title: Asxl1, replicate 2, scRNAseq

first: Tian

last: Mi

address: 262 Danny Thomas Pl MS351

description:
10x Genomics 3' kit
TGK248

data_processing:
The demultiplexing, barcoded processing, mapping, counting and aggregation were done by Cell Ranger 6.0.0 software.
Assembly: mm10
Supplementary files format and content: Tab separated files of genes
Supplementary files format and content: Tab separated files of cell barcodes
Supplementary files format and content: MEX file of gene-barcode matrix

source_name: Spleen

extract_protocol:
P14 cells were FACS-purified from spleen at 30 days post LCMV infection. Purified P14 cells were washed with PBS and 0.04% BSA before loading into a Chromium Next GEM Chip G (10X Genomics). GEM generation, cDNA amplification and library construction were performed following the protocol of Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10X Genomics) with target recovery of 5000-10000 cells per library/sample. The final 4 libraries were sequenced on the Illumina NovaSeq platform using 100bp paired-end with target reads of 500 million per sample.
GEM generation, cDNA amplification and library construction were performed following the protocol of Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10X Genomics) with target recovery of 5000-10000 cells per library/sample

value: Spleen

tag: cells loaded

value: CD8 T cells

tag: genetic modification

value: Asxl1 KO


title: Asxl1, replicate 1, scRNAseq

status: Public on Oct 10 2024

type: SRA

city: Memphis

state: TN

department: Immunology

country: USA

institute: St. Jude Children's Research Hospital

description:
10x Genomics 3' kit
TGK247

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: MCF-7 palbociclib + fulvestrant: palbociclib + fulvestrant + INX-315 biol rep 1

city: New York

first: Jessica

middle: Sarah

last: Armand

state: NY

department: Pathology and Cell Biology

institute: Columbia University Irving Medical Center

library_source: transcriptomic

data_processing:
Sequence reads were trimmed to remove adaptors and low-quality reads with an average Phred quality score below 30
Trimmed sequence reads were mapped to the transcriptome reference GRCh38_tran using HISAT2 (default parameters: maximum mismatch cost = 6, minimum mismatch cost = 2, gap penalty = 5 + N * 3).
Reference annotation GTF file GRCh38 was used to generate the read count matrix. All references were obtained from Ensembl.org.
Assembly: hg38
Supplementary files format and content: Text file with raw counts for each sample

organism: Homo sapiens

source_name: Breast, mammary gland

growth_protocol: MCF-7 cells were cultured in DMEM plus 10% FBS and housed in a humidified incubator at 37C and 5% CO2.

extract_protocol:
RNA isolation was performed using the GeneJET RNA Purification Kit (Thermo Scientific, #K0732) according to manufacturer’s instruction.
Isolated RNA was shipped to Azenta for library preparation and sequencing; please contact Azenta life sciences for further information

treatment_protocol: Cells were cultured to dual palbociclib (Selleck) + fulvestrant (Selleck) resistance for 2 months. Cells were then either discontinued, maintained in palbociclib + fulvestrant, switched to INX-315 (MedChemExpress) +fulvestrant, or switched to palbociclib + INX-315 + fulvestrant for 20 days.

value: Breast, mammary gland

tag: cell line

value: epithelial cell

value: WT

tag: treatment

value: Palbociclib + INX-315 + fulvestrant


title: Tet2, replicate 2, scRNAseq

description:
10x Genomics 3' kit
TGK246

value: Tet2 KO


title: Blood sample from dengue with warning sign patient 2

city: Shah Alam

first: Jeyanthi

last: Suppiah

address: Jalan Setia Murni U13/52, Setia Alam

department: Virology Unit

country: Malaysia

institute: Institute for Medical Research, National Institutes of Health Malaysia

data_processing:
To compare gene expression profile between 3 groups, healthy control, severe dengue and dengue with warning sign
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001). Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: excel files which included TPM, FPKM and read counts for each sample.

source_name: blood/pbmc

extract_protocol:
Total RNA was extracted using the innuPREP RNA mini kit 2.0 (Analytical Jenna)
Enrichment of mRNA was performed using Dynabeads mrRNA Purification Kit (Invitrogen) and library preparation was carried out using MGIEasy RNA Library Prep Set (MGI)
2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: blood/pbmc

tag: disease state

value: dengue virus


title: MCF-7 palbociclib + fulvestrant: INX-315 + fulvestrant biol rep 2

value: INX-315 + fulvestrant


title: MCF-7 palbociclib + fulvestrant: INX-315 + fulvestrant biol rep 1


title: Blood sample from dengue with warning sign patient 6


title: MCF-7 palbociclib + fulvestrant: palbocicib + fulvestrant biol rep2

value: Palbociclib + fulvestrant


title: Dnmt3a, replicate 2, scRNAseq

description:
10x Genomics 3' kit
TGK244

value: Dnmt3a KO


title: MCF-7 palbociclib + fulvestrant: palbocicib + fulvestrant biol rep1


title: Blood sample from dengue with warning sign patient 1


title: Blood sample from dengue with warning sign patient 11


title: Tet2, replicate 1, scRNAseq

description:
10x Genomics 3' kit
TGK245


title: Blood sample from dengue with warning sign patient 12


title: MCF-7 palbociclib + fulvestrant: discontinued biol rep 1

value: DMSO


title: Dnmt3a, replicate 1, scRNAseq

description:
10x Genomics 3' kit
TGK243


title: MCF-7 palbociclib + fulvestrant: discontinued biol rep 2


title: ΔCyaR, late exponential phase, 37°C, biol rep 3

city: Bochum

first: Franz

last: Narberhaus

address: Universitätsstraße 150

department: LS Biologie der Mikroorganismen

country: Germany

institute: Ruhr-Universität Bochum

data_processing:
Adapter sequences were removed via cutadapt 1.18 with Python 3.7.9 (options: -j 4 -q 10)
Cleaned reads were mapped with bwa (0.7.17-r1188) mem on default settings.
Duplicate reads were removed with Samtools 1.10.
Differential gene expression was analyzed  with DESeq2. A maximal adjusted p value of 0.05 was used as threshold.
Assembly: NCBI RefSeq: for the chromosome NC_010465.1 from US DOE Joint Genome Institute; Identical to CP000950.1. For the pIB plasmid NZ_CP032567.1 from UC Santa Cruz.
Supplementary files format and content: Files include the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Yersinia pseudotuberculosis YPIII

source_name: bacteria

growth_protocol: Cells were grown at 25°C and 37°C in LB medium. Samples were taken at OD600 0.5 and 1.5

extract_protocol:
RNA was extracted via hot-phenol method as described in (Pienkoß et al., 2021, DOI: https://doi.org/10.1371/journal.ppat.1009650). Samples were treated with RNAse-free DNase.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adapt or ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: bacteria

value: CyaR deletion mutant


title: Rosa, replicate 2, scRNAseq

description:
10x Genomics 3' kit
TGK242

value: Rosa KO


title: ΔCyaR, exponential phase, 37°C, biol rep 3


title: ΔCyaR, late exponential phase, 37°C, biol rep 2


title: ΔCyaR, late exponential phase, 25°C, biol rep 3


title: Blood sample from severe dengue patient 1


title: ΔCyaR, late exponential phase, 25°C, biol rep 2


title: Rosa, replicate 1, scRNAseq

description:
10x Genomics 3' kit
TGK241

value: Spleen


title: ΔCyaR, exponential phase, 25°C, biol rep 3


title: Asxl1, Cut&Tag replicate 2, H3K9ac

library_source: genomic

data_processing:
Raw reads in fastq format were processed with skewer 0.2.2 to remove potential adapters and quality trim 3’ end of reads. Then CUT&Tag FASTQ files were mapped to mm10 by Bowtie2 v2.2.9 using the following parameters: -k 1 -X2000 -t --quiet –mm. PCR duplicates were marked using Picard before the removal of unmapped, unpaired, mitochondrial reads and ENCODE blacklist regions.
Assembly: mm10
Supplementary files format and content: bigWig files normalized by total reads
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: spleen

extract_protocol:
P14 cells were FACS-purified from LCMV-infected mice at 30 days post infection. 0.5-2x10^5 cells were collected per sample and subjected to library construction.
Library construction was performed following the Epicypher CUTANA Direct-to-PCR CUT&TAG protocol with slight modifications and all the buffer used were freshly prepared.

value: spleen

value: CD8 T cells

tag: antibody


title: Blood sample from healthy control 9

value: healthy


title: ΔCyaR, exponential phase, 25°C, biol rep 2


title: Blood sample from healthy control 10


title: ΔCyaR, late exponential phase, 37°C, biol rep 1


title: ΔCyaR, exponential phase, 37°C, biol rep 2


title: Blood sample from healthy control 8


title: Asxl1, Cut&Tag replicate 1, H3K9ac

value: Asxl1 KO


title: Rosa, Cut&Tag replicate 2, H3K9ac


title: ΔCyaR, exponential phase, 37°C, biol rep 1


title: ΔCyaR, exponential phase, 25°C, biol rep 1


title: Blood sample from healthy control 7


title: Rosa, Cut&Tag replicate 1, H3K9ac


title: B175_0h_2

city: Qinhuangxdao

first: Yucui

last: Han

address: No. 360, West Section, Hebei Street

country: China

institute: Hebei Normal University Of Science and Technology

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads  were generated. About xxxxx raw reads  for each sample were generated. Raw reads of fastq format  were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.  Then about xxxxxx clean reads  for each sample were retained for subsequent analyses. The clean  reads were mapped to the reference genome  using HISAT2. FPKM of each gene was calculated and  the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R  (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and  foldchange > 2 or foldchange < 0.5  was set as the threshold for significantly differential expression  gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the  expression pattern of genes in different groups and samples. The radar map of top 30 genes was  drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways  enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0),  respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble  diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential  expression in the two types of samples. Then it is tested whether the predefined gene set was  enriched at the top or bottom of the ranking list.
Assembly: mm10
Supplementary files format and content: Setaria italica v2.2
Supplementary files format and content: tab-delimited text file include FPKM values

organism: Setaria italica

source_name: leaf

growth_protocol: mRNAsequencing experimental method

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.RNA purity and quantification were evaluated using the NanoDrop 2000  spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100  Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using  VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The  transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: RNAIsolation and Library Preparatio and RNASequencing and Differentially Expressed Genes Analysis

value: leaf


title: Blood sample from healthy control 6


title: Wild type, late exponential phase, 25°C, biol rep 3

value: wild type


title: Blood sample from healthy control 5


title: Naive, Cut&Tag replicate 4, H3K9ac


title: Wild type, exponential phase, 25°C, biol rep 3


title: Naive, Cut&Tag replicate 3, H3K9ac


title: Wild type, late exponential phase, 37°C, biol rep 2


title: Blood sample from healthy control 4


title: Wild type, late exponential phase, 25°C, biol rep 2


title: Naive, Cut&Tag replicate 2, H3K9ac


title: Wild type, exponential phase, 25°C, biol rep 2


title: Blood sample from healthy control 3


title: Naive, Cut&Tag replicate 1, H3K9ac


title: Wild type, exponential phase, 37°C, biol rep 2


title: Wild type, late exponential phase, 37°C, biol rep 1


title: ΔCyaR, late exponential phase, 25°C, biol rep 1


title: Wild type, late exponential phase, 25°C, biol rep 1


title: Wild type, exponential phase, 37°C, biol rep 1


title: Asxl1, Cut&Tag replicate 4, H3K4me3


title: Blood sample from healthy control 1


title: Wild type, exponential phase, 25°C, biol rep 1


title: Wild type, late exponential phase, 37°C, biol rep 3


title: 64COvary008Stroma

city: Pittsburgh

first: Ian

middle: Philip

last: MacFawn

state: PA

address: 5115 Centre Ave

institute: University of Pittsburgh

data_processing:
RNA-seq; LOQ 2pct by target, 3rd quartile normalized.
Assembly: GRCh38.p13
Supplementary files format and content: Columns represent individual ROIs with descriptions designating tissue type, cell type, and sample ID. Rows represent genes.

source_name: Ovary

growth_protocol: Slides were stored at 4C in a desiccator after sectioning, then DSP was performed within the timeframe specified by Nanostring.

extract_protocol:
Extract was performed according to UPMC Cytometry Facility, UPMC Health Sciences Sequencing Core and Nanostring GeoMx DSP protocols.
direct PCR. Read pattern: 27x27. 8bp index.

value: Ovary

tag: roi

tag: type

value: Stroma

tag: batch


title: ET0267.Dataset_207128090030/207128090030_R02C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.
The 'Normalized Data.csv' contains normalized (Sesame) Beta values

label_protocol: Standard Illumina Protocol

extract_protocol: not provided

value: not provided

tag: sid

tag: specieslatinname

value: Mus musculus


title: Asxl1, Cut&Tag replicate 3, H3K4me3


title: ET0267.Dataset_207101810031/207101810031_R02C01


title: Wild type, exponential phase, 37°C, biol rep 3


title: 64COvary008CD20


title: 64COvary006Stroma


title: 64COvary007Full ROI

value: Full ROI


title: Asxl1, Cut&Tag replicate 2, H3K4me3


title: Rosa, Cut&Tag replicate 5, H3K4me3


title: 64COvary006Immune

value: Immune


title: 64COvary006CD20


title: ET0267.Dataset_207128090030/207128090030_R03C01


title: 64COvary005Full ROI


title: ET0267.Dataset_207101810031/207101810031_R03C01


title: Rosa, Cut&Tag replicate 3, H3K4me3


title: Blood sample from healthy control 2

value: blood/pbmc


title: 64COvary004Full ROI


title: 64COvary003Full ROI


title: ET0267.Dataset_207128090030/207128090030_R03C02


title: 64COvary002Full ROI


title: 64COvary001Full ROI


title: Asxl1, Cut&Tag replicate 1, H3K4me3


title: ET0267.Dataset_207101810031/207101810031_R03C02


title: 64AOmentum015Stroma

source_name: Omentum

value: Omentum


title: 64AOmentum014Stroma


title: ET0267.Dataset_207101810031/207101810031_R06C01


title: Rosa, Cut&Tag replicate 1, H3K4me3


title: 64AOmentum013Stroma


title: 64AOmentum010Full ROI


title: 64AOmentum012Full ROI


title: ET0267.Dataset_207128090030/207128090030_R05C01


title: Naive, Cut&Tag replicate 4, H3K4me3


title: Rosa, Cut&Tag replicate 4, H3K4me3


title: 64AOmentum009Full ROI


title: 64AOmentum008Full ROI


title: 64AOmentum006Full ROI


title: 64AOmentum007Full ROI


title: Naive, Cut&Tag replicate 2, H3K4me3


title: 64AOmentum005Full ROI


title: ET0267.Dataset_207128090030/207128090030_R04C01


title: 64AOmentum004Full ROI


title: ET0267.Dataset_207101810031/207101810031_R04C01


title: 64AOmentum002Full ROI


title: Asxl1 Cut&Tag replicate 3, H2AK119Ub


title: Naive, Cut&Tag replicate 1, H3K4me3


title: 64AOmentum003Full ROI


title: 64AOmentum001Full ROI


title: Rosa, Cut&Tag replicate 2, H3K4me3


title: ET0267.Dataset_207128090030/207128090030_R06C01


title: 65COvary022Immune


title: 65COvary021Full ROI


title: ET0267.Dataset_207128090030/207128090030_R01C01


title: Naive, Cut&Tag replicate 3, H3K4me3


title: ET0267.Dataset_207101810031/207101810031_R01C01


title: Asxl1 Cut&Tag replicate 2, H2AK119Ub


title: ET0267.Dataset_207128090030/207128090030_R02C02


title: Asxl1 Cut&Tag replicate 1, H2AK119Ub


title: ET0267.Dataset_207101810031/207101810031_R05C01


title: Rosa, Cut&Tag replicate 2, H2AK119Ub


title: ET0267.Dataset_207101810031/207101810031_R02C02


title: Rosa, Cut&Tag replicate 1, H2AK119Ub


title: 65COvary016Immune


title: 65COvary017Immune


title: 65COvary016CD20


title: 65COvary015Full ROI


title: 65COvary014Full ROI


title: Asxl1, Cut&Tag replicate 5, H3K27me3


title: ET0267.Dataset_207101810031/207101810031_R01C02


title: 65COvary013Full ROI


title: 65COvary012Full ROI


title: ET0267.Dataset_207128090030/207128090030_R06C02


title: 65COvary011Full ROI


title: Asxl1, Cut&Tag replicate 4, H3K27me3


title: Asxl1, Cut&Tag replicate 3, H3K27me3


title: ET0267.Dataset_207101810031/207101810031_R06C02


title: 65COvary020Full ROI


title: 65COvary019Full ROI


title: 65COvary010Full ROI


title: 65COvary018Immune


title: 65COvary008Immune


title: ET0267.Dataset_207128090030/207128090030_R05C02


title: Rosa, Cut&Tag replicate 4, H3K27me3


title: Rosa, Cut&Tag replicate 3, H3K27me3


title: ET0267.Dataset_207128090030/207128090030_R01C02


title: 65COvary009Full ROI


title: 65COvary006Immune


title: ET0267.Dataset_207101810031/207101810031_R05C02


title: 65COvary006CD20


title: Rosa, Cut&Tag replicate 2, H3K27me3


title: 65COvary005Immune


title: Rosa, Cut&Tag replicate 1, H3K27me3


title: 65COvary005CD20


title: ET0267.Dataset_207128090030/207128090030_R04C02


title: ET0267.Dataset_207101810031/207101810031_R04C02


title: 65COvary004CD20


title: 65COvary003Immune


title: Asxl1, Cut&Tag replicate 2, H3K27me3


title: ET0267.Dataset_207101810032/207101810032_R03C01


title: Asxl1, Cut&Tag replicate 1, H3K27me3


title: 65COvary002Immune


title: 65COvary007Immune


title: Naive, Cut&Tag replicate 1, H3K27me3


title: ET0267.Dataset_207101810032/207101810032_R02C02


title: 65COvary001Immune


title: 65COvary001CD20


title: 65COvary002CD20


title: ET0267.Dataset_207101810050/207101810050_R03C01


title: Asxl1, replicate 4, RNA seq

data_processing:
Raw reads in fastq format were processed with skewer 0.2.2 to remove potential adapters and quality trim 3’ end of reads. Reads were then mapped to mm10 reference genome by STAR 2.5.3a with options --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000. Raw read count matrix was generated using R function summarizeOverlaps, and pairwise differential gene expression is done by DESeq2 1.26.0.
Assembly: mm10
Supplementary files format and content: tab delimited text files includes raw counts for each sample

extract_protocol:
RNA was isolated using the Direct-zol RNA MicroPrep Kit (Zymo research) according to the manufacturer’s protocols. RNA was quantified using the Quant-iT RiboGreen assay (Life Technologies) and quality-checked by 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or LabChip RNA PicoSensitivitiy assay (PerkinElmer) before library generation.
Libraries were prepared from total RNA with TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina).


title: 64BFallopian Tube014Full ROI

source_name: Fallopian Tube

value: Fallopian Tube


title: ET0267.Dataset_207101810050/207101810050_R02C02


title: ET0267.Dataset_207101810032/207101810032_R06C02


title: 64BFallopian Tube012Full ROI


title: 64BFallopian Tube013Full ROI


title: 65COvary004Immune


title: Tet2, replicate 4, RNA seq

value: Tet2 KO


title: Asxl1, replicate 3, RNA seq

value: Spleen


title: 64BFallopian Tube011Immune


title: 64BFallopian Tube011CD20


title: ET0267.Dataset_207101810032/207101810032_R02C01


title: 64BFallopian Tube010Full ROI


title: 64BFallopian Tube009Full ROI


title: ET0267.Dataset_207101810032/207101810032_R01C02


title: 65COvary003CD20


title: Tet2, replicate 3, RNA seq


title: Rosa, replicate 5, RNA seq

value: Rosa KO


title: ET0267.Dataset_207101810050/207101810050_R02C01


title: 64BFallopian Tube007Full ROI


title: 64BFallopian Tube006Immune


title: Rosa, replicate 4, RNA seq

value: CD8 T cells


title: ET0267.Dataset_207101810050/207101810050_R01C02


title: 64BFallopian Tube005Immune


title: 64BFallopian Tube004Immune


title: Rosa, replicate 3, RNA seq


title: ET0267.Dataset_207101810032/207101810032_R01C01


title: 64BFallopian Tube003Immune


title: 64BFallopian Tube004CD20


title: Rosa, replicate 2, RNA seq


title: 64BFallopian Tube002Immune


title: Asxl1, replicate 2, RNA seq


title: ET0267.Dataset_207101810032/207101810032_R06C01


title: ET0267.Dataset_207101810050/207101810050_R06C01


title: ET0267.Dataset_207101810050/207101810050_R01C01


title: 58COvary022Immune


title: 64BFallopian Tube001Immune


title: Tet2, replicate 2, RNA seq


title: 58COvary023Immune


title: 64BFallopian Tube002CD20


title: 58COvary020Full ROI


title: ET0267.Dataset_207101810032/207101810032_R05C02


title: Tet2, replicate 1, RNA seq


title: 58COvary019Full ROI


title: 64BFallopian Tube008Full ROI


title: 58COvary021Full ROI


title: 58COvary018Full ROI


title: ET0267.Dataset_207101810032/207101810032_R05C01


title: Dnmt3a, replicate 4, RNA seq

value: Dnmt3a KO


title: ET0267.Dataset_207101810032/207101810032_R04C02


title: 58COvary017Full ROI


title: Dnmt3a, replicate 3, RNA seq


title: Asxl1, replicate 1, RNA seq

value: Asxl1 KO


title: 58COvary016Full ROI


title: 58COvary014Full ROI


title: ET0267.Dataset_207101810050/207101810050_R05C01


title: 58COvary013Full ROI


title: 58COvary015Full ROI


title: 58COvary012Full ROI


title: Dnmt3a, replicate 2, RNA seq


title: ET0267.Dataset_207101810050/207101810050_R04C02


title: ET0267.Dataset_207101810050/207101810050_R06C02


title: 58COvary009Immune


title: 58COvary011Immune


title: 58COvary008Full ROI


title: Dnmt3a, replicate 1, RNA seq


title: ET0267.Dataset_207101810032/207101810032_R04C01


title: Rosa, replicate 1, RNA seq


title: ET0267.Dataset_207101810032/207101810032_R03C02


title: 58COvary007Full ROI


title: Asxl1 Tim3, replicate 4, ATAC

data_processing:
Raw reads in fastq format were processed with skewer 0.2.2 to remove potential adapters and quality trim 3’ end of reads. Then ATACseq FASTQ files were mapped to mm10 by Bowtie2 v2.2.9 using the following parameters: -k 1 -X2000 -t --quiet –mm. PCR duplicates were marked using Picard before the removal of unmapped, unpaired, mitochondrial reads and ENCODE blacklist regions.
Assembly: mm10
Supplementary files format and content: bigWig files normalized by total reads

extract_protocol:
P14 cells were FACS-purified from LCMV-infected mice at 30 days post infection. 5000 - 20000 cells were collected per sample and subjected to library construction according to the optimized Omni-ATAC protocol (46) with slight modification of the library cleanup step.
Library constructed according to the optimized Omni-ATAC protocol with slight modification of the library cleanup step. Double-sided size selection (0.6X and 1.2X) was performed with SPRIselect (Beckman Coulter) to enrich sequenceable fragments in the final library.


title: 58COvary005Full ROI


title: Asxl1 Tim3, replicate 3, ATAC


title: 58COvary006Full ROI


title: Asxl1 Tim3, replicate 2, ATAC


title: 58COvary002Immune


title: 58COvary003Immune


title: 58COvary001Immune


title: Asxl1 Tim3, replicate 1, ATAC


title: ET0267.Dataset_207101810050/207101810050_R05C02


title: 60AOmentum013Immune


title: 60AOmentum013CD20


title: ET0318.Dataset_207505380016_R03C02

tag: age


title: Asxl1 Ly108, replicate 4, ATAC


title: Asxl1 Ly108, replicate 3, ATAC


title: 60AOmentum012Immune


title: 58COvary010Immune


title: 60AOmentum012CD20


title: ET0267.Dataset_207101810050/207101810050_R04C01


title: ET0318.Dataset_207505380016_R03C01


title: Asxl1 Ly108, replicate 1, ATAC


title: 60AOmentum009Immune


title: 60AOmentum010Immune


title: ET0318.Dataset_207505380016_R02C02


title: 60AOmentum010CD20


title: Asxl1 Ly108, replicate 2, ATAC


title: ET0267.Dataset_207101810050/207101810050_R03C02


title: 60AOmentum008CD20


title: ET0318.Dataset_207505380016_R01C02


title: 60AOmentum014CD20


title: 60AOmentum009CD20


title: 60AOmentum007Full ROI


title: Rosa Tim3, replicate 1, ATAC


title: Rosa Tim3, replicate 2, ATAC


title: Rosa Ly108, replicate 2, ATAC


title: ET0318.Dataset_207505380016_R01C01


title: 60AOmentum006CD20


title: 60AOmentum011Full ROI


title: 58COvary004Immune


title: ET0318.Dataset_207505380016_R06C02


title: 60AOmentum004Full ROI


title: ET0318.Dataset_207505380016_R02C01


title: Rosa Ly108, replicate 1, ATAC


title: ET0318.Dataset_207505380016_R06C01


title: 60AOmentum005Full ROI


title: 60AOmentum008Immune


title: Asxl1, replicate 2, ATAC


title: 60AOmentum003Immune


title: 60AOmentum002Full ROI


title: 60AOmentum006Immune


title: 60AOmentum001Immune


title: 60AOmentum003CD20


title: 60AOmentum001CD20


title: 60BFallopian Tube016Full ROI


title: ET0318.Dataset_207505380016_R04C02


title: Rosa, replicate 2, ATAC


title: 60BFallopian Tube015CD20


title: 60BFallopian Tube015Immune


title: 60BFallopian Tube013Full ROI


title: Rosa, replicate 1, ATAC


title: ET0318.Dataset_207505380016_R04C01


title: Asxl1 D30 rep1, WGBS

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the mm10 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: mm10
Supplementary files format and content: txt files with columns of chr, loc, cov, meth

extract_protocol:
DNA was extracted from the sorted cells and then bisulfite treated using an EZ DNA Methylation-Direct kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina NovaSeq 6000 systems


title: ET0318.Dataset_207505380016_R05C02


title: 60BFallopian Tube014Full ROI


title: 60BFallopian Tube011Full ROI


title: ET0213.Dataset_207101810021_R03C02

value: sorted bone marrow


title: 60BFallopian Tube012Full ROI


title: ET0318.Dataset_207505380016_R05C01


title: 60BFallopian Tube010Immune


title: ET0213.Dataset_207101810021_R02C02


title: Asxl1, replicate 1, ATAC


title: 60BFallopian Tube009Immune


title: 60BFallopian Tube008Full ROI


title: Tet2 D30 rep1, WGBS


title: ET0213.Dataset_207101810021_R05C01


title: Dnmt3a D30 rep2, WGBS


title: ET0213.Dataset_207101810021_R01C02


title: 60BFallopian Tube007Full ROI


title: 60BFallopian Tube006Immune


title: ET0213.Dataset_207101810021_R06C01


title: Asxl1 D30 rep2, WGBS


title: 60BFallopian Tube004Full ROI


title: ET0213.Dataset_207101810021_R04C01


title: 60BFallopian Tube005Immune


title: Dnmt3a D30 rep1, WGBS


title: 60BFallopian Tube003Immune


title: 60BFallopian Tube002Immune


title: Rosa D30 rep2, WGBS


title: Tet2 D30 rep2, WGBS


title: ET0213.Dataset_207101810021_R03C01

value: ET0213_B62moF6 CLP


title: 60COvary013Full ROI

value: Ovary


title: 60BFallopian Tube001Immune


title: ET0213.Dataset_207101810021_R02C01

value: ET0213_B62moF5 CLP


title: 60COvary011Full ROI


title: Day 4_Lmod2 W405*6

city: Tucson

first: Jared

last: Churko

state: Arizona

address: 1501 N CAMPBELL AVE LSN 461

department: CMM

institute: University of Arizona

description:
Lmod2miceGeneMatrixGEO.txt
D9

data_processing:
Fastq files were aligned using STAR to Ensembl GRCh38 annotation for human samples and Ensembl GRCm38 annotation for mus musculus samples. Differentially expressed genes were calculated using DESeq2.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: LV

extract_protocol:
For bulk RNA-seq, hiPSC-CMs and mouse heart (LV) tissue were lysed using TRIzol reagent (Zymo Research) and total RNA was extracted using the Direct-zol RNA Miniprep Plus kit (Zymo Research). DuringRNA isolation, on-column DNAse digestion was performed for 15mins at room temperature.
RNA-seq library prep using the Illumina TruSeq stranded mRNA kit and sequencing using a NovaSeq (PE150) system was performed at MedGenome Inc., CA.

value: LV

tag: day

value: Day 4

value: Lmod2 W405*


title: ET0213.Dataset_207101810021_R01C01

value: ET0213_B62moF4 CLP

value: Mus musculus


title: Rosa D30 rep1, WGBS


title: 60COvary012Full ROI

value: Full ROI


title: 60COvary010Immune

value: Immune


title: 60COvary009Immune


title: 60COvary008Full ROI


title: Day 4_Lmod2 W405*5

description:
Lmod2miceGeneMatrixGEO.txt
D3


title: ET0213.Dataset_207101810015_R03C02


title: 60COvary007Full ROI


title: Day 14_Lmod2 W405*3

description:
Lmod2miceGeneMatrixGEO.txt
D25

value: Day 14


title: 60COvary006Immune


title: 60COvary005Immune


title: ET0213.Dataset_207101810015_R02C02


title: Day 14_Lmod2 W405*2

description:
Lmod2miceGeneMatrixGEO.txt
D22


title: ET0213.Dataset_207101810015_R01C02


title: Day 4_Lmod2 W405*4

description:
Lmod2miceGeneMatrixGEO.txt
D12


title: 60COvary004Immune


title: 60COvary004CD20


title: 60COvary001Full ROI


title: 60COvary002Full ROI


title: 60COvary003Immune


title: ET0213.Dataset_207101810015_R06C01


title: ET0213.Dataset_207101810015_R05C01


title: 58BFallopian Tube016Full ROI

value: Fallopian Tube


title: Day 4_Lmod2 W405*3

description:
Lmod2miceGeneMatrixGEO.txt
D11


title: ET0213.Dataset_207101810015_R04C01


title: 58BFallopian Tube015Full ROI


title: ET0213.Dataset_207101810015_R03C01

value: ET0213_B62moF6 LK


title: Day 4_Lmod2 W405*2

description:
Lmod2miceGeneMatrixGEO.txt
D10


title: ET0213.Dataset_207101810015_R02C01

value: ET0213_B62moF5 LK


title: 58BFallopian Tube014Full ROI


title: Day 4_Lmod2 W405*1

description:
Lmod2miceGeneMatrixGEO.txt
D1


title: 58BFallopian Tube012Tumor

value: Tumor


title: ET0213.Dataset_207101810015_R01C01

value: ET0213_B62moF4 LK


title: 58BFallopian Tube010Full ROI


title: 58BFallopian Tube013Full ROI


title: Day 4_wildtype11

description:
Lmod2miceGeneMatrixGEO.txt
C8

value: wildtype


title: 58BFallopian Tube011Tumor


title: 58BFallopian Tube009Full ROI


title: 58BFallopian Tube007Full ROI


title: ET0213.Dataset_207101810014_R02C02

value: sorted bone marrow


title: Day 14_Lmod2 W405*1

description:
Lmod2miceGeneMatrixGEO.txt
D21


title: Day 4_wildtype9

description:
Lmod2miceGeneMatrixGEO.txt
C5


title: 58BFallopian Tube003Immune


title: Day 4_wildtype8

description:
Lmod2miceGeneMatrixGEO.txt
C4


title: Day 4_wildtype10

description:
Lmod2miceGeneMatrixGEO.txt
C7


title: 58BFallopian Tube001Immune


title: Day 4_wildtype6

description:
Lmod2miceGeneMatrixGEO.txt
C1


title: ET0213.Dataset_207101810014_R03C02


title: 58BFallopian Tube006Immune


title: 58BFallopian Tube002Immune


title: ET0213.Dataset_207101810014_R06C01


title: ET0213.Dataset_207101810014_R01C02


title: 58BFallopian Tube004Full ROI


title: 58AOmentum015Full ROI

value: Omentum


title: 58BFallopian Tube001CD20


title: 58BFallopian Tube008Full ROI


title: ET0213.Dataset_207101810014_R05C01


title: 58BFallopian Tube003CD20


title: 58AOmentum014Other

value: Other


title: ET0213.Dataset_207101810014_R04C01


title: Day 4_Lmod2KO6

description:
Lmod2miceGeneMatrixGEO.txt
B6

value: LV


title: 58AOmentum014CD20


title: ET0213.Dataset_207101810014_R03C01

value: ET0213_B62moF6 LSK


title: Day 4_Lmod2KO5

description:
Lmod2miceGeneMatrixGEO.txt
B5

value: Day 4


title: 58AOmentum013Tumor


title: 58AOmentum012Tumor


title: Day 4_Lmod2KO4

description:
Lmod2miceGeneMatrixGEO.txt
B4


title: ET0213.Dataset_207101810014_R02C01

value: ET0213_B62moF5 LSK


title: 58AOmentum011Other


title: Day 4_Lmod2KO3

description:
Lmod2miceGeneMatrixGEO.txt
B3


title: Day 4_wildtype7

description:
Lmod2miceGeneMatrixGEO.txt
C2


title: 58AOmentum010Full ROI


title: 58AOmentum011CD20


title: ET0213.Dataset_207101810014_R01C01

value: ET0213_B62moF4 LSK

value: Mus musculus


title: 58BFallopian Tube005Full ROI

value: Full ROI


title: 58AOmentum009Other


title: ET0213.Dataset_207036290009_R03C02

value: ET0213_B690wF7 Linplus


title: 58AOmentum009CD20


title: 58AOmentum008Other


title: Day 14_Lmod2KO3

description:
Lmod2miceGeneMatrixGEO.txt
B18

value: Day 14


title: 58AOmentum007Other


title: 58AOmentum006Other


title: Day 14_Lmod2KO1

description:
Lmod2miceGeneMatrixGEO.txt
B13


title: 58AOmentum007CD20


title: ET0213.Dataset_207036290009_R06C01

value: ET0213_B652wF3 Linplus


title: ET0213.Dataset_207036290009_R01C02

value: ET0213_B690wF5 Linplus


title: Day 4_Lmod2KO2

description:
Lmod2miceGeneMatrixGEO.txt
B10


title: 58AOmentum006CD20


title: 58AOmentum005Full ROI


title: 58AOmentum003Other


title: Day 4_Lmod2KO1

description:
Lmod2miceGeneMatrixGEO.txt
B1


title: ET0213.Dataset_207036290009_R05C01

value: ET0213_B652wF2 Linplus


title: 58AOmentum004Full ROI


title: Day 4_wildtype4

description:
Lmod2miceGeneMatrixGEO.txt
A3


title: 58AOmentum003CD20


title: 58AOmentum008CD20


title: ET0213.Dataset_207036290009_R02C02

value: ET0213_B690wF6 Linplus


title: Day 14_Lmod2KO2

description:
Lmod2miceGeneMatrixGEO.txt
B15


title: ET0213.Dataset_207036290009_R03C01

value: ET0213_B62moF6 Linplus


title: 58AOmentum002CD20


title: 58AOmentum001Other


title: Day 14_wildtype3

description:
Lmod2miceGeneMatrixGEO.txt
A26

value: wildtype


title: 58AOmentum001CD20

value: Omentum


title: Day 14_wildtype2

description:
Lmod2miceGeneMatrixGEO.txt
A20


title: 65AOmentum015Full ROI


title: ET0213.Dataset_207036290009_R02C01

value: sorted bone marrow

value: ET0213_B62moF5 Linplus


title: ET0213.Dataset_207036290009_R01C01

value: ET0213_B62moF4 Linplus


title: 65AOmentum014Stroma

value: Stroma


title: 65AOmentum013Stroma


title: 65AOmentum012Stroma


title: P28.Dataset_206604260001_R01C01

value: Muscle

tag: female

tag: conditiondetailed

value: Bulk Tissue (2 months)

value: AT27 whole muscle


title: Day 14_wildtype1

description:
Lmod2miceGeneMatrixGEO.txt
A19

value: LV


title: Day 4_wildtype5

description:
Lmod2miceGeneMatrixGEO.txt
A9

value: Day 4


title: ET0213.Dataset_207036290009_R04C01

value: ET0213_B652wF1 Linplus

value: Mus musculus


title: Day 4_wildtype3

description:
Lmod2miceGeneMatrixGEO.txt
A13


title: P28.Dataset_206604260007_R01C01

value: SatelliteCells

value: Stem Cells (2 months)

value: AT27 satellite cells


title: 65AOmentum012Tumor

value: Tumor


title: 65AOmentum009Full ROI

value: Full ROI


title: 58AOmentum002Other

value: Omentum

value: Other


title: P28.Dataset_206604260001_R03C01

value: AT26 whole muscle


title: 65AOmentum010Full ROI


title: P28.Dataset_206604260007_R03C01

value: AT26 satellite cells


title: Day 4_wildtype1

description:
Lmod2miceGeneMatrixGEO.txt
A10

value: wildtype


title: P28.Dataset_206604260001_R02C01

value: Muscle

value: AT25 whole muscle


title: 65AOmentum007Full ROI


title: 65AOmentum006Full ROI


title: 65AOmentum008Full ROI


title: 65AOmentum005Full ROI


title: 65AOmentum004Full ROI


title: 65AOmentum003Full ROI


title: CUT&RUN_ZT20_Zolpidem_IgG_1

first: Benjamin

middle: H

last: Weekley

address: 1470 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Samples were demultiplexed using bcl2fastq2 (Illumina, v2.20).
Samples were aligned to the hg19 or mm10 genome using bowtie2 (2.5.0), with the following parameters: --local --very-sensitive-local --phred33 -I 10 -X 700 --dovetail --no-unal --no-mixed --no-discordant
Low quality reads were filtered out using Samtools (1.9) with a cutoff MAPQ of 30, and only unique reads kept for further processing.
Unique read files for each replicate/timepoint/antibody  were merged and  used for peak calling using MACS2 (3.0.0a6) using the callpeaks function with the options -f BAMPE -q 0.05 --broad --broad-cutoff .05 –min-length 147, using the corresponding IgG sample as the -c.
For visualization, each sample was normalized by scaling the samples based off of the E. coli spike in, and genome coverage tracks (bigwig files) were produced using deepTools (3.5.1) bamCoverage function with the options –binSize 10 –smoothLength 30 --normalizeUsing None --scaleFactor # and using an ENCODE hg19 or mm10 blacklist file (https://doi.org/10.1038/s41598-019-45839-z) to discard regions with consistent non-specific signal
Assembly: hg19/mm10
Supplementary files format and content: Bigwig files for visualization (merged and scaled based off of E. coli spike in DNA)
Supplementary files format and content: Macs2 peak files (.narrowPeak/.broadPeak) on merged files, and corresponding TSS annotations
Library strategy: CUT&RUN

source_name: Brain-TMN

growth_protocol: HeLa cells were grown in DMEM with glucose,, 10% fetal bovine serum and 1X pen-Strep. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Tissue or cells were resuspended in a cell lysis buffer and homogenized using a dounce homogenizer. Nuclei were isolated, washed, and counted. 30k nuclei were used per replicate per time point (tissue) or cell line. Nuclei were bound to concavalin-A beads. Nuclei were incubated overnight with primary antibody at 4 degrees celsius, then washed, and incubated with pA/G-MNase for 1 hour at 4 degrees celsius. Residual pA/G-MNase was washed, the sample resupsended in calcium activation buffer and incubated for 30 minutes at 4 degrees celsius. 2X STOP mix containing RNAse A was added to samples, and incubated at 37 degrees celsius for 15 minutes. Supernatant was collected and DNA isolated using column purification prior to library prep.
NEB Next Ultra II Kit

treatment_protocol: Mice brains were collected every 4 hours across the zeitgeber time following IACUC protocols. They were flash-frozen using methylbutane and stored at -80 degrees celsius. Brains were sliced and TMN punched (1 mm punches) according to previously published coordinates. TMN were frozen at -80 degrees celsius until CUT&RUN was performed.

value: Brain-TMN

tag: time

value: Zolpidem

tag: replicate

value: Rabbit IgG, Abcam ab172730


title: CUT&RUN_ZT20_Vehicle_IgG_1

tag: tissue

value: Vehicle


title: 65AOmentum002Full ROI


title: 65AOmentum011Full ROI


title: 65AOmentum001Full ROI


title: 65BFallopian Tube014Full ROI

value: Fallopian Tube


title: 65BFallopian Tube013Full ROI


title: P28.Dataset_206604260007_R05C01

value: SatelliteCells

value: Stem Cells (8 months)

value: AR32 satellite cells

value: Mus musculus


title: 65BFallopian Tube012Full ROI

value: Full ROI


title: 65BFallopian Tube010Full ROI


title: CUT&RUN_ZT20_Zolpidem_H3K4me3Q5ser_1

tag: genotype

value: H3K4me3Q5ser, Millipore ABE2580


title: P28.Dataset_206604260001_R05C01

value: Bulk Tissue (8 months)

value: AR32 whole muscle


title: CUT&RUN_ZT20_Vehicle_H3K4me3Q5ser_3


title: CUT&RUN_ZT20_Zolpidem_H3K4me3Q5ser_2


title: 65BFallopian Tube009Full ROI


title: P28.Dataset_206604260001_R06C01

value: AR23 whole muscle


title: 65BFallopian Tube011Full ROI


title: P28.Dataset_206604260007_R06C01

value: AR23 satellite cells


title: P28.Dataset_206604260007_R02C01

value: Stem Cells (2 months)

value: AT25 satellite cells


title: 65BFallopian Tube008Full ROI


title: 65BFallopian Tube006Tumor

value: Tumor


title: P28.Dataset_206604260007_R04C01

value: AR20 satellite cells


title: CUT&RUN_ZT20_Vehicle_H3K4me3Q5ser_1

value: Brain-TMN


title: CUT&RUN_ZT20_Vehicle_H3K4me3Q5ser_2

value: Vehicle


title: 65BFallopian Tube005Immune

value: Fallopian Tube

value: Immune


title: 65BFallopian Tube005CD20


title: CUT&RUN_ZT20_Zolpidem_H3K4me3Q5ser_3

value: Zolpidem


title: P28.Dataset_206604260001_R04C01

value: Muscle

value: AR20 whole muscle


title: CUT&RUN_ZT20_Zolpidem_H3K4me3Q5his_3

value: H3K4me3Q5his, Millipore ABE2570


title: 65BFallopian Tube003Full ROI

value: Full ROI


title: CUT&RUN_ZT20_Zolpidem_H3K4me3Q5his_2


title: Day 4_wildtype2

description:
Lmod2miceGeneMatrixGEO.txt
A12

value: LV

value: Day 4

value: wildtype


title: P28.Dataset_206604260001_R01C02

value: Bulk Tissue (12 months)

value: AN43 whole muscle

value: Mus musculus


title: 65BFallopian Tube002Full ROI


title: P28.Dataset_206604260007_R01C02

value: SatelliteCells

value: Stem Cells (12 months)

value: AN43 satellite cells


title: P28.Dataset_206604260001_R03C02

value: AN37 whole muscle


title: 64COvary011Stroma

value: Ovary

value: Stroma


title: 64COvary012Stroma


title: CUT&RUN_ZT20_Zolpidem_H3K4me3Q5his_1

value: Brain-TMN

value: Zolpidem


title: 65BFallopian Tube001Immune

value: Fallopian Tube

value: Immune


title: 64COvary011CD20


title: CUT&RUN_ZT20_Vehicle_H3K4me3Q5his_3

value: Vehicle

value: H3K4me3Q5his, Millipore ABE2570


title: P28.Dataset_206604260001_R02C02

value: Muscle

value: AN35 whole muscle


title: CUT&RUN_ZT20_Vehicle_H3K4me3Q5his_1


title: 65BFallopian Tube007Full ROI

value: Full ROI


title: 64COvary010Stroma


title: 64COvary009CD20


title: 65BFallopian Tube004Full ROI


title: CUT&RUN_ZT20_Zolpidem_WDR5_3

value: WDR5, CST D9E1I


title: 54Omentum005Stroma

value: Omentum


title: 54Omentum006Tumor

value: Tumor


title: P28.Dataset_206604260007_R03C02

value: SatelliteCells

value: Stem Cells (12 months)

value: AN37 satellite cells

value: Mus musculus


title: P28.Dataset_206604260007_R05C02

value: Stem Cells (23 months)

value: AI33 satellite cells


title: CUT&RUN_ZT20_Vehicle_H3K4me3Q5his_2

value: Brain-TMN


title: 64COvary010CD20

value: Ovary


title: 54Omentum005CD20


title: 54Omentum005Immune

value: Immune


title: 54Omentum004Tumor


title: P28.Dataset_206604260007_R06C02

value: AI31 satellite cells


title: 54Omentum003Stroma

value: Stroma


title: 64COvary009Stroma


title: CUT&RUN_ZT20_Vehicle_WDR5_2

value: Vehicle


title: P28.Dataset_206604260007_R02C02

value: AN35 satellite cells


title: 54Omentum003Tumor


title: 54Omentum006Stroma


title: P28.Dataset_206604260001_R05C02

value: Muscle

value: Bulk Tissue (23 months)

value: AI33 whole muscle


title: P28.Dataset_206604260007_R04C02

value: AI30 satellite cells


title: CUT&RUN_ZT20_Zolpidem_WDR5_2

value: Zolpidem

value: WDR5, CST D9E1I


title: 54Omentum003CD20

value: Omentum


title: CUT&RUN_ZT20_Vehicle_WDR5_1


title: HCT116, arsenite, rep1, RNA

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

data_processing:
The RNA-Seq libraries were sequenced on NovaSeqX 1.5B at SingleRead 100 mode at the Vienna BioCenter NGS facility producing ~35 million reads per sample. BCL files were converted to demultiplexed fastq files with bcl2fastq v2.20.0.422. The quality of fastq files was checked with fastqc 0.11.9.
The fastq files were trimmed and aligned to human genome hg38 using GENCODE annotation (release 46) with STAR v2.7.11b allowing for the two mismatches. Gene counts were obtained using FeatureCounts function of the Subread package v2.0.6.
Assembly: hg38, GENCODE annotation (release 46)
Supplementary files format and content: tsv, gene read counts

molecule: polyA RNA

growth_protocol: HCT116 conditionally expressing Tet-OsTIR1 were obtained from Masato Kanemaki Lab and cultured in McCoy's 5A (Modified) Medium (Sigma) with 10% Fetal Bovine Serum (Gibco), 2 mM Glutamine (Sigma), 1% Pen/Step (Sigma).

extract_protocol:
Cells were washed with ice-cold PBS, scraped, centrifuged (3500 rpm, 4 min) and the pellet flash frozen and stored at -80°C. On the day of the experiment, the pellets were thawed and 150 µL of lysis buffer (25 mM HEPES pH 7.3, 150 mM NaCl, 5 mM MgCl2, 0.5% NP-40, 1 mM DTT). 1x protease inhibitor cocktail (Roche), 1x phosphatase inhibitor PhosSTOP (Roche) and 1 U / µL of Murine RNase Inhibitor (New England Biolabs) were added for lysis. Cells were lysed by vortexing for 20 minutes (3 seconds with 2-minute intervals). The lysate was centrifuged at 20.000 rpm for 15 minutes. For total transcriptome sequencing total RNA was extracted from 5 µL aliquot of clarified cell lysate (IP input) using the KingFisher Flex Purification System (Thermo) with the High-Performance RNA Isolation kit (Molecular Tools Shop, Vienna BioCenter). During the isolation RNA was treated with RNase-free DNase I (NEB). PolyA mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and used for library preparation.
Libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: To induce stress cells were treated with 500 µM sodium arsenite (Sigma) for two hours before collection. PBS was added to the control cells.

tag: cell line

tag: cell type

value: human colorectal carcinoma

value: Sodium arsenite 2 hours 500 µM

tag: sample type

value: RNA-Seq


title: P28.Dataset_206604260001_R06C02

value: AI31 whole muscle

value: Mus musculus


title: 54Omentum001Immune

value: Immune


title: 54Omentum005Tumor

value: Tumor


title: CUT&RUN_ZT20_Zolpidem_WDR5_1

value: Brain-TMN

tag: treatment


title: HCT116, control, rep1, RNA

value: PBS control


title: CUT&RUN_ZT16_IgG_1

value: Rabbit IgG, Abcam ab172730


title: 54Omentum001CD20

tag: roi


title: CUT&RUN_ZT20_Vehicle_WDR5_3

value: Vehicle


title: 40Ovary015Immune

value: Ovary

tag: type


title: 40Ovary013Stroma

value: Stroma

tag: batch


title: P28.Dataset_206604260001_R04C02

value: Muscle

value: Bulk Tissue (23 months)

tag: sid

value: AI30 whole muscle


title: 54Omentum003Immune

value: Omentum


title: 54Omentum002Stroma


title: CUT&RUN_ZT20_IgG_1


title: 40Ovary012Tumor


title: 40Ovary011Stroma


title: CUT&RUN_ZT4_IgG_1


title: 40Ovary011Immune


title: 54Omentum002Tumor


title: 54Omentum001Stroma


title: 40Ovary010Stroma


title: CUT&RUN_ZT20_WDR5_2

value: WDR5, CST D9E1I


title: mCherry-IGF2BP1 Y396E, control, rep3, RNA

value: human colorectal carcinoma

value: mCherry-IGF2BP1 Y396E, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: CUT&RUN_ZT12_IgG_1


title: 54Omentum004Stroma


title: mCherry-IGF2BP1 S181E, control, rep3, RNA

value: mCherry-IGF2BP1 S181E, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO

value: RNA-Seq


title: 40Ovary015Stroma


title: CUT&RUN_ZT8_IgG_1


title: mCherry-IGF2BP1 Y396E, arsenite, rep3, RNA

value: Sodium arsenite 2 hours 500 µM


title: 40Ovary009Stroma


title: mCherry-IGF2BP1 S181E, arsenite, rep3, RNA


title: 40Ovary014Tumor

value: Tumor


title: CUT&RUN_ZT20_WDR5_1

value: Brain-TMN


title: mCherry-IGF2BP1 RQ, arsenite, rep3, RNA

value: mCherry-IGF2BP1 RQ, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: 40Ovary009CD20


title: 40Ovary008Stroma


title: 40Ovary011CD20


title: CUT&RUN_ZT20_WDR5_3


title: 40Ovary010CD20


title: mCherry-IGF2BP1 Y396E, arsenite, rep2, RNA


title: 40Ovary007Immune

value: Immune


title: CUT&RUN_ZT0_IgG_1

value: Rabbit IgG, Abcam ab172730


title: 40Ovary007CD20

value: Ovary


title: CUT&RUN_ZT12_WDR5_3


title: mCherry-IGF2BP1 RQ, control, rep3, RNA

value: PBS control


title: CUT&RUN_ZT16_WDR5_2

description:
16_WD_merged.scaled.bs10.bw
WDR5_16_IgG.05_peaks.narrowPeak


title: mCherry-IGF2BP1 WT, arsenite, rep3, RNA

value: mCherry-IGF2BP1 WT, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: 40Ovary009Immune


title: 40Ovary006Immune


title: 40Ovary008Immune


title: 40Ovary006CD20


title: CUT&RUN_ZT12_WDR5_2


title: mCherry-IGF2BP1 RQ, arsenite, rep2, RNA


title: 40Ovary008CD20


title: mCherry-IGF2BP1 S181E, arsenite, rep2, RNA


title: 40Ovary007Stroma

value: Stroma


title: 40Ovary010Immune


title: mCherry-IGF2BP1 WT, arsenite, rep2, RNA


title: 40Ovary005Stroma


title: CUT&RUN_ZT16_WDR5_3


title: mCherry-IGF2BP1 WT, control, rep3, RNA


title: 40Ovary005Immune


title: mCherry-IGF2BP1 Y396E, control, rep2, RNA


title: CUT&RUN_ZT12_WDR5_1


title: 40Ovary004Stroma


title: CUT&RUN_ZT8_WDR5_3


title: CUT&RUN_ZT8_WDR5_2


title: 40Ovary004Tumor


title: 40Ovary006Stroma


title: 40Ovary003Immune


title: 40Ovary002Stroma


title: mCherry-IGF2BP1 RQ, control, rep2, RNA


title: mCherry-IGF2BP1 WT, control, rep2, RNA


title: CUT&RUN_ZT8_WDR5_1


title: 40Ovary003CD20


title: 40Ovary002Immune


title: CUT&RUN_ZT4_WDR5_3


title: 40Ovary001Stroma


title: mCherry-IGF2BP1 Y396E, arsenite, rep1, RNA


title: 40Ovary001Immune


title: CUT&RUN_ZT4_WDR5_2


title: 36Omentum009Stroma


title: mCherry-IGF2BP1 S181E, arsenite, rep1, RNA


title: 40Ovary001CD20


title: 40Ovary005CD20


title: mCherry-IGF2BP1 RQ, arsenite, rep1, RNA


title: 36Omentum009Immune


title: CUT&RUN_ZT0_WDR5_3


title: mCherry-IGF2BP1 S181E, control, rep2, RNA


title: 36Omentum009CD20


title: CUT&RUN_ZT16_WDR5_1


title: 36Omentum008CD20


title: mCherry-IGF2BP1 WT, arsenite, rep1, RNA


title: 36Omentum008Stroma


title: 36Omentum007CD20


title: 36Omentum007Stroma


title: 36Omentum005Stroma


title: CUT&RUN_ZT0_WDR5_1


title: mCherry-IGF2BP1 RQ, control, rep1, RNA


title: CUT&RUN_ZT20_H3K4me3Q5ser_2

value: H3K4me3Q5ser, Millipore ABE2580


title: 36Omentum004Stroma

value: Omentum


title: 36Omentum006Tumor


title: 36Omentum003Stroma


title: 36Omentum004Tumor


title: CUT&RUN_ZT20_H3K4me3Q5ser_3


title: 36Omentum006Stroma


title: mCherry-IGF2BP1 WT, control, rep1, RNA


title: 36Omentum002Tumor


title: CUT&RUN_ZT20_H3K4me3Q5ser_1


title: 36Omentum002Stroma


title: 36Omentum001Stroma


title: CUT&RUN_ZT16_H3K4me3Q5ser_3


title: HCT116, arsenite, rep1, RIP

data_processing:
The RIP-Seq libraries were sequenced on NovaSeqX 1.5B at SingleRead 100 mode at the Vienna BioCenter NGS facility producing ~35 million reads per sample. BCL files were converted to demultiplexed fastq files with bcl2fastq v2.20.0.422. The quality of fastq files was checked with fastqc 0.11.9.
The fastq files were trimmed and aligned to human genome hg38 using GENCODE annotation (release 46) with STAR v2.7.11b allowing for the two mismatches. Gene counts were obtained using FeatureCounts function of the Subread package v2.0.6.
Assembly: hg38, GENCODE annotation (release 46)
Supplementary files format and content: tsv, gene read counts

extract_protocol:
Cells were washed with ice-cold PBS, scraped, centrifuged (3500 rpm, 4 min) and the pellet flash frozen and stored at -80°C. On the day of the experiment, the pellets were thawed and 150 µL of lysis buffer (25 mM HEPES pH 7.3, 150 mM NaCl, 5 mM MgCl2, 0.5% NP-40, 1 mM DTT). 1x protease inhibitor cocktail (Roche), 1x phosphatase inhibitor PhosSTOP (Roche) and 1 U / µL of Murine RNase Inhibitor (New England Biolabs) were added for lysis. Cells were lysed by vortexing for 20 minutes (3 seconds with 2-minute intervals). The lysate was centrifuged at 20.000 rpm for 15 minutes. 20 µL of RPF-Trap magnetic agarose (rtma) were used per 10 cm dish. Lysates were incubated at 4°C for 1 h rotating, and then washed three times with lysis buffer and twice with wash buffer (25mM HEPES pH 7.3, 150mM NaCl, 1mM MgCl2, 0.5% NP40). Then the beads were resuspended in 150 µL of wash buffer containing 0.1% SDS and 2 mg/mL proteinase K (Ambion), and incubated at 55°C for 30min. The eluate was collected and purified with an RNA cleanup kit (Zymo Research). The purified RNA samples were rRNA depleted using human riboPOOL probes (siTOOLs) according to the manufacturer’s instructions. The RNA was then purified with an RNA cleanup kit (Zymo Research) and treated with 0.2 U of RNase-free DNase I (NEB) at 37°C for 15 min, and re-purified with an RNA cleanup kit (Zymo Research)
Libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

value: RIP-Seq


title: CUT&RUN_ZT0_WDR5_2

value: WDR5, CST D9E1I


title: mCherry-IGF2BP1 S181E, control, rep1, RNA

value: human colorectal carcinoma


title: HCT116, control, rep1, RIP


title: CUT&RUN_ZT4_WDR5_1


title: 36Omentum001CD20


title: CUT&RUN_ZT16_H3K4me3Q5ser_1


title: 36Omentum001Tumor


title: 81Omentum008Stroma


title: CUT&RUN_ZT16_H3K4me3Q5ser_2


title: 36Omentum001Immune


title: mCherry-IGF2BP1 Y396E, arsenite, rep3, RIP

value: mCherry-IGF2BP1 Y396E, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: CUT&RUN_ZT12_H3K4me3Q5ser_3


title: 81Omentum008Tumor


title: mCherry-IGF2BP1 S181E, arsenite, rep3, RIP

value: mCherry-IGF2BP1 S181E, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: 81Omentum007Stroma


title: mCherry-IGF2BP1 Y396E, control, rep1, RNA

value: RNA-Seq


title: 81Omentum006Stroma


title: 81Omentum005Stroma


title: 81Omentum005Immune


title: CUT&RUN_ZT12_H3K4me3Q5ser_1


title: 81Omentum005Tumor

value: Tumor


title: mCherry-IGF2BP1 Y396E, control, rep3, RIP


title: mCherry-IGF2BP1 S181E, control, rep3, RIP


title: mCherry-IGF2BP1 WT, arsenite, rep3, RIP

value: Sodium arsenite 2 hours 500 µM


title: 81Omentum005CD20


title: CUT&RUN_ZT8_H3K4me3Q5ser_3

value: Brain-TMN


title: CUT&RUN_ZT12_H3K4me3Q5ser_2


title: mCherry-IGF2BP1 RQ, control, rep3, RIP

value: mCherry-IGF2BP1 RQ, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: 81Omentum004Tumor


title: CUT&RUN_ZT8_H3K4me3Q5ser_2


title: 81Omentum004Stroma


title: CUT&RUN_ZT8_H3K4me3Q5ser_1


title: 81Omentum003Stroma


title: mCherry-IGF2BP1 Y396E, arsenite, rep2, RIP


title: 81Omentum004Immune

value: Immune


title: mCherry-IGF2BP1 WT, control, rep3, RIP


title: 81Omentum003Tumor


title: 81Omentum004CD20


title: CUT&RUN_ZT4_H3K4me3Q5ser_3


title: 81Omentum003Immune


title: 81Omentum003CD20


title: CUT&RUN_ZT4_H3K4me3Q5ser_2


title: mCherry-IGF2BP1 RQ, arsenite, rep2, RIP


title: 81Omentum002Tumor


title: 81Omentum002Stroma


title: 81Omentum002Immune


title: mCherry-IGF2BP1 WT, arsenite, rep2, RIP


title: 81Omentum002CD20


title: CUT&RUN_ZT0_H3K4me3Q5ser_3


title: 81Omentum001Stroma


title: mCherry-IGF2BP1 Y396E, control, rep2, RIP


title: CUT&RUN_ZT0_H3K4me3Q5ser_2


title: 81Omentum001Immune


title: mCherry-IGF2BP1 S181E, control, rep2, RIP


title: 81Omentum001Tumor


title: 81Omentum001CD20


title: LNLymph Node005Stroma

description: LN

source_name: Lymph Node

value: Lymph Node


title: CUT&RUN_ZT0_H3K4me3Q5ser_1


title: mCherry-IGF2BP1 RQ, control, rep2, RIP

value: PBS control


title: mCherry-IGF2BP1 S181E, arsenite, rep2, RIP


title: mCherry-IGF2BP1 WT, control, rep2, RIP

value: mCherry-IGF2BP1 WT, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: CUT&RUN_ZT20_H3K4me3Q5his_3

value: H3K4me3Q5his, Millipore ABE2570


title: LNLymph Node004Immune

description: LN


title: LNLymph Node005CD20

description: LN


title: LNLymph Node004Stroma

description: LN

value: Stroma


title: CUT&RUN_ZT20_H3K4me3Q5his_2


title: CUT&RUN_ZT20_H3K4me3Q5his_1


title: LNLymph Node004CD20

description: LN


title: LNLymph Node003Stroma

description: LN


title: mCherry-IGF2BP1 S181E, arsenite, rep1, RIP


title: CUT&RUN_ZT4_H3K4me3Q5ser_1

value: H3K4me3Q5ser, Millipore ABE2580


title: LNLymph Node003Immune

description: LN


title: CUT&RUN_ZT16_H3K4me3Q5his_2

description:
16_DH_merged.scaled.bs10.bw
DualHis_ZT16_IgG.BROAD.05_peaks.broadPeak


title: CUT&RUN_ZT12_H3K4me3Q5his_3


title: LNLymph Node001CD20

description: LN


title: 38Ovary010Stroma

value: Ovary


title: mCherry-IGF2BP1 WT, arsenite, rep1, RIP

value: RIP-Seq


title: CUT&RUN_ZT16_H3K4me3Q5his_3


title: LNLymph Node003CD20

description: LN


title: CUT&RUN_ZT12_H3K4me3Q5his_2


title: 38Ovary009Stroma


title: mCherry-IGF2BP1 RQ, arsenite, rep1, RIP

value: human colorectal carcinoma


title: LNLymph Node001Stroma

description: LN


title: 38Ovary009CD20


title: LNLymph Node002Stroma

description: LN


title: CUT&RUN_ZT16_H3K4me3Q5his_1


title: 38Ovary008Stroma


title: CUT&RUN_ZT12_H3K4me3Q5his_1


title: 38Ovary009Immune


title: LNLymph Node001Immune

description: LN


title: mCherry-IGF2BP1 RQ, control, rep1, RIP


title: mCherry-IGF2BP1 WT, control, rep1, RIP


title: LNLymph Node002CD20

description: LN


title: 38Ovary006Tumor


title: mCherry-IGF2BP1 Y396E, control, rep1, RIP

value: mCherry-IGF2BP1 Y396E, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: mCherry-IGF2BP1 Y396E, arsenite, rep1, RIP


title: CUT&RUN_ZT8_H3K4me3Q5his_2


title: 38Ovary006Immune


title: 38Ovary006CD20


title: 38Ovary004Stroma


title: CUT&RUN_ZT8_H3K4me3Q5his_3


title: LNLymph Node005Immune

description: LN


title: 38Ovary003Stroma


title: CUT&RUN_ZT4_H3K4me3Q5his_2


title: CUT&RUN_ZT4_H3K4me3Q5his_3


title: 38Ovary003Immune


title: 38Ovary006Stroma


title: CUT&RUN_ZT4_H3K4me3Q5his_1


title: MDA-MB-231/RR, control, 2

city: Seoul

first: Lee

last: Seungcheol

address: Heukseokro 84

country: South Korea

institute: Chungang university

data_processing:
Trimmomatic v 0.38
The resulting clean reads were aligned to the Homo sapiens (GRCh38) reference genome using HISAT (version 2.1.0), based on HISAT and Bowtie2 implementations.
The aligned data in the SAM file format were sorted and indexed using SAMtools (version 1.9.) Following alignment, transcripts were assembled and quantified using StringTie (version 2.1.3b).
Gene- and transcript-level quantifications were calculated as the raw read count, fragments per kilobase of transcript per million mapped reads, and transcripts per million.
Assembly: GRCh38
Supplementary files format and content: Gene- and transcript-level quantifications were calculated as the raw read count
Supplementary files format and content: fragments per kilobase of transcript per million mapped reads, and transcripts per million.

growth_protocol: MDA-MB-231/RR cells were cultured in DMEM with 10% heat-inactivated FBS and 1% penicillin-streptomycin. The cells were cultured at 37°C in a humidified incubator (95% air and 5% CO2).

extract_protocol:
The cells were incubated until confluency was approximately 70–90% and then harvested following dislodging of the cells by trypsin-EDTA. The harvested cells were centrifuged at 1,000 g, the medium was removed, and the cells were washed twice with 1× PBS. Following the final wash, the cells were resuspended in 0.1× PBS and aliquots were immediately frozen in liquid nitrogen.
The filtered dataset was normalized using relative log expression to correct for variations in library sizes among the samples.

value: Breast cancer cell


title: MDA-MB-231/RR, control, 1


title: 38Ovary008Tumor


title: 38Ovary001Immune


title: CAFs, YBX1 shRNA, 72 h, rep 5

city: Shenyang

first: Qijun

last: Wu

address: No. 36, San Hao Street

institute: Shengjing Hospital of China Medical University

data_processing:
Illumina Sequencing
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Fastp v0.23.1
Trimmed sequence reads were mapped to GRCh38.109 using Hisat2 v2.2.1 with default settings
Read count extraction was performed using Htseq
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa;Homo_sapiens.GRCh38.109.gtf
Supplementary files format and content: processed data.xlsx

source_name: cancer-associated fibroblasts

extract_protocol:
RNA was extracted by using TRIzol reagent.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified. After the library construction is completed, preliminary quantification is carried out using Qubit, and the library is diluted to 1.5ng/ul. Subsequently, the inserted fragments of the library are detected. Once the inserted fragments meet expectations, the effective concentration of the library is accurately quantified using qRT PCR to ensure the quality of the library.

value: cancer-associated fibroblasts

value: YBX1 knockdown


title: 38Ovary001CD20


title: MDA-MB-231/RR, experiment, oTR, Melatonin, 3

value: ortho-topolin riboside(oTR), Meatonin


title: MDA-MB-231/RR, experiment, oTR, Melatonin, 2


title: mCherry-IGF2BP1 S181E, control, rep1, RIP

value: mCherry-IGF2BP1 S181E, IGF2BP2 KO, IGF2BP3 KO, Tet-OsTIR1-PURO


title: 38Ovary005Tumor

value: Tumor


title: CUT&RUN_ZT8_H3K4me3Q5his_1

value: Brain-TMN


title: CUT&RUN_ZT0_H3K4me3Q5his_1


title: MDA-MB-231/RR, control, 3


title: 41Ovary015Immune

value: Immune


title: CUT&RUN_ZT20_H3K4me3_3

value: H3K4me3, Epicypher 13-0041


title: 38Ovary003CD20


title: CAFs, YBX1 shRNA, 72 h, rep 2


title: 41Ovary013Immune


title: CUT&RUN_ZT20_H3K4me3_2


title: CUT&RUN_ZT0_H3K4me3Q5his_3


title: 38Ovary001Stroma


title: 38Ovary002Stroma


title: CUT&RUN_ZT0_H3K4me3Q5his_2


title: 38Ovary002CD20


title: CAFs,YBX1 shRNA, 72 h, rep 1


title: CAFs, YBX1 shRNA, 72 h, rep 4


title: 41Ovary013CD20


title: 38Ovary004Tumor


title: CUT&RUN_ZT16_H3K4me3_3


title: MDA-MB-231/RR, experiment, oTR, Melatonin, 1


title: CUT&RUN_ZT16_H3K4me3_2


title: 41Ovary014Tumor


title: 41Ovary015Stroma


title: CAFs,YBX1 shRNA, 72 h, rep 3


title: 41Ovary015CD20


title: CAFs, NC shRNA, 72 h, rep1

value: WT


title: 41Ovary012Stroma


title: CUT&RUN_ZT20_H3K4me3_1


title: CAFs, NC shRNA, 72 h, rep 4


title: 41Ovary012Tumor


title: 41Ovary011Stroma


title: CUT&RUN_ZT12_H3K4me3_2


title: CAFs, NC shRNA, 72 h, rep 3


title: 41Ovary010Stroma


title: SUM159 DAPK3 KO R2

city: Houston

first: Charles

middle: E

last: Foulds

state: TX

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
Alignments were performed against human genome version GRCh38 using RSEM and Bowtie 2.
TPM (Transcripts Per Million) values calculated by RSEM were log2 transformed.
Differential expression analysis was performed using R package edgeR.
Gene set enrichment analysis (GSEA) was performed using publicly available software (GSEA version 4.2). The input of GSEA is the ranked gene list based on the signed (by direction of change) log10 p-values from the differential expression analysis. The Hallmark gene sets within the Molecular Signatures Database (MSigDB) were used for GSEA.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text includes raw counts for each sample

growth_protocol: SUM159 was maintained in Ham’s F-12 medium with 5% FBS, 10 mM HEPES, 5 μg/mL insulin, and 1 μg/mL hydrocortisone.

extract_protocol:
RNA was extracted from SUM159 control and DAPK3 KO #3 cells using the RNeasy Mini Kit (QIAGEN, #74106) and treated with DNase (QIAGEN, #79254) to remove genomic DNA.
The Genomic and RNA Profiling (GARP) Core at BCM confirmed concentration (using a NanoDrop spectrophotometer) and integrity (using an Agilent Bioanalyzer). The GARP core then made mRNA libraries and performed sequencing on an Illumina NovaSeq 6000 sequencing instrument.

value: triple-negative breast cancer cell line

value: DAPK3 KO


title: 41Ovary011Tumor


title: 41Ovary013Stroma

value: Stroma


title: 41Ovary007Tumor

value: Ovary


title: 41Ovary007Immune


title: SUM159 DAPK3 KO R1


title: 41Ovary010Immune


title: CUT&RUN_ZT12_H3K4me3_1


title: CUT&RUN_ZT8_H3K4me3_3


title: CAFs, NC shRNA, 72 h, rep 2


title: 41Ovary006Stroma


title: 41Ovary010CD20


title: 41Ovary009CD20


title: CUT&RUN_ZT16_H3K4me3_1


title: SUM159 DAPK3 KO R3


title: 41Ovary007Stroma


title: CUT&RUN_ZT12_H3K4me3_3


title: 41Ovary006Tumor


title: 41Ovary008CD20


title: 41Ovary008Stroma


title: SUM159 control R1

value: DAPK3 WT


title: 41Ovary004Stroma


title: CUT&RUN_ZT4_H3K4me3_3


title: CUT&RUN_ZT4_H3K4me3_2


title: 41Ovary003Immune


title: SUM159 control R3


title: CUT&RUN_ZT4_H3K4me3_1


title: clone 35 cells, resting SN, 43-hr

city: Kyoto

first: Jun

last: Shimizu

state: Kyoto

address: Nishikyo-ku, 1-36 Goryo-ohara, KKVP 206

country: Japan

institute: MiCAN Technologies Inc.

data_processing:
Following adapter sequence removal with Trimmomatic v0.38, the sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat (ver. 2.1.1). The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff (ver. 2.2.1).
Assembly: hg19
Supplementary files format and content: Excel file includes the number of fragments per kilobase of exon per million mapped fragments (FPKMs), fold change and normalized counts for each sample.

source_name: clone 35

extract_protocol:
Total RNA was extracted from cells with an miRNeasy Micro kit (QIAGEN) according to the manufacturer’s protocol.
Library preparation was performed based on the manufacturer’s instructions using a TruSeq stranded mRNA Library Prep kit (Illumina).

treatment_protocol: Human CD4+ T cells (2x104/well) were cultured in the presence of anti-CD3/CD28-beads along with or without IL-2 (10 U/mL) for 1-2 weeks (stimulation culture). After these periods, cells were harvested, depleted from beads, washed and cultured in the presence of IL-2 (resting culture). These stimulation and resting cultures were repeated every 1-2 weeks. Culture SNs after stimulation or resting culture were harvested, filtrated and used as stimulation- or resting-SNs (stim- or rest-SNs, respectively). Clone 35 cells were cultured with these SNs from 24- or 43-hrs.

value: clone 35

value: monocyte cells

value: resting-SN, 43-hr


title: 41Ovary007CD20


title: CUT&RUN_ZT0_H3K4me3_3

description:
0_K3.scaled.bs10.bw
K4me3_ZT0_IgG.BROAD.05_peaks.broadPeak


title: 41Ovary001Immune


title: 41Ovary006Immune


title: 41Ovary001CD20


title: CUT&RUN_ZT8_H3K4me3_2


title: 41Ovary006CD20


title: 41Ovary005Stroma


title: SUM159 control R2


title: 41Ovary003Stroma


title: CUT&RUN_ZT0_H3K4me3_1


title: clone 35 cells, stimulating SN, 24-hr

value: stimulating-SN, 24-hr


title: 41Ovary003Tumor


title: CUT&RUN_ZT8_H3K4me3_1


title: clone 35 cells, stimulating SN, 43-hr

value: stimulating-SN, 43-hr


title: 41Ovary003CD20


title: 41Ovary002Stroma


title: DPSCS, neural induction, rep1

city: Tsukuba

first: Shohei

last: Takaoka

state: Ibaraki

address: 2-1-1 Amakubo

department: oral and maxillofacial surgery

institute: Tsukuba university hospital

description: 10X Genommics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v7.1.0.(https://www.10xgenomics.com/jp/support/software/cell-ranger/latest/release-notes/cr-release-notes#v7-1-0）
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dental pulp

extract_protocol:
The adherent cells were dissociated using trypsin, and following singlet processing, they were filtered using a 40-µm cell strainer. Cells were stained with trypan blue and observed under a microscope to assess cell counts and viability; single-cell suspensions with viability >80% were employed for library preparation.
The cDNA synthesis and gene expression libraries were performed according to the protocol provided by 10x Genomics (Chromium Next GEM Single Cell 3ʹReagent Kits v3.1 (Dual Index) CG000315 Rev E).

value: dental pulp

value: neural lineage cells

value: cultured cells

value: human

value: neural induction


title: 80Omentum008Stroma

value: Omentum


title: CUT&RUN_ZT20_H3K4me2_3

value: Brain-TMN


title: 41Ovary001Stroma


title: clone 35 cells, medium, 43-hr

value: WT

value: medium, 43-hr


title: clone 35 cells, medium, 24-hr

value: medium, 24-hr


title: 41Ovary002Tumor

value: Ovary

value: Tumor


title: CUT&RUN_ZT0_H3K4me3_2

value: H3K4me3, Epicypher 13-0041


title: 80Omentum009Tumor


title: 80Omentum007Stroma

value: Stroma


title: iPSC-CMs_LMOD2 -/+3

description:
BXYGeneMatrixGEO.txt
CL81D

source_name: iPSC-CMs

value: iPSC-CMs

value: iPSCs

value: LMOD2 -/+


title: 80Omentum008Immune

value: Immune


title: clone 35 cells, resting SN, 24-hr

value: clone 35

value: monocyte cells

value: resting-SN, 24-hr


title: 80Omentum008CD20


title: CUT&RUN_ZT16_H3K4me2_2


title: 80Omentum009Stroma


title: CUT&RUN_ZT20_H3K4me2_2


title: 80Omentum007Tumor


title: 80Omentum007Immune


title: 80Omentum004CD20


title: 80Omentum003Stroma


title: iPSC-CMs_LMOD2 -/+2

description:
BXYGeneMatrixGEO.txt
CL81C


title: 80Omentum007CD20


title: CUT&RUN_ZT12_H3K4me2_2


title: CUT&RUN_ZT16_H3K4me2_3


title: 80Omentum006Stroma


title: CUT&RUN_ZT20_H3K4me2_1


title: iPSC-CMs_LMOD2-/-4

description:
BXYGeneMatrixGEO.txt
CL4H


title: iPSC-CMs_LMOD2 -/+1

description:
BXYGeneMatrixGEO.txt
CL81B


title: 80Omentum005Stroma


title: CUT&RUN_ZT12_H3K4me2_3


title: 80Omentum006Tumor


title: CUT&RUN_ZT12_H3K4me2_1


title: 80Omentum004Stroma


title: CUT&RUN_ZT16_H3K4me2_1


title: CUT&RUN_ZT8_H3K4me2_3


title: 80Omentum004Tumor


title: iPSC-CMs_LMOD2+/+1

description:
BXYGeneMatrixGEO.txt
CL68B


title: CUT&RUN_ZT8_H3K4me2_2


title: 80Omentum003Tumor


title: iPSC-CMs_LMOD2-/-1

description:
BXYGeneMatrixGEO.txt
CL4A


title: 3D MDA-MB-231 dSRF MRTF-A OX 3

last: Eder

state: Pennsylvania

address: 300 Technology Drive

department: Bioengineering

data_processing:
Quality of sequencing reads were determined with FastQC before transcripts from the Ensembl v.93 transcriptome (hg38) were quantified with Salmon v.11.3
Gene-level expression  was calculated using tximport v.1.12.0
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts (as estimated by Salmon) for each Sample
Supplementary files format and content: tab-delimited text file include TPM values for each Sample

source_name: Breast Cancer

growth_protocol: MDA-MB-231 cells were maintained with 10% fetal bovine serum (FBS), antibiotics, and 2% matrigel in case of the 3D cultures in an incubator with 5% CO2 at 37C in (2D) culture plates or (3D) on top of matrigel.

extract_protocol:
RNA collevtion was performed with the Qiagen Rneasy Mini Plus Kit
Libraries were obtaining from the total RNA following the Illumina Stranded Total RNA preparation Ligation with Ribo-Zero Plus protcol

treatment_protocol: MRTF-A overexpression was induced for 72h prior to RNA collection by doxycline induction

value: Breast Cancer

value: dSRF MRTF-A OX

value: 1ug/ml doxycline for 72h


title: CUT&RUN_HeLa_IgG_1

source_name: HeLa

value: HeLa

value: Rabbit IgG, Abcam ab172730


title: iPSC-CMs_LMOD2+/+2

description:
BXYGeneMatrixGEO.txt
CL68E


title: 3D MDA-MB-231 dSRF MRTF-A OX 2

value: dSAP MRTF-A OX


title: 3D MDA-MB-231 dSRF MRTF-A OX 1

value: WT MRTF-A OX


title: CUT&RUN_ZT4_H3K4me2_3

value: Brain-TMN


title: 80Omentum003CD20

value: Omentum


title: 80Omentum003Immune


title: iPSC-CMs_LMOD2-/-3

description:
BXYGeneMatrixGEO.txt
CL4D


title: 80Omentum002Stroma

value: Stroma


title: 80Omentum004Immune


title: 80Omentum002Tumor

value: Tumor


title: CUT&RUN_ZT4_H3K4me2_2


title: iPSC-CMs_LMOD2-/-2

description:
BXYGeneMatrixGEO.txt
CL4C

value: iPSC-CMs

value: iPSCs


title: 80Omentum001Immune

value: Immune


title: 3D MDA-MB-231 WT MRTF-A OX 3


title: 80Omentum001CD20


title: CUT&RUN_ZT8_H3K4me2_1


title: 3D MDA-MB-231 dSAP MRTF-A OX 3

value: Control


title: CUT&RUN_HeLa_H3Q5his_3

description:
HELA_Q5_merged.bs10.bw
singleHisHela_.BROAD.05_peaks.broadPeak

value: H3Q5his, Millipore ABE2578


title: 3D MDA-MB-231 WT MRTF-A OX 1


title: CUT&RUN_HeLa_H3Q5his_1


title: 3D MDA-MB-231 dSAP MRTF-A OX 2


title: CUT&RUN_HeLa_H3Q5his_2


title: CUT&RUN_ZT4_H3K4me2_1


title: 3D MDA-MB-231 Control 2


title: 3D MDA-MB-231 WT MRTF-A OX 2


title: 3D MDA-MB-231 Control 1


title: 3D MDA-MB-231 dSAP MRTF-A OX 1


title: CUT&RUN_ZT0_H3K4me2_3

description:
0_K2.scaled.bs10.bw
K4me2_ZT0_IgG.BROAD.01_peaks.broadPeak


title: CUT&RUN_HeLa_H3K4me3Q5his_3

description:
HELA_DH_merged.bs10.bw
DualHisHela_.BROAD.05_peaks.broadPeak

value: H3K4me3Q5his, Millipore ABE2570


title: CUT&RUN_ZT0_H3K4me2_2


title: Transgenic line 3

city: Zhengzhou

first: han

last: xingzhou

address: 100 Science Avenue

institute: Zhengzhou University

data_processing:
The clean and filtered reads were aligned to the references genome of Arabidopsis thaliana using TopHat2 (ftp.ensem blgen omes.org/pub/plant s/relea se-25/fasta /arabidopsisthaliana/).
The differentially expressed genes (DEGs) were determined using the DESeq program with a log-fold expression change (log FC) of ≥ 2 and false discovery rate (FDR) threshold of < 0.01.
The FDR of DEGs was based on P < 0.05 which was adjusted by the Benjamini–Hochberg correction method.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

growth_protocol: First of all, the seeds of wild-type plants (WT) and transgenic Arabidopsis lines were sterilized with 5% NaClO solution, and washed with double-distilled H2O three times, and then sowed on the MS solid medium (3% sucrose, pH 5.8) under sterile conditions. After a week of growth in the incubator (22℃, 16 h light / 8 h dark), transferred the seeding into soil and grown in a growth chamber with 16 h light / 8 h dark periodically, and the growth temperature was set around 22 ℃

extract_protocol:
The fresh leaves were collected from 4-week-old WT plants and transgenic Arabidopsis lines under drought treatments. The total RNA was first extracted using TRIzol Reagent (TaKaRa, Tokyo, Japan), and treated with RNase-free DNase I (TaKaRa)
mRNA purification using the Magnetic Oligo (dT) Beads (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. The preparation of cDNA library construction was performed using random hexamer primers and reverse transcriptase (Invitrogen, Waltham, MA, USA). The cDNA libraries were sequenced using the Illumina HiSeq 2000 platform (Illu-mina). Finally, the raw data were transformed into sequenc-ing information by base calling and stored as FastQ for-mat files

tag: cultivar

value: leaf

tag: genotype/variation

value: transgenic line


title: 2D MDA-MB-231 dSRF MRTF-A OX 2

value: Breast Cancer

value: 1ug/ml doxycline for 72h


title: CUT&RUN_HeLa_H3K4me3Q5his_2

value: HeLa


title: 2D MDA-MB-231 dSRF MRTF-A OX 3

value: dSRF MRTF-A OX


title: MlxKO 5 month, skeletal muscle [SK-X5S5238]

city: pittsburgh

first: Huabo

last: Wang

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

data_processing:
CLC Genomics Workbench v 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Mus musculus (GRCm38.p6) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include CPM(TMM-adjusted) values for each Sample

source_name: skeletal muscle

growth_protocol: Animal work was conducted in compliance with the Public Health Service Policy on Humane Care and Use of Laboratory Animal Research (ILAR) Guide for Care and Use of Laboratory Animals. All experimental procedures, diets and tests were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Pittsburgh. All mice were housed in a specific pathogen-free facility, maintained under standard conditions at UPMC Children’s Hospital of Pittsburgh.

extract_protocol:
RNAs were isolated from mouse tissues using RNeasy kit,according to the directions of the supplier (Qiagen, Inc. Germantown, MD). Exceptions to this were made in the case of adipose tissue and skeletal muscle for which we utilized an RNeasy Lipid Tissue extraction Kit(Qiagen, Inc., Germantown, MD).
Sequencing libraries were generated using a NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, Beverly, MA).Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms.

treatment_protocol: CreER activation and Mlx excision were initiated at the time of weaning in mice that had attained a weight of 15 g or greater.  Each mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil.

value: skeletal muscle

tag: strain

value: B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J x Mlx Flox/Flox

tag: age

value: 5 month

value: MlxKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: MlxKO 5 month, skeletal muscle [SK-X5S5239]


title: Transgenic line 2


title: 2D MDA-MB-231 dSAP MRTF-A OX 3


title: 2D MDA-MB-231 dSRF MRTF-A OX 1

value: WT MRTF-A OX


title: Transgenic line 1


title: 3D MDA-MB-231 Control 3

value: dSAP MRTF-A OX


title: WT plants rep1

value: WT


title: 2D MDA-MB-231 dSAP MRTF-A OX 1


title: PBMC, Cycle1, patient 208 TCR

first: Yiqian

last: Gu

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

description: 10x Genomics

data_processing:
Cellranger multi 7.1.0 was used for read alignment to reference genome hg38 and gene quantification.
Assembly: hg38
Supplementary files format and content: Tab separated value files, comma seperated value files, and matrix files
Library strategy: scTCR-seq

source_name: PBMC

extract_protocol:
Frozen PBMC thawed and Ficoll purified
10X Single Cell TCR & 5' Gene Expression Sequencing Library Prep

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

tag: cycle

tag: patient id

value: patient 208


title: MlxKO 5 month, skeletal muscle [SK-X5S4299]


title: PBMC, At progression, patient 208 TCR

description: 10x Genomics

value: At progression


title: PBMC, Cycle1, patient 207 TCR

description: 10x Genomics

value: patient 207


title: PBMC, Cycle7, patient 208 TCR

description: 10x Genomics


title: MlxKO 20 month, skeletal muscle [SK-X18S60]

value: 20 month


title: WT plants rep2

value: leaf


title: CUT&RUN_HeLa_H3K4me3Q5his_1

value: HeLa

tag: time

tag: replicate

value: H3K4me3Q5his, Millipore ABE2570


title: PBMC, At progression, patient 207 TCR

description: 10x Genomics

tag: tissue


title: PBMC, At progression, patient 206 TCR

description: 10x Genomics

value: patient 206


title: 2D MDA-MB-231 WT MRTF-A OX 3

value: Breast Cancer

tag: cell line

tag: genotype

value: 1ug/ml doxycline for 72h


title: I19-1290-06

city: Oss

first: Monica

last: Raimo

state: Noord-Brabant

address: Kloosterstraat 9

department: Research

country: Netherlands

institute: Glycostem

description: donor 7 replicate A

data_processing:
Illumina adapter and poly-A sequences were trimmed off with an in-house adapter-trimming script
The trimmed reads were mapped against the human GRCh38 reference using HiSat2 (version 2.1.0)
Gene expression values were determined using htseq-count (version 0.11.2) and Ensembl release-91 gene and transcript annotation
Assembly: human GRCh38
Supplementary files format and content: xlsx format with normalized gene counts for each sample

source_name: NK cell derived from UCB CD34+ cells

growth_protocol: CD34+ cells from 10 UCB donors were seeded in 6-wells tissue culture treated plates (Corning Incorporated) for expansion culture in Glycostem Basal Growth Medium (GBGM®; Fertipro) supplemented with human serum (Sanquin), thrombopoietin (TPO), interleukin (IL)-7, FMS-like tyrosine kinase 3 ligand (Flt-3L), granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-6, stem cell factor (SCF) (all from Cellgenix) and Neupogen (G-CSF; Amgen) as previously described. After 9 days, TPO was replaced by IL-15 (Cellgenix) and after 14 days of NK progenitor expansion, Flt-3L was replaced by Proleukin (IL-2; Novartis) for the NK cell differentiation phase. Cells were cultured until day 28 and cryopreserved. Upon thawing, cells were directly used for assays, or cultured for an additional 7 days in differentiation medium before use. 10 donors were sequenced at day 35, after a week of recovery.

extract_protocol:
RNA was isolated using the RNAeasy Plus Mini kit (Qiagen) according to manufacturer's instructions
RNA-Seq libraries were prepared according to the Illumina TruSeq stranded mRNA protocol

tag: cell type

value: NK cell derived from UCB CD34+ cells

tag: day of_culture


title: 2D MDA-MB-231 WT MRTF-A OX 2

value: Control

tag: treatment


title: I19-1278-40

description: donor 6 replicate A


title: 2D MDA-MB-231 dSAP MRTF-A OX 2

value: dSRF MRTF-A OX


title: MlxKO 20 month, skeletal muscle [SK-X18S58]

value: skeletal muscle

value: B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J x Mlx Flox/Flox

value: MlxKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: PBMC, Cycle1, patient 206 TCR

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: MlxKO 5 month, skeletal muscle [SK-X5S5001]

value: 5 month


title: 2D MDA-MB-231 WT MRTF-A OX 1


title: WT plants rep3

value: WT


title: MlxKO 20 month, skeletal muscle [SK-X18S57]

value: 20 month


title: MlxKO 20 month, skeletal muscle [SK-X18S59]


title: MlxKO 5 month, Liver [Liver-X5L5239]

source_name: Liver

value: Liver


title: MlxKO 5 month, Liver [Liver-X5L5238]


title: PBMC, Cycle1, patient 205 TCR

description: 10x Genomics

value: patient 205


title: Non-Responder 2 (864)

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

description: 864 nonresponder

data_processing:
Base calling was performed using RTA 3.9.25, demultiplexing was performed using cellranger v7.0.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.0.0 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: H5 file filtered gene barcode matrix

source_name: oral tongue squamous epithelial carcinoma

extract_protocol:
Tumors were mechanically and chemically digested into single-cell suspensions using the gentleMACS Dissociator and the mouse tumor dissociation kit by Miltenyi Biotec (130-096-730, Miltenyi Biotec, Auburn, CA) respectively, per manufacturer’s protocol.
Library preparation and quality control were performed as described in the 10X User Guide (3’ v3.1).

value: oral squamous cell carcinoma


title: I19-1290-04

description: donor 2 replicate A


title: I19-1278-44

description: donor 5 replicate A


title: PBMC, Cycle7, patient 206 TCR

description: 10x Genomics

value: patient 206


title: 2D MDA-MB-231 Control 3

value: Breast Cancer

value: dSAP MRTF-A OX

value: 1ug/ml doxycline for 72h


title: I20-1188-39

description: donor 10 replicate B

value: NK cell derived from UCB CD34+ cells


title: MlxKO 20 month, Liver [Liver-X18L74]


title: CUT&RUN_ZT0_H3K4me2_1

city: New York

value: Brain-TMN


title: MlxKO 20 month, skeletal muscle [SK-X18S56]

value: skeletal muscle

value: B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J x Mlx Flox/Flox


title: I19-1278-42

description: donor 4 replicate A


title: I20-1188-40

description: donor 8 replicate B


title: 2D MDA-MB-231 Control 1

value: Control


title: PBMC, Cycle7, patient 205 TCR

description: 10x Genomics

value: PBMC


title: 2D MDA-MB-231 Control 2

value: WT MRTF-A OX


title: PBMC,  At progression, patient 205 TCR

description: 10x Genomics

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: At progression


title: I19-1290-02

description: donor 3 replicate A


title: Smyd3 ASOs, rep3

data_processing:
Base calling was performed using RTA 3.9.25, demultiplexing was performed using cellranger v7.0.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.0.0 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: h5 file filtered gene barcode matrix

extract_protocol:
Tumors were mechanically and chemically digested into single-cell suspensions using the gentleMACS Dissociator and the mouse tumor dissociation kit by Miltenyi Biotec (130-096-730, Miltenyi Biotec, Auburn, CA) respectively, per manufacturer’s protocol.
Library preparation and quality control were performed as described in the 10X User Guide (3’ v3.1). Two NextSeq runs were performed.

value: oral tongue squamous epithelial carcinoma


title: I20-1188-37

description: donor 7 replicate B


title: MlxKO 20 month, Liver [Liver-X18L17]

value: Liver

value: 20 month

value: MlxKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: MlxKO 5 month, Liver [Liver-X5L5001]

value: 5 month


title: I19-1290-05

description: donor 1 replicate A


title: I20-1188-33

description: donor 6 replicate B


title: Non-Responder 1 (838)

description: 838 nonresponder

value: oral squamous cell carcinoma


title: PBMC,  At progression, patient 204 TCR

description: 10x Genomics

value: patient 204


title: Smyd3 ASOs, rep1


title: MlxKO 5 month, Liver [Liver-X5L4299]


title: I20-1188-35

description: donor 4 replicate B

value: NK cell derived from UCB CD34+ cells


title: PBMC, Cycle17, patient 107 TCR

description: 10x Genomics

value: patient 107


title: MlxKO 5 month, omental adipose tissue [Fat-X5F5239]

source_name: omental adipose tissue

value: omental adipose tissue


title: I20-1188-32

description: donor 3 replicate B


title: PBMC, Cycle7, patient 107 TCR

description: 10x Genomics


title: PBMC, Cycle7, patient 202 TCR

description: 10x Genomics

value: patient 202


title: Responder 2 (870)

description: 870 responder


title: PBMC, Cycle7, patient 204 TCR

description: 10x Genomics


title: I20-1188-38

description: donor 9 replicate B


title: MlxKO 5 month, omental adipose tissue [Fat-X5F5238]

value: B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J x Mlx Flox/Flox


title: I20-1188-34

description: donor 2 replicate B


title: iPSC-CMs_LMOD2+/+3

description:
BXYGeneMatrixGEO.txt
CL68F

value: iPSC-CMs

value: iPSCs


title: PBMC, Cycle1, patient 204 TCR

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: Control ASOs, rep1

value: oral tongue squamous epithelial carcinoma


title: Responder 1 (83)

description: 83 responder


title: I20-1188-36

description: donor 1 replicate B


title: MlxKO 20 month, Liver [Liver-X18L19]

value: Liver


title: MlxKO 5 month, omental adipose tissue [Fat-X5F4299]


title: PBMC, Cycle17, patient 105 TCR

description: 10x Genomics

value: patient 105


title: PBMC,  At progression, patient 202 TCR

description: 10x Genomics

value: At progression


title: MlxKO 20 month, Liver [Liver-X18L18]

value: 20 month

value: MlxKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: Smyd3 ASOs, rep2

value: oral squamous cell carcinoma


title: MlxKO 20 month, omental adipose tissue [Fat-X18F40]


title: Smyd3 ASOs + anti-PD-1, non-R (989)

data_processing:
Basecalling was performed using RTA version 2.4.11, demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v1.18 (parameters: --pair-filter=any nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35)
Trimmed reads were mapped to mm10 sequences using STAR 2.7.0f aligner with the following parameters: "--limitSjdbInsertNsj 2500000 --outSAMtype BAM Unsorted --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10 --sjdbScore 1 --quantMode TranscriptomeSAM"
Read count extraction was performed using RSEM v1.3.0
Assembly: mm10/M21
Supplementary files format and content: tab-delimited text file containing raw counts for all samples

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) following the manufacturer’s instructions with the addition of 1.5 ml volumes of 100% ethanol to the aqueous phase.
TruSeq Stranded mRNA Prep kit

value: Smyd3 ASOs + anti-PD-1

tag: group


title: MlxKO 20 month, omental adipose tissue [Fat-X18F39]


title: SHP-77-JIB-04_1

city: Dallas

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

description:
Gene_FPKM_uqnorm.txt
SHP-77-JIB-04_1

data_processing:
Illumina sequencer from UTSW Sequencing Core (single-end) or Novogene (paired-end)
fastq files were aligned to GRCh38 (human) reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2. Mouse reads were filtered out from CLX samples
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Assembly: GRCh38
Supplementary files format and content: Gene_FPKM_uqnorm.txt

growth_protocol: See publication

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Library preparation was done with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina or according to Novogene specifications (https://en.novogene.com)

treatment_protocol: See publication

value: SCLC

tag: xenograft

value: no

value: 24 hours


title: PBMC, Cycle1, patient 202 TCR

description: 10x Genomics

value: patient 202


title: Control ASOs, rep3


title: PBMC, Cycle7, patient 104 TCR

description: 10x Genomics

value: patient 104


title: PBMC, Cycle17, patient 104 TCR

description: 10x Genomics


title: MlxKO 20 month, Liver [Liver-X18L16]

value: B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J x Mlx Flox/Flox


title: SHP-77-DMSO_1

description:
Gene_FPKM_uqnorm.txt
SHP-77-DMSO_1

value: DMSO


title: PBMC, Cycle1, patient 104 TCR

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: Control ASOs, rep2

value: oral tongue squamous epithelial carcinoma


title: MlxKO 20 month, omental adipose tissue [Fat-X18F37]

value: omental adipose tissue


title: H82-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
H82-JIB-04_2


title: Control ASOs + anti-PD-1, rep3 (850)

value: Control ASOs + anti-PD-1


title: MlxKO 5 month, omental adipose tissue [Fat-X5F5001]

value: 5 month


title: SHP-77-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
SHP-77-JIB-04_2


title: Control ASOs + anti-PD-1, rep2 (880)


title: PBMC, Cycle7, patient 105 TCR

description: 10x Genomics

value: patient 105


title: Smyd3 ASOs + anti-PD-1, non-R (847)