title: DMSO_HTB4643_G3

description: TC-83 nsP2-4

data_processing:
Basecalling was done using Nanopore Guppy (ver. 5.1.12)
Sequencing reads were checked for read quality and de-multiplexed using 9 nt-long barcode sequence plus adjacent 10 nt primer sequence
Reads were aligned to Venezuelan equine encephalitis virus genome L01443.1 using Minimap2 (version 2.17-r941)
VCF for each sample was generated by SAMtools mpileup function using mapped BAM file.
Assembly: L01443.1
Supplementary files format and content: vcf format


title: msi2msi3nasp_RNAseq_rep2

status: Public on Oct 25 2024

type: SRA

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

library_source: transcriptomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (DNBSEQ platform, single-end 50bp).

tag: cell type

value: Arabidopsis seedlings

tag: genotype

tag: time


title: DMSO_HTB4643_G2

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

country: USA

institute: University of Louisville

description: TC-83 nsP2-4

library_source: genomic

molecule: genomic DNA

organism: Venezuelan equine encephalitis virus (strain TC-83)

extract_protocol:
VEEV TC-83 nsP234 region is PCR-amplified from cDNA synthesized from viral RNA.
For samples sequenced with Nanopore MinION, Nanopore ligation-based sequencing kit was used. For samples sequenced with PacBio Sequel IIe, samples were prepared into SMRTbell template libraries.

tag: cell line

tag: treatment

value: DMSO


title: BeWo_hSTELLA-KO-c2

type: genomic

city: Guangzhou

first: Wenbin

last: Gu

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Chinese Academy of Sciences

institute: Guangzhou Institutes of Biomedicine and Health

description:
Clone 2 from hSTELLA-targeting sgRNA transduced BeWo cells
BeWo_hSTELLA-KO-c2

scan_protocol: Polymer-coated chips were image-processed in Illumina iScan scanner.

data_processing: Data were extracted using Illumina GenomeStudio V2011.1 software. Methylation status of each CpG site was presented as beta value based on following definition: beta value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

label: Cy5 and Cy3

organism: Homo sapiens

source_name: BeWo, hSTELLA sgRNA transduced, clone2

label_protocol: DNA bisulfite conversion was carried out using EZ DNA Methylation Kit (Zymo Research) by following manufacturer's manual with modifications for Illumina Infinium Methylation Assay. Briefly, 0.5~1.0 ug of genomic DNA was first mixed with 5 ul of M-Dilution Buffer and incubate at 37C for 15 minutes and then mixed with 100 ul of CT Conversion Reagent prepared as instructed in the kit's manual. Mixtures were incubated in a thermocycler with 16 thermal cycles at 95C for 30 seconds and 50C for one hour. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification. Concentration of eluted DNA was measured using Nanodrop-1000 spectrometer. Bisulfite-converted DNA was analyzed using Illumina Infinium MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer's manual. Beadchip contains more than 850,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

growth_protocol: BeWo cells were maintained in Ham‘s F-12K complete medium.  NCCIT cells were maintained in RPMI 1640 complete medium. HCT116 cells were maintained in McCoy's 5A complete medium, and RKO cells were maintained in MEM complete medium.

extract_protocol: Genomic DNA was extracted and purified from cell pellets using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer's instructions. Genomic DNA quality was assessed by low concentration agarose gel (0.6%) electrophoresis and spectrometry of OD260/280 and OD 260/230 ratio.

treatment_protocol: BeWo and NCCIT cells were transduced by lentivirus expressing Cas9/sgRNA targeting hSTELLA. The single-cell clones were subsequently selected through serial dilution of these transduced cells, and verified by western blot and sequencing. CRC cells (HCT116 and RKO cells) with lentivirus-mediated stable overexpression of STELLA orthologs were harvested on Day 9 post virus-transduction. HCT116 cells treated with LNP-mRNA or vehicle control were harvested on Days 2, 6 and 10.

tag: tumor type

value: choriocarcinoma

value: BeWo

value: hSTELLA-targeting sgRNA transduced


title: WTnoIR, H3K36me3, regen, rep2

city: Boulder

first: Alison

middle: Rae Swearingen

last: Pashos

state: CO

address: 1945 Colorado Avenue

department: MCDB

institute: University of Colorado Boulder

data_processing:
All samples were normalized to background using CPM. H3K36M H3K36me3 and H3K36me2 samples were normalized to Epicypher K-metstat spike in panel using in house scripts to quantify barcodes.
CUT&Tag reads were mapped to the mouse mm10 genome using Bowtie version 2.2.9.
DeepTools v3.0.1 was used with normalization as above to create bigWig files.
Assembly: mm10
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: organoid

growth_protocol: WT organoid samples were grown in ENR media. H3K36M organoid samples were grown in ENR with 2 ug/mL doxycycline added for 4 weeks before harvest.

