title: Cx3cr1cre_M38, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected
Supplementary files format and content: surface_protein.csv: comma-delimited text file including barcodes associated with each hashtag ID
Supplementary files format and content: Hashtag-condition.csv: comma-delimited text file including condition/treatment information for each hashtag

value: tumor or spleen


title: IMR90NUT_3

status: Public on Nov 07 2024

type: SRA

city: Philadelphia

first: Ruofan

last: Yu

state: PA

address: 3400 civic center blvd

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
STAR2.7.1a: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
htseq-counts
Assembly: hg19
Supplementary files format and content: tab limited RNA-seq raw count

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Hela and passage 25-35 IMR90 cells grown in DMEM high glucose with 10% FBS. LCLs in RPMI with 20% FBS

extract_protocol:
Trizol
NEB ultra2 directional RNA library prep kit

treatment_protocol: as described in sample information

tag: cell line

tag: cell type

value: fetal lung fibroblast

tag: genotype

value: wt

tag: treatment

value: siNeg+6hr nutlin-3a


title: Larvae_Sec_OS1

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

department: Biology

institute: Wesleyan University

data_processing:
FASTQC on each of the 72 raw fastq files
Bowtie2 alignment using the D. simulans or D. sechellia reference genome available at the time of analysis.
Cufflinks for quantification and normalization was followed tiht custom R scripts to perform statiistical analyses.
Hybrids had allele specific expression measured by aligning hybrid sample reads to one secies genome then taking the unaligned reads and aligning to the other species genome in both directions to determine which reads were allele specific for each speices in the F1 hybrids. This results in two data columns in the processed data with the species of allele indicated in the header name as _Sim or _Sec for hybrid sample quantification.
Assembly: Drosophila_simulans_ASM75419v3.39.gff3 and Drosophila_simulans_ASM75419v3.dna.toplevel.fa or Drosophila_sechellia.dsec_caf1.38.gff3 and Drosophila_sechellia.dsec_caf1.dna.toplevel.fa
Supplementary files format and content: Processed data are all in one lager table that is a tab delimited text ffile

organism: Drosophila sechellia

source_name: Larvae

growth_protocol: Fruit  flies were reared on standard food or food supplemented with octanoic acid and mainteind in a 16:8 light:dark cycle at 20 ̊C

extract_protocol:
RNA was extracted from a single tissue homogenate of either 10 whole adult females or 10 whole female L3 larvae using the Promega SV total RNA extraction system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fruit flies were fed standard media or octanoic acid media and these treatments were conducted on both species and hybrids in both larval and adult flies in all different combinations of standard or octanoic acid food provided in the previous generation and the current generation.

tag: developmental stage

value: Larvae

tag: previous media

value: Octanoic Acid Media

tag: current media

value: Standard Media

tag: biological replicate

tag: tissue


title: IMR90NUT_2


title: 1dpa-drp1-2

city: 杭州市

first: li

last: yucong

state: 浙江省

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

country: China

institute: 西湖大学生命科学学院博士研究生

data_processing:
fastaq RNA-seq data adapter trimming by fastap
RNA-seq data quality control
Quantification of feature counts to obtain raw counts by STAR  methods
Assembly: smed_20140614_60aa_genes-noref.gtf
Supplementary files format and content: high_filtered_feature_bc_matrix
Supplementary files format and content: low_filtered_feature_bc_matrix

molecule: total RNA

organism: Schmidtea mediterranea

source_name: whole body

extract_protocol:
RNA was harvested using TRIGene Reagent(Genstar Cat#ZP118-101S). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA SMARTER Library Prep Kit for Illumina following manufacturer's protocols.

value: whole body

value: RNAi

tag: time


title: Larvae_Sec_SS3


title: Cx3cr1cre_M38, mRNA-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: poly A RNA

library_source: transcriptomic single cell

organism: Mus musculus

source_name: tumor or spleen

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.


title: IMR90NUT_1


title: 1dpa-drp1-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Larvae_Sec_SS2


title: IMR90NC_3

value: siNeg


title: scRNAseq + scATACseq, Th0

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

country: Spain

institute: IDIBAPS

library_source: other

data_processing:
Aligment - Bowtie2, Cellranger v6
PeakCalling - MACS2
Downstream - DiffBind, Seurat, Signac, GenomicRanges, Trackviewer…
Assembly: GRCm38.p6
Supplementary files format and content: Peakset; differential peaks called
Supplementary files format and content: feature count matrices

molecule: other

source_name: Spleen

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630), washed, and right after resuspended in transposase reaction mix.
Library fragments were amplified using 1x NEB Next PCR master mix (New England BioLabs) and 1.25 μM of custom Nextera PCR primers forward and reverse. Libraries were rendered using the barcoded primers Ad1_noMX as forward and Ad2.1-6 as reverse and purified using a PCR cleanup kit (Qiagen), yielding a final concentration of about 30 nM in 20 μL. Libraries were then analyzed on Bioanalyzer using an Agilent DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA) to estimate the quantity and size distribution. Next, they were quantified by qPCR using the KAPA Library Quantification Kit before amplification with Illumina’s cBot.
Libraries were loaded at 3.33 pM onto the flowcell and sequenced 1 x 50 on Illumina’s HiSeq 2500

value: Spleen

tag: strain

value: NOD mouse

value: KLH immunization

tag: chip antibody


title: scRNAseq + scATACseq, vaccination-induced TFH

value: Vaccionation-induced TFH


title: Larvae_Sec_SS1


title: scRNAseq + scATACseq, Tet+

value: Tet+

value: pMHCII-NP


title: Adult_Sec_OO3

source_name: Adult

value: Adult


title: Methylome Tconv, replicate 3

library_source: genomic

molecule: genomic DNA

value: Tconv


title: Adult_Sec_OO2


title: H-sod2-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: homo


title: IMR90NC_1

value: fetal lung fibroblast

value: wt


title: Hela_HS_WAPLsi3

source_name: HeLa kyoto

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID

value: WAPL si+HS


title: Adult_Sec_OO1

value: Octanoic Acid Media


title: Methylome Tconv, replicate 2


title: Hela_HS_WAPLsi2


title: OV, CD, replicate 1, scRNAseq

city: Hong Kong

first: Ka Chi

last: Chu

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: HKU

data_processing:
Raw reads were processed with Cell Ranger (v6.0)
Assembly: mm39
Supplementary files format and content: Cell Ranger output (barcodes, features, matrix)

source_name: Otic vesicle

extract_protocol:
E10.5 OVs were pooled and digested in TryplE (Invitrogen) with 0.05% collagenase (Worthington Biochemical) and dispase (Worthington Biochemical) at 37°C for 30 min. 5U/ml DNaseI (Invitrogen) was added to the digestion mix after 15 min digestion. DPBS with 10% FBS was added to quench the digestion. Dissociated cells were spined at 300 g x 5 min, washed with DPBS with 0.04% BSA, and filtered with 40 μm strainer. Filtered cells were spined at 300 g x 5 min, washed with DPBS with 0.04% BSA, re-spined, and resuspended in 50 μl DPBS with 0.04% BSA for downstream processing.
Single cell encapsulation and cDNA libraries were prepared with Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit. Sequencing was carried out with Illumina NovaSeq 6000 for Pair-End 151bp sequencing.

value: Otic vesicle


title: H-sod2-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: whole body

value: RNAi


title: Methylome Tconv, replicate 1

value: Spleen

value: NOD mouse

value: KLH immunization


title: Adult_Sec_OS3

value: Standard Media


title: 1dpa-E-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp


title: Adult_Sec_OS2

value: Adult


title: Adult_Sec_OS1


title: Methylome vaccination-induced TFH, replicate 3

value: Vaccionation-induced TFH


title: Methylome vaccination-induced TFH, replicate 2


title: H-opa1-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: homo


title: Hela_HS_NEG3

value: neg si +HS


title: IMR90NC_2

value: fetal lung fibroblast

value: wt

value: siNeg


title: 1dpa-E-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: 1dpa-E-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Hela_HS_NEG2

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: H-opa1-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: whole body


title: Methylome vaccination-induced TFH, replicate 1


title: Adult_Sec_SO3

value: Octanoic Acid Media


title: Hela_HS_NEG1


title: Adult_Sec_SO2


title: Methylome Tet+, replicate 3

value: Spleen

value: Tet+

value: pMHCII-NP


title: Hela_WAPLsi3

value: WAPL si


title: H-opa1-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: H-drp1-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Adult_Sec_SO1

value: Adult

value: Standard Media


title: Hela_HS_WAPLsi1

value: WAPL si+HS


title: Hela_WAPLsi2


title: H-sod2-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: homo


title: H-drp1-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Methylome Tet+, replicate 2

value: NOD mouse


title: Hela_NEG3

value: neg si


title: Methylome Tet+, replicate 1


title: Adult_Sec_SS3


title: Hela_NEG2


title: GSK101_1

city: Beijing

first: Xiaotong

address: 22# Zhongguancun South Avenue, Haidian District

institute: Peking university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Rattus_norvegicus from Rattus_norvegicus.Rnor_6.0 using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Rnor_6.0
Supplementary files format and content: All_samples_rpkm.txt

organism: Rattus norvegicus

source_name: TMJ disc cell

extract_protocol:
Total RNAs were extracted from disc cells in control group and GSK101 group using TRIzol Reagent (Invitrogen, cat. NO 15596026). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: TMJ disc cell


title: H-E-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp


title: H-drp1-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Adult_Sec_SS2


title: Adult_Sec_SS1


title: mESC, Ldhb KO, RNA-seq

city: New York

first: XIANLE

last: SHI

state: NY

address: 168 street

institute: CUMC

data_processing:
Alignment was done by Bowtie2 (v2.3.4.3).
Sorting was done by name using Samtools (v1.9)
Count was done by Htseq (v0.11.2)
Normalization was done by using edgeR (v3.26.8)
Assembly: mm9
Supplementary files format and content: normalized expression levels for every gene

source_name: mouse embryonic stem cells

growth_protocol: The ESC medium was prepared as follows: 85% Dulbecco’s Modified Eagle Media (DMEM) (Gibco, Waltham, Massachusetts, USA), 15% fetal bovine serum (HyClone, Logan, Utah, USA), 2 mM L-glutamine (Invitrogen, Carlsbad, CA, USA), 100 units/ml penicillin and 100 µg/ml streptomycin (Invitrogen), 0.1 mM nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, United States), and 1000 units/mL LIF. Mouse ESCs were plated on tissue culture dishes which were pre-coated with 0.2% gelatin (Sigma-Aldrich) for at least 20 min and grown in humidified 5% CO2 at 37°C incubator. The medium was changed every day and ESCs were passaged every 2-3 days.

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Library construction and sequencing were performed by BGI Tech (Shenzhen, China)

treatment_protocol: Under normal culture

value: mouse embryonic stem cells

value: mESC

value: Ldhb knockout

value: Ldhb KO


title: mESC, Ldha KO, RNA-seq

value: Ldha knockout

value: Ldha KO


title: Hela_NEG1

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: H-E-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: whole body

value: RNAi


title: H-E-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Pcgf5_siRNA_H3K27me3_rep1

city: Kyoto

first: Satoshi

last: Mashiko

address: Sakyoku oiwakecho

institute: Kyoto university

description: The file mapped to the B6 genome was named genome1 and PWK genome was named genome4

data_processing:
Sequencing reads were aligned to the N-masked B6 mouse genome (mm10) using single nucleotide polymorphisms with PWK mice (https://www.ebi.ac.uk/pub/databases/eva/PRJEB43298/mgp_REL2005_snps_indels.vcf.gz) using bowtie2 (ver. 2.4.5) with “-t-q -N 1 -L 25 --no-mixed --no-discordant” options.The reads of the generated BAM files were sorted to B6 or PWK mice using UniversalSNPsplit (https://github.com/lanjiangboston/). BAM files comprising reads specific to each strain were converted to bigwig files using counts per million (CPM) normalization by bamCoverage in deepTools.ChIP sample peaks were obtained by MACS2 (ver. 2.2.7.1) by comparison to baseline. Landscapes of gene-specific ChIP peaks were visualized by loading BW files into Integrative Genomics Viewer (IGV) (ver. 2.12.1).
Assembly: mm10 and PWK mice ((https://www.ebi.ac.uk/pub/databases/eva/PRJEB43298/mgp_REL2005_snps_indels.vcf.gz) )
Supplementary files format and content: bw files

source_name: Embryo

growth_protocol: mouse morula stage embryos were in vitro produced by in vitro fertilization (IVF) using B6 oocytes and PWK sperm and further cultured in KSOM up to 72 hpi.

extract_protocol:
Morula-stage embryos at 72 h post IVF were collected as approximately 40 embryos per biological replicate for ChIP. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The morulae were freed from the zona pellucida by using pronaseK before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was processed for ChIP using anti-H3K27me3 antibody (61017, Active Motif). The ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer.
Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.

treatment_protocol: The culture was chemically semi-defined (bovine serum albumin was added). The one-cell stage embryos at 3 hpi were electropolated with siControl or siPcgf5 and further cultured up to morula stage (72 hpi).

value: Embryo

value: morula stage embryo

value: in vitro produced, siPcgf5 treated from the one-cell stage


title: mESC, WT, RNA-seq

value: Wild type

value: WT


title: CTCF_HS_aux2

value: IAA+HS


title: opa1;drp1_2dpa_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

source_name: tails

value: tails


title: CTCF_HS_aux1


title: Pcgf5_siRNA_H3K27me3_rep2

description: The file mapped to the B6 genome was named genome1 and PWK genome was named genome5


title: MC38_mche-_3

description: RFP(-) TAMs in MC38

data_processing:
Sequencing was performed on NovaSeq X platform in a 101-base single-end mode.
Illumina RTA4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: tumor (MC38)

extract_protocol:
Total RNA was extracted using TRI Reagent.
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

value: tumor (MC38)


title: opa1;drp1_2dpa_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Mouse embryonic stem cell, H3K27ac (wildtype on Hdac1), ChIP-seq

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality.
Alignment was done by using Bowtie2
Reads that mapped to multiple locations in the genome were discarded
Annotation was done by using the script annotatePeaks.pl of HOMER.
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
Chromatin fragmentation by Mnase and immunoprecipitation were carried out following the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocols.
Purified ChIP DNA was used for library construction following the Illumina ChIP–seq library generation protocol (NEB)

value: mouse embryonic stem cells

value: mESC

value: wildtype on Hdac1

value: H3K27ac (Cell Signaling Technology, 8173S,1:100)

value: normal culture


title: Mouse embryonic stem cell, H3K27ac  (lysine to arginine substitutionon Hdac1), ChIP-seq

value: lysine to arginine substitutionon Hdac1

value: H3K27ac (Cell Signaling Technology, 8173S,1:102)


title: CTCF_HS_dmso2

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID

value: DMSO+HS


title: opa1;drp1_2dpa_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: opa1;egfp_2dpa_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: MC38_mche-_2

description: RFP(-) TAMs in MC38


title: CTCF_HS_dmso3


title: MC38_mche-_1

description: RFP(-) TAMs in MC38


title: siRNA_Control_H3K27me3_rep2

description: The file mapped to the B6 genome was named genome1 and PWK genome was named genome3

value: Embryo

value: morula stage embryo

value: in vitro produced, siControl treated from the one-cell stage


title: siRNA_Control_H3K27me3_rep1

description: The file mapped to the B6 genome was named genome1 and PWK genome was named genome2


title: CTCF_HS_dmso1


title: EpiSCs, Ad libitum, rep2

city: Hangzhou

first: Bing

last: Zhang

state: Zhejiang

address: No. 600 Dunyu Road, Sundun Town, Xihu District

department: School of Life Sciences

institute: Westlake University

data_processing:
Adaptor triming: fastp_0.23.1
Mapping and quantification: Salmon_1.4.0
Differential Expression Analysis: DESeq2_1.36.0
Assembly: mm10
Supplementary files format and content: .xlsx

source_name: skin

extract_protocol:
RNA were purified using RNeasy Plus Micro Kit (Qiagen 74034).
RNA-seq libraries were generated using Single Cell Full Length mRNA-Amplification Kit (Vazyme N712) and TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD503).

value: skin

value: epidermal stem cells (EpiSCs)

value: WT

value: Ad libitum


title: CTCF_HS_aux3

value: IAA+HS


title: EpiSCs, Ad libitum, rep1


title: opa1;egfp_2dpa_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: tails


title: CTCF_aux3

value: IAA


title: Mouse embryonic stem cell, H3K27ac (lysine to glutamine substitutionon Hdac1), ChIP-seq

value: mouse embryonic stem cells

value: mESC

value: H3K27ac (Cell Signaling Technology, 8173S,1:101)

value: normal culture


title: HFSCs, Fasting for 48hrs, rep3

value: hair follicle stem cells (HFSCs)

value: Fasting for 48 hours


title: mESC, SO treatment, RNA-seq

description: SO

value: Wild type

value: SO treatment


title: opa1;egfp_2dpa_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: egfp;egfp_2dpa_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp;egfp


title: MC38_mche+_2

description: RFP(+) TAMs in MC38

value: tumor (MC38)


title: CTCF_aux2

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: egfp;egfp_2dpa_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: CTCF_aux1


title: MC38_mche+_1

description: RFP(+) TAMs in MC38


title: HFSCs, Fasting for 48hrs, rep1

value: skin

value: WT


title: CTCF_dmso3

value: DMSO


title: B16_mche_neg_3

description: RFP(-) TAMs in B16F10

source_name: tumor (B16F10)

value: tumor (B16F10)


title: CTCF_dmso2


title: B16_mche_neg_11

description: RFP(-) TAMs in B16F10


title: HFSCs, Fasting for 24hrs, rep2

value: Fasting for 24 hours


title: HFSCs, Fasting for 24hrs, rep3


title: HFSCs, Fasting for 24hrs, rep1


title: opa1;drp1_1dpa_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: tails


title: opa1;drp1_1dpa_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: opa1;egfp_1dpa_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: RAD21_aux2

value: IAA


title: MC38_mche+_3

description: RFP(+) TAMs in MC38


title: B16_mche_neg_12

description: RFP(-) TAMs in B16F10


title: CTCF_dmso1


title: HFSCs, Ad libitum, rep2

value: hair follicle stem cells (HFSCs)

value: Ad libitum


title: HFSCs, Fasting for 48hrs, rep2

value: Fasting for 48 hours


title: RAD21_aux3


title: B16_mche_pos_11

description: RFP(+) TAMs in B16F10


title: opa1;egfp_1dpa_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: B16_mche_pos_12

description: RFP(+) TAMs in B16F10


title: HFSCs, Ad libitum, rep3


title: HFSCs, Ad libitum, rep1


title: RAD21_dmso3


title: RAD21_aux1


title: egfp;egfp_2dpa_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: opa1;egfp_1dpa_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: V4E16-E3M2R

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

data_processing:
Illumina bcl2fastq2 v2.17.1.14 for basecalling
The RNAseq reads were processed and aligned to reference genome using nf-core/rnaseq v3.11.2 of the nf-core collection of workflows (Ewels et al., 2020). The RNAseq reads were evaluated and adapter sequences were filtered out using FastQC [v. 0.11.9 ] and Cutadapt [v. 3.4 ], and ribosomal RNA was removed using Sortmerna [v. 4.3.4 ].
The reads were aligned to reference genome using Salmon [v. 1.10.1].
Assembly: de novo genome of Myodes glareolus (GenBank PRJNA1050237)
Supplementary files format and content: Tab-delimited gene expression count values of each samples

organism: Myodes glareolus

source_name: Molar 2

growth_protocol: Tooth and jaw germs were dissected carefully under microscope from E13.5, E14.5, E15.5 or E16.5 bank vole.

extract_protocol:
The tooth germ was homogenised into TRI Reagent (Merck, Darmstadt, Germany) using Precellys 24 -homogenizer (Bertin Instruments, Montigny-le-Bretonneux, France). The RNA was extracted by guanidium thiocyanate-phenol-chloroform method and then further purified by RNeasy Plus micro kit (Qiagen GmbH, Hilden, Germany) according to manufacturer's instructions.
The cDNA libraries were prepared with Ovation Mouse Universal RNAseq System (Tecan, Zürich, Schwitzerland).

value: Molar 2

tag: age

value: Vole embryonic cells


title: Pancreatic Islets 7dpi SH

first: Paul

last: Zumbo

address: 1300 York Ave

department: Applied Bioinformatics Core

institute: Weill Cornell Medicine

data_processing:
Demultiplexing, alignment, filtering, and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. The 10X provided refernce was used for alingment and annotation (mm10-2020-A).
Sample integration (batch correction), expression value normalization, clustering, cell type annotation and so on were done scater and scran. For more details and the cell type annotation information, see https://github.com/abcwcm/CZI_MI_mouseZebrafish
Assembly: mm10
Supplementary files format and content: CellRanger produced filtered feature-barcode matrix in H5 format.

source_name: Pancreatic Islets

extract_protocol:
Whole blood was collected by cardiac puncture. Red blood cells where lysed with ACK buffer and removed by density centrifugation in a 7.5% BSA cushion (300g for 5min).  Cells were strained with a 40um sieve.     For kidney cells isolation, animals were perfused with PBS-5mM EDTA through the left ventricle, then kidneys where collected and  minced into pieces with a razor blade. Tissue fragments were digested in HBBS – 0.15mg/ml Liberase TM for 25min at 37deg C with vigorous agitation. Digestion was stopped with FBS. The digestion mix was passed through a 70um sieve and spun down for 5min at 300g. The pellet was spun down on a 7.5% BSA cushion, for 4min at 250g, twice, to clear debris.     For heart, non-myocyte cells, hearts were perfused by the Langendorff method and digested with 0.15mg/ml Liberase TM. The LV of sham-operated animals or the infarcted area of the LV of infarcted hearts was cut and triturated with a plastic Pasteur pipette. Digestion was stopped with FBS. Myocytes were separated by centrifugation at 50g for 5 mins. The supernatant with the rest of the cells was pelleted at 300g for 5 mins. Cells where then passed through a 70um strainer.    For liver cells, livers were perfused and then digested in Liver Digest Medium. Livers were dissected and hepatocytes were separated by centrifugation at 30g for 4minutes. The rest of the cells (supernatant) were pelleted by centrifugating 5min at 300g. Non-hepatocyte liver cells were passed through a 70um sieve. Hepatocytes and the rest of the liver cells were combined 1:1.    Pancreatic islets were isolated by perfusion of the pancreases with CiZyme through the common hepatic duct. Pancreases were removed and digested at 37 °C for 17 min. After two washes with RPMI medium with 3% FBS, islets were separated into a gradient using RPMI medium and Histopaque (Sigma-Aldrich). Islets were then hand-picked and rendered single by digesting for 10min at 37deg C in Accutase.
Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3, and Chromium Single Cell B Chip Kit.

treatment_protocol: LAD ligation or sham surgery

value: Pancreatic Islets

value: wild type

value: Sham


title: opa1;drp1_1dpa_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: RAD21_dmso2

value: HeLa kyoto

value: cervical cancer cells


title: Larvae_Sec_OO3

value: Larvae

value: Octanoic Acid Media


title: V4E16-E2M2R

value: WT


title: egfp;egfp_1dpa_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp;egfp


title: B16_mche_pos_3

description: RFP(+) TAMs in B16F10

value: tumor (B16F10)


title: egfp;egfp_1dpa_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: tails


title: RAD21_dmso1

value: DMSO


title: egfp;egfp_1dpa_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: V4E16-E1M2R


title: Blood 30dpi SH

source_name: Blood

value: Blood

value: Whole tissue


title: neg2-igg

description:
CUT&RUN with IGG/SON antibody
negIMR90.bw.srt.bw

data_processing:
Bowtie2:--local --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 1000- x hg19
filtered with samtools view -q 5 and deduplicated with Picard
Bigwig and BedGraph files were generated with deepTools: bamCompare -b1 $SON -b2 $IGG -bs 5000 --smoothLength 15000 --effectiveGenomeSize 2864785220 --exactScaling --normalizeUsing RPKM --scaleFactorsMethod None -bl blacklistPEAK.merge.bed
Assembly: hg19
Supplementary files format and content: SON/IGG normalized bigwig file
Library strategy: CUT&RUN

extract_protocol:
For each condition, nuclei from ~600k cells was isolated using nuclear isolation buffer [10mM HEPES-KOH (pH 7.9), 10mM KCl, 0.1% NP40, 0.5mM spermidine, 1x Halt protease inhibitor cocktail] and bound to concanavalin A lectin beads which had been washed in binding buffer [BioMag Plus; binding buffer: 20mM HEPES-KOH (pH 7.9), 10mM KCl, 1mM CaCl2, 1mMnCl2], as described. After bead binding, samples were split into two tubes, one for each antibody, where binding buffer was replaced with 1:100 antibody diluted in blocking buffer [20mM HEPES-KOH (pH 7.5), 150mM NaCl, 0.1% BSA, 0.5mM spermidine, 1x Halt protease inhibitor cocktail, 2mM EDTA](IgG antibody: Millipore 06-371); SON antibody: abcam ab121759) and incubated overnight at 4°C. Samples were washed in washing buffer [20mM HEPES-KOH (pH 7.5), 150mM NaCl, 0.1% BSA, 0.5mM spermidine, 1x Halt protease inhibitor cocktail], and treated with pA-MNase and CaCl2 for 30 minutes on an ice cold pre-chilled metal block on ice. The reaction was stopped by addition of STOP buffer [200mM NaCl, 20mM EDTA, 4mM EGTA, 50µg/mL RNase A, 40µg/mL glycogen] while gently vortexing, and DNA fragments were released by incubation at 37°C for 10 minutes. The DNA fragments were collected from bead supernatants, treated with Proteinase K for 10 minutes at 70°C, then subject to PCI-choroform purification.
NEBNext Ultra II DNA Library Prep Kit

value: fetal lung fibroblast

value: wt

value: siNeg


title: opa1;drp1_6h_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: V10E16-E2M2L

value: Molar 2

value: Vole embryonic cells


title: neg2-son


title: V10E16-E3M2L


title: neg1-son


title: V10E16-E4M2R


title: V10E16-E1M2L


title: Blood 30dpi MI

value: wild type

value: LAD ligation


title: ct2-son

description:
CUT&RUN with IGG/SON antibody
CTIMR90.bw.srt.bw

value: siCTCF


title: opa1;egfp_6h_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: opa1;drp1_6h_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: V4E16-E3M1R

source_name: Molar 1

value: Molar 1


title: opa1;egfp_6h_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Liver 7dpi MI

source_name: Liver

value: Liver


title: Liver 7dpi SH

value: Sham


title: Pancreatic Islets 30dpi MI

value: Pancreatic Islets


title: ct1-son


title: Pancreatic Islets 30dpi SH


title: Kidney 7dpi MI

source_name: Kidney

value: Kidney


title: ct2-igg


title: Pancreatic Islets 7dpi MI


title: opa1;egfp_6h_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: tails


title: V4E16-E2M1R

value: WT


title: V4E16-E1M1R


title: opa1;drp1_6h_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: ct1-igg


title: Heart 7dpi SH

source_name: Heart

value: Heart

value: Left ventricle, non-myocytes


title: egfp;egfp_6h_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp;egfp


title: Kidney 7dpi SH

value: Whole tissue


title: 561S2-SON

description:
CUT&RUN with IGG/SON antibody
561.bw

value: patient derived Lymphoblastoid cell lines

value: Blood cells


title: neg1-igg

value: fetal lung fibroblast

value: wt

value: siNeg


title: egfp;egfp_6h_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: opa1;drp1_0h_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: V10E16-E3M1L

value: Molar 1

value: Vole embryonic cells


title: 561S1-SON

description:
CUT&RUN with IGG/SON antibody
561.bw


title: V10E16-E2M1L


title: Heart 7dpi MI

value: wild type

value: LAD ligation


title: 561S1-IGG

description:
CUT&RUN with IGG/SON antibody
561.bw


title: egfp;egfp_6h_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: V9E15-E5M1L


title: Blood 7dpi SH

value: Blood

value: Sham


title: V9E15-E3M1L

value: WT


title: 561S2-IGG

description:
CUT&RUN with IGG/SON antibody
561.bw


title: V10E16-E1M1L


title: opa1;drp1_0h_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: tails


title: Liver 30dpi SH

value: Liver


title: Liver 30dpi MI


title: V9E15-E1M1L


title: S2S1-IGG

description:
CUT&RUN with IGG/SON antibody
S2.bw

value: Healthy control 2


title: Kidney 30dpi SH

value: Kidney

value: Whole tissue


title: opa1;egfp_0h_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: S2S2-IGG

description:
CUT&RUN with IGG/SON antibody
S2.bw

value: patient derived Lymphoblastoid cell lines

value: Blood cells


title: S2S2-SON

description:
CUT&RUN with IGG/SON antibody
S2.bw


title: V9E15-E2M1R


title: V17E15-E1M1R


title: S2S1-SON

description:
CUT&RUN with IGG/SON antibody
S2.bw


title: Heart 30dpi MI

value: Heart

value: Left ventricle, non-myocytes


title: V16E15-E2M1R


title: Kidney 30dpi MI


title: opa1;egfp_0h_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: RNAi


title: opa1;drp1_0h_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: egfp;egfp_0h_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp;egfp


title: S1S2-IGG

description:
CUT&RUN with IGG/SON antibody
S1.bw

value: Healthy control 1


title: VXE14-E2M1R

value: Molar 1

value: Vole embryonic cells


title: Liver 1dpi MI

value: wild type

value: LAD ligation


title: S1S2-SON

description:
CUT&RUN with IGG/SON antibody
S1.bw


title: Blood 7dpi MI

value: Blood


title: V16E15-E1M1L

value: WT


title: HelaWAPL2-SON

description:
CUT&RUN with IGG/SON antibody
CTCFHelaWAPL.bw.srt.bw

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID

value: siWAPL

tag: time point


title: egfp;egfp_0h_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: tails


title: opa1;egfp_0h_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Pancreatic Islets 1dpi SH

value: Pancreatic Islets

value: Sham


title: Liver 1dpi SH

value: Liver

value: Whole tissue


title: S1S1-SON

description:
CUT&RUN with IGG/SON antibody
S1.bw

value: patient derived Lymphoblastoid cell lines

value: Blood cells


title: V7E14-E1M1L

value: Molar 1


title: TL2067 ,Hypoxia, Control

city: Oxford

first: Lee

last: Page

state: Oxfordshire

address: Centre for Clinical Vaccinology and Tropical Medicine (CCVTM), Churchill Hospital, Old Road, Headington, Oxford

department: Department of Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
Quantification of the libraries was performed using a Qubit 2.0 fluorometer (Life Technologies). Sequencing was executed on the NovaSeq 6000 Illumina® platform, generating 150-base pair (bp) paired-end reads at a sequencing depth of 40 million reads per sample.
To ensure high-quality data reads containing adapter sequences, poly-N stretches, and low-quality reads were removed, resulting in clean reads. The Spliced Transcripts Alignment to a Reference (STAR) software (version 2.5) was utilized for mapping the reads to the human genome (GRCh38), with reads quantified using HTSeq (Anders et al., 2015).
Assembly: GRCh38
Supplementary files format and content: tab-limited text file containing raw counts for each sample

source_name: Lung Tissue Explants

growth_protocol: Resected lung tissue was obtained from patients undergoing surgical lobectomy at University Hospital Southampton. Parenchymal tissue from donors was dissected into small cubes (1–3 mm3). Lung explants were cultured in RPMI media containing antibiotics (Sigma-Aldrich, Paisley, UK) for 24 h.

extract_protocol:
Total RNA was extracted from samples using Qiazol reagent (Qiagen), with the RNA isolated according to the manufacturer’s instructions. The cDNA was produced using reverse transcription which was carried out according to the manufacturer’s instructions using a High-Capacity cDNA Reverse Transcription Kit (Life Technologies) with random hexamers
Libraries were generated using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA), and their quality was evaluated on the Agilent Bioanalyzer 2100 system.

treatment_protocol: On the day of infection, media was replaced with antibiotic-free RPMI, and explants were either left uninfected or infected with 5x106 CFU of NTHi for 24 h under normoxic (21% O2) or hypoxic (1% O2, 5% CO2, BAL N2) conditions in a hypoxic chamber (MIC-101, Stem Cell Technologies) at 37°C

value: Lung Tissue Explants

value: Uninfected in hypoxia


title: V10E16-E4M1R

value: Vole embryonic cells


title: egfp;egfp_0h_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp;egfp

value: RNAi


title: Heart 30dpi SH

value: Heart

value: Left ventricle, non-myocytes

value: wild type


title: HelaWAPL1-SON

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID

value: siWAPL


title: V6E14-E2M1L

value: WT


title: S1S1-IGG

description:
CUT&RUN with IGG/SON antibody
S1.bw

value: Healthy control 1


title: VXE14-E1M1L


title: Heart 1dpi SH

value: Sham


title: HelaWAPL1-IGG


title: V6E14-E1M1L


title: TL2067 ,Normoxia, Infected

value: Infected in normoxia


title: TL2067 ,Hypoxia, Infected

value: Infected in hypoxia


title: Pancreatic Islets 1dpi MI

value: Pancreatic Islets

value: LAD ligation


title: HelaWAPL2-IGG


title: V18E14-E3M1R

value: Molar 1

value: Vole embryonic cells


title: HelaIAARAD212-SON

description:
CUT&RUN with IGG/SON antibody
RAD21HelaIAA.bw.srt.bw

value: IAA


title: TL2067 ,Normoxia, Control

value: Lung Tissue Explants

value: Uninfected in normoxia


title: TL2058 ,Hypoxia, Infected


title: HelaIAARAD211-SON


title: HelaIAARAD212-IGG


title: Heart 1dpi, MI

value: Heart

value: Left ventricle, non-myocytes

value: wild type


title: TL2058 ,Normoxia, Infected


title: Blood 1dpi MI

value: Blood

value: Whole tissue


title: V18E14-E1M1R

value: WT


title: Blood 1dpi SH


title: TL2058 ,Hypoxia, Control

value: Uninfected in hypoxia


title: V23E14-E3JR

source_name: Jaw

value: Jaw


title: HelaDMSORAD212-SON

description:
CUT&RUN with IGG/SON antibody
RAD21HelaDMSO.bw.srt.bw

value: HeLa kyoto

value: cervical cancer cells

value: DMSO


title: WT_REF (rep3)

type: RNA

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Log-phase rep3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Precultures of propolis stress-resistant Saccharomyces cerevisiae (FD11) mutant strain and reference strain were prepared in yeast minimal medium (2% glucose and 0.67% yeast nitrogen base without amino acid (Difco)) by incubating at 30°C and 150 rpm for about ~ 16 hour. Precultures were inoculated into fresh yeast minimal medium to an initial OD600 of 0.1. Then, cultures were incubated at 30°C and 150 rpm. When cultures OD600 value reaches about 1.0 (corresponding to the mid-exponential phase). Cells were harvested and total RNA extraction was done.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: There is no treatment protocol in this study.

value: CEN.PK 113-7D Reference Strain


title: HelaDMSORAD212-IGG


title: V23E14-E4JL


title: HelaIAARAD211-IGG


title: TL2054 ,Hypoxia, Infected

value: Infected in hypoxia


title: V23E14-E2JR

value: Vole embryonic cells


title: TL2054 ,Normoxia, Control


title: WT_REF (rep4)


title: TL2054 ,Hypoxia, Control


title: V23E14-E1JR


title: V23E14-E3JL


title: FD11-Log phase-Rep4

source_name: Propolis stress-resistant Saccharomyces cerevisiae, log phase, rep4


title: WT_REF (rep1)

source_name: Log-phase rep1


title: V23E14-E4JR


title: HelaDMSORAD211-SON


title: TL2058 ,Normoxia, Control


title: TL2054 ,Normoxia, Infected

value: Infected in normoxia


title: FD11-Log phase-Rep3

source_name: Propolis stress-resistant Saccharomyces cerevisiae, log phase, rep3


title: HelaDMSORAD211-IGG


title: TL2052, Hypoxia, Control

value: Lung Tissue Explants


title: V8E13-E3M1L

value: Molar 1


title: CTCFHelaDMSO2-IGG

description:
CUT&RUN with IGG/SON antibody
CtcfHELADMSO.bw.srt.bw

value: CTCF-AID


title: TL2052 ,Normoxia, Infected


title: FD11-Log phase-Rep2

source_name: Propolis stress-resistant Saccharomyces cerevisiae, log phase, rep2


title: V8E13-E2M1L


title: WT_REF (rep2)

source_name: Log-phase rep2


title: LLC CMTM4 KO 3

first: Won-Min

last: Song

state: New York

address: One Gustave L. Levy Place, Box 1123

institute: Icahn school of medicine at Mount Sinai

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to the reference genome (mm10) using the Spliced Transcripts Alignment to a Reference (STAR) software.
Salmon was used to count the read numbers mapped of each gene.
Assembly: mm10
Supplementary files format and content: A comma-separated values (CSV) file contains raw counts for all samples

source_name: Lewis lung carcinoma

growth_protocol: Both control and CMTM4 KD cells were cultured in RPMI media with 10% FBS.

extract_protocol:
RNA was isolated using Trizol per the manufacturer’s specifications.
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® Ultra TM 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, adaptor[1]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: Lewis lung carcinoma

value: Mouse lung cancer cell

value: CMTM4 KO


title: CTCFHelaDMSO1-SON


title: V8E13-E1M1L


title: LLC CMTM4 KO 2


title: CTCFHelaDMSO2-SON


title: CTCFHelaDMSO1-IGG


title: FD11-Log phase-Rep1

source_name: Propolis stress-resistant Saccharomyces cerevisiae, log phase, rep1


title: CTCFHelaAUX2-SON

description:
CUT&RUN with IGG/SON antibody
CTCFHELAIAA.bw.srt.bw

value: IAA


title: V23E14-E1JL

value: WT


title: V5E13-E1M1R


title: V15E13-E2M1R


title: TL1667, Hypoxia, Control

value: Uninfected in hypoxia


title: TL2052 ,Hypoxia, Infected


title: LLC CMTM4 KO 1


title: TL2052 ,Normoxia, Control

value: Uninfected in normoxia


title: TL1667, Normoxia, Infected


title: LLC Control 2

value: wild type


title: CTCFHelaAUX2-IGG

value: HeLa kyoto

value: cervical cancer cells


title: CTCFHelaAUX1-SON


title: TL1667, Normoxia, Control


title: V5E13-E3M1L


title: LLC Control 1


title: V15E13-E1M1R


title: CTCFHelaAUX1-IGG


title: effector NCOR1-cKO Treg 3

status: Public on Nov 06 2024

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/DanieleBarreca/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.0.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: spleen and lymph nodes

extract_protocol:
Between 5 x 10e4 and 5 x 10e5 cells were sorted per sample and total RNA was prepared from cell lysates using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to manufacturer’s protocol.
Full-length cDNA was prepared with the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006). The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina). The libraries were sequenced on a Illumina HiSeq 3000 instrument with 50-bp single-read configuration.

value: CD4+ FOXP3+ regulatory T cell

value: NCOR1fl/fl DEREG-GFP+ CD4-Cre+


title: effector NCOR1-cKO Treg 2


title: effector NCOR1-cKO Treg 1


title: TL1667, Hypoxia, Infected

value: Infected in hypoxia


title: naive NCOR1-cKO Treg 1


title: effector WT Treg 1

value: NCOR1fl/fl DEREG-GFP+ CD4-Cre-


title: effector WT Treg 2


title: effector WT Treg 3


title: naive NCOR1-cKO Treg 2


title: LLC Control 3


title: naive WT Treg 3


title: naive WT Treg 2


title: Total nuclei sample for Individual 236 [205854150008_R07C01]

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

hyb_protocol: nuclei samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: nuclei samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package bigmelon idat function. Data was then pre-processed using dasen function.

label: Cy5 and Cy3

source_name: Total

label_protocol: 500 ng DNA from each nuclei sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gold Kit (Cambridge Bioscience, UK) according to the manufacturer's standard protocol.

extract_protocol: Genomic DNA was extracted from frozen nuclei aliquots using a modified proteinase K-based extraction method.

value: Total

tag: antibody combination

value: unstained

tag: individual id

tag: Sex

value: F

tag: basename


title: Total nuclei sample for Individual 237 [205854150041_R01C01]

tag: cell type

value: M


title: NeuNPos nuclei sample for Individual 237 [205854150041_R02C01]

source_name: NeuNPos

value: NeuNPos

value: NeuN+


title: DoubleNeg nuclei sample for Individual 237 [205854150041_R03C01]

source_name: DoubleNeg

value: DoubleNeg


title: Sox10Pos nuclei sample for Individual 236 [205854150008_R05C01]


title: Sox10Pos nuclei sample for Individual 237 [205854150041_R04C01]


title: DoubleNeg nuclei sample for Individual 236 [205854150008_R06C01]


title: naive WT Treg 1

tag: genotype


title: Sox10Pos nuclei sample for Individual 236 [205854150008_R03C01]


title: DoubleNeg nuclei sample for Individual 236 [205854150008_R01C01]


title: NeuNPos nuclei sample for Individual 236 [205854150008_R08C01]


title: Total nuclei sample for Individual 236 [205854150008_R02C01]


title: NeuNPos nuclei sample for Individual 236 [205854150008_R04C01]


title: Total nuclei sample for Individual 233 [205854150007_R01C01]


title: naive NCOR1-cKO Treg 3


title: Sox10Pos nuclei sample for Individual 235 [205854150007_R06C01]


title: Total nuclei sample for Individual 235 [205854150007_R05C01]


title: Sox10Pos nuclei sample for Individual 233 [205854150007_R04C01]


title: DoubleNeg nuclei sample for Individual 234 [205862300133_R01C01]


title: DoubleNeg nuclei sample for Individual 235 [205854150007_R08C01]


title: Total nuclei sample for Individual 234 [205862300133_R03C01]


title: NeuNPos nuclei sample for Individual 234 [205862300133_R02C01]


title: Total nuclei sample for Individual 234 [205862300138_R06C01]


title: NeuNPos nuclei sample for Individual 234 [205862300138_R07C01]


