x supplied protocol and sequenced at the Mount Sinai Genomics Core Facility. Gel-bead in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and then sequenced in paired-end mode on a HiSeq 2500 instrument (Illumina, San Diego, CA).


title: Tumor_raw_TCR_P12

description:
T cell receptor
10x Genomics


title: SMARCA4_BRM-IgG

data_processing:
CUT&RUN-seq data were preprocessed and analyzed using cutRunTools pipeline.
This pipeline automated the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data was further utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalized by subtracting the treatment file to the corresponding control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Peak bed files
Supplementary files format and content: bigWig files

growth_protocol: MOLT-4 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep and were treated with 250nM BRM014 or DMSO.

extract_protocol:
Library construction from the Cut&Run-seq samples and sequencing of paired-end-150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end Cut&Run-Seq sequencing

value: T-ALL


title: Hom 1-1 l

description:
p.Gly1170Ser homozygous substitution in COL2A14
Hom_1-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: PBMC_P2_P7_P9_Raw_GEX-2-1

description:
mRNA
10x Genomics


title: SMARCA4_DMSO-IgG

value: DMSO


title: Het 3-4 l

description:
p.Gly1170Ser heterozygous substitution in COL2A12
Het_3-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: iMSBmal1KO Exercise Trained 5

first: Mark

last: Viggars

address: University of Florida, M531

institute: University of Florida

data_processing:
Partek Flow
Quality score trimmed for Phred <20, 3-prime right end, min-read length 25,
Trimmed sequence reads were mapped to mm10, GRCm39. Annotated to genomes. Star alignment 2.7.8a
CPM values used in processed data file. Deseq2 median of ratios and Deseq2 differential expression analysis used.
Assembly: mm10 (GRCm39)
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Gastrocnemius Muscle, Exercise Trained, Muscle-Specific Bmal1KO

extract_protocol:
Trizol with Qiagen, RNEasy Kit
Illumina library kit.

value: Tibialis Anterior Muscle

value: Cre+:iMSBmal1 fl/fl

value: iMSBMal1KO + Exercise Training

value: 48-hours post


title: iMSBmal1KO Exercise Trained 1


title: MOLT4_BRM_IgG


title: Tumor_Raw_GEX_P13

description:
mRNA
10x Genomics


title: H3K27ac_BRM

tag: antibody

value: H3K27ac (ab4729, Abcam)

tag: control


title: iMSBmal1KO Exercise Trained 4

tag: genotype

tag: treatment


title: Tumor_Raw_GEX_P12

description:
mRNA
10x Genomics


title: Het 2-2 l

description:
p.Gly1170Ser heterozygous substitution in COL2A6
Het_2-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Het 3-1 l

description:
p.Gly1170Ser heterozygous substitution in COL2A9
Het_3-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: MOLT4_DMSO_IgG


title: iMSBmal1KO Exercise Trained 2

tag: time


title: iMSBmal1KO Exercise Trained 3


title: Tumor_Raw_GEX_P11

description:
mRNA
10x Genomics


title: Vehicle Exercise Trained 4

source_name: Gastrocnemius Muscle, Exercise Trained

value: Vehicle + Exercise Training


title: Tumor_raw_TCR_P11

description:
T cell receptor
10x Genomics


title: Tumor_Raw_GEX_P10

description:
mRNA
10x Genomics


title: RUNX1_BRM

value: RUNX1 (ab23980, Abcam)


title: Het 2-4 l

description:
p.Gly1170Ser heterozygous substitution in COL2A8
Het_2-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte


title: Vehicle Exercise Trained 3


title: Het 2-3 l

description:
p.Gly1170Ser heterozygous substitution in COL2A7
Het_2-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: LATE (day 44)


title: Phoxinus gills, Reference, biol rep 2

data_processing:
Quality improvement via an adaptor and low-quality reads filtering using TRIMMOMATIC, with a threshold of phred + 33 quality score of at least 25 for all bases, and a minimum length of 50 bp for all reads kept for downstream analyses
TRINITY v2.9.1 was used to create a de novo assembly using the nine pairs of clean sequences.
The reads of the raw nine paired sequences were aligned to the de novo transcriptome using SALMON
BUSCO v5.2.2 was used to assess transcriptome assembly completeness by searching against the actinopterygii_odb10 (Creation date: 2021-02-19) dataset.
The expression matrix was generated and the low expressions transcripts (minimum expression of 1.0) were filtered using TRINITY v2.9.1, the expression levels were normalized as transcripts per million transcripts (TPM). Identification of likely protein-coding regions in transcripts was performed with TRANSDECODER v5.5.0.
The filtered transcriptome sequencing reads were aligned to protein, signal peptides, and transmembrane domains using the tools, DIAMOND v2.0.8 [49], SIGNALP 6.0 [50], TMHMM v2.0 [51], and, HMMER v3.3.2 [52]. The de novo transcriptome was then functionally annotated using the tool TRINOTATE v3.2.2 [45].
Before the differential gene expression analysis, the SALMON tool was used to align the clean reads of the three sites to the filtered transcriptome and the mapping rate was calculated. The mapping tables were merged according to the stations and using TMM [53] normalization. Differential expression analysis with three biological replicates of the two stations with higher chloride (A and C) were compared to the reference condition (Station B) using the DESeq2 [54] package, the fold change cut-off was set at >2, and the FDR≤0.05.
Assembly: de novo (trinity)
Supplementary files format and content: tab-delimited text file with annotated TMM counts for each sample output of deseq2

extract_protocol:
RNA was extracted using an RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
Illumina Tru-Seq™ RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) was applied in generating sequencing libraries following the manufacturer’s protocol

value: gills

value: Reference


title: Vehicle Exercise Trained 5


title: Vehicle Exercise Trained 1


title: Patient P3 Primary Tumor, gene expression

data_processing:
Pair-ended FASTQ files were mapped to the GRCh38 human transcriptome using the count function in Cell Ranger
The count matrices obtained were normalized, log-transformed and scaled using the Seurat version 3 package in R
Cells with < 400 genes, < 1000 unique molecular identifier (UMI) counts or > 25% mitochondrial gene expression detected were removed from downstream analyses
Assembly: GRCh38
Supplementary files format and content: cell-filtered count matrices, TCR contig info

source_name: Primary Tumor Surgical Resection

extract_protocol:
Tumor samples were transported in RPMI stored at 4°C, rinsed with PBS, minced and incubated in a rotation shaker for 40 minutes at 37°C in Collagenase IV 0.25mg/ml, Collagenase D 200U/ml and DNAse I 0.1mg.ml (all Sigma). Cell suspensions were then aspirated through a 18G needle ten times and strained through a 70-micron mesh prior to RBC lysis. Dead cells were removed using an EasySep Dead Cell Removal (Annexin V) Kit. Cell suspensions were sorted into CD45+ and CD45- cells using the EasySep™ Human CD45 Depletion Kit per kit instructions.
PBMCs from the blood samples were isolated within 3 hours of collection via Ficoll density gradient centrifugation for 10 min at 1200g room temperature. The supernatant was then spun down at 500g for 10 min at 4 degrees C and the pellet resuspended to a concentration of 10x10^6 cells/ml cold Human Serum AB (GemCell HAB and HAB + 20% DMSO in 1:1 ratio). The resulting PBMCs were stored in 2ml Cryogenic vials in liquid nitrogen. Previously frozen PBMCs were thawed, washed 2X in RPMI 2% FCS, treated with ACK lysis buffer (Lonza) to remove RBCs and briefly incubated with DAPI. 300,000 cells were then sorted on a DAPI negative gate. Cells were then stained for 30 minutes at room temperature with a panel of 138 Total-Seq-C antibodies (Biolegend, Stoeckius et al 2017) and washed 3x using the HT1000 laminar wash system (Curiox). Cells were then counted using the Cellaca MX High-throughput Automated Cell Counter as described in the manufacturer’s protocol (Nexcelom), pooled and loaded on the 10x Chromium Next GEM Chip K Kit using a superloading strategy mixing cells from the same sample across lanes.
For tumor samples, 10x libraries were constructed using the 10x supplied protocol and sequenced at the Mount Sinai Genomics Core Facility.
For PBMCs in the blood samples, libraries were prepared according to manufacturer’s protocol (10x Genomics).
scRNA-seq, CITE-seq (blood only), TCR-seq

value: Primary Tumor Surgical Resection

tag: tumor stage

value: IIIB

tag: molecule type

value: mRNA


title: H3K27ac_DMSO

tag: cell line

value: T-ALL


title: Het 2-1 l

description:
p.Gly1170Ser heterozygous substitution in COL2A5
Het_2-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: female

value: Gly1170Ser heterozygote

tag: technical replicate

tag: biological replicate


title: SMARCA4_DMSO

value: DMSO

value: BRG1 (#49360, Cell Signaling Technology)


title: RUNX1_DMSO


title: Het 1-4 l

description:
p.Gly1170Ser heterozygous substitution in COL2A4
Het_1-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: Sex

tag: included


title: Vehicle Exercise Trained 2

value: Tibialis Anterior Muscle

value: Cre+:iMSBmal1 fl/fl

value: 48-hours post


title: Patient P8 Primary Tumor, gene expression


title: Patient P5 Primary Tumor, gene expression


title: Het 1-3 l

description:
p.Gly1170Ser heterozygous substitution in COL2A3
Het_1-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: replicate


title: SMARCA4_BRM014


title: Het 1-2 l

description:
p.Gly1170Ser heterozygous substitution in COL2A2
Het_1-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: iMSBmal1KO Control 4

source_name: Gastrocnemius Muscle, Sedentary, Muscle-Specific Bmal1KO

value: iMSBmal1KO + No Exercise


title: Patient P4 Primary Tumor, gene expression

value: IIB


title: Macrophage, resting, normoxia, 2hr, unfed control [S01]

extract_protocol:
Cells were scraped from dishes and extracted in trizol
Total RNA was subjected to the TimeLapse-seq oxidation protocol before constructing libraries using Takara biosiences SMARTer seq Pico V3 Kit
nucleoside recoding RNA-seq (TimeLapse

treatment_protocol: See sample record

value: macrophage

tag: agent

value: unfed

tag: activation state

value: resting

value: normoxia (17% sea level O2)


title: WT 3-4 l

description:
wild-type control
WT_3-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: tissue

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte

value: Wild-type

tag: time point

value: LATE (day 44)


title: iMSBmal1KO Control 5


title: iMSBmal1KO Control 2


title: WT 3-3 l

description:
wild-type control
WT_3-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: cell type

value: female


title: iMSBmal1KO Control 3


title: Macrophage, activated, hypoxia, 24hr, rep3 [S18]

value: s4U 500 uM, 2 hr

value: activated (5 ug/mL LPS & 50 ng/mL interferon gamma)

value: hypoxia (1% sea level O2)


title: Patient P1 Primary Tumor, gene expression, CD45neg

value: Primary Tumor Surgical Resection

value: IIIB

value: mRNA


title: iMSBmal1KO Control 1

value: Tibialis Anterior Muscle

value: Cre+:iMSBmal1 fl/fl

value: iMSBmal1KO + No Exercise

value: 48-hours post


title: Macrophage, activated, hypoxia, 24hr, rep2 [S17]

value: macrophage


title: WT 3-2 l

description:
wild-type control
WT_3-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Macrophage, activated, hypoxia, 24hr, rep1 [S16]


title: WT 3-1 l

description:
wild-type control
WT_3-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Vehicle Control 5

source_name: Gastrocnemius Muscle, Sedentary

value: Vehicle + No Exercise


title: Het 1-1 l

description:
p.Gly1170Ser heterozygous substitution in COL2A1
Het_1-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: Gly1170Ser heterozygote


title: Macrophage, resting, normoxia, 2hr, 500uM s4U [S19]

value: resting

value: normoxia (17% sea level O2)


title: Macrophage, activated, normoxia, 24hr, rep3 [S15]

value: female


title: Vehicle Control 4


title: WT 2-4 l

description:
wild-type control
WT_2-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived chondrocyte

value: Wild-type

value: LATE (day 44)


title: Vehicle Control 3


title: Patient P1 Primary Tumor, gene expression, CD45pos

value: Primary Tumor Surgical Resection


title: WT 2-3 l

description:
wild-type control
WT_2-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Macrophage, activated, normoxia, 24hr, rep2 [S14]

value: s4U 500 uM, 2 hr

value: activated (5 ug/mL LPS & 50 ng/mL interferon gamma)


title: WT 2-1 l

description:
wild-type control
WT_2-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Macrophage, activated, normoxia, 24hr, rep1 [S13]


title: WT 2-2 l

description:
wild-type control
WT_2-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Vehicle Control 1

value: Tibialis Anterior Muscle


title: WT 1-10 l

description:
wild-type control
WT_1-10_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: WT 1-9 l

description:
wild-type control
WT_1-9_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Macrophage, resting, normoxia, 24hr, rep2 [S11]


title: Macrophage, resting, normoxia, 24hr, rep3 [S12]


title: Macrophage, resting, normoxia, 24hr, rep1 [S10]


title: Neuroblastoma cell line, Differentited 1.5 days; treated with si-CyCoNP; Replicate2

data_processing:
Trimmomatic (v0.39; Bolger et al., 2014) and Cutadapt (v3.2; Martin, 2011) were used to remove adapter sequences and poor quality bases; minimum read length after trimming was set to 18.
Reads aligning to rRNAs were filtered out; this first alignment was performed using Bowtie2 software (v2.4.2, https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
STAR software (v2.7.7a, Dolbin et al., 2013) was used to align reads to GRCh38 genome.
Uniquely mapping fragments were counted for each annotated gene (ensembl release 99) through STAR software (v2.7.7a, Dolbin et al., 2013). See Material and Methods section for further explanation.
Assembly: GRCh38
Supplementary files format and content: counts_table.tsv contains gene level fragment counts related to analyzed samples
Supplementary files format and content: gene_expression_table.FPKM.tsv contains the gene expression data (FPKM) related to analyzed samples

source_name: SK-N-BE

extract_protocol:
Total RNA from cells was extracted with the Direct-zol RNA Purification Kit (Zymo Research)
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus was used to prepare cDNA libraries for RNA‐Seq
Total RNA, Paired end

treatment_protocol: 1.5 days differentiated SK-N-BE cells treated with si-SCR or si-CyCoNP

value: SK-N-BE

value: Neuroblastoma


title: CD71+/Ter119+ cells, WT/WT, rep2

city: Melbourne

first: Graham

middle: William

last: Magor

state: Victoria

address: 99 Commercial Rd

country: Australia

institute: ACBD

description:
mouse_267
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv

data_processing:
Read were mapped to mm9 with hisat2
Gene features were counted with featureCounts
Differential testing was performed with Voom/limma
Assembly: mm9
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with counts per million for each sample

source_name: spleen

extract_protocol:
Trizol
Swift Rapid RNA library kit

treatment_protocol: CD71+Ter119+ cells FACS sorted from spleen

value: spleen

value: CD71+/TER119+ sorted erythoblasts

value: WT/WT


title: No Treatment_3

type: RNA

city: Suita

first: Masahito

last: Shimojo

address: 1-6 Yamadaoka

country: Japan

institute: Osaka University

description:
Gene expression after 48hr in 22Rv1 without ASO
No Treatment_3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 22Rv1 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: without ASO


title: CD71+/Ter119+ cells, WT/D45, rep3

description:
mouse_320
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: AmNA7168_3

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA7168
AmNA7168_3(normalized)

value: transfected with Negative Control


title: Neuroblastoma cell line, Differentited 1.5 days; treated with si-CyCoNP; Replicate3

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

institute: Sapienza University of Rome


title: Negative Control_3

description:
Gene expression after 48hr in 22Rv1 transfected with Negative Control
Negative Control_3

value: transfected with AmNA[+23/+44]


title: AmNA[+23/+44]_3

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA[+23/+44]
2344_3(normalized)

value: transfected with AmNA[+21/+40]


title: WT 1-7 l

description:
wild-type control
WT_1-7_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: female


title: AmNA[+21/+40]_3

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA[+21/+40]
2140_3(normalized)

value: transfected with AmNA7168


title: WT 1-8 l

description:
wild-type control
WT_1-8_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived chondrocyte

value: Wild-type

value: LATE (day 44)


title: CD71+/Ter119+ cells, WT/WT, rep1

description:
mouse_169
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: WT 1-6 l

description:
wild-type control
WT_1-6_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Vehicle Control 2

city: Gainesville

value: Cre+:iMSBmal1 fl/fl

value: Vehicle + No Exercise

value: 48-hours post


title: Neuroblastoma cell line, Differentited 1.5 days; treated with si-CyCoNP; Replicate1

value: SK-N-BE

value: Neuroblastoma


title: CD71+/Ter119+ cells, WT/WT, rep3

description:
mouse_268
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv

value: spleen

value: CD71+/TER119+ sorted erythoblasts


title: Neuroblastoma cell line, Differentited 1.5 days; treated with si-SCR; Replicate3


title: Negative Control_2

description:
Gene expression after 48hr in 22Rv1 transfected with Negative Control
Negative Control_2


title: CD71+/Ter119+ cells, WT/D45, rep2

description:
mouse_291
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: WT 1-4 l-2

description:
wild-type control
WT_1-4_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: CD71+/Ter119+ cells, WT/D45, rep1

description:
mouse_179
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: Neuroblastoma cell line, Differentited 1.5 days; treated with si-SCR; Replicate2


title: No Treatment_2

description:
Gene expression after 48hr in 22Rv1 without ASO
No Treatment_2


title: WT 1-4 l


title: AmNA7168_2

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA7168
AmNA7168_2(normalized)


title: CD71+/Ter119+ cells, WT/KO, rep5

description:
mouse_262
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv

value: WT/KO


title: Neuroblastoma cell line, Differentited 1.5 days; treated with si-SCR; Replicate1


title: WT 1-3 l

description:
wild-type control
WT_1-3_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: CD71+/Ter119+ cells, WT/KO, rep3

description:
mouse_166
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: Tumor-899

description: Fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generte fastq files.
Sequences were aligned to hg38 genome using Space Ranger's default settings.
Gene expression of reference coding genes was quantifies uisng Space Ranger's deault settings.
Assembly: hg38
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of genes ID
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue with spots
Supplementary files format and content: scalefactors_json.json.gz: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv list of spatial barcodes and the coordinates of corresponding spots
Library strategy: Spatial Transcriptomics

source_name: tumor

growth_protocol: Hypoxia fate-mapping MDA-MB-231 tumors (Godet et. al, 2019) were harvested 18 days post-implantation and immediately frozen in clear OCT. 10 μm tumor slices were placed within the fiducial frame of the Visium slide. The tissue was pre-fixed in cold methanol and imaged at 10X magnification using a Cytation5 in the RFP and GFP channels to acquire native fluorescence. The slide was immediately transferred to cold methanol with DAPI. DAPI staining was imaged at 10X using Cytation5.

extract_protocol:
The Visium spatial gene expression protocol was followed according to the manufacturer’s instructions (#PN-1000187, 10X Genomics). Briefly, tissue permeabilization was followed by cDNA synthesis, second strand synthesis and cDNA denaturation. The ideal cycle number was determined by qPCR and cDNA was amplified and cleaned using SPRIselect. The amount of cDNA was measured to determine the cDNA input for library construction.
Library construction was performed following the Visium protocol. Briefly, cDNA was fragmented and submitted to end repair and A-tailing. Adaptor sequences were ligated, and the post-ligation product was cleaned and subjected to Index PCR.
Overall, the P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 were added.

treatment_protocol: No treatment was performed.

value: tumor

value: breast cancer


title: CD71+/Ter119+ cells, WT/KO, rep2

description:
mouse_252
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: WT 1-1 l

description:
wild-type control
WT_1-1_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: DMSO-IgG_2

first: Tze King

last: Tan

address: 14 Medical Drive

growth_protocol: DND-41 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep and were treated with 100nM ACBI-1 or DMSO or no treatment.

value: T-ALL

value: DMSO

tag: antibody

value: IgG


title: Hom 3-4 e

description:
p.Gly1170Ser homozygous substitution in COL2A24
Hom_3-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: female

tag: genotype

value: Gly1170Ser homozygote

value: EARLY (day 34)


title: Negative Control_1

description:
Gene expression after 48hr in 22Rv1 transfected with Negative Control
Negative Control_1(normalized)

tag: treatment

value: without ASO


title: PCL_Week6_Rep3

city: Rochester

first: Hani

middle: A

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

data_processing:
Data Formatting bcl2fastq version 2.20.0
Data Cleaning FastP version 0.23.1 with parameters --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r
Genome Alignment STAR_2.7.9a with parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx
Read Quantification subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Assembly: Rnor_6.0 GCA_000001895.4
Supplementary files format and content: tab-delimited text file of gene counts

organism: Rattus norvegicus

source_name: Repair bone tissue

extract_protocol:
For the bone marrow, tissue dissociation was achieved with red blood cell lysis buffer, followed by enzymatic digestion using Type IV collagenase, dispase, and DNase. Bone tissue was mechanically disrupted into fine pieces and further digested with Type I collagenase. Cells released from the marrow and bone were pooled and submitted to the GRC for mRNA extraction.
mRNA libraries for RNA-Seq were prepared using the Illumina mRNA prep kit following manufacturers protocols

value: Repair bone tissue

value: WT

value: PCL Scaffold at 6 weeks


title: CD71+/Ter119+ cells, WT/KO, rep1

description:
mouse_182
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: AmNA[+21/+40]_2

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA[+21/+40]
2140_2(normalized)

value: transfected with AmNA[+23/+44]


title: PCL_Week6_Rep2


title: Tumor-897


title: AmNA[+23/+44]_2

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA[+23/+44]
2344_2(normalized)


title: DMSO-H3K27ac_2

institute: National University of Singapore

value: H3K27ac (ab4729, Abcam)


title: CD71+/Ter119+ cells, D45/D45, rep3

description:
mouse_263
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv

value: spleen

value: CD71+/TER119+ sorted erythoblasts


title: Hom 3-3 e

description:
p.Gly1170Ser homozygous substitution in COL2A23
Hom_3-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived chondrocyte


title: PCL_Week6_Rep1


title: ACBI-IgG_2

value: ACBI


title: Hom 3-2 e

description:
p.Gly1170Ser homozygous substitution in COL2A22
Hom_3-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: PCL_Week2_Rep3

value: PCL Scaffold at 2 weeks


title: CD71+/Ter119+ cells, WT/KO, rep4

description:
mouse_259
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv

value: WT/KO


title: WT 1-2 l

description:
wild-type control
WT_1-2_l
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: Wild-type

value: LATE (day 44)


title: No Treatment_1

description:
Gene expression after 48hr in 22Rv1 without ASO
No Treatment_1

value: transfected with AmNA7168


title: AmNA7168_1

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA7168
AmNA7168_1(normalized)


title: AmNA[+21/+40]_1

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA[+21/+40]
2140_1(normalized)

value: transfected with AmNA[+21/+40]


title: CD71+/Ter119+ cells, D45/D45, rep1

description:
mouse_171
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: Hom 3-1 e

description:
p.Gly1170Ser homozygous substitution in COL2A21
Hom_3-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: female

value: Gly1170Ser homozygote

value: EARLY (day 34)


title: Hom 2-4 e

description:
p.Gly1170Ser homozygous substitution in COL2A20
Hom_2-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: AmNA[+23/+44]_1

description:
Gene expression after 48hr in 22Rv1 transfected with AmNA[+23/+44]
2344_1(normalized)

value: transfected with Negative Control


title: CD71+/Ter119+ cells, D45/KO, rep4

description:
mouse_260
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: PCL_Week2_Rep1

value: Repair bone tissue

value: WT


title: NP_Week6_Rep3

value: ACPC-NP Scaffold at 6 weeks


title: Hom 2-3 e

description:
p.Gly1170Ser homozygous substitution in COL2A19
Hom_2-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Hom 2-2 e

description:
p.Gly1170Ser homozygous substitution in COL2A18
Hom_2-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: DND_BRG1

value: T-ALL

value: BRG1 (#49360, Cell Signaling Technology)


title: NP_Week6_Rep2


title: CD71+/Ter119+ cells, D45/KO, rep1

description:
mouse_164
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv

value: spleen

value: CD71+/TER119+ sorted erythoblasts


title: DND_H3K4me3

value: H3K4me3 (Epicypher)


title: NP_Week6_Rep1


title: DND_IgG

value: IgG


title: CD71+/Ter119+ cells, D45/KO, rep2

description:
mouse_256
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: CD71+/Ter119+ cells, D45/D45, rep2

description:
mouse_241
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: CD71+/Ter119+ cells, D45/KO, rep3

description:
mouse_163
MommeD45-raw-counts.csv
MommeD45-processed-counts.csv


title: PCL_Week2_Rep2

value: PCL Scaffold at 2 weeks


title: ACBI-H3K27ac_2

value: ACBI

value: H3K27ac (ab4729, Abcam)


title: Hom 1-4 e

description:
p.Gly1170Ser homozygous substitution in COL2A16
Hom_1-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte


title: MOLT4_SMA4

value: MOLT4_SMA4 (#49360, Cell Signalling Technology)


title: NP_Week2_Rep3

value: ACPC-NP Scaffold at 2 weeks


title: Hom 1-3 e

description:
p.Gly1170Ser homozygous substitution in COL2A15
Hom_1-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: female

value: Gly1170Ser homozygote

value: EARLY (day 34)


title: DND_RUNX1

value: RUNX1 (ab23980, Abcam)


title: Old, 8, spatial transcriptomics

city: Philadelphia

first: Yicheng

last: Wu

state: Pennsylvania

address: 415 Curie Boulevard

department: Neuroscience

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
Raw data was processed using the Cell Ranger (v6) and Space Ranger (v2) softwares.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Whole brain

extract_protocol:
For scRNA-seq, freshly collected brain cells from dentate gyrus of C57Bl6/JRj mice were dissociated using Neural Tissue Dissociation Kit (P) and Myelin Removal Beads II (Miltenyi Biotec).  For spatial transcriptomics, mouse brains were collected and embedded in OCT.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, spatial gene expression protocol, 10x Genomics).

value: Brain cells

value: Whole brain

tag: strain

tag: age

value: 16-21 month old


title: Hom 2-1 e

description:
p.Gly1170Ser homozygous substitution in COL2A17
Hom_2-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Old, 7, spatial transcriptomics

description: 10x Genomics


title: MOLT4_RUNX1

value: T-ALL

value: MOLT4_RUNX1 (ab23980, Abcam)


title: DND_Input_RUNX1

value: IgG


title: NP_Week2_Rep2

value: Repair bone tissue

value: WT


title: Old, 6, spatial transcriptomics

description: 10x Genomics


title: NP_Week2_Rep1


title: MOLT4_Input


title: Hom 1-1 e

description:
p.Gly1170Ser homozygous substitution in COL2A13
Hom_1-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz