title: Female_mice_F23_5XFAD_Trem2_T96K_p

description:
Library name: F23_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: WT 01

status: Public on Sep 17 2025

type: SRA

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Brain/Hypothalamus

extract_protocol:
Rneasy
Illumina TruSeq

tag: tissue

value: Brain/Hypothalamus

tag: genotype

value: Wild-type


title: scRNAseq_HW3125_24h_PoolA

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: 2837F10

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole animal

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

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

tag: strain

value: Whole animal

tag: time


title: scRNAseq_HW3125_22h_PoolC

description: Library name: 2837F9


title: Lip-1MI3

city: Shanghai

first: chang

middle: yu

last: chen

address: yishan Rd 600#

country: China

institute: shanghai sixth people's hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced. The raw sequence data have been submitted to the NCBI Gene Expression Omnibus (GEO) datasets with accession number < GEO accession > or NCBI Short Read Archive (SRA) with accession number with accession number < SRA accession >.
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
We use R to perform correlation analysis. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The pearson correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments.
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: ventricle tissue

growth_protocol: Male, C57BL/6J, 6-8weeks old, housed under standard conditions with a 12/12 h light-dark cycle, with unrestricted access to water and food. The housing environment was controlled to maintain a temperature of 20–25 °C and a relative humidity of 40% to 70%.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Mice were divided into four groups: Sham, MI, Fer-1+MI, and Lip-1+MI. Mice were anesthetized with an intraperitoneal injection of pentobarbital sodium at a dose of 80 mg/kg. After achieving anesthesia, a thoracotomy was conducted between the fourth and fifth intercostal spaces to expose the heart. The left anterior descending coronary artery was then ligated with a 6-0 polyester suture, positioned proximally to the left atrium and near the pulmonary artery outflow tract. The Fer-1 and Lip-1 groups received pre-treatment with Fer-1 (1 mg·kg-1·d-1) and Lip-1 (3 mg·kg-1·d-1) (obtained from MCE), respectively, 24 hours prior to the MI procedure.

value: ventricle tissue

value: Wild Type

tag: treatment

value: Lip-1 (3 mg·kg-1·d-1)  24 hours before permanent ligation of the left anterior descending artery


title: mRNAseq_N2_26h_Rep1

description: Library name: 2772F13

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

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

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


title: mRNAseq_N2_21h_Rep1

description: Library name: 2772F8


title: Lip-1MI2


title: mRNAseq_N2_20h_Rep1

description: Library name: 2772F7


title: scRNAseq_HW3125_22h_PoolB

description: Library name: 2837F8


title: Female_mice_F18_5XFAD_Trem2_T96K_p

city: Charlestown

first: Ana

last: Griciuc

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital

description:
Library name: F18_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx

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

source_name: brain

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

value: brain

tag: cell type

value: microglia

tag: Sex

value: female

tag: age

value: 8 months old


title: scRNAseq_HW3125_22h_PoolA

description: Library name: 2837F7


title: Lip-1MI1


title: Female_mice_F17_5XFAD_Trem2_T96K_p

description:
Library name: F17_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: mRNAseq_N2_19h_Rep1

description: Library name: 2772F6


title: Fer-1MI3

value: Fer-1 (1 mg·kg-1·d-1) 24 hours before permanent ligation of the left anterior descending artery


title: Fer-1MI2


title: scRNAseq_HW3125_20h_PoolB

description: Library name: 2837F5


title: Female_mice_F8_5XFAD_Trem2_T96K_p

description:
Library name: F8_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: scRNAseq_HW3125_20h_PoolC

description: Library name: 2837F6


title: Female_mice_F16_5XFAD_Trem2_T96K_p

description:
Library name: F16_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: mRNAseq_N2_17h_Rep1

description: Library name: 2772F4


title: mRNAseq_N2_16h_Rep1

description: Library name: 2772F3


title: scRNAseq_HW3125_20h_PoolA

description: Library name: 2837F4


title: Female_mice_F2_5XFAD_Trem2_T96K_p

description:
Library name: F2_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Female_mice_F22_5XFAD_Trem2_T96K_p

description:
Library name: F22_5XFAD_Trem2_T96K_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: mRNAseq_N2_15h_Rep1

description: Library name: 2772F2


title: scRNAseq_HW3125_18h_PoolC

description: Library name: 2837F3


title: MI2

value: permanent ligation of the left anterior descending artery


title: Female_mice_F25_5XFAD_Trem2_p_p

description:
Library name: F25_5XFAD_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: MI3


title: Female_mice_F13_5XFAD_Trem2_p_p

description:
Library name: F13_5XFAD_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: mRNAseq_N2_MoltExit

description: Library name: 2571F2

data_processing:
The RNA-seq samples were mapped to the c.elegans genome (ce10) with the R package QuasR using the spliced alignment algorithm HISAT2. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",splicedAlignment=TRUE,aligner="Rhisat2")". For gene quantification, gene annotation from WormBase was used (WS220). The command used to create the expression count table was qCount(proj,exons,orientation="opposite").
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with amplitudes and calibrated phases for all oscillating genes from (PMID: 32687264). Calibration was performed by rotating the phases from (PMID: 32687264) such that zero degrees represents molt exit. The amplitudes are identical to (PMID: 32687264). Also included is a classification of the genes into 4 gene sets based on their calibrated phases (0,90,180,270). This information can be used to visualize developmental trajectories based on the orthogonal gene set method.

growth_protocol: Synchronized L1 animals (strain HW1939) expressing ubiquitous luciferase, were grown (1 animal per well) in two 384-well plates in S-Basal containing OP50 bacteria and luciferin. Developmental trajectories were then recorded on a luminometer for 26 and 28 hours so that the majority of animals were at L3 molt entry and L3 molt exit respectively, prior to freezing the plates. After identifying wells contianing animals at the appropriate developmental timepoint, the plates were thawed, and individual animals were collected from their wells and pooled for RNA isolation and library preparation.

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

tag: developmental stage

value: L3 Molt Exit


title: MI1


title: mRNAseq_N2_18h_Rep1

description: Library name: 2772F5


title: scRNAseq_HW3125_18h_PoolB

description: Library name: 2837F2


title: Female_mice_F19_5XFAD_Trem2_p_p

description:
Library name: F19_5XFAD_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: scRNAseq_HW3125_18h_PoolA

description: Library name: 2837F1


title: Female_mice_F14_5XFAD_Trem2_p_p

description:
Library name: F14_5XFAD_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: sham3

value: sham


title: mRNAseq_N2_MoltEntry

description: Library name: 2571F1

value: L3 Molt Entry


title: sham2


title: Fer-1MI1


title: Female_mice_F1_5XFAD_Trem2_p_p

description:
Library name: F1_5XFAD_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Trim66_KO_homo_10X_scRNA_seq

first: Yalei

last: Kong

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University

data_processing:
Reads were processed using the Cell Ranger (Trim66 knockout data: version 6.1.2; Goofy-cre; Cbx4 flox: version 5.0.0) pipeline with default parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome (GRCm38, mm10) using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat R toolkit (Trim66 knockout data: version 4.3.0; Goofy-cre; Cbx4 flox: version 5.0.1) for downstream analysis. The different filtering thresholds are suitable for Trim66 knockout and Goofy-cre; Cbx4 flox data. For Trim66 knockout data, cells with less than 700 transcripts, or less than 200 genes, or more than 15000 transcripts, or more than 10% of mitochondrial genes expression were filtered out as low-quality cells; genes expressed in less than 3 cells were excluded. But for Goofy-cre; Cbx4 flox data, cells with less than 1500 transcripts, or less than 200 genes. or more than 15000 transcripts, or more than 10% of mitochondrial genes expression, or more than 1% hemoglobin-genes expression were filtered out as low-quality cells. The normalized data (NormalizeData function in Seurat package) after merging the different datasets was performed for extracting a subset of variable genes. Next, we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data with the vars.to.regress parameter to remove the mitochondrial variables. Then we used the Harmony package to integrate the different data. And the integrated data was displayed on a 2D map produced with uniform manifold approximation and projection (UMAP) using harmony embeddings (Trim66 knockout: 1-20; Goofy-cre; Cbx4 flox: 1-30).
The clusters were obtained using the FindNeighbors and FindClusters functions with the resolution set to 0.9 for Trim66 knockout and 0.6 for Goofy-cre; Cbx4 flox, resulting in 25 and 23 cell clusters, respectively. The cell types were annotated by overlapping the cluster markers found using the FindAllMarkers function with the known cell-type marker genes. The following cell types were annotated with selected marker genes listed below: HBCs (Krt5, Krt14, Trp63, Cxcl14, Sox2, Meg3); GBCs (Ascl1, Sox2, Lgr5, Hes6, Cxcr4, Ezh2, Neurog1, Neurod1, Tmprss4, Kit, Mki67, Top2a); INPs (Neurog1, Neurod1, Neurod2, Top2a, Mki67, Lhx2, Ebf1); immature OSNs (Ablim1, Drd4, Dbn1, Dpysl5, Crmp1, Ppp2cb, Marcksl1, Atf5, Gnas, Hdac2, Gng8, Dpysl3, Gap43, Stmn1, Stmn2, Ebf2, Lhx2, Cbx8, Trib3); mature OSNs (Cngb1, Adcy3, Slc17a6, Cnga4, Cnga2, Gnal, Omp, Gng13, Stoml3, Ebf2, Cbx8, Rtp1); sustentacular cells (Cyp2g1, Cyp1a2, Notch2, Notch3, Hes1, Hes5, Gpx6, Ermn, Sox2, Hey1, Sult1c1); olfactory ensheathing glia (S100b, Plp1, Mpz, Alx3); olfactory microvillar cells (Coch, Ascl3, Cftr, Hepacam2, Sox9, Trpm5); GC-D cells (Ms4a4c, Ms4a6c, Ms4a7, Pde2a, Car2, Cnga3); immune cells (Cd3d, Cd3e, Cd8a, Cd4, Il7r, Fgfbp2, Fcgr3a, Cx3cr1, Cd19, Cd79a, Ms4a4a); blood cells (Ptprc, Hba-a1, Mzb1, Sdc1, Cd14, S100a12, Clec10a, C1qa, C1qb, C1q)
For identifying the OSNs identity, we set different thresholds to analysis. Mature OSNs expressing single OR (UMI >= 2) were identified based on the OR that they expressed, while immature OSNs may simultaneously express several OR genes (UMI >= 1) at low levels.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Main Olfactory Epithelium (MOE)