title: Sox10Pos nuclei sample for Individual 234 [205862300138_R08C01]


title: NeuNPos nuclei sample for Individual 233 [205862300133_R05C01]


title: Sox10Pos nuclei sample for Individual 233 [205862300133_R07C01]


title: Total nuclei sample for Individual 232 [205862300118_R01C01]


title: DoubleNeg nuclei sample for Individual 233 [205862300133_R06C01]


title: Total nuclei sample for Individual 233 [205862300133_R08C01]


title: DoubleNeg nuclei sample for Individual 231 [205862300110_R02C01]


title: Sox10Pos nuclei sample for Individual 232 [205862300118_R04C01]


title: NeuNPos nuclei sample for Individual 231 [205862300118_R07C01]


title: DoubleNeg nuclei sample for Individual 231 [205862300118_R05C01]


title: Total nuclei sample for Individual 231 [205862300110_R03C01]


title: Sox10Pos nuclei sample for Individual 231 [205862300110_R01C01]


title: NeuNPos nuclei sample for Individual 232 [205862300118_R03C01]


title: NeuNPos nuclei sample for Individual 231 [205862300110_R04C01]


title: Total nuclei sample for Individual 231 [205862300118_R06C01]


title: Total nuclei sample for Individual 232 [205862300110_R05C01]


title: DoubleNeg nuclei sample for Individual 232 [205862300110_R08C01]


title: NeuNPos nuclei sample for Individual 232 [205862300110_R06C01]


title: DoubleNeg nuclei sample for Individual 234 [205862300138_R05C01]


title: Total nuclei sample for Individual 230 [205862300109_R01C01]


title: Sox10Pos nuclei sample for Individual 234 [205862300133_R04C01]


title: DoubleNeg nuclei sample for Individual 230 [205862300109_R03C01]


title: NeuNPos nuclei sample for Individual 235 [205854150007_R07C01]


title: Sox10Pos nuclei sample for Individual 230 [205862300109_R02C01]


title: NeuNPos nuclei sample for Individual 230 [205862300109_R04C01]


title: NeuNPos nuclei sample for Individual 222 [205862300095_R04C01]


title: Total nuclei sample for Individual 222 [205862300095_R01C01]


title: Sox10Pos nuclei sample for Individual 222 [205862300095_R02C01]


title: DoubleNeg nuclei sample for Individual 232 [205862300118_R02C01]


title: Total nuclei sample for Individual 221 [205862300094_R01C01]


title: NeuNPos nuclei sample for Individual 221 [205862300094_R02C01]


title: DoubleNeg nuclei sample for Individual 222 [205862300095_R03C01]


title: Sox10Pos nuclei sample for Individual 221 [205862300094_R03C01]


title: Sox10Pos nuclei sample for Individual 231 [205862300118_R08C01]


title: DoubleNeg nuclei sample for Individual 221 [205862300094_R04C01]


title: Sox10Pos nuclei sample for Individual 220 [205862300096_R01C01]


title: NeuNPos nuclei sample for Individual 219 [205862300064_R01C01]


title: Total nuclei sample for Individual 220 [205862300096_R03C01]


title: DoubleNeg nuclei sample for Individual 220 [205862300096_R02C01]


title: NeuNPos nuclei sample for Individual 220 [205862300096_R04C01]


title: Total nuclei sample for Individual 219 [205862300064_R03C01]


title: DoubleNeg nuclei sample for Individual 219 [205862300064_R04C01]


title: Sox10Pos nuclei sample for Individual 232 [205862300110_R07C01]


title: Total nuclei sample for Individual 218 [205862300095_R05C01]


title: DoubleNeg nuclei sample for Individual 218 [205862300095_R07C01]


title: NeuNPos nuclei sample for Individual 218 [205862300095_R06C01]


title: Total nuclei sample for Individual 217 [205854150120_R03C01]


title: Sox10Pos nuclei sample for Individual 217 [205854150120_R04C01]


title: Total nuclei sample for Individual 216 [205862300094_R05C01]


title: Sox10Pos nuclei sample for Individual 216 [205862300094_R08C01]


title: NeuNPos nuclei sample for Individual 216 [205862300094_R07C01]


title: DoubleNeg nuclei sample for Individual 217 [205854150120_R02C01]


title: DoubleNeg nuclei sample for Individual 216 [205862300094_R06C01]


title: Total nuclei sample for Individual 215 [205862300064_R06C01]


title: Total nuclei sample for Individual 214 [205854150120_R05C01]


title: DoubleNeg nuclei sample for Individual 215 [205862300064_R05C01]


title: NeuNPos nuclei sample for Individual 215 [205862300064_R08C01]


title: Sox10Pos nuclei sample for Individual 214 [205854150120_R06C01]


title: Sox10Pos nuclei sample for Individual 219 [205862300064_R02C01]


title: WT6

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

description: instrument model: Singular Genomics G4

data_processing:
Fastq files were generated with the Illumina off-line basecaller (olb) v. 1.9.4.
Reads were aligned against mm10 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics
Fastq files were processed using the nf-core/rnaseq v 3.11.1 pipeline [https://zenodo.org/records/10171269] in the Nextflow 22.10.4 environment, using the GRCm39 reference genome and ENSEMBL GRCm39.110 murine annotation.
Gene-level expression tables of counts and transcript-per-million (TPM) generated by STAR/Salmon processing were retrieved [Dobin2013, Soneson2015, Patro2017] .
Assembly: GRCm39 / ENSEMBL 110 annotation
Supplementary files format and content: Gene-level raw counts and transcript per million (TPM) data generated by Salmon, tab-separated format

source_name: Muscle

growth_protocol: High glucose DMEM w/ l-glutamine, sodium pyruvate and glucose as the base, with 10% fetal bovine serum and 1% pen-strep for growth of these myoblasts.

extract_protocol:
We extracted the multinucleated myofibril monolayers using the Rneasy mini kit with standard extraction protocols for adherent cell monolayers. Lysed the cells for 5 minutes and passed the lysate through the QIAshredder before continuing the Rneasy mini kit extraction protocol.
Ten microliters of undiluted total RNA was incubated with 10ul of NEB Dynabeads for polyaA+ RNA selection, eluted, and fragmented in 20ul. Illumina libraries were constructed using NEB Ultra II protocol; 5ul of the fragmented solution using half the amount of reagent and 1,2 PrD instead of enhancer in the ligation step, with 14 PCR cycles of final amplification and TS Singular index barcoding.Library sizes were quantified and verified by QPCR and on a Fragmen t Analyzer before loading for sequencing on a Singular G4 instrument in a 50-base paired-end configuration. Low-input samples were prepared by ribodepletion using the ZapR v2 protocol and mammalian-specific R-probe V2 kit at full volume (7.5 min fragmentation time).

treatment_protocol: Suspended 100k cells in a 24 wellplate (n=6) for each genotype. Seeded the cells onto a 1mm thick fibrin hydrogel consisting of 8 mg of fibrinogen/mL of GM+ media. GM+ consists of high glucose DMEM with sodium pyruvate, l-glutamine and glucose. We add 10% fetal bovine serum, 1% l-glutamine and 1% pen-strep alongside 1 mg/mL of aminocaproic acid to form GM+. They were cultured in GM+ for two days prior to being swapped onto DM++ media. DM++ media consists of the same high glucose DMEM base but with 10% inactivated horse serum, 1% l-glutamine, 1% pen-strp, 1 mg/mL of aminocaproic acis and 0.05 uL/mL of IGF-1.

value: Muscle

tag: cell line

value: myoblast

value: Wild-Type

tag: treatment

value: Differentiation media for 6 days


title: WT4

description: instrument model: Singular Genomics G4


title: WT3

description: instrument model: Singular Genomics G4


title: WT2

description: instrument model: Singular Genomics G4


title: Total nuclei sample for Individual 213 [205854150118_R07C01]


title: DoubleNeg nuclei sample for Individual 212 [205854150118_R02C01]


title: WT1

description: instrument model: Singular Genomics G4


title: NeuNPos nuclei sample for Individual 213 [205854150118_R08C01]


title: NeuNPos nuclei sample for Individual 214 [205854150120_R08C01]


title: Total nuclei sample for Individual 211 [205854150109_R05C01]


title: O6

description: instrument model: Singular Genomics G4


title: Sox10Pos nuclei sample for Individual 211 [205854150109_R06C01]


title: DoubleNeg nuclei sample for Individual 213 [205854150118_R06C01]


title: DoubleNeg nuclei sample for Individual 214 [205854150120_R07C01]


title: Sox10Pos nuclei sample for Individual 213 [205854150118_R05C01]


title: Total nuclei sample for Individual 212 [205854150118_R01C01]


title: DoubleNeg nuclei sample for Individual 211 [205854150109_R08C01]


title: NeuNPos nuclei sample for Individual 212 [205854150118_R03C01]


title: NeuNPos nuclei sample for Individual 211 [205854150109_R07C01]


title: Total nuclei sample for Individual 210 [205854150099_R08C01]


title: O5

description: instrument model: Singular Genomics G4


title: NeuNPos nuclei sample for Individual 210 [205854150099_R05C01]


title: TripleNeg nuclei sample for Individual 212 [205854150117_R02C01]

source_name: TripleNeg

value: TripleNeg


title: O3

description: instrument model: Singular Genomics G4


title: IRF8Pos nuclei sample for Individual 212 [205854150117_R01C01]


title: O4

description: instrument model: Singular Genomics G4


title: O2

description: instrument model: Singular Genomics G4


title: Sox10Pos nuclei sample for Individual 212 [205854150118_R04C01]


title: DoubleNeg nuclei sample for Individual 212 [205854150117_R04C01]


title: WT5

description: instrument model: Singular Genomics G4


title: O1

description: instrument model: Singular Genomics G4


title: CRISPRa+ sample 4

city: San Francisco

first: Dena

last: Dubal

state: California

address: 675 Nelson Rising Lane, Rm 292

department: Department of Neurology

institute: University of California San Francisco

data_processing:
The quality of the reads was obtainedd using FastQC
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts from exons were calculated usig featureCounts from the Subread package v.1.5.2.
Downstream differential expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel files include normalised mean gene counts for each Sample

source_name: Brain

extract_protocol:
Cells were stored in TRIzol and extracted using a Qiagen Rneasy micro kit
Library was prepared using the SMART-Seq v4 Ultra Low input RNA kit following the manufacturer's protocol

value: Brain

value: Neurons

value: CRISPRa+ lentivirus


title: Sox10Pos nuclei sample for Individual 209 [205854150087_R07C01]


title: CRISPRa+ sample 3


title: DoubleNeg nuclei sample for Individual 208 [205854150109_R04C01]


title: NeuNPos nuclei sample for Individual 208 [205854150109_R02C01]


title: Control sample 2

value: Control lentivirus


title: Control sample 4


title: Sox10Pos nuclei sample for Individual 208 [205854150109_R03C01]


title: CRISPRa+ sample 2


title: CRISPRa+ sample 1


title: Xp Sample 3_Young

description:
Xp3-Y
Differential_expression_analysis_table XpY v XmY.csv

value: Xp cells


title: Control sample 1


title: Control sample 3


title: Total nuclei sample for Individual 206 [205854150066_R05C01]

value: Total


title: DoubleNeg nuclei sample for Individual 209 [205854150087_R04C01]


title: Xp Sample 4_Young

description:
Xp4-Y
Differential_expression_analysis_table XpY v XmY.csv


title: Total nuclei sample for Individual 207 [205854150099_R04C01]

value: unstained


title: DoubleNeg nuclei sample for Individual 207 [205854150099_R03C01]


title: NeuNPos nuclei sample for Individual 207 [205854150099_R01C01]


title: Total nuclei sample for Individual 208 [205854150109_R01C01]


title: Xp Sample 1_Young

description:
Xp1-Y
Differential_expression_analysis_table XpY v XmY.csv


title: NeuNPos nuclei sample for Individual 206 [205854150066_R07C01]


title: Xp Sample 2_Young

description:
Xp2-Y
Differential_expression_analysis_table XpY v XmY.csv


title: Sox10Pos nuclei sample for Individual 206 [205854150066_R08C01]


title: Fgfr3CE_Cxcl12GFP_21-49

city: Houston

first: Shion

last: Orikasa

state: TX

address: 7500 Cambridge St

institute: University of Texas Health Science Center at Houston School of Dentistry

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: mm10_trans_nono
Supplementary files format and content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Femur bone marrow

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. GFP+ and tdTomato+ cells were FACS-isolated. ~71,956 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2
10X Genomics Chromium Single Cell 3' v2 Libraries

value: Femur bone marrow

value: Postnatal day 49

value: Cxcl12-GFP; Fgfr3CE; R26R-tdTomato


title: Sox10Pos nuclei sample for Individual 207 [205854150099_R02C01]

value: M


title: Total nuclei sample for Individual 209 [205854150087_R08C01]


title: Xm Sample 5_Young

description:
Xm5-Y
Differential_expression_analysis_table XpY v XmY.csv

value: Xm cells


title: NeuNPos nuclei sample for Individual 209 [205854150087_R06C01]

value: NeuNPos

value: NeuN+


title: DoubleNeg nuclei sample for Individual 206 [205854150066_R06C01]

value: DoubleNeg


title: Xp Sample 5_Young

description:
Xp5-Y
Differential_expression_analysis_table XpY v XmY.csv


title: Xm Sample 4_Young

description:
Xm4-Y
Differential_expression_analysis_table XpY v XmY.csv


title: Total nuclei sample for Individual 200 [205096370021_R03C01]


title: Xm Sample 3_Young

description:
Xm3-Y
Differential_expression_analysis_table XpY v XmY.csv


title: Sox10Pos nuclei sample for Individual 199 [205096370019_R01C01]


title: Xm Sample 2_Young

description:
Xm2-Y
Differential_expression_analysis_table XpY v XmY.csv


title: NeuNPos nuclei sample for Individual 199 [205096370019_R04C01]


title: Total nuclei sample for Individual 199 [205096370019_R03C01]


title: DoubleNeg nuclei sample for Individual 198 [205097260047_R02C01]


title: Xp Sample 4_Old

description:
Xp4-O
Differential_expression_analysis_table XpO v XmO.csv


title: Total nuclei sample for Individual 198 [205097260047_R03C01]


title: Xp Sample 2_Old

description:
Xp2-O
Differential_expression_analysis_table XpO v XmO.csv


title: NeuNPos nuclei sample for Individual 198 [205097260047_R04C01]


title: Total nuclei sample for Individual 196 [205096370013_R05C01]


title: Xp Sample 1_Old

description:
Xp1-O
Differential_expression_analysis_table XpO v XmO.csv


title: Xm Sample 5_Old

description:
Xm5-O
Differential_expression_analysis_table XpO v XmO.csv


title: Xp Sample 3_Old

description:
Xp3-O
Differential_expression_analysis_table XpO v XmO.csv


title: Xm Sample 3_Old

description:
Xm3-O
Differential_expression_analysis_table XpO v XmO.csv


title: Sox10Pos nuclei sample for Individual 198 [205097260047_R01C01]


title: NeuNPos nuclei sample for Individual 196 [205096370013_R06C01]


title: Xm Sample 4_Old

description:
Xm4-O
Differential_expression_analysis_table XpO v XmO.csv


title: Sox10Pos nuclei sample for Individual 196 [205096370013_R07C01]


title: Total nuclei sample for Individual 197 [205096370019_R06C01]


title: DoubleNeg nuclei sample for Individual 196 [205096370013_R08C01]


title: Xm Sample 2_Old

description:
Xm2-O
Differential_expression_analysis_table XpO v XmO.csv


title: Xm Sample 1_Old

description:
Xm1-O
Differential_expression_analysis_table XpO v XmO.csv


title: NeuNPos nuclei sample for Individual 195 [205096370026_R04C01]


title: DoubleNeg nuclei sample for Individual 195 [205096370026_R03C01]


title: Xm Sample 1_Young

description:
Xm1-Y
Differential_expression_analysis_table XpY v XmY.csv


title: DIV6 primary neurons, WT, rep3

city: Illkirch

first: Juliette

last: GODIN

address: 1 rue LAurent Fries

country: France

institute: IGBMC

data_processing:
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis. Reads mapping to rRNA were also discarded (this mapping was performed using bowtie version 2.2.8).
Reads were then mapped onto the mm10 assembly of mouse genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 102.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: E15.5 cortex

growth_protocol: Cortices from E15.5 Tm1b mouse embryos were dissected in cold PBS supplemented with BSA (3 mg/mL), MgSO4 (1 mM, Sigma), and D-glucose (30 mM, Sigma). They were then dissociated in Neurobasal media containing papain (20U/mL, Worthington) and DNase I (100 μg/mL, Sigma) for 20 min at 37°C with brief vortexing every 6-7 min. Cells were then incubated for 7 min with Neurobasal media containing Ovomucoïde (15 mg/mL, Worthington), and manually triturated 10 times with a 1000 ml pipette in OptiMeM supplemented with D-Glucose (20mM). Cells were then plated at 1 × 106 cells per 6 well  plate coated with poly-D-lysine (1 mg/ml, Sigma) overnight at 4°C and cultured for up to 10 days in Neurobasal medium supplemented with B27 (1×), L-glutamine (2 mM), and penicillin (5 units/ml)-streptomycin (50 mg/ml). Half of the media was changed with fresh supplemented Neurobasal media every 3 days.

extract_protocol:
Total RNA was extracted from  DIV6 primary neuronal cultures using the NucleoSpin RNA purification kit (Macherey-Nagel)
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: E15.5 cortex

value: primary cortical neurons

value: WT


title: Xp Sample 5_Old

description:
Xp5-O
Differential_expression_analysis_table XpO v XmO.csv

value: Brain

value: Neurons


title: DIV6 primary neurons, mut, rep3

value: HOM (Wdr47 deficient)


title: Sox10Pos nuclei sample for Individual 194 [205096370025_R08C01]


title: NeuNPos nuclei sample for Individual 194 [205096370025_R05C01]


title: Total nuclei sample for Individual 193 [205096370013_R03C01]


title: NeuNPos nuclei sample for Individual 193 [205096370013_R01C01]


title: Sox10Pos nuclei sample for Individual 192 [205061420185_R07C01]


title: DIV6 primary neurons, WT, rep2


title: Total nuclei sample for Individual 192 [205061420185_R06C01]


title: Sox10Pos nuclei sample for Individual 193 [205096370013_R02C01]


title: sm10c2

city: Shanghai

first: Yuanjie

last: Tang

state: Shanghai

address: 300 Fenglin Road, Xuhui District

department: CAS Center for Excellence in Molecular Plant Sciences

institute: CHINESE ACADEMY OF SCIENCES

data_processing:
This involved purity-filtered read trimming for adapters and low-quality sequences with Trimmomatic v0.32.
The cleaned reads were aligned against Arabidopsis thaliana TAIR10 genome (GCF_000001735.4) using STAR 2.7.9a
Data alignment quality was assessed with RSeQC v5.0.1. DEG analysis was performed using the DESeq2 R package v1.38.0.
Assembly: TAIR10.1
Supplementary files format and content: comma-delimited text file includes rawcounts for each samples

organism: Arabidopsis thaliana

source_name: sgn3 myb36 root inoculated with CHA0 for 10h replicate 2

extract_protocol:
RNA was harvested using Trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries. 10μg of total RNA was digested with 5U of DNaseI (from Takara, Japan) at 37°C for 30 minutes. The DNase-digested RNA was purified using the RNeasy MinElute Cleanup Kit (from QIAGEN, Germany). The purified RNA was eluted with 15μl of RNase-free water to obtain the RNA sample. The purified RNA was subjected to rRNA depletion using the Ribo-off™ rRNA Depletion Kit (Plant) (from Vazyme, China).
Take 100ng of rRNA-depleted RNA and use the NEB Next® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA) to construct a library.

value: root

value: CHA0 for 10h


title: sm10c3

source_name: sgn3 myb36 root inoculated with CHA0 for 10h replicate 3


title: DIV6 primary neurons, mut, rep1


title: DIV6 primary neurons, mut, rep2


title: sm6c2

source_name: sgn3 myb36 root inoculated with CHA0 for 6h replicate 2

value: CHA0 for 6h


title: sm6c3

source_name: sgn3 myb36 root inoculated with CHA0 for 6h replicate 3


title: sm10c1

source_name: sgn3 myb36 root inoculated with CHA0 for 10h replicate 1


title: DIV6 primary neurons, WT, rep1


title: DoubleNeg nuclei sample for Individual 192 [205061420185_R08C01]


title: DIV6 primary neurons, WT, rep4


title: NeuNPos nuclei sample for Individual 192 [205061420185_R05C01]


title: Total nuclei sample for Individual 191 [205061420166_R07C01]

value: Total

value: unstained


title: Sox10Pos nuclei sample for Individual 191 [205061420166_R06C01]


title: sm3c3

source_name: sgn3 myb36 root inoculated with CHA0 for 3h replicate 3

value: CHA0 for 3h


title: DIV6 primary neurons, mut, rep4


title: Total nuclei sample for Individual 194 [205096370025_R07C01]

value: M


title: sm6c1

source_name: sgn3 myb36 root inoculated with CHA0 for 6h replicate 1


title: NeuNPos nuclei sample for Individual 191 [205061420166_R05C01]


title: sm3c2

source_name: sgn3 myb36 root inoculated with CHA0 for 3h replicate 2


title: Total nuclei sample for Individual 190 [205061420161_R08C01]


title: Sox10Pos nuclei sample for Individual 189 [205096370025_R01C01]

value: F


title: smk3

source_name: sgn3 myb36 root CK replicate 3

value: CK


title: DoubleNeg nuclei sample for Individual 194 [205096370025_R06C01]


title: NeuNPos nuclei sample for Individual 189 [205096370025_R04C01]

value: NeuNPos

value: NeuN+


title: sm3c1

source_name: sgn3 myb36 root inoculated with CHA0 for 3h replicate 1


title: Total nuclei sample for Individual 188 [205096370020_R06C01]

source_name: Total


title: Sox10Pos nuclei sample for Individual 188 [205096370020_R07C01]


title: NeuNPos nuclei sample for Individual 188 [205096370020_R05C01]

source_name: NeuNPos


title: c10c1

source_name: Col-0 root inoculated with CHA0 for 10h replicate 1

value: Wild type, Col--0


title: NeuNPos nuclei sample for Individual 187 [205096370020_R03C01]


title: c10c2

source_name: Col-0 root inoculated with CHA0 for 10h replicate 2


title: c6c1

source_name: Col-0 root inoculated with CHA0 for 6h replicate 1


title: c6c3

source_name: Col-0 root inoculated with CHA0 for 6h replicate 3


title: Sox10Pos nuclei sample for Individual 187 [205096370020_R02C01]


title: c6c2

source_name: Col-0 root inoculated with CHA0 for 6h replicate 2


title: c3c3

source_name: Col-0 root inoculated with CHA0 for 3h replicate 3


title: Total nuclei sample for Individual 187 [205096370020_R04C01]


title: c10c3

source_name: Col-0 root inoculated with CHA0 for 10h replicate 3


title: smk1

source_name: sgn3 myb36 root CK replicate 1


title: Total nuclei sample for Individual 186 [205061420185_R03C01]


title: c3c1

source_name: Col-0 root inoculated with CHA0 for 3h replicate 1


title: c3c2

source_name: Col-0 root inoculated with CHA0 for 3h replicate 2


title: Sox10Pos nuclei sample for Individual 186 [205061420185_R02C01]


title: ck3

source_name: Col-0 root CK replicate 3


title: Sox10Pos nuclei sample for Individual 190 [205061420161_R06C01]


title: DoubleNeg nuclei sample for Individual 187 [205096370020_R01C01]

source_name: DoubleNeg

value: DoubleNeg


title: smk2

source_name: sgn3 myb36 root CK replicate 2


title: DoubleNeg nuclei sample for Individual 189 [205096370025_R02C01]


title: ck2

source_name: Col-0 root CK replicate 2


title: Total nuclei sample for Individual 185 [205096370018_R05C01]


title: DoubleNeg nuclei sample for Individual 188 [205096370020_R08C01]


title: ck1

source_name: Col-0 root CK replicate 1


title: NeuNPos nuclei sample for Individual 186 [205061420185_R04C01]


title: Sox10Pos nuclei sample for Individual 185 [205096370018_R08C01]


title: NeuNPos nuclei sample for Individual 185 [205096370018_R07C01]


title: NeuNPos nuclei sample for Individual 184 [205061420166_R02C01]


title: DoubleNeg nuclei sample for Individual 185 [205096370018_R06C01]


title: Sox10Pos nuclei sample for Individual 183 [205096370018_R02C01]


title: NeuNPos nuclei sample for Individual 183 [205096370018_R03C01]


title: Total nuclei sample for Individual 184 [205061420166_R01C01]

source_name: Total


title: Sox10Pos nuclei sample for Individual 184 [205061420166_R03C01]


title: Total nuclei sample for Individual 183 [205096370018_R01C01]


title: ST-00022617-B

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

data_processing:
Data was processed as part of the Adaptive Biotechnologies service.
Data was analyzed using the Adaptive Biotechnologies "immunoSeq ANALYZER 3.0" tool.
Processed data was exported from the Adaptive Biotechnologies "immunoSeq ANALYZER 3.0" tool using the "Export" function with the default option (not the v2 option).
Data can be viewed in the Adaptive Biotechnologies "immunoSeq ANALYZER 3.0" tool at this link: https://clients.adaptivebiotech.com/pub/link-2023-nc
Supplementary files format and content: Tab separated value (*.tsv) text file.  Contains sequences of templates detected, details of specific test used, multiple annotations and metrics for each template, plus metadata and metrics for each associated specimen (sample).

source_name: blood

extract_protocol:
Adaptive Biotechnologies human TCRB sequencing service
Adaptive Biotechnologies human TCRB sequencing service

tag: sample type

value: matched blood

value: blood

tag: public patient_id

value: Female

tag: age at_diagnosis

tag: blood matched_to

value: Primary


title: Total nuclei sample for Individual 182 [205097260048_R07C01]


title: DoubleNeg nuclei sample for Individual 183 [205096370018_R04C01]


title: ST-00022617-T

source_name: Pancreas

value: primary tumor

tag: tissue

value: Pancreas


title: NeuNPos nuclei sample for Individual 182 [205097260048_R06C01]

source_name: NeuNPos


title: DoubleNeg nuclei sample for Individual 182 [205097260048_R05C01]


title: ST-00022635-B

value: Male


title: ST-00022484-T


title: ST-00022354-T


title: ST-00022484-B


title: Total nuclei sample for Individual 181 [205061420123_R03C01]

value: Total


title: Total nuclei sample for Individual 179 [205097260048_R02C01]

value: unstained


title: ST-00022200-Ma

source_name: metastatic tumor

value: metastatic tumor


title: HT29 DMSO

city: Sendai

first: Yuya

last: Yoshida

state: Miyagi

address: Seiryomachi 4-1, Aoba-ku

department: clinical oncology

institute: Tohoku University Hospital

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.3.0 Microarray (Agilent, G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array(Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%). Raw data were extracted using the Agilent Feature Extraction software, version 10.7.3.1., protocol GE1_107_Sep09.

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9.1 (Agilent) , and was 75% percentile-normalized.

source_name: HT29 cells, DMSO 0.1%, 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop One.

growth_protocol: Cell lines were caltured using DMEMDMEM with 10% fetal bovine serum in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA of the cells was extracted using the RNeasy Mini kit (Qiagen) according to manufacture's protocol.

treatment_protocol: Cell lines were treated with DMSO, tretinoin, encorafenib/binimetinib, or tretinoin/encorafenib/binimetinib at 24 hours.

value: colon cancer cell line

value: DMSO


title: HT29 ENC/BIN

source_name: HT29 cells, encorafenib 10 µM/binimatinib 10 µM, 24 hours

value: encorafenib/binimetinib


title: ST-00022635-T

source_name: Ampulla of Vater

value: Ampulla of Vater


title: HT29 TRE

source_name: HT29 cells, tretinoin 1 µM, 24 hours

value: tretinoin


title: ST-00022200-B

value: Met


title: Total nuclei sample for Individual 178 [205097260047_R05C01]

value: M


title: NeuNPos nuclei sample for Individual 179 [205097260048_R01C01]

value: NeuNPos

value: NeuN+


title: RKO ENC/BIN

source_name: RKO cells, encorafenib 10 µM/binimatinib 10 µM, 24 hours

value: RKO


title: HT29 TRE/ENC/BIN

source_name: HT29 cells, encorafenib 10 µM/binimatinib 10 µM/tretinoin 1 µM, 24 hours

value: tretinoin/encorafenib/binimetinib


title: RKO TRE/ENC/BIN

source_name: RKO cells, encorafenib 10 µM/binimatinib 10 µM/tretinoin 1 µM, 24 hours


title: RKO DMSO

source_name: RKO cells, DMSO 0.1%, 24 hours


title: ST-00022177-T

value: primary tumor


title: RKO TRE

source_name: RKO cells, tretinoin 1 µM, 24 hours


title: ST-00022166-B

value: matched blood

value: blood


title: Sox10Pos nuclei sample for Individual 178 [205097260047_R07C01]


title: NeuNPos nuclei sample for Individual 178 [205097260047_R06C01]


title: ST-00022177-B

value: Male

value: Primary


title: NeuNPos nuclei sample for Individual 180 [205097260049_R03C01]


title: ST-00022354-B


title: DoubleNeg nuclei sample for Individual 178 [205097260047_R08C01]

source_name: DoubleNeg

value: DoubleNeg


title: ST-00021900-M

source_name: Lymph Node

value: metastatic tumor

value: Lymph Node


title: Total nuclei sample for Individual 177 [205061420093_R01C01]

value: Total

value: unstained

value: F


title: ST-00021900-B

value: Met


title: ST-00021843-T

value: Pancreas


title: NeuNPos nuclei sample for Individual 177 [205061420093_R04C01]

value: NeuNPos


title: DoubleNeg nuclei sample for Individual 177 [205061420093_R02C01]


title: ST-00021837-T

value: Female


title: ST-00021843-B


title: Total nuclei sample for Individual 176 [205096370045_R02C01]


title: DoubleNeg nuclei sample for Individual 176 [205096370045_R03C01]


title: ST-00021832-T


title: ST-00021837-B


title: Total nuclei sample for Individual 175 [205061420063_R05C01]

value: M


title: Sox10Pos nuclei sample for Individual 174 [205097260046_R02C01]


title: ST-00021789-T


title: ST-00021789-B


title: NeuNPos nuclei sample for Individual 174 [205097260046_R01C01]

value: NeuN+


title: ST-00021786-T

value: primary tumor


title: Sox10Pos nuclei sample for Individual 175 [205061420063_R06C01]


title: Total nuclei sample for Individual 174 [205097260046_R03C01]


title: ST-00021786-B

value: matched blood


title: ST-00021737-B

value: blood


title: Total nuclei sample for Individual 172 [205096370074_R02C01]


title: NeuNPos nuclei sample for Individual 172 [205096370074_R03C01]


title: DoubleNeg nuclei sample for Individual 174 [205097260046_R04C01]


title: Total nuclei sample for Individual 173 [205097260022_R03C01]


title: ST-00021412-T


title: NeuNPos nuclei sample for Individual 176 [205096370045_R04C01]


title: ST-00021563-T

value: Male


title: NeuNPos nuclei sample for Individual 171 [205096370040_R07C01]


title: ST-00021611-B

value: blood only


title: DoubleNeg nuclei sample for Individual 172 [205096370074_R04C01]

value: DoubleNeg


title: ST-00021412-B

value: Primary


title: DoubleNeg nuclei sample for Individual 171 [205096370040_R05C01]


title: ST-00021370-B


title: ST-00021220-B


title: ST-00021832-B


title: Total nuclei sample for Individual 170 [205061420036_R05C01]


title: ST-00021194-M

source_name: Liver

value: metastatic tumor

value: Liver


title: ST-00021194-B


title: Total nuclei sample for Individual 169 [205096370040_R01C01]

source_name: Total

value: Total

value: unstained


title: ST-00021190-T


title: ST-00021563-B

source_name: blood


title: ST-00021096-B


title: ST-00021190-B


title: NeuNPos nuclei sample for Individual 168 [205096370050_R04C01]


title: ST-00021074-B


title: Sox10Pos nuclei sample for Individual 172 [205096370074_R01C01]

value: F


title: Total nuclei sample for Individual 167 [205096370033_R04C01]


title: Total nuclei sample for Individual 166 [205096370028_R08C01]


title: ST-00021071-B


title: Total nuclei sample for Individual 165 [205096370028_R02C01]


title: ST-00021067-B

value: Met


title: ST-00021066-B


title: Sox10Pos nuclei sample for Individual 164 [205097260022_R05C01]


title: ST-00021060-B


title: ST-00021059-B


title: ST-00021039-B


title: Total nuclei sample for Individual 163 [205096370074_R05C01]


title: ST-00020969-T

source_name: Pancreas

value: Pancreas


title: Sox10Pos nuclei sample for Individual 170 [205061420036_R06C01]


title: Total nuclei sample for Individual 164 [205097260022_R06C01]


title: DoubleNeg nuclei sample for Individual 164 [205097260022_R08C01]


title: Sox10Pos nuclei sample for Individual 163 [205096370074_R08C01]


title: ST-00020969-B

value: Female


title: ST-00020952-T


title: NeuNPos nuclei sample for Individual 163 [205096370074_R07C01]

source_name: NeuNPos

value: NeuNPos

value: M


title: DoubleNeg nuclei sample for Individual 163 [205096370074_R06C01]


title: ST-00020952-B


title: ST-00020947-B


title: Total nuclei sample for Individual 168 [205096370050_R03C01]


title: ST-00020936-T

value: primary tumor


title: Total nuclei sample for Individual 161 [205096370029_R01C01]


title: Sox10Pos nuclei sample for Individual 161 [205096370029_R02C01]


title: NeuNPos nuclei sample for Individual 161 [205096370029_R04C01]

value: NeuN+


title: ST-00020936-B

value: matched blood

value: blood


title: ST-00020922-B

value: Male

value: blood only


title: NeuNPos nuclei sample for Individual 164 [205097260022_R07C01]


title: ST-00020905-B


title: ST-00020904-T


title: NeuNPos nuclei sample for Individual 160 [205096370027_R04C01]


title: DoubleNeg nuclei sample for Individual 160 [205096370027_R01C01]

value: DoubleNeg


title: Total nuclei sample for Individual 159 [205096370054_R06C01]


title: ST-00020824-B


title: ST-00020904-B

value: Primary


title: ST-00020640-B


title: ST-00020640-T


title: Total nuclei sample for Individual 158 [205096370050_R06C01]


title: Sox10Pos nuclei sample for Individual 158 [205096370050_R08C01]


title: NeuNPos nuclei sample for Individual 159 [205096370054_R08C01]


title: DoubleNeg nuclei sample for Individual 162 [205096370027_R08C01]


title: ST-00020650-B


title: ST-00020523-B


title: ST-00020630-B


title: NeuNPos nuclei sample for Individual 158 [205096370050_R07C01]


title: Total nuclei sample for Individual 157 [205096370033_R05C01]


title: ST-00020482-B


title: ST-00020482-T


title: ST-00020366-B


title: ST-00020344-B


title: Sox10Pos nuclei sample for Individual 157 [205096370033_R06C01]


title: Total nuclei sample for Individual 156 [205096370026_R05C01]


title: Sox10Pos nuclei sample for Individual 160 [205096370027_R03C01]


title: ST-00020339-B


title: DoubleNeg nuclei sample for Individual 156 [205096370026_R07C01]


title: ST-00020336-B


title: Total nuclei sample for Individual 155 [205097260046_R06C01]


title: ST-00020312-B


title: Sox10Pos nuclei sample for Individual 155 [205097260046_R05C01]


title: DoubleNeg nuclei sample for Individual 159 [205096370054_R05C01]


title: ST-00020301-B


title: NeuNPos nuclei sample for Individual 155 [205097260046_R07C01]


title: ST-00020287-B


title: ST-00020291-T


title: ST-00020291-B


title: DoubleNeg nuclei sample for Individual 155 [205097260046_R08C01]


title: Sox10Pos nuclei sample for Individual 153 [205096370021_R05C01]


title: Sox10Pos nuclei sample for Individual 154 [205096370029_R07C01]


title: ST-00020285-T


title: ST-00020282-B


title: ST-00020285-B


title: NeuNPos nuclei sample for Individual 156 [205096370026_R06C01]


title: ST-00020281-M

value: metastatic tumor

value: Liver


title: Total nuclei sample for Individual 153 [205096370021_R07C01]

value: Total

value: unstained


title: Total nuclei sample for Individual 154 [205096370029_R06C01]


title: NeuNPos nuclei sample for Individual 157 [205096370033_R07C01]


title: Total nuclei sample for Individual 126 [205862290091_R02C01]


title: IRF8Pos nuclei sample for Individual 126 [205862290091_R01C01]


title: ST-00020281-B

value: Met


title: DoubleNeg nuclei sample for Individual 154 [205096370029_R08C01]


title: ST-00020277-M


title: ST-00020279-B


title: ST-00020260-M


title: DoubleNeg nuclei sample for Individual 153 [205096370021_R08C01]


title: ST-00020277-B


title: NeuNPos nuclei sample for Individual 126 [205862290091_R04C01]


title: Sox10Pos nuclei sample for Individual 126 [205862290091_R05C01]


title: ST-00020260-B


title: DoubleNeg nuclei sample for Individual 125 [205862300030_R05C01]

value: F


title: ST-00020258-T

value: Pancreas

value: Female


title: Total nuclei sample for Individual 125 [205862300030_R07C01]


title: Sox10Pos nuclei sample for Individual 125 [205862300030_R06C01]


title: ST-00020258-B


title: ST-00020236-T


title: ST-00020251-B


title: ST-00020251-M

source_name: Peritoneum

value: Peritoneum


title: NeuNPos nuclei sample for Individual 125 [205862300030_R08C01]

value: NeuNPos


title: ST-00020232-M

source_name: Retroperitoneum

value: Retroperitoneum


title: NeuNPos nuclei sample for Individual 123 [205862290123_R07C01]

value: NeuN+

value: M


title: DoubleNeg nuclei sample for Individual 126 [205862290091_R03C01]


title: DoubleNeg nuclei sample for Individual 124 [205862300109_R07C01]


title: Sox10Pos nuclei sample for Individual 123 [205862290123_R08C01]


title: Total nuclei sample for Individual 123 [205862290123_R06C01]


title: ST-00020225-T

value: primary tumor

value: Male


title: Total nuclei sample for Individual 124 [205862300109_R05C01]


title: Total nuclei sample for Individual 122 [205862290091_R07C01]


title: Sox10Pos nuclei sample for Individual 121 [205862300030_R01C01]


title: NeuNPos nuclei sample for Individual 121 [205862300030_R03C01]


title: ST-00020223-B

value: matched blood

value: blood


title: ST-00020223-T


title: DoubleNeg nuclei sample for Individual 121 [205862300030_R02C01]

value: DoubleNeg


title: ST-00020225-B

value: Primary


title: NeuNPos nuclei sample for Individual 124 [205862300109_R06C01]


title: ST-00020232-B


title: ST-00020222-B


title: Total nuclei sample for Individual 120 [205862290072_R08C01]

value: Total


title: Total nuclei sample for Individual 121 [205862300030_R04C01]

value: unstained


title: ST-00020222-T


title: Total nuclei sample for Individual 119 [205862290123_R01C01]


title: ST-00020236-B


title: ST-00020208-B


title: DoubleNeg nuclei sample for Individual 119 [205862290123_R02C01]


title: ST-00020207-B


title: ST-00020226-B

value: Met


title: NeuNPos nuclei sample for Individual 119 [205862290123_R04C01]


title: ST-00020206-M

value: metastatic tumor

value: Liver


title: Sox10Pos nuclei sample for Individual 118 [205862290056_R01C01]

value: F


title: Total nuclei sample for Individual 118 [205862290056_R03C01]


title: ST-00020206-B


title: DoubleNeg nuclei sample for Individual 118 [205862290056_R02C01]


title: ST-00020204-B

value: Female


title: ST-00020201-B


title: Total nuclei sample for Individual 117 [205862290079_R06C01]


title: Total nuclei sample for Individual 115 [205862290056_R05C01]


title: ST-00020190-B


title: Total nuclei sample for Individual 116 [205862290057_R06C01]


title: NeuNPos nuclei sample for Individual 115 [205862290056_R07C01]

value: NeuNPos


title: ST-00020191-B

value: blood only


title: ST-00020211-B


title: Sox10Pos nuclei sample for Individual 115 [205862290056_R06C01]


title: ST-00020190-M


title: ST-00020183-B


title: DoubleNeg nuclei sample for Individual 115 [205862290056_R08C01]


title: ST-00020176-M

value: Peritoneum


title: ST-00020207-T

value: Pancreas


title: NeuNPos nuclei sample for Individual 114 [205854150087_R03C01]

value: NeuN+

value: M


title: ST-00020176-B

value: matched blood

value: Male


title: NeuNPos nuclei sample for Individual 113 [205862290046_R05C01]


title: ST-00020169-B

value: blood


title: ST-00020203-B


title: ST-00020168-M

source_name: Tissue near left hepatic artery

value: Tissue near left hepatic artery


title: ST-00020165-T

value: primary tumor


title: Total nuclei sample for Individual 113 [205862290046_R08C01]

value: Total

value: unstained


title: ST-00020168-B

value: Met


title: Total nuclei sample for Individual 111 [205061420176_R07C01]


title: Total nuclei sample for Individual 112 [205061420034_R01C01]


title: Sox10Pos nuclei sample for Individual 112 [205061420034_R04C01]


title: Sox10Pos nuclei sample for Individual 111 [205061420176_R05C01]


title: ST-00020164-M

value: metastatic tumor

value: Liver


title: ST-00020165-B

value: Female

value: Primary


title: Total nuclei sample for Individual 110 [205061420172_R06C01]

value: F


title: ST-00020164-B


title: DoubleNeg nuclei sample for Individual 109 [205061420160_R05C01]

value: DoubleNeg


title: ST-00020159-B

value: blood only