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Nuclei were isolated from cells following Heinekoff et al. "Benchtop CUT&Tag". Organoids were harvested using EDTA to remove matrigel and TrypLE to digest to single cell, at which point nuclei were isolated following H3inekoff et al. "Benchtop CUT&Tag".
CUT&Tag was performed as in Heinekoff et al. "Benchtop CUT&Tag" for each antibody. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

treatment_protocol: Mice were irradiated with 2 Gy at day 0 and harvested at 2 and 3 days post-IR. Organoids were irradiated with 6 Gy and harvested at 24, 48, and 96 hours post-IR.

tag: tissue

value: organoid

value: WT H3


title: DMSO_HTB4643_H11

description: TC-83 nsP2-4


title: DMSO_HTB4643_L7

description: TC-83 nsP2-4


title: msi2msi3nasp_RNAseq_rep1


title: WTnoIR, H3K27me3, regen, rep2


title: DMSO_HTB4643_G11

description: TC-83 nsP2-4


title: DMSO_HTB4643_F2

description: TC-83 nsP2-4


title: WTnoIR, H3K36me3, regen, rep1


title: hag2nasp_RNAseq_rep3

value: hag2-/- nasp-/-


title: DMSO_HTB4643_F12

description: TC-83 nsP2-4


title: hag2nasp_RNAseq_rep2


title: DMSO_HTB4643_E24

description: TC-83 nsP2-4


title: DMSO_HTB4643_F3

description: TC-83 nsP2-4


title: DMSO_HTB4643_D2

description: TC-83 nsP2-4


title: WTnoIR, H3K27me3, regen, rep1


title: hag2msi2msi3_RNAseq_rep3


title: DMSO_HTB4643_D3

description: TC-83 nsP2-4


title: BeWo_hSTELLA-KO-c3

description:
Clone 3 from hSTELLA-targeting sgRNA transduced BeWo cells
BeWo_hSTELLA-KO-c3

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina Infinium MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer's manual. Beadchip contains more than 850,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

source_name: BeWo, hSTELLA sgRNA transduced, clone3


title: DMSO_HTB4643_C3

description: TC-83 nsP2-4


title: DMSO_HTB4643_E3

description: TC-83 nsP2-4


title: BeWo_SCR-c3

description:
Clone 3 from sgSCR transduced BeWo cells
BeWo_SCR-c3

source_name: BeWo, scramble sgRNA transduced, clone3

value: sgSCR transduced


title: BeWo_hSTELLA-KO-c1

description:
Clone 1 from hSTELLA-targeting sgRNA transduced BeWo cells
BeWo_hSTELLA-KO-c1

source_name: BeWo, hSTELLA sgRNA transduced, clone1


title: DMSO_HTB4643_C23

description: TC-83 nsP2-4


title: H3K36M, H3K36me2, regen, rep2


title: DMSO_HTB4643_E2

description: TC-83 nsP2-4


title: hag2msi2msi3_RNAseq_rep2


title: hag2nasp_RNAseq_rep1


title: H3K36M, H3K27me3, regen, rep2


title: hag2msi2msi3_RNAseq_rep1


title: DMSO_HTB4643_B5

description: TC-83 nsP2-4


title: DMSO_HTB4643_C13

description: TC-83 nsP2-4


title: DMSO_HTB4643_C2

description: TC-83 nsP2-4


title: Col-0_RNAseq_rep3

value: wild type


title: DMSO_HTB4643_A22

description: TC-83 nsP2-4


title: DMSO_HTB4643_A3

description: TC-83 nsP2-4


title: H3K36M, H3K36me2, regen, rep1


title: Col-0_RNAseq_rep2


title: H3K36M, H3K36me3, regen, rep1


title: H3K36M, H3K36me3, regen, rep2


title: H3K36M, H3K27me3, regen, rep1


title: DMSO_HTB4643_A21

description: TC-83 nsP2-4


title: DMSO_HTB4278_O2

description: TC-83 nsP2-4


title: IR96, H3K36me3, regen, rep2


title: DMSO_HTB4643_B2

description: TC-83 nsP2-4


title: IR96, H3K36me2, regen, rep2


title: hind paw, control-2

type: RNA

city: Chihuahua

first: Mercedes

last: Bermúdez

state: Chihuahua

address: Chihuahua

department: Dentistry

country: Mexico

institute: Universidad autónoma de Chihuahua

hyb_protocol: Transcript expression analysis of both groups was conducted using Mouse Clariom D® microarrays (GeneChip, Affymetrix, USA). The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, complementary DNA (cDNA) preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cDNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.

data_processing: Partek ® Genomic Suite (GS) ® v7.20.0831 software was employed for the subsequent analysis. All samples were normalized using the Robust Multiarray Average (RMA) method, which encompasses background correction, normalization, and calculation of expression values. Differential expression analysis was performed using one-way ANOVA. Differentially expressed genes (DEGs) were selected between the groups based on an absolute log2 fold change (log2FC) >1.5 or < -1.5, and the Benjamini and Hochberg false discovery rate (16) was applied to account for multiple hypothesis testing. Genes with an adjusted p-value < 0.01 were considered significant.   Enrichment analysis with QIAGEN Ingenuity Pathway Analysis (IPA) was used to assess the biological relevance of DEGs. The analysis and integration of direct protein-protein interactions centered on the functional association and its downstream regulation were obtained in the IPA, selecting the interactions with minimal confidence (interaction score > 0.5) and considering the pathway's activation or inhibition by the z-score of each molecule.

label: biotin

source_name: mice hind paw

extract_protocol: The effect of IF on transcriptome was evaluated in the RNA microarray by comparing the IF group (experimental group) and the control group. One hind paw of each mouse was used for this analysis. After the dissection of the paw, the skin, hair, nails, and muscle were removed entirely, and the resulting joint structure containing bones, joints, and tarsal ligaments was immediately placed in liquid nitrogen and disrupted using a biopulverizer. Total RNA was extracted using RNeasy® Lipid Tissue Mini Kit (QIAGEN, Germantown, MD, USA) according to the manufacturer´s instructions. The RNA quality and integrity were verified in the fluorometer Qubit 4 (ThermoFisher Scientific, Waltham, MS, USA).

treatment_protocol: The Collagen induced arthritis was induced, all animals were fed with a standard chow diet and water ad libitum until day 21, when the second collagen injection was done. On this day,mice were randomly divided into two groups of eight mice each; one received every-other-day Intermittent Fasting for four weeks (experimental group), and the other did not (control group) transcript expression analysis was conducted using Mouse Clariom D® microarrays (GeneChip, Affymetrix, USA),   The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, complementary DNA (cDNA) preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cDNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.  Partek ® Genomic Suite (GS) ® v7.20.0831 software was employed for the subsequent analysis. All samples were normalized using the Robust Multiarray Average (RMA) method, which encompasses background correction, normalization, and calculation of expression values. Differential expression analysis was performed using one-way ANOVA. Differentially expressed genes (DEGs) were selected between the groups based on an absolute log2 fold change (log2FC) >1.5 or < -1.5, and the Benjamini and Hochberg false discovery rate (16) was applied to account for multiple hypothesis testing. Genes with an adjusted p-value < 0.01 were considered significant.

tag: strain

value: DBA/1 mice

tag: Sex

value: male

tag: disease state

value: Collagen induced arthritis

value: control

value: after 4 weeks of intervention


title: DMSO_HTB4278_F7

description: TC-83 nsP2-4


title: DMSO_HTB4278_H5

description: TC-83 nsP2-4


title: DMSO_HTB4643_B3

description: TC-83 nsP2-4


title: DMSO_HTB4278_N22

description: TC-83 nsP2-4


title: hind paw, control-1

scan_protocol: Transcript expression analysis of both groups was conducted using Mouse Clariom D® microarrays (GeneChip, Affymetrix, USA). The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, complementary DNA (cDNA) preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cDNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.


title: IR96, H3K27me3, regen, rep2


title: hind paw, intermittent fasting-2

label_protocol: Transcript expression analysis of both groups was conducted using Mouse Clariom D® microarrays (GeneChip, Affymetrix, USA). The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, complementary DNA (cDNA) preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cDNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.

value: IF


title: DMSO_HTB4278_C7

description: TC-83 nsP2-4


title: DMSO_HTB4278_C10

description: TC-83 nsP2-4


title: IR96, H3K36me3, regen, rep1


title: Col-0_RNAseq_rep1


title: DMSO_HTB4643_A2

description: TC-83 nsP2-4


title: DMSO_HTB4278_A13

description: TC-83 nsP2-4


title: EIDD1931_50uM_3

description: TC-83 nsP2-4


title: hind paw, intermittent fasting-1


title: IR96, H3K27me3, regen, rep1


title: DMSO_HTB4277_P22

description: TC-83 nsP2-4


title: DMSO_HTB4277_P21

description: TC-83 nsP2-4


title: IR96, H3K36me2, regen, rep1


title: DMSO_HTB4278_A12

description: TC-83 nsP2-4


title: DMSO_HTB4277_P1

description: TC-83 nsP2-4


title: EIDD1931_50uM_2

description: TC-83 nsP2-4


title: IR48, H3K36me3, regen, rep2


title: DMSO_HTB4277_O18

description: TC-83 nsP2-4


title: EIDD1931_50uM_1

description: TC-83 nsP2-4


title: DMSO_HTB4277_O1

description: TC-83 nsP2-4


title: IR48, H3K36me2, regen, rep2


title: EIDD1931_1uM_3

description: TC-83 nsP2-4

value: 1uM EIDD-1931


title: IR48, H3K27me3, regen, rep2


title: DMSO_HTB4277_N1

description: TC-83 nsP2-4


title: EIDD1931_1uM_2

description: TC-83 nsP2-4


title: DMSO_HTB4277_M7

description: TC-83 nsP2-4


title: DMSO_HTB4277_N22

description: TC-83 nsP2-4


title: DMSO_HTB4278_A9

description: TC-83 nsP2-4


title: EIDD1931_1uM_1

description: TC-83 nsP2-4


title: DMSO_HTB4277_M11

description: TC-83 nsP2-4


title: DMSO_HTB4277_L1

description: TC-83 nsP2-4


title: IR48, H3K36me2, regen, rep1


title: DMSO_HTB4277_M1

description: TC-83 nsP2-4


title: DMSO_HTB4277_K1

description: TC-83 nsP2-4


title: DMSO_HTB4277_K19

description: TC-83 nsP2-4


title: EIDD1931_10uM_3

description: TC-83 nsP2-4


title: BeWo_SCR-c2

description:
Clone 2 from sgSCR transduced BeWo cells
BeWo_SCR-c2

source_name: BeWo, scramble sgRNA transduced, clone2


title: DMSO_HTB4277_I10

description: TC-83 nsP2-4


title: IR24, H3K36me3, regen, rep2


title: EIDD1931_10uM_2

description: TC-83 nsP2-4


title: DMSO_HTB4277_J1

description: TC-83 nsP2-4


title: EIDD1931_10uM_1

description: TC-83 nsP2-4


title: IR24, H3K36me2, regen, rep2


title: DMSO_HTB4277_I1

description: TC-83 nsP2-4


title: DMSO_HTB4277_H24

description: TC-83 nsP2-4


title: DMSO_HTB4277_H2

description: TC-83 nsP2-4


title: DMSO_HTB4277_K9

description: TC-83 nsP2-4


title: IR48, H3K27me3, regen, rep1


title: IR48, H3K36me3, regen, rep1


title: DMSO_HTB4277_H1

description: TC-83 nsP2-4


title: DMSO_2

description: TC-83 nsP2-4


title: IR24, H3K27me3, regen, rep2


title: DMSO_HTB4277_G1

description: TC-83 nsP2-4


title: DMSO_3

description: TC-83 nsP2-4


title: IR24, H3K36me3, regen, rep1


title: DMSO_HTB4277_F1

description: TC-83 nsP2-4


title: DMSO_1

description: TC-83 nsP2-4


title: DMSO_HTB4277_E24

description: TC-83 nsP2-4


title: DMSO_HTB4277_E1

description: TC-83 nsP2-4


title: IR24, H3K36me2, regen, rep1


title: DMSO_HTB4277_D1

description: TC-83 nsP2-4


title: IR24, H3K27me3, regen, rep1


title: DMSO_HTB4277_E17

description: TC-83 nsP2-4


title: NCCIT_hSTELLA-KO-c2

description:
Clone 2 from hSTELLA-targeting sgRNA transduced NCCIT cells
NCCIT_hSTELLA-KO-c2

source_name: NCCIT, hSTELLA sgRNA transduced, clone2

value: embryonal carcinoma

value: NCCIT


title: KOA3_SF_CD14posCD16pos

city: Olomouc

first: Eva

last: Kriegová

address: Hněvotínská 976/3

country: Czech Republic

institute: Univerzita Palackého v Olomouci

description: synovial fluid-derived immune cells

data_processing:
Data were analysed using nextflow (v23.04.1) pipeline using rnaseq module (v3.11.2).
Adapters were trimmed using fastp and reads mapped using STAR aligner.
For quantification of the data Salmon tool was used.
Read counts, TPM and differential gene analysis was performed using 3D RNA-Seq APP.
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample
Supplementary files format and content: comma-delimited text file includes TPM values for each sample

source_name: monocyte-macrophage lineage cells

growth_protocol: SF samples from KOA patients were processed within four hours of aspiration, and the resulting pellet of cells isolated by gradient centrifugation was used for subsequent cell sorting by FACS.

extract_protocol:
Total RNA was isolated from the bulk of sorted subpopulations using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Sci Inc., Waltham, MA, USA) according to the manufacturer’s protocol. All samples were pretreated by HL-dsDNAse (ArcticZymes Technologies, Tromsø, Norway) according to the manufacturer's instructions.
The libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit - Pico input Mammalian v3 (Takara Bio USA, Mountain View, CA, USA) according to the manufacturer's instructions. Quality control of the libraries was performed using an Agilent DNA HS Chip on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer's protocol.

treatment_protocol: A dry pellets of sorted CD11b+ CD14−CD16−, CD14+CD16−, and CD14+CD16+ cells were stored at -80°C prior to RNA isolation.

value: monocyte-macrophage lineage cells

tag: cell subtype


title: DMSO_HTB4277_C11

description: TC-83 nsP2-4

value: DMSO


title: DMSO_HTB4277_C12

description: TC-83 nsP2-4


title: C23_7 [191_Sub_11]

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description:
each of the clonal sublines (C1-C24) was derived from B2905 mouse melanoma cell line (Nature Med. 2020, 26:781)
Expression_CountValue.tsv, Expression_FPKM.tsv, Expression_TPM.tsv, Mutations.tsv

library_source: transcriptomic single cell

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples

source_name: Clonal subline C23

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

value: Melanoma cell line

value: HGF-tg C57BL6

tag: microbiota status

tag: sorting strategy

value: single cells sorted from homogeneous culture


title: KOA2_SF_CD14posCD16pos

description: synovial fluid-derived immune cells


title: C23_8 [192_Sub_12]


title: DMSO_HTB4277_C9

description: TC-83 nsP2-4


title: KOA4_SF_CD14posCD16pos

description: synovial fluid-derived immune cells


title: DMSO_HTB4277_C1

description: TC-83 nsP2-4


title: C23_6 [190_Sub_10]


title: KOA4_SF_CD14posCD16neg

description: synovial fluid-derived immune cells


title: DMSO_HTB4277_B4

description: TC-83 nsP2-4


title: DMSO_HTB4277_B17

description: TC-83 nsP2-4


title: DMSO_HTB4277_B1

description: TC-83 nsP2-4


title: KOA3_SF_CD14posCD16neg

description: synovial fluid-derived immune cells


title: C23_5 [189_Sub_9]


title: DMSO_HTB4277_A7

description: TC-83 nsP2-4


title: BeWo_SCR-c1

description:
Clone 1 from sgSCR transduced BeWo cells
BeWo_SCR-c1

source_name: BeWo, scramble sgRNA transduced, clone1

value: choriocarcinoma

value: BeWo


title: C23_4 [188_Sub_8]


title: C23_3 [187_Sub_7]


title: DMSO_HTB4277_A1

description: TC-83 nsP2-4


title: KOA1_SF_CD14posCD16neg

description: synovial fluid-derived immune cells


title: DMSO_HTB4276_P7

description: TC-83 nsP2-4


title: DMSO_HTB4276_P4

description: TC-83 nsP2-4


title: DMSO_HTB4276_P12

description: TC-83 nsP2-4


title: KOA4_SF_CD14negCD16neg

description: synovial fluid-derived immune cells


title: KOA3_SF_CD14negCD16neg

description: synovial fluid-derived immune cells


title: KOA1_SF_CD14posCD16pos

description: synovial fluid-derived immune cells


title: C8_8 [184_Sub_4]

source_name: Clonal subline C8


title: DMSO_HTB4276_P1

description: TC-83 nsP2-4


title: C23_2 [186_Sub_6]


title: DMSO_HTB4276_O15

description: TC-83 nsP2-4


title: C23_1 [185_Sub_5]


title: DMSO_HTB4277_B9

description: TC-83 nsP2-4


title: DMSO_HTB4276_P11

description: TC-83 nsP2-4


title: C8_7 [183_Sub_3]


title: DMSO_HTB4276_N1

description: TC-83 nsP2-4


title: DMSO_HTB4276_M1

description: TC-83 nsP2-4


title: KOA2_SF_CD14negCD16neg

description: synovial fluid-derived immune cells


title: KOA1_SF_CD14negCD16neg

description: synovial fluid-derived immune cells


title: DMSO_HTB4276_O1

description: TC-83 nsP2-4


title: DMSO_HTB4276_L11

description: TC-83 nsP2-4


title: C4_8 [182_Sub_2]

source_name: Clonal subline C4


title: WTnoIR, H3K36me2, regen, rep1

value: organoid

value: WT H3


title: DMSO_HTB4276_L1

description: TC-83 nsP2-4


title: DMSO_HTB4276_K1

description: TC-83 nsP2-4


title: C3_8 [181_Sub_1]

source_name: Clonal subline C3


title: DMSO_HTB4276_J1

description: TC-83 nsP2-4


title: C24_8 [180_P02_H12]

source_name: Clonal subline C24


title: C24_7 [179_P02_G12]


title: DMSO_HTB4276_F12

description: TC-83 nsP2-4


title: EG40, EG41 VDJ-seq

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
L20
Bone marrow from diagnosis, refractory anemia with excess blasts, RAEB-2

data_processing:
scRNA- and scADT-seq data was aligned with Cell Ranger 6.0 version to human reference (hg19) from 10x Genomics with default parameters.
The VDJ-data for BCR and TCR were separately processed using Cell Ranger version 6.0 by alignment to VDJ-reference (hg20) with default parameters.
Assembly: hg19 (transcriptome), hg20 (VDJ sequencing)
Supplementary files format and content: CITE-seq: barcode annotation;  feature annotation: 10x Cell Ranger feature list; count matrix: 10x Cell Ranger raw UMI count matrix, VDJ-seq: all_contig_annotations.csv
Library strategy: VDJ-seq

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Bone marrow cells or control cell line samples (Nalm-6, HL-60 and Jurkat) were thawn from the viably cryopreserved samples. If indicated in sample metadata, excess dead cells were depleted from samples using bead-based Dead Cell Removal Kit (catalog number 130-090-101, MACS Miltenyi Biotech). Cells were thawn in a 37C water bath, immediately after adding 0.5 ml RPMI 1640 media (Thermo Fisher Scientific) + 10% FBS (Gibco)+ 20 ul DNAse (Roche 100U/ul) on top, then moving cells to 15 mL Falcon and filling the volume drop-wise, gently swirling. Cells were washed two times, counted, then 100 000-200 000 cells centrifuged and re-suspended in 50 ul Cell Staining Buffer (BioLegend) and blocked with 5ul of Human TruStain FcX Blocking Solution (BioLegend) for 10 min at 4C. Antibody pool (0.25 ug per million cells per specific antibody, except 0.125 ug for CD45 and CD8; 0.1 ug per hashtag antibodies) was added per sample and incubated for 30 min at 4C. Samples were washed three times with cell staining buffer, counted and assessed for viability using trypan blue staining with EVE analysis, and then sample pools were prepared, centrifuged and loaded to Chromium lanes. If post-stain viability was >70% for all samples, equal ratios were loaded aiming at 10 000 cells. Otherwise, loading ratio was adjusted such that half target cell count was used for samples with viability 50-70% and one fifth of viability was 20-50%.
The 5prime gene expression, ADT- and VDJ (BCR and TCR) libraries were prepared following manufacturer instructions (10x Genomics). cDNA qualities were assessed using Bioanalyzer. For some samples, wetting failure occured and in this case run was repeated. Libraries were index barcoded and sequenced using Novaseq S1, S2 or S4 runs.
10x Chromium 5' kit for CITE-seq and VDJ-seq

tag: donor

tag: batch

value: bone marrow

tag: disease

value: refractory anemia with excess blasts

value: diagnosis


title: EG46, EG47, CellLineMix10 VDJ-seq

description:
L23
Bone marrow from diagnosis, myelodysplastic syndrome, del(5q), progressed from MDS to AML

value: D32, D33, CellLineMix

value: Nalm-6, HL-60, Jurkat

value: myelodysplastic syndrome


title: DMSO_HTB4276_D9

description: TC-83 nsP2-4


title: DMSO_HTB4276_I1

description: TC-83 nsP2-4


title: DMSO_HTB4276_M17

description: TC-83 nsP2-4


title: C24_6 [178_P02_F12]


title: EG57, EG58 VDJ-seq

description:
L28
Bone marrow from diagnosis, myelodysplastic syndrome


title: EG38, EG39, CellLineMix8 VDJ-seq

description:
L19
Bone marrow from diagnosis, refractory anemia with excess blasts, RAEB-2

value: D24, D25, CellLineMix


title: C24_5 [177_P02_E12]


title: DMSO_HTB4276_D21

description: TC-83 nsP2-4


title: DMSO_HTB4276_B19

description: TC-83 nsP2-4


title: C24_4 [176_P02_D12]


title: EG36, EG37, CellLineMix7 VDJ-seq

description:
L18
Bone marrow from follow-up, aplastic anemia. This pool contains also few cells from AML donor that failed in sample preparation.