extract_protocol:
The MOE tissues were dissected and transported in sterile culture dish with 10 ml 1´Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used the dissociation enzyme, 0.25% Trypsin (Thermo Fisher, 25200-072) and 10 μg/mL DNase I (Sigma, 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, SV30087.02) to digest the tissues. The MOE tissues were dissociated at 37 °C with a shaking speed of 50 rpm for about 40 min. We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1´Red Blood Cell Lysis Solution (Thermo Fisher, 00-4333-57). Dissociated cells were washed with 1´DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher). Each of the solutions above contained transcriptional inhibitors (5 μg/mL Actinomycin D., 10 μg/mL Anisomycin, and 10 μM Triptolide, Sigma)
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10´beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 Rev D). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2´150 chemistry.

value: Main Olfactory Epithelium (MOE)


title: Sham1


title: ATACseq_N2_29h_Rep2

description: Library name: 2919F16

library_source: genomic

data_processing:
Paired-end ATAC-seq reads were trimmed with Cutadapt v 1.18 using the parameters “-a NCTGTCTCTTATA -A NCTGTCTCTTATA --minimum-length=10 --overlap=1”. The N in the adapter was used to remove one additional nucleotide in every read in order to ensure correct downstream alignment of adapter reads with Bowtie. Trimmed reads were mapped to the C. elegans genome (ce11) using the qAlign function from the R package QuasR (v 1.42.1) with standard parameters which deploys the aligner Bowtie. The fragment size distributions of the individual libraries showed multiple peaks, the short fraction corresponding to transcription factor footprints (<120bp) and long fraction to nucleosomes (>120bp). We thus considered fragments with a read length of less than 120 bp for further analysis. To obtain ATAC-seq peaks we combined the alignments of all samples and ran MACS2 peak finder (v 2.2.6) with the parameters “-g ce -f BAMPE -q 0.5 --keep-dup all”. We quantified the number of reads in all the peaks using the function qCount() in the package QuasR. We further performed quantile normalization to correct for non-linear trends in the data, followed by log2 transformation with a pseudocount of 8 (log2(x+8)).
To study potential oscillations in the ATAC-seq data, we performed cosine curve fitting separately for every ATAC-seq peak using a linear model. In addition to the two oscillatory predictors cos(φ) and sin(φ), we also included a linear term λ to capture graded changes in intensity. For φ we directly used the inferred unwrapped pseudo times (in radians) obtained from the matching RNA-seq experiments. This allowed us to compensate for slight differences in the timing between the two replicates, to combine the two replicates in one single cosine curve fitting procedure and to obtain calibrated phases (molt-sync). ATAC-seq peaks with an amplitude > 0.25 were classified as oscillating, and ATAC-seq peaks with an amplitude < 0.25 and an absolute graded coefficient > 0.25 were defined as graded.
Assembly: ce11
Supplementary files format and content: tab-delimited text file with ATAC-seq peaks called (MACS2) on all samples together
Supplementary files format and content: tab-delimited text file with raw ATAC-seq read counts for all ATAC-seq peaks
Supplementary files format and content: tab-delimited text file with normalized log2 ATAC-seq read counts for all ATAC-seq peaks
Supplementary files format and content: tab-delimited text file with amplitudes and phases obtained by a cosine fit. Each peaks is classified as oscillating, graded or flat
Supplementary files format and content: bed file with genomic coordinates for oscillating ATAC-seq peaks
Supplementary files format and content: bed file with genomic coordinates for graded ATAC-seq peaks
Supplementary files format and content: bed file with genomic coordinates for flat ATAC-seq peaks
Supplementary files format and content: tab-delimited text file with activity vectors x’ y’ for molting clock TFs (coefficients of the linear model)
Supplementary files format and content: Tab-delimited text file with peak id, peak classification, genomic coordinate, linked Gene (if available), x and y from a cosine fit performed on the ATAC-seq data (cartesian coordinates of amplitude and phase), predicted x and y by the linear model, training variable that specifies the set of ATAC-seq peaks that were used for training, ChIP enrichments for the molting clock Tfs, TF cluster membership and contribution vectors for the molting clock TFs

molecule: genomic DNA

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

extract_protocol:
Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Briefly, 7 rounds of douncing (3 times / round) were performed in Omni-ATAC buffer, and nuclei were seperated from worm debry by slow centrifugation. Isolated nuclei were then tagmented according to the Omni-ATAC protocol (Corces et al., 2017, Nat Methods), and DNA isolated using the MinElute PCR purification kit (28004, Qiagen).
Isolated DNA was amplified using NEB Next High-Fidelity PCR Master Mix (M0541S, NEB), and barcoded illumina sequencing primers before Ampure XP bead purification.

tag: replicate


title: D8_NuclearRNA_WT_1

first: Eric

last: Van Nostrand

address: 1 Baylor Plaza Rm T334

department: Therapeutic Innovation Center

description:
Library name: D8_NuclearRNA_WT_1
0

data_processing:
Remove 10nt UMI from 5' end of read (293T experiment only): umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
Adapter trimming: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.2 --quality-cutoff 6 -m 18 -a AGATCGGAAGAGCACACGTC -a AAAAAAAAAAAAAAAAAAAA -a GGGGGGGGGGGGGGGGGGGG -A AGATCGGAAGAGCGTCGTGT -A TTTTTTTTTTTTTTTTTTTT -O 5 -o $prefix.fastq.r1.gz -p $prefix.fastq.r2.gz
UMI removal from end of R2 (293T experiment only): cutadapt -j 8 -U -10 -o $fastq1_working_trim2 -p $fastq2_working_trim2 $fastq1_working_trim $fastq2_working_trim
Repeat removal: STAR --runMode alignReads --runThreadN 8 --genomeDir $rep_star_database --readFilesCommand zcat --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFileNamePrefix $output_rep_database --outSAMtype BAM Unsorted --outFilterType BySJout --outBAMcompression 10 --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outStd Log --readFilesIn $fastq1_working_trim2 $fastq2_working_trim2
Sort: fastq-sort --id $prefix.sorted.RepUnmapped.out.mate1 > $prefix.sorted.RepUnmapped.out.mate1.sorted.fq fastq-sort --id $prefix.sorted.RepUnmapped.out.mate2 > $prefix.sorted.RepUnmapped.out.mate2.sorted.fq
Genome mapping: STAR --runMode alignReads --runThreadN 8 --genomeDir /hg19/star_2.4.0j_encode/ --genomeLoad NoSharedMemory --readFilesIn $prefix.RepUnmapped.out.mate1.s.fq $prefix.RepUnmapped.out.mate2.s.fq --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix $prefix.rmRep.genomemap --outSAMattributes All --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outStd Log --alignEndsType EndToEnd --outBAMcompression 10 --outSAMmode Full
Remove PCR duplicates (293T experiment only): umi_tools dedup --random-seed 1 --stdin $output_genome_sorted_bam --method unique --stdout $output_rmDup_bam
Gene-level expression quantification: featureCounts -p -a /path/to/gencode.v19.annotation.gtf -s 2 -o $prefix1.feature.count /path/to/sortedbam1.bam /path/to/sortedbam2.bam /path/to/sortedbam3.bam …
Isolate protein-coding genes only: perl pull_proteincodinggenes.pl $prefix1.feature.count hg19
Gene-level expression analysis: deseq $prefix1.feature.count.proteincodingonly.txt $prefix1.experiment.design.tsv $prefix1.feature.count.tsv.proteincodingonly.deseq.txt
Splicing analysis (rmats v4.3.0): rmats.py --b1 bamfilist.siNC.txt --b2 bamfilist.siQKI.txt --gtf gencode.v19.annotation.gtf -t paired --libType fr-secondstrand --variable-read-length --readLength 150 --nthread 8 --od rmats/ --tmp rmats/tmp/
Assembly: hg19
Supplementary files format and content: Bigwig genome coverage files (.bw), rmats splicing analysis output (.rmats), Gene-level read counts (featureCounts .txt file)

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: For D0 (pluripotency), cells were dissociated (Accutase), plated in FTDA growth medium (Rao, et al. Cell Stem Cell 2016 PMID 26748419), and cultured overnight prior to UV crosslinking. Cardiomyocyte differentiation was conducted following a previously established protocol (M. Zhang et al., 2015 PMID 25639979, Rao, et al. Cell Stem Cell 2016 PMID 26748419). In summary, confluent human embryonic stem cells (hESCs) dissociated (Accutase), pelleted, resuspended in ITS buffer supplemented with CHIR and BMP4 based on differentiation efficiency screening (WT: 1.5 uM CHIR, 1.5 ng/mL BMP4 ; QKI KO: 1.25 uM CHIR, 1.5 ng/mL BMP4), and plated. After 24 hours, media was replaced with TS media and cultured for 24 hours, followed by replacement with TS media supplemented with 100nM C59 for 48 hours (D4 (cardiac progenitors) were crosslinked at this stage). Fresh media (TS+100 mM C59) was added, followed by 24 hours, followed by media changes with TS media every 48 hours. D8 (cardiomyocyte) samples were UV crosslinked after confirmation of beating at days 7-8.

extract_protocol:
RNA was extracted by standard Trizol extraction.
For cardiomyocytes, RNA was polyA-enriched, followed by library preparation with Illumina stranded mRNA kits. For 293T experiments, polyA-enriched RNA was isolated with NEBNext® High Input Poly(A) mRNA Isolation kit, followed by library preparation utilizing the same protocol as seCLIP (Blue SM et al, Nature Protocols. 2022 PMID 35322209), based off of a published RNA-seq approach (Shishkin AA, Nature Methods. 2015 PMID 25730492).

treatment_protocol: For 293T QKI siRNA knockdown experiments, non-targeting siRNA (Silencer® select Negative control# 1, Invitrogen) or siRNA against QKI (Silencer® select-ID s18084, Invitrogen) was transfected at a concentration of 10 µM per well using Lipofectamine™ RNAimax (Cat# 13778150, Invitrogen) according to the manufacturer’s guidelines.

tag: cell line

value: D8 of hSC differentiation to cardiomyocyte


title: D8_NuclearRNA_WT_3

description:
Library name: D8_NuclearRNA_WT_3
0


title: ATACseq_N2_28h_Rep2

description: Library name: 2919F15


title: Female_mice_F30_Trem2_p_p

description:
Library name: F30_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Trim66_KO_het_10X_scRNA_seq


title: mRNAseq_N2_14h_Rep1

description: Library name: 2772F1


title: Goofy_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_5

data_processing:
Trimmomatic (version 0.39) was used to filter out low-quality reads
Reads were mapped to the mouse reference genome (mm10) with Hisat2 (version 2.1.0).
Raw read counts mapped to genes were calculated using featureCounts from Subread package (version 2.0.1).
DEG analyses were performed using DESeq2 (version 1.40.1) package with the default settings.
Significantly changed genes were identified with adjusted p value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: csv files containing normalized counts and TPM value obtained from DESeq2 package

extract_protocol:
mRNAs from the whole MOE tissues were extracted and purified with a Cell/Tissue total RNA isolation kit V2 (Vazyme, RC112-01).
Libraries were prepared with Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604-02).


title: ATACseq_N2_30h_Rep2

description: Library name: 2919F17


title: D8_NuclearRNA_KO_3

description:
Library name: D8_NuclearRNA_KO_3
0


title: ATACseq_N2_26h_Rep2

description: Library name: 2919F13


title: Female_mice_F24_Trem2_p_p

description:
Library name: F24_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: D8_NuclearRNA_KO_2

description:
Library name: D8_NuclearRNA_KO_2
0


title: D8_NuclearRNA_KO_1

description:
Library name: D8_NuclearRNA_KO_1
0


title: ATACseq_N2_25h_Rep2

description: Library name: 2919F12


title: ATACseq_N2_24h_Rep2

description: Library name: 2919F11


title: Female_mice_F10_Trem2_p_p

description:
Library name: F10_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Goofy_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_4


title: D8_NuclearRNA_WT_2

description:
Library name: D8_NuclearRNA_WT_2
0


title: ATACseq_N2_27h_Rep2

description: Library name: 2919F14


title: Goofy_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_3


title: Kang4_020 | 010

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th AVE NE

department: tumor microenvironment and metastasis

institute: the Hormel Institute

description: Fresh frozen Spatial transcriptome sequncing

data_processing:
FASTQ fileswere processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI. The number of raw reads was highly linearly correlated with the number of unique UMIs at all AOI sizes, suggesting largely uniform library amplification. However, to correct for any PCR amplification bias, all analyses in this study use UMI deduplicated counts. Data were exported to Excel for further analysis.
Assembly: N/A
Supplementary files format and content: xlsx
Library strategy: GeoMx Spatial transcriptome

source_name: liver

extract_protocol:
Frozen sections of murine livers were fixed with formalin overnight, and sent to the University of Minnesota Genomics Center for probe hybridization, immunofluorescence staining, and selection of ROIs for analysis. 1x Tris-EDTA (pH9.0) solution and steaming the solution to 95⁰C method were used for antigen retrieval followed by Proteinase K digestion at 37⁰C for 5 minutes (1 µg/mL) to expose RNA targets.
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual. The DSP aspirate was dried and resuspended in 10 μL DEPC-treated water, and 4 μL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled either in equal volumes or in proportion relative to AOI size, depending on the experiment, and purified with two rounds of AMPure XP beads (Beckman Coulter).Libraries were sequenced on an Illumina NextSeq 2000, according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.

value: liver

value: Activated-hepatic stellate cells of PD-L1 knockout mouse liver


title: Kang4_020 | 009


title: D0-WT-3

description:
Library name: D0-WT-3
0

value: D0 of hSC differentiation to cardiomyocyte


title: Female_mice_F7_5XFAD_Trem2_p_p

description:
Library name: F7_5XFAD_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: ATACseq_N2_23h_Rep2

description: Library name: 2919F10

value: Whole animal


title: Female_mice_F4_Trem2_p_p

description:
Library name: F4_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Goofy_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_2


title: ATACseq_N2_22h_Rep2

description: Library name: 2919F9


title: D0-KO-2

description:
Library name: D0-KO-2
0


title: Goofy_Cre_Trim66_flox_het_bulk_RNA_seq_rep_4


title: ATACseq_N2_20h_Rep2

description: Library name: 2919F7


title: ATACseq_N2_18h_Rep2

description: Library name: 2919F5


title: Kang4_020 | 005

value: Activated-hepatic stellate cells of control mouse liver


title: Goofy_Cre_Trim66_flox_het_bulk_RNA_seq_rep_3


title: ATACseq_N2_17h_Rep2

description: Library name: 2919F4


title: D0-WT-1

description:
Library name: D0-WT-1
0


title: Goofy_Cre_Trim66_flox_het_bulk_RNA_seq_rep_2


title: Kang4_020 | 004


title: Female_mice_F28_Trem2_p_p

description:
Library name: F28_Trem2_p_p
Samples_Control_ and_Mutant_Females_RPKM_Table.xlsx


title: Goofy_Cre_Trim66_flox_het_bulk_RNA_seq_rep_1


title: Goofy_Cre_Trim66_flox_het_bulk_RNA_seq_rep_5


title: D8-KO-2

description:
Library name: D8-KO-2
0


title: Goofy_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_1


title: ATACseq_N2_21h_Rep2

description: Library name: 2919F8


title: Kang4_020 | 008


title: D0-KO-3

description:
Library name: D0-KO-3
0


title: D8-KO-4

description:
Library name: D8-KO-4
0


title: D0-WT-2

description:
Library name: D0-WT-2
0


title: ATACseq_N2_16h_Rep2

description: Library name: 2919F3


title: Kang4_020 | 003


title: ATACseq_N2_19h_Rep2

description: Library name: 2919F6


title: D0-KO-1

description:
Library name: D0-KO-1
0


title: D8-KO-1

description:
Library name: D8-KO-1
0


title: Kang4_020 | 007


title: Kang4_020 | 002


title: monocytes_propranolol_4

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Data alinged using STAR (V.2.7.9). Reads in genes (Ensembl gene transcripts GRCm39.104.gtf) were quantified using featureCounts within the Subread package (V.2.0.3).
Assembly: GRCm39
Supplementary files format and content: count matrix text file generated by featureCounts

source_name: murine B16F10 metastasis

extract_protocol:
RNA was isolated using an RNA purification kit (Qiagen)
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA (500 ng) was prepared for sequencing using polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina. Library quality was assessed using the Fragment Analyzer (AATI) followed by library quantification (Illumina library quantification kit). Sequencing was carried out on a NovaSeq 6000 platform (Illumina).

value: lung monocytes

value: Propranolol


title: ATACseq_N2_15h_Rep2

description: Library name: 2919F2


title: ATACseq_N2_14h_Rep2

description: Library name: 2919F1


title: D8-WT-3

description:
Library name: D8-WT-3
0


title: ATACseq_N2_29h_Rep1

description: Library name: 2771F16


title: AB R55 inj.

city: Linköping

first: David

last: Ramonet

address: US campus - BKV floor 10

department: BKV

country: Sweden

institute: University of Linköping

data_processing:
bioconductor
Assembly: GRCmm39
Supplementary files format and content: delimited with expression values in one single file

growth_protocol: 5xFAD mice

extract_protocol:
RNAeasy +
Illumina Stranded mRNA

treatment_protocol: intracelebral delivery of tool compounds R55, R33 or vehicle in the cortex via sterotaxic microinjection

value: brain

tag: drug treatment

tag: brain hemisphere

value: injected hemisphere


title: monocytes_propranolol_3


title: ATACseq_N2_30h_Rep1

description: Library name: 2771F17


title: D8-WT-4

description:
Library name: D8-WT-4
0


title: AD R33 inj.


title: monocytes_propranolol_2


title: ATACseq_N2_28h_Rep1

description: Library name: 2771F15


title: monocytes_control_4

value: no treatment


title: Kang4_020 | 001


title: D4-KO-3

description:
Library name: D4-KO-3
0

value: D4 of hSC differentiation to cardiomyocyte


title: monocytes_control_3


title: AB R55 con.

value: uninjected hemisphere


title: ATACseq_N2_26h_Rep1

description: Library name: 2771F13


title: D4-KO-1

description:
Library name: D4-KO-1
0


title: D4-KO-2

description:
Library name: D4-KO-2
0


title: ATACseq_N2_27h_Rep1

description: Library name: 2771F14


title: D8-WT-2

description:
Library name: D8-WT-2
0


title: AH veh. inj.

value: vehicle


title: monocytes_control_2


title: D4-WT-3

description:
Library name: D4-WT-3
0


title: ATACseq_N2_25h_Rep1

description: Library name: 2771F12


title: monocytes_propranolol_1


title: AD R33 con.


title: AH veh. con.


title: ATACseq_N2_24h_Rep1

description: Library name: 2771F11


title: D4-WT-2

description:
Library name: D4-WT-2
0


title: monocytes_control_1


title: total_lung_propranolol_5

value: lung


title: N R33 con.


title: ATACseq_N2_23h_Rep1

description: Library name: 2771F10


title: total_lung_propranolol_4


title: QKI_D8_input3

description: Library name: QKI_D8_input3

library_source: other

data_processing:
eCLIP analysis was performed as described in Van Nostrand et al. Nature Methods 2016 (PMID 27018577).
Demutiplexing: python demux.py --fastq_1 $fastq1_working --fastq_2 $fastq2_working --expectedbarcodeida $bc1 --expectedbarcodeidb $bc2 -b $bc_fi --length 10 --max_hamming_distance 0 -m $metric_fi --newname $newname --dataset $dataset
Adapter trimming: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTAAGCAAT -g CTTCCGATCTGGCTTGT -A ATTGCTTAGATCGGA -A ACAAGCCAGATCGGA -A TTGCTTAGATCGGAA -A CAAGCCAGATCGGAA -A TGCTTAGATCGGAAG -A AAGCCAGATCGGAAG -A GCTTAGATCGGAAGA -A AGCCAGATCGGAAGA -A CTTAGATCGGAAGAG -A GCCAGATCGGAAGAG -A TTAGATCGGAAGAGC -A CCAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A CAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -A GAAGAGCGTCGTGTA -A AAGAGCGTCGTGTAG -o $fastq1_tr -p $fastq2_tr $fastq1 $fastq2 > $cutadapt_metrics
Adapter trimming round 2: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A ATTGCTTAGATCGGA -A ACAAGCCAGATCGGA -A TTGCTTAGATCGGAA -A CAAGCCAGATCGGAA -A TGCTTAGATCGGAAG -A AAGCCAGATCGGAAG -A GCTTAGATCGGAAGA -A AGCCAGATCGGAAGA -A CTTAGATCGGAAGAG -A GCCAGATCGGAAGAG -A TTAGATCGGAAGAGC -A CCAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A CAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -A GAAGAGCGTCGTGTA -A AAGAGCGTCGTGTAG -o $fastq1_trtr -p $fastq2_trtr $fastq1_tr $fastq2_tr > $cutadapt_metrics2
Sort: fastq-sort --id $fastq1_trtr > $fastq1_trtrsort fastq-sort --id $fastq2_trtr > $fastq2_trtrsort
Remove repeat-mapping reads: STAR --runMode alignReads --runThreadN 8 --genomeDir homo_sapiens_repbase_v2 --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outFileNamePrefix $prefix.sorted.Rep --outSAMtype BAM Unsorted --outFilterType BySJout --outBAMcompression 10 --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outStd Log --readFilesIn $fastq1_trtrsort $fastq2_trtrsort
Sort: fastq-sort --id $prefix.sorted.RepUnmapped.out.mate1 > $prefix.sorted.RepUnmapped.out.mate1.sorted.fq fastq-sort --id $prefix.sorted.RepUnmapped.out.mate2 > $prefix.sorted.RepUnmapped.out.mate2.sorted.fq
Genome mapping: STAR --runMode alignReads --runThreadN 8 --genomeDir $genome_star_sjdb/ --genomeLoad NoSharedMemory --readFilesIn $prefix.sorted.RepUnmapped.out.mate1.sorted.fq $prefix.sorted.RepUnmapped.out.mate2.sorted.fq --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix $prefix.sorted.rmRep --outSAMattributes All --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outStd Log --alignEndsType EndToEnd --outBAMcompression 10 --outSAMmode Full
Sort bam: samtools sort -n -o $prefix.rmRep.sorted.bam $prefix.rmRep.bam
Remove PCR duplicates: python barcodecollapsepe.py -b $prefix.rmRep.sorted.bam -o $prefix.rmRep.rmDup.bam -m $prefix.rmRep.rmDup.bam.metrics
Merge barcodes: samtools merge $prefix.merged.rmDup.bam $prefix.X1A.r1.fq.Tr1Tr2.sorted.rmRep.rmDup.bam $prefix.X1B.r1.fq.Tr1Tr2.sorted.rmRep.rmDup.bam
Peak calling: clipper --species hg19 --bam $prefix.merged.rmDup.bam --save-pickle --outfile $prefix.bed
Input normalization: overlap_peakfi_with_bam_PE.pl $IPprefix.merged.rmDup.bam $Inputprefix.merged.rmDup.bam $prefix.bed $mappedreadnums $prefix.IPvsInput.bed
Compress overlapping peaks: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl $prefix.IPvsInput.bed
3 replicate IDR: perl run_IDR_3sample.pl  $rep1_full_fi $rep2_full_fi $rep3_full_fi $final.IDR.010203merged.bed
Assembly: hg19
Supplementary files format and content: Bigwig genome coverage files (.bw), narrowPeak format peak bed files (.narrowPeak.bed.gz)

molecule: other

growth_protocol: For D0 (pluripotency), cells were dissociated (Accutase), plated in FTDA growth medium (Rao, et al. Cell Stem Cell 2016 PMID 26748419), and cultured overnight prior to UV crosslinking. Cardiomyocyte differentiation was conducted following a previously established protocol (M. Zhang et al., 2015 PMID 25639979, Rao, et al. Cell Stem Cell 2016 PMID 26748419). In summary, confluent human embryonic stem cells (hESCs) dissociated (Accutase), pelleted, resuspended in ITS buffer supplemented with CHIR and BMP4 based on differentiation efficiency screening (1.5 uM CHIR, 1.5 ng/mL BMP4), and plated. After 24 hours, media was replaced with TS media and cultured for 24 hours, followed by replacement with TS media supplemented with 100nM C59 for 48 hours (D4 (cardiac progenitors) were crosslinked at this stage). Fresh media (TS+100 mM C59) was added, followed by 24 hours, followed by media changes with TS media every 48 hours. D8 (cardiomyocyte) samples were UV crosslinked after confirmation of beating at days 7-8.

extract_protocol:
eCLIP was performed as described in Van Nostrand et al. Nature Methods 2016 (PMID 27018577). Briefly, cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest as indicated and Protein G sheep anti-rabbit Dynabeads, and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter was ligated to the 3’ end (T4 RNA Ligase, NEB). Samples were then run on SDS-PAGE gels and transferred to nitrocellulose membranes, and a region from 40-115 kDa (75 kDa = 225 nt of RNA above the protein size) was isolated and proteinase K (NEB) treated to isolate RNA. RNA was reverse transcribed and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 10 (N10) random bases at the 5’ end) was then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample was first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder was PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: Cells were UV crosslinked as previously described (Van Nostrand et al. Nature Methods 2016 (PMID 27018577)). Briefly, cells were rinsed with PBS, a minimal amount of PBS was added to cover (~2 mL per 10cm plate), followed by crosslinking (254 nM, 400 mJ/cm2) on ice. After crosslinking, cells were scraped and moved to conical tubes and pelleted, followed by removal of PBS and snap freezing.

tag: eclip antibody

tag: in-line barcode


title: L veh. inj.


title: total_lung_propranolol_1


title: L veh. con.


title: ATACseq_N2_20h_Rep1

description: Library name: 2771F7


title: total_lung_propranolol_3


title: D4-WT-1

description:
Library name: D4-WT-1
0


title: total_lung_control_5


title: ATACseq_N2_21h_Rep1

description: Library name: 2771F8


title: R R55 con.


title: QKI_D8_input2

description: Library name: QKI_D8_input2


title: ATACseq_N2_22h_Rep1

description: Library name: 2771F9


title: total_lung_propranolol_2


title: ATACseq_N2_19h_Rep1

description: Library name: 2771F6


title: QKI_D8_IP3

description: Library name: QKI_D8_IP3

value: X1A, X1B


title: QKI_D8_input1

description: Library name: QKI_D8_input1


title: Q R55 con.


title: QKI_D8_IP2

description: Library name: QKI_D8_IP2


title: total_lung_control_4


title: ATACseq_N2_18h_Rep1

description: Library name: 2771F5


title: R R55 inj.


title: total_lung_control_3


title: QKI_D8_IP1

description: Library name: QKI_D8_IP1


title: N R33 inj.


title: ATACseq_N2_16h_Rep1

description: Library name: 2771F3


title: total_lung_control_2


title: Q R55 inj.


title: ATACseq_N2_17h_Rep1

description: Library name: 2771F4


title: AA R55 con.


title: AA R55 inj.


title: total_lung_control_1


title: QKI_D4_input1

description: Library name: QKI_D4_input1


title: Des+/+_kap6_12, RNA

city: Alexandroupolis

first: Panagiotis

last: Liakopoulos

address: Dragana

department: Molecular Biology and Genetics

country: Greece

institute: Democritus University of Thrace

data_processing:
Raw reads from RNA-Seq experiments were aligned to the GRCm38 (mm10) reference genome using the HISAT2 aligner version 2.2.1 with default options. SAM files were converted to sorted and indexed BAM files using Samtools version 1.13. Counting reads to genes was done using the HTSeq – Count program version 1.99.2 with the options -s no --additional-attr gene_name. Differentially expressed genes (DEGs) were identified using the NOISeq R package version 2.44.0 considering 5 technical replicates in each conditions. DEGs with q >= 0.8 were considered significant.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

source_name: heart

growth_protocol: For induced Cardiomyocytes (iCM) samples: fibroblasts were isolated by enzymatic digestion with 1mg/ml Trypsin (Gibco) and 1mg/ml Collagenase type2 (worthington) from  hearts of 1-3 day old mouse pups as descibed in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)." Then, they transduced with the viral coctail Gat4+Mef2C+Tbx5 as described in "Qian, L., Berry, E.C., Fu, J.D., Ieda, M. & Srivastava, D. Reprogramming of mouse fibroblasts into cardiomyocyte-like cells in vitro. Nature protocols 8, 1204-1215 (2013)."  These iCMs were grown in DME/M199 edis+10%FBS for 7 days and then underwent FACS sorting analysis.

extract_protocol:
RNA was purified using Nucleospin RNA extraction Kit from Mackerey and Nagel
RNAseq libraries were prepared with the Illumina TruSeq RNA v2 kit using 1 μg of total RNA. Libraries were checked with the Agilent bioanalyzer DNA1000 chip, quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. 100 bp Single-End reads were generated with the Illumina NovaSeq sequencer.

value: heart

value: primary cells:7 day old induced cardiomyocytes from cardiac fibrobalsts isolated from hearts of Des+/+ mouse pups after viral transduction with viral cocktail :Gata4+Mef2C+Tbx5+ DsRED

value: Des+/+

value: WT+RGMT


title: QKI_D4_IP3

description: Library name: QKI_D4_IP3


title: O R33 inj.


title: ATACseq_N2_14h_Rep1

description: Library name: 2771F1


title: QKI_D4_IP2

description: Library name: QKI_D4_IP2


title: P R55 inj.


title: RNA,Des-/-_Swim_Replicate2

data_processing:
Raw reads from RNA-Seq experiments were aligned to the GRCm38 (mm10) reference genome using the HISAT2 aligner version 2.2.1 with default options. SAM files were converted to sorted and indexed BAM files using Samtools version 1.13. Counting reads to genes was done using the HTSeq – Count program version 1.99.2 with the options -s reverse --additional-attr gene_name. Differentially expressed genes (DEGs) were identified using the DESeq2 R package version 1.40.2. DEG matrices from DESeq2 were filtered using the following criteria: log2 fold change >= 0.6, p-value ≤ 0.05, and a mean count of ≥ 20 across all replicates in B condition or log2 fold change <= -0.6, p-value ≤ 0.05, and a mean count of ≥ 20 across all replicates in A condition. Gene ontology analysis was performed using the clusterProfiler R package version 4.8.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

growth_protocol: The adult cardiomyocytes (ACM) were isolated with enzymatic perfutsion using  an enzymatic cocktail of Trypsin (Gibco) and CollagenaseD (ROCHE) as described in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)". ACM were isolated form 3 month old mice that have or not undergone swimming excersise as described in ""Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)" and "Diokmetzidou, A., et al. Desmin and alphaB-crystallin interplay in the maintenance of mitochondrial homeostasis and cardiomyocyte survival. Journal of cell science 129, 3705-3720 (2016)". ACM harvested immediately after isolation.

value: Primary cardiomyocytes isolated from 3month old mice

value: Des-/-


title: QKI_D4_IP1

description: Library name: QKI_D4_IP1


title: Intermediate, Clone_31

city: New Haven

first: Jason

last: Sheltzer

state: CT

address: 300 George Street

department: Surgery

institute: Yale University

description: Library name: Intermediate_Clone_31

data_processing:
Custom nextflow copy number calling pipeline, described in methods
Reads filtered by fastp 0.23.4. Removed low quality reads. Removed adapter sequences.
Reads mapped to hg38 by bwa 0.7.17
Copy number determined by CNVKit.
Assembly: hg38
Supplementary files format and content: bin-level normalized log2 copy ratios and copy number for each sample

growth_protocol: iPS cells were maintained in mTeSR+ in humidified atmosphere with 5% CO2 and 5% O2 at 37C. Media was replenished every day. If cells were plated as single cells, media was supplemented with 10 uM Y-27632

extract_protocol:
DNA was harvested using Dneasy Blood and Tissue kit (Qiagen).
DNA libraries were prepared by Azenta following Azenta's standard protocols.

treatment_protocol: To generate Revertant cells, JE03 294 cells were treated with 1.5 uM AZ3146 for 48 hours to generate cell line with trisomy for chromosome 8.  This trisomic intermediate was then transiently transfected with KaryoCreate plasmids to induce missegregation events at Chromsoome 8

value: Induced pluripotent stem cell

value: invdupdel(8p), + additional copy of euploid chromosome 8

value: Was derived from JE03 294 after treatment with AZ3146


title: Intermediate, Clone_33

description: Library name: Intermediate_Clone_33


title: Des+/+_kap8_14, RNA

value: primary cells:7 day old induced cardiomyocytes from cardiac fibrobalsts isolated from hearts of Des-/- mouse pups after viral transduction with viral cocktail :Gata4+Mef2C+Tbx5+Desmin

value: WT+DGMT


title: QKI_D4_input2

description: Library name: QKI_D4_input2


title: ATACseq_N2_15h_Rep1

description: Library name: 2771F2

value: Whole animal


title: O R33 con.

value: brain


title: RNA,Des-/-_Swim_Replicate3


title: RNA,Des-/-_Swim_Replicate1


title: QKI_D4_input3

description: Library name: QKI_D4_input3

value: D4 of hSC differentiation to cardiomyocyte


title: P R55 con.

value: uninjected hemisphere


title: QKI_D0_input3

description: Library name: QKI_D0_input3

value: D0 of hSC differentiation to cardiomyocyte


title: Probrand, JE03-294

description: Library name: JE03_294


title: M veh. con.

value: vehicle


title: M veh. inj.

value: injected hemisphere


title: QKI_D0_input2

description: Library name: QKI_D0_input2


title: RNA,Des-/-_Non_Swim_Replicate2

value: heart


title: SW620 cells biol rep 2

city: DOWNERS GROVE

first: Cai

last: Roberts

state: IL

address: 555 31ST STREET, SCIENCE HALL 322-E

department: Pharmacology

institute: Midwestern University

description:
Library name: SW620-2
Column in processed files: SW620.2

data_processing:
Reads trimmed with Trimmomatic v.0.36
Reads mapped to reference genome using STAR aligner v.2.5.2b
Counts calculated using featureCounts from the Subread package v.1.5.2
Differerentially expressed genes were determines using DESeq2. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Gene ontology analysis was done using GeneSCF v.1.1-p2
Assembly: Homo sapiens GRCh38
Supplementary files format and content: CSV file contains raw counts for each sequence
Supplementary files format and content: CSV files contain DEG names and expression levels

growth_protocol: PEO4 cells were grown in RPMI 1640 with 10% FBS and 1% penicillin/streptomycin. SW480 and SW620 cells were grown in DMEM with 10% FBS and 1% penicillin/streptomycin. All cells were maintained at 37degC and 5% CO2.

extract_protocol:
RNA was extracted using the Total RNA Mini Kit from IBI Scientific according to the manufacturer instructions.
Illumina RNA library preparation with rRNA depletion and DNAse treatment

treatment_protocol: PEO4 -T cells were treated with recombinant human TGFbeta for 6 days at a concentration of 10ng/mL

value: colorectal


title: QKI_D0_input1

description: Library name: QKI_D0_input1


title: SW620 cells biol rep 1

description:
Library name: SW620-1
Column in processed files: SW620.1


title: K R33 con.


title: QKI_D0_IP3

description: Library name: QKI_D0_IP3

value: X1A, X1B


title: RNA,Des+/+_Swim_Replicate3

value: Primary cardiomyocytes isolated from 3month old mice

value: Des+/+

value: WT


title: SW620 cells biol rep 3

description:
Library name: SW620-3
Column in processed files: SW620.3


title: QKI_D0_IP2

description: Library name: QKI_D0_IP2


title: SW480 cells biol rep 3

description:
Library name: SW480-3
Column in processed files: SW480.3


title: SW480 cells biol rep 2

description:
Library name: SW480-2
Column in processed files: SW480.2


title: K R33 inj.


title: patient TH85 cells, normal fibroblast from lung (non-tumor)

city: Seoul

first: Sang-Won

last: Um

address: 81 Irwon-ro

department: Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center

country: South Korea

institute: Sungkyunkwan University School of Medicine

description: Library name: TH85_NF

data_processing:
After trimming poor quality bases from the FASTQ files, reads were aligned to the human reference genome (hg19) with STAR v2.5.2b (https://github.com/alexdobin/STAR) and estimated gene expression was calculated in terms of estimated expected counts using RSEM v1.3 (https://github.com/deweylab/RSEM).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw count values for for every gene and every sample

source_name: lung

extract_protocol:
The total RNA from cultured cell pellets of CAFs or NFs was extracted with an RNeasy Mini Kit (Qiagen). Nucleic acid extraction was performed according to the manufacturer’s instructions.
Sequencing libraries were prepared with or TruSeq RNA Sample Preparation Kit v2, set A and B (Illumina, Inc., Cat# RS-122-2001 and RS-122-2002) following manufacturer’s protocols.

value: lung

value: SqCC


title: RNA,Des-/-_Non_Swim_Replicate1

value: Des-/-


title: J veh. con.


title: Revertant, Clone_31.3

description: Library name: JE03_294_31_3

value: Induced pluripotent stem cell

value: diploid

value: Was derived from JE03 294 after treatment with AZ3146, and transfection of KaryoCreate plasmids


title: J veh. inj.

value: brain


title: QKI_D0_IP1

description: Library name: QKI_D0_IP1


title: patient TH165 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH165_CAF


title: SW480 cells biol rep 1

description:
Library name: SW480-1
Column in processed files: SW480.1


title: RNA,Des+/+_Non_Swim_Replicate3


title: RNA,Des+/+_Swim_Replicate1


title: PEO4 TGFbeta biol rep 3

description:
Library name: PEO4-T-3
Column in processed files: PEO.T.3

value: ovarian

value: TGFbeta


title: RNA,Des-/-_Non_Swim_Replicate3


title: RNA,Des+/+_Non_Swim_Replicate2


title: patient TH160 cells, cancer-associated fibroblast from lymph node

description: Library name: TH160_CAF

source_name: lymph node

value: lymph node


title: Atlas_medLN_T-B-myeloid_CITEseq

city: Würzburg

first: Angela

last: Riedel

state: Bavaria

address: Josef-Schneider-Straße 2

department: Mildred-Scheel-Nachwuchszentrum (MSNZ) für Krebsforschung

country: Germany

institute: University Hospital Würzburg

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
medLN_CTRL_barcodes.tsv.gz
medLN_CTRL_features.tsv.gz
medLN_CTRL_matrix.mtx.gz
m_med_001_LNA_T-B-myeloid_citeseq_library

data_processing:
Raw BCL files were de-multiplexed and corresponding FASTQ files for GEX. libraries were processed with Cellranger version 7.0 using the count  mode with default parameters and mouse assembly 10 (mm10).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz.: Tab-separated file of cell barcodes
Supplementary files format and content: features.tsv.gz: Tab-separated file of gene names and feature name
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange

molecule: protein

source_name: Lymph node (mediastinal)

growth_protocol: Female BALB/C 8-weeks old mice were used in all experiments fed with standard chow

extract_protocol:
Samples were processed using 10X Genomics Chromium Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) according to the manufacturer’s instructions.
The libraries were prepared using 10X Genomics Chromium Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) according to the manufacturer’s instructions.

treatment_protocol: Control mice were untreated (naïve), 4T1 and 67NR were orthotopically injected with breast cancer cells in the 4th mammary pad and sacrificed 18 days after tumor injection when tumor size reached the endpoint (500mm3), LPS and poly(I:C) mice were injected subcutaneously and sacrificed after 72 hours.

value: Lymph node (mediastinal)

value: BALB/C

value: Myeloid cells, T cells and B cells

value: Control (naïve)

tag: library type

value: ADT

tag: adt

value: TotalSeq-A anti-mouse CD11c, TotalSeq-A anti-mouse Ly-6G, , TotalSeq-A anti-mouse Ly-6C, TotalSeq-A anti-mouse MHC-II, TotalSeq-A anti-mouse CX3CR1, TotalSeq-A anti-mouse CD103, TotalSeq-A anti-mouse PDPN, TotalSeq-A anti-mouse CR2/CR1, TotalSeq-A anti-mouse CD31, TotalSeq-A anti-mouse CD34, TotalSeq-A anti-mouse CD3, TotalSeq-A anti-mouse CD4, TotalSeq-A anti-mouse CD8, and TotalSeq-A anti-mouse CD62L, TotalSeq-A anti-mouse CD25 , TotalSeq-A anti-mouse CD44, TotalSeq-A anti-mouse PD-1 , TotalSeq-A anti-mouse CXCR5, TotalSeq-A anti-mouse TCRgd, TotalSeq-A anti-mouse CD127, TotalSeq-A anti-mouse NKp46, TotalSeq-A anti-mouse CD19, TotalSeq-A anti-mouse CD21, TotalSeq-A anti-mouse IgM, TotalSeq-A anti-mouse IgD, TotalSeq-A anti-mouse CD23, and TotalSeq-A anti-mouse CD2.


title: AE R33 inj.

tag: tissue

value: injected hemisphere


title: PEO4 TGFbeta biol rep 2

description:
Library name: PEO4-T-2
Column in processed files: PEO.T.2


title: Atlas_medLN_T-B-myeloid_GX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
medLN_CTRL_barcodes.tsv.gz
medLN_CTRL_features.tsv.gz
medLN_CTRL_matrix.mtx.gz
m_med_001_LNA_T-B-myeloid_gene_library

tag: genotype

value: WT

value: mRNA


title: patient TH157 cells, cancer-associated fibroblast from lymph node

description: Library name: TH157_CAF

value: SqCC


title: RNA,Des+/+_Non_Swim_Replicate1

value: heart

value: Primary cardiomyocytes isolated from 3month old mice

value: Des+/+


title: patient TH153 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH153_CAF

value: lung

value: ADC


title: RNA,Des+/+_Swim_Replicate2


title: Atlas_axLN_T-B-myeloid_CITEseq

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
axLN_CTRL_barcodes.tsv.gz
axLN_CTRL_features.tsv.gz
axLN_CTRL_matrix.mtx.gz
m_ax_001_LNA_T-B-myeloid_citeseq_library

source_name: Lymph node (axillary)

value: Lymph node (axillary)

tag: strain


title: ChIP,Input for H3K27Ac, Null Swim

data_processing:
Raw reads from ChIP-Seq experiments were aligned to the GRCm38 (mm10) reference genome using the Bowtie2 aligner version 2.4.4 with default options. SAM files were converted to sorted and indexed BAM files using Samtools version 1.13. Peak calling was performed as previously described (Stadhouders et al. 2015, https://github.com/supatt-lab/rChIPSeqTools). Annotation of the peak lists was done using the ChIPseeker R package version 1.36.0.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: tab delimited txt filtered peak list files (except Input files)

growth_protocol: The adult cardiomyocytes (ACM) were isolated with enzymatic perfutsion using  an enzymatic cocktail of Trypsin (Gibco) and CollagenaseD (ROCHE) as described in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)". ACM were isolated form 3 month old mice that have or not undergone swimming excersise as described in ""Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)" and "Diokmetzidou, A., et al. Desmin and alphaB-crystallin interplay in the maintenance of mitochondrial homeostasis and cardiomyocyte survival. Journal of cell science 129, 3705-3720 (2016)".ACM harvested immediately after isolation.

extract_protocol:
chip DNA was isolated using protein G-Dynabeads (Thermofisher)
Input and IP DNAs were quantified with qubit. 5-10 ng DNA from each sample were used as input for ChIPSeq library prep with the NEBNext Ultra II DNA library prep kit for Illumina, according to manufacturer’s instructions

value: Des-/-

tag: chip antibody

value: H3K27Ac :Abcam ab4736


title: PEO4 TGFbeta biol rep 1

description:
Library name: PEO4-T-1
Column in processed files: PEO.T.1

value: ovarian

tag: treatment

value: TGFbeta


title: PEO4 control media biol rep 3

description:
Library name: PEO4-D-3
Column in processed files: PEO.D.3

tag: cell type

value: control


title: patient TH153 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH153_NF


title: patient TH137 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH137_CAF


title: PEO4 control media biol rep 2

description:
Library name: PEO4-D-2
Column in processed files: PEO.D.2


title: TDLN-NDLN_axLN_T-cells_Stroma_m_002_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
mT002_barcodes.tsv.gz
mT002_features.tsv.gz
mT002_matrix.mtx.gz
m_002_4T1_67NR_LPS_CTRL_Tcell_HTO

value: BALB/C

value: T cells

value: Tumor mice (67NR+4T1) and control (naïve)

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, TotalSeq-B0303 anti-mouse Hashtag 3, TotalSeq-B0304 anti-mouse Hashtag 4


title: PEO4 control media biol rep 1

description:
Library name: PEO4-D-1
Column in processed files: PEO.D.1


title: patient TH137 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH137_NF


title: TDLN-NDLN_axLN_T-cells_Stroma_m_002_GX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
mT002_barcodes.tsv.gz
mT002_features.tsv.gz
mT002_matrix.mtx.gz
m_002_4T1_67NR_LPS_CTRL_Tcell_gene_library

value: WT

value: mRNA


title: ChIP,H3K27Ac,Null Non Swim

value: heart

value: Primary cardiomyocytes isolated from 3month old mice

value: H3K27Ac :Abcam ab4733


title: ChIP,Input for H3K27Ac, Null Non Swim

value: H3K27Ac :Abcam ab4734


title: TDLN-NDLN_axLN_Myeloid_Stroma_m_001_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
m001_barcodes.tsv.gz
m001_features.tsv.gz
m001_matrix.mtx.gz
m_001_4T1_67NR_CTRL_FRC_CD11b_HTO

value: Lymph node (axillary)

value: Myeloid cells and stromal cells (endothelial+fibroblasts)


title: patient TH127 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH127_CAF

value: lung

value: ADC


title: ChIP,Input for H3K27Ac, WT Swim

value: Des+/+

value: H3K27Ac :Abcam ab4732


title: DMSO Static Replicate3

city: Chapel Hill

first: William

last: Polacheck

state: North Carolina

address: 10010B Mary Ellen Jones Bldg CB 7575

institute: UNC

description: Library name: DMSO_Static_rep3

data_processing:
Sequencing reads were trimmed using bbmap and reads were aligned to GRCh38.p14 using Salmon. Differential expression was performed in R using DESeq2.
Assembly: GRCh38.p14
Supplementary files format and content: CSV, counts

source_name: Endothelium

growth_protocol: Cells were maintained in EGM-2 (Lonza).

extract_protocol:
RNA was extracted using Quick RNA Microprep kit (Zymo, R1050). 200ng RNA was used to prepare libraries.
Libraries were prepared using the KAPA stranded RNA-Seq Library Preparation Kit (Roche, 07962240001) per manufacturer's protocols.

treatment_protocol: Cells were treated with 5uM A-485 or DMSO for 24 hours under either static or flow conditions.

value: Endothelium

value: Human umbilical vein endothelial cells

value: Static + vehicle

tag: batch

value: Batch 3


title: DMSO Static Replicate2

description: Library name: DMSO_Static_rep2

value: Batch 2


title: patient TH127 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH127_NF


title: TDLN-NDLN_axLN_Myeloid_Stroma_m_001_GX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
m001_barcodes.tsv.gz
m001_features.tsv.gz
m001_matrix.mtx.gz
m_001_4T1_67NR_CTRL_FRC_CD11b_gene_library

value: BALB/C

value: WT

value: Tumor mice (67NR+4T1) and control (naïve)


title: ChIP,Input for H3K27Ac, WT Non Swim

value: heart

value: Primary cardiomyocytes isolated from 3month old mice

value: H3K27Ac :Abcam ab4730


title: patient TH100 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH100_CAF


title: TDLN-NDLN_axLN_FRCs_Stroma_m_002_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
mF002_barcodes.tsv.gz
mF002_features.tsv.gz
mF002_matrix.mtx.gz
m_002_4T1_67NR_LPS_CTRL_FRC_HTO

value: Lymph node (axillary)

value: Stromal cells (endothelial+fibroblasts)

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, TotalSeq-B0303 anti-mouse Hashtag 3, TotalSeq-B0304 anti-mouse Hashtag 4


title: DMSO Static Replicate1

description: Library name: DMSO_Static_rep1

value: Batch 1


title: Atlas_axLN_T-B-myeloid_GX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
axLN_CTRL_barcodes.tsv.gz
axLN_CTRL_features.tsv.gz
axLN_CTRL_matrix.mtx.gz
m_ax_001_LNA_T-B-myeloid_gene_library

value: Myeloid cells, T cells and B cells

value: Control (naïve)

value: mRNA


title: DMSO Flow Replicate3

description: Library name: DMSO_Flow_rep3

value: Endothelium

value: Human umbilical vein endothelial cells

value: Flow + vehicle


title: ChIP,H3K27Ac,Null Swim

value: Des-/-

value: H3K27Ac :Abcam ab4735


title: TDLN-NDLN_axLN_FRCs_Stroma_m_002_GX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
mF002_barcodes.tsv.gz
mF002_features.tsv.gz
mF002_matrix.mtx.gz
m_002_4T1_67NR_LPS_CTRL_FRC_gene_library

value: BALB/C

value: WT

value: Tumor mice (67NR+4T1) and control (naïve)


title: DMSO Flow Replicate2

description: Library name: DMSO_Flow_rep2

value: Batch 2


title: patient TH100 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH100_NF

value: lung

value: ADC


title: ChIP,H3K27Ac,WT Non Swim

value: heart

value: Primary cardiomyocytes isolated from 3month old mice

value: Des+/+

value: H3K27Ac :Abcam ab4729


title: ChIP,Input, Null Swim

value: LaminA/C:Millipore MABT 1348


title: ST_TDLN_4T1_pre-met_2axLN

description:
ST_axLN_4T1_pre-met_C1
Fresh Frozen Spatial transcriptomics sequencing

data_processing:
*library strategy: Spatial transcriptomics, 10XVisium
The raw BCL files were de-multiplexed, resulting in corresponding FASTQ files for gene expression (GEX) libraries.
These FASTQ files were processed using SpaceRanger version 1.3.1 with default parameters, with the images and alignment files generated by the Loupe software by 10x Genomics.
The gene expression data were aligned to the mouse assembly 10 (mm10).
Assembly: mm10
Supplementary files format and content: A compressed files that contain barcodes.tsv.gz:Tab seperated list of spatial barcodes, features.tsv.gz: Tab seperated list of gene IDs, matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format, aligned_fiducials.jpg.gz: aligned fiducials of the tissue image, scalefactors_json.json: scalefactors in json format, tissue_hires_image.png: hi-res image of tissue, tissue_lowres_image.png: low-res image of tissue, and tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

growth_protocol: Female BALB/C 8-weeks old mice were used in all experiments

extract_protocol:
Samples were processed using 10X Genomics Visium Spatial Gene Expression Slide & Reagent Kit (4 rxns PN-1000187) according to the manufacturer’s instructions.
The libraries were prepared using 0X Genomics Visium Spatial Gene Expression Slide & Reagent Kit (4 rxns PN-1000187)  according to the manufacturer’s instructions.

treatment_protocol: Control mice were untreated (naïve), 4T1 and 67NR were orthotopically injected with breast cancer cells in the 4th mammary pad and harvested 18 days after tumor injection when tumor size reached the endpoint (500mm3) .

value: Lymph node (axillary)

value: all axillary lymph node cell types

value: Tumor mice 4T1


title: ST_TDLN_67NR_2axLN

description:
ST_axLN_67NR_B1
Fresh Frozen Spatial transcriptomics sequencing

value: Tumor mice 67NR


title: ChIP,LMNAC,Null Swim

value: Des-/-

value: LaminA/C:Millipore MABT 1347


title: A485 Static Replicate3

description: Library name: A485_Static_rep3

value: Endothelium

value: Human umbilical vein endothelial cells

value: Static + P300i

value: Batch 3


title: DMSO Flow Replicate1

description: Library name: DMSO_Flow_rep1

value: WT

value: Flow + vehicle

value: Batch 1


title: patient TH110 cells, cancer-associated fibroblast from lymph node

description: Library name: TH110_CAF

value: lymph node

value: SqCC


title: patient TH89 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH89_NF

value: lung

value: ADC


title: ST_NDLN_CTRL_2axLN

description:
ST_axLN_CTRL_A1
Fresh Frozen Spatial transcriptomics sequencing

value: Lymph node (axillary)

value: BALB/C

value: Control (naïve)


title: ChIP,LMNAC,Null Non Swim

value: heart

value: Primary cardiomyocytes isolated from 3month old mice

value: LaminA/C:Millipore MABT 1345


title: Teleogryllus_oceanicus_eggs_sRNA_rep1

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: Teleogryllus_oceanicus_eggs_sRNA_rep1
Small RNA sequencing from Teleogryllus oceanicus eggs replicate 1

data_processing:
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting. The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses. Trimmed reads were first mapped to infrastructural RNAs including ribosomal RNA, small nuclear RNA, small nucleolar RNA, microRNA, and transfer RNA, which are annotated in their respetive genomes or genomes from closely related species using bowtie v1.2.3 allowing up to one mismatch. Reads that did not map to these infrastructural RNAs were subsequently mapped to the corresponding species' genomes. The sam file was further processed to the bam file, then to the bed file using samtools/1.19 and bedtools/2.28.0. The coverage of uniquely mappable reads on 0.5kb genomic tiles was measured using bedtools intersect.
Assembly: GCA_905231855.2_idEriTena2.2 for Eristalis tenax GCF_016617805.1_CSIRO_BtryS06_freeze2 for Bactrocera tryoni GCF_002204515.2_AaegL5.0 for Aedes aegypti GCF_013141755.1_UCI_ANSTEP_V1.0 for Anopheles stephensi GCA_032399595.1_TetCarb_2.0 for Tetragonula carbonaria GCA_031308135.1_ado_dt_MfTpo_fix for Acheta domesticus GCA_964035755.1_iqTelOcea1 for Teleogryllus oceanicus
Supplementary files format and content: *_genomic-tile-coverage.txt: coverage of uniquely mappable piRNA (>22nt) reads on individual 0.5kb genomic tiles <tile position with genomic coodinate and strand> <coverage per 1 million piRNA reads>

organism: Teleogryllus oceanicus

source_name: eggs

growth_protocol: Insects were kept at standard conditions at room temperature.

extract_protocol:
Small RNA sequencing was performed on ovaries and eggs collected from a variety of insects. About 10 pairs of ovaries from 1 week to up to 3 months old females and eggs within up to 8 hours of egg laying have been collected per replicate. Total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
Small RNAs were first size-selected from the total RNA by 12% w/v UREA-PAGE using radio-labelled 19mer (5′-CGUACGCGGGUUUAAACGA) and 35mer (5'-CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU) spikes, and oxidised using sodium periodate. The oxidised small RNAs were further size-selected by PAGE. The size-selected oxidised small RNAs were ligated to the 3' adapter 5rApp/NNNNAGATCGGAAGAGCACACGTCT/3ddC, and then to the 5' adapter ACACUCUUUCCCUACACGACGCUCUUCCGAUCUNNNN where Ns are randomised. The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the RT primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT. The library was amplified using KAPA LongRange DNA polymerase (Sigma) with a universal TruSeq forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcode-containing TruSeq reverse primer (e.g. CAAGCAGAAGACGGCATACGAGATxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where xxxxxx were the barcode).

value: eggs

tag: Sex

value: mixed

value: wild type

value: oxidized

tag: age

value: 0 - 8 hour old


title: ChIP,Input, Null Non Swim

tag: cell line

value: Des-/-

value: LaminA/C:Millipore MABT 1346


title: patient TH147 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH147_CAF


title: A485 Static Replicate1

description: Library name: A485_Static_rep1

value: Endothelium

value: Human umbilical vein endothelial cells

value: WT

value: Static + P300i

value: Batch 1


title: A485 Static Replicate2

description: Library name: A485_Static_rep2

value: Batch 2


title: ChIP,H3K27Ac,WT Swim

value: Des+/+

value: H3K27Ac :Abcam ab4731


description:
Library name: Teleogryllus_oceanicus_ovaries_sRNA_rep1
Small RNA sequencing from Teleogryllus oceanicus ovaries replicate 1

source_name: ovaries

value: ovaries

value: female

value: 2 weeks old


title: ChIP,Input, WT Swim

value: heart

value: Primary cardiomyocytes isolated from 3month old mice

value: LaminA/C:Millipore MABT 1344


title: patient TH141 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH141_CAF

value: lung

value: ADC


title: patient TH138 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH138_CAF


title: Acheta_domesticus_eggs_sRNA_rep2

description:
Library name: Acheta_domesticus_eggs_sRNA_rep2
Small RNA sequencing from Acheta domesticus eggs replicate 2

organism: Acheta domesticus

value: eggs

value: mixed

value: wild type

value: oxidized

value: 0 - 8 hour old


title: ChIP,LMNAC,WT Swim

value: WT

value: LaminA/C:Millipore MABT 1343


title: patient TH89 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH89_CAF


title: A485 Flow Replicate3

description: Library name: A485_Flow_rep3

value: Endothelium

value: Human umbilical vein endothelial cells

value: Flow + P300i

value: Batch 3


title: A485 Flow Replicate2

description: Library name: A485_Flow_rep2

value: Batch 2


title: Acheta_domesticus_eggs_sRNA_rep1

description:
Library name: Acheta_domesticus_eggs_sRNA_rep1
Small RNA sequencing from Acheta domesticus eggs replicate 1


title: ChIP,Input, WT Non Swim

value: heart

value: Des+/+

value: LaminA/C:Millipore MABT 1342


title: Acheta_domesticus_ovaries_sRNA_rep2

description:
Library name: Acheta_domesticus_ovaries_sRNA_rep2
Small RNA sequencing from Acheta domesticus ovaries replicate 2

value: ovaries

value: female

value: 2 weeks old


title: ChIP,LMNAC,WT Non Swim

value: Primary cardiomyocytes isolated from 3month old mice

value: LaminA/C:Millipore MABT 1341


title: patient TH122 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH122_CAF

value: lung

value: SqCC


title: A485 Flow Replicate1

description: Library name: A485_Flow_rep1

value: WT

value: Batch 1


title: Acheta_domesticus_ovaries_sRNA_rep1

description:
Library name: Acheta_domesticus_ovaries_sRNA_rep1
Small RNA sequencing from Acheta domesticus ovaries replicate 1

value: wild type

value: oxidized


title: Tetragonula_carbonaria_eggs_sRNA_rep2

description:
Library name: Tetragonula_carbonaria_eggs_sRNA_rep2
Small RNA sequencing from Tetragonula carbonaria eggs replicate 2

organism: Tetragonula carbonaria

value: eggs

value: mixed

value: 0 - 8 hour old


title: HiC,ICM,Des-/-

data_processing:
Hi-C data were analyzed using FAN-C version 0.9.26. Raw reads for each pair were aligned to the mm10 mouse genome version and the generated sam files were sorted and used to generate filtered pair files, which were used to create Knight–Ruiz (KR) normalized multybinned HiC matrices (5mb, 2mb, 1mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, 5kb) using FAN-C – auto with default parameters.   TAD boundaries were called using the insulation score method from FAN-C. Insulation scores were calculated for 10-kb binned HiC matrices at multiple window sizes (10kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 1.5Mb, 2Mb, 2.5Mb, 3Mb, 3.5Mb, 4Mb). Domain boundaries were calculated from the insulation scores. Genome contact matrices were produced using 10kb binned HiC matrices with color scale of 0.1 for iCM, 0.03 for NCM and 0.01 for ACM and ACM swim. A/B compartment heatmaps were produced using fanc compartments with eigenvector binning at 10 20 30 40 50 60 70 80 90 100 using normalized 1mb binned HiC matrices.
Assembly: mm10
Supplementary files format and content: filtered for coverage (bins with less reads than 10% of the median bin coverage) and corrected using Knight-Ruiz matrix balancing binned Hic files at 5mb, 2mb, 1mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb resolution
Supplementary files format and content: unfiltered and unbalanced fragment-level Hic files

growth_protocol: For induced Cardiomyocytes (iCM) samples: fibroblasts were isolated by enzymatic digestion with 1mg/ml Trypsin (Gibco) and 1mg/ml Collagenase type2 (worthington) from  hearts of 1-3 day old mouse pups as descibed in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)." Then, they transduced with the viral coctail Gat4+Mef2C+Tbx5 as described in "Qian, L., Berry, E.C., Fu, J.D., Ieda, M. & Srivastava, D. Reprogramming of mouse fibroblasts into cardiomyocyte-like cells in vitro. Nature protocols 8, 1204-1215 (2013)."  These iCMs were grown in DME/M199 edis+10%FBS for 7 days and then underwent FACS sorting analysis. For Neonatal cardiomyocytes (NCM) samples: NCM were isolated by enzymatic digestion using 1mg/ml Trypsin (Gibco) and 1mg/ml Collagenase type2 (worthington) from hearts of 1-3 day old mouse pups as descibed in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)." Then cultured for 3-4 days in  DMEM 7%FBS (with 1% pen/strep and 1.5mM vitamin B12). The adult cardiomyocytes (ACM) were isolated with enzymatic perfutsion using  an enzymatic cocktail of Trypsin (Gibco) and CollagenaseD (ROCHE) as described in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)". ACM were isolated form 3 month old mice that have or not undergone swimming excersise as described in ""Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)" and "Diokmetzidou, A., et al. Desmin and alphaB-crystallin interplay in the maintenance of mitochondrial homeostasis and cardiomyocyte survival. Journal of cell science 129, 3705-3720 (2016)". The ACM harvested immediately after isolation.

extract_protocol:
DNA was extracted with phenol-chloroform-isoamyl alcohol mixture and ethanol percipitated
Libraries were built using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: For induced Cardiomyocytes (iCM) samples: fibroblasts  were tranduced with a retroviral cocktail for 24 hrs

value: heart

value: primary cells:7 day old induced cardiomyocytes from cardiac fibrobalsts isolated from hearts of Des-/- mouse pups after viral transduction with viral cocktail :Gata4+Mef2C+Tbx5

value: Des-/-


title: patient TH122 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH122_NF


title: HiC,ICM,Des+/+

value: primary cells:7 day old induced cardiomyocytes from cardiac fibrobalsts isolated from hearts of Des+/+  mouse pups after viral transduction with viral cocktail :Gata4+Mef2C+Tbx5

value: Des+/+


title: Tetragonula_carbonaria_eggs_sRNA_rep1

description:
Library name: Tetragonula_carbonaria_eggs_sRNA_rep1
Small RNA sequencing from Tetragonula carbonaria eggs replicate 1


title: patient TH120 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH120_CAF

value: ADC


title: TR3, After treatment [miRNA-seq]

city: Nanning

first: Pingping

last: Zeng

state: Guangxi

address: Guangxi Medical University, No. 8, Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, China.

institute: Guangxi Medical University

description:
Library name: Sample TR3_miRNA
Peripheral blood 5ml
miRNA_Expression(TD-TR).xlsx

data_processing:
Downtime data quality control
Match the genome
Modification site recognition (RNA quantification)
Differential site identification (differential RNA identification)
Functional enrichment analysis
Assembly: HG38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: Nasopharyngeal cancer

extract_protocol:
Using the PAXgene Blood RNA Kit (BD, USA), the total RNAs were extracted from samples of the rise distress group (Class 4) and decline distress group (Class 1) divided by LCGM following the manufacturer’s instructions. A Nanodrop ND-1000 (Thermo Fisher, USA) was applied to measure the concentration and quality of total RNAs.
The sequencing library was built using around 1–2 μg of total RNAs per sample. RNA sequencing services were provided by CloudSeq Inc. (Shanghai, China). Trizol (Invitrogen, USA) was utilized to extract Total RNA, and rRNA was removed via the GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China). Directional RNA libraries were built via the GenSeq® Directional RNA Library Prep Kit. RNA was fragmented to ~300 nt in length. Reverse transcriptase and random hexamers were utilized to synthesize the first-strand cDNA. Moreover, the dUTP Mix was applied to synthesize the second-strand cDNA. The double-stranded cDNA fragments underwent end repair, adapter ligation, and dA-tailing. The cDNA, ligated with adapters, was PCR-amplified and purified to generate the final sequencing libraries. Furthermore, the libraries were sequenced in paired-end 150 bp mode.

value: Nasopharyngeal cancer

value: male

tag: subject group

value: decline distress upon admission group

value: Radiotherapy

tag: time point

value: After treatment