value: D21, D23, CellLineMix

value: aplastic anemia

value: follow-up


title: DMSO_HTB4276_D16

description: TC-83 nsP2-4

value: DMSO


title: EG34, EG35 VDJ-seq

description:
L17
Bone marrow from diagnosis, aplastic anemia


title: DMSO_HTB4276_A7

description: TC-83 nsP2-4


title: DMSO_HTB4276_B12

description: TC-83 nsP2-4


title: EG54, EG55, EG56 VDJ-seq

description:
L27
Bone marrow from diagnosis, myelodysplastic syndrome


title: DMSO_HTB4276_A20

description: TC-83 nsP2-4


title: C24_3 [175_P02_C12]

value: Melanoma cell line

value: HGF-tg C57BL6


title: DMSO_HTB4276_I10

description: TC-83 nsP2-4


title: DMSO_HTB4275_P5

description: TC-83 nsP2-4


title: C24_2 [174_P02_B12]

source_name: Melanoma cell line

value: single cells sorted from homogeneous culture


title: EG57, EG58 CITE-seq

data_processing:
scRNA- and scADT-seq data was aligned with Cell Ranger 6.0 version to human reference (hg19) from 10x Genomics with default parameters.
The VDJ-data for BCR and TCR were separately processed using Cell Ranger version 6.0 by alignment to VDJ-reference (hg20) with default parameters.
Assembly: hg19 (transcriptome), hg20 (VDJ sequencing)
Supplementary files format and content: CITE-seq: barcode annotation;  feature annotation: 10x Cell Ranger feature list; count matrix: 10x Cell Ranger raw UMI count matrix, VDJ-seq: all_contig_annotations.csv
Library strategy: CITE-seq


title: DMSO_HTB4277_A24

description: TC-83 nsP2-4


title: DMSO_HTB4275_M18

description: TC-83 nsP2-4


title: DMSO_HTB4276_C7

description: TC-83 nsP2-4


title: EG54, EG55, EG56 CITE-seq


title: C24_1 [173_P02_A12]


title: DMSO_HTB4275_K22

description: TC-83 nsP2-4


title: EG46, EG47, CellLineMix10 CITE-seq


title: DMSO_HTB4275_K12

description: TC-83 nsP2-4


title: C22_8 [172_P02_H10]

source_name: Clonal subline C22


title: DMSO_HTB4275_H1

description: TC-83 nsP2-4


title: C22_7 [171_P02_G10]


title: EG40, EG41 CITE-seq


title: DMSO_HTB4275_G10

description: TC-83 nsP2-4


title: DMSO_HTB4275_G17

description: TC-83 nsP2-4


title: C22_6 [170_P02_F10]


title: DMSO_HTB4275_H3

description: TC-83 nsP2-4


title: EG36, EG37, CellLineMix7 CITE-seq


title: C22_5 [169_P02_E10]


title: EG34, EG35 CITE-seq


title: C22_4 [168_P02_D10]


title: C22_3 [167_P02_C10]


title: DMSO_HTB4275_D1

description: TC-83 nsP2-4


title: DMSO_HTB4275_B7

description: TC-83 nsP2-4


title: DMSO_HTB4275_F1

description: TC-83 nsP2-4


title: DMSO_HTB4275_E1

description: TC-83 nsP2-4


title: DMSO_HTB4275_C1

description: TC-83 nsP2-4


title: DMSO_HTB4275_L11

description: TC-83 nsP2-4


title: DMSO_HTB4275_D22

description: TC-83 nsP2-4


title: DMSO_HTB4275_B24

description: TC-83 nsP2-4


title: EG38, EG39, CellLineMix8 CITE-seq


title: DMSO_HTB4275_B21

description: TC-83 nsP2-4


title: DMSO_HTB4275_G1

description: TC-83 nsP2-4


title: C22_1 [165_P02_A10]


title: DMSO_HTB4275_B1

description: TC-83 nsP2-4


title: DMSO_HTB4275_B11

description: TC-83 nsP2-4


title: Deceased

city: Shanghai

first: Zhong

last: Fang

address: Dongan Road 131#

institute: Fudan University

description: Visium Spatial Gene expression for FFPE tissue Sequencing

data_processing:
Raw sequencing data were processed using the 10x Gnomics Space Ranger's default stetting
Sequence were aligned to GRCh38-2020-A genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Rnger's default settinggs
Assembly: GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducial.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: liver

extract_protocol:
Liver tissue were FFPE embedded, and 5um FFPE selctions were cut
Spatial transcriptome sequencing librariers were prepared with VisiumCytAssist_GeneExpression kit according to manufacturer's construction

value: liver

tag: group

value: Deceased


title: C21_8 [164_P02_H09]

source_name: Clonal subline C21

tag: cell type


title: Moderate

value: Moderate


title: Severe

value: Severe


title: DMSO_HTB4275_A6

description: TC-83 nsP2-4


title: DMSO_HTB4275_A1

description: TC-83 nsP2-4


title: C21_7 [163_P02_G09]


title: Rh41,BRG1

city: AURORA

first: Etienne

last: Danis

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The quality of fastq files was accessed using FastQC (v.0.11.8), FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads.
The ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (v.2.3.4.3).
Samtools (v. 1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool (v.2.21.1).
Bedtools genomecov (v.2.27.1) was used to create bedgraph files from the bam files.
Bigwig files were created using deepTools bamCoverage (v.3.2.1) and visualized using IGV (v.2.8.2).
Peaks were called using MACS2 (v2.1.2) (Ref. 10) using ENCODE recommendations.
Metagene plots and heatmaps were generated using ngs.plot (v.2.61).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: cancer cell

growth_protocol: Rh41 and Rh30 cells were grown in RPMI with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol:
Cells were harvested, immobilized on Con-A beads, permeabilized with digitonin, and incubated with antibodies overnight. Antibody-bound chromatin was released using pAG-MNase with CaCl2 activation. DNA was purified using NEB Monarch DNA cleanup kit.
CUT&RUN libraries were assembled using the NEBNext Ultra II DNA Library Prep Kit for Illumina and dual-index primers, followed by size selection/adaptor cleanup using AMPure XP beads, and size distribution assessment using high-sensitivity Agilent DNA chips.

treatment_protocol: None, shRNA-mediated factor depletion or drug treatment.

value: cancer cell

value: Rhabdomyosarcoma


title: Rh41,Scramble,BRG1

value: control


title: Rh41,YK,ETS1

value: drug


title: C21_6 [162_P02_F09]


title: Rh41,DMSO,ETS1


title: A375, CO1 mtDNA, replicate (mouse) 2

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Reads were trimmed (TrimGalore v.0.6.0), aligned with HISAT2 to the GRCH38 reference genome.
Assembly: GRCH38
Supplementary files format and content: Excel file reports raw counts for genes in each sample.

source_name: Subcutaneous tumor grown in flank of NSG mouse

growth_protocol: Animals were maintained on a standard chow diet, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
RNA extraction was carried out from frozen tissue using the RNEasy kit (Qiagen) following manufacturer's instructions.
Libraries were constructed using Lexogen's QuantSeq 3' mRNA-Seq Library Prep Kit FWD following manufacturer's instructions.

treatment_protocol: 10,000 A375 cells were injected subcutaneously into the flank of an NSG mouse and allowed to grow until 20-25mm in diameter.

value: melanoma

tag: genotype

value: CO1 mtDNA


title: C22_2 [166_P02_B10]


title: A375, CO1 mtDNA, replicate (mouse) 3

value: Subcutaneous tumor grown in flank of NSG mouse


title: DMSO_HTB4274_P1

description: TC-83 nsP2-4


title: Rh41,YK,P3F


title: C21_5 [161_P02_E09]


title: C21_4 [160_P02_D09]


title: DMSO_HTB4274_O1

description: TC-83 nsP2-4


title: A375, ND1 mtDNA, replicate (mouse) 3

value: ND1 mtDNA


title: DMSO_HTB4275_A17

description: TC-83 nsP2-4


title: A375, CO1 mtDNA, replicate (mouse) 4


title: Rh41,DMSO,P3F


title: C21_3 [159_P02_C09]


title: DMSO_HTB4274_N1

description: TC-83 nsP2-4


title: A375, ND1 mtDNA, replicate (mouse) 2


title: Rh41,Scramble,P3F,rep2


title: C21_2 [158_P02_B09]


title: A375, ND1 mtDNA, replicate (mouse) 1


title: DMSO_HTB4274_P17

description: TC-83 nsP2-4


title: DMSO_HTB4274_M21

description: TC-83 nsP2-4


title: DMSO_HTB4274_M10

description: TC-83 nsP2-4


title: Rh41,Scramble,P3F,rep1


title: C20_8 [156_P02_H08]

source_name: Clonal subline C20


title: C21_1 [157_P02_A09]


title: A375, ATP6 mtDNA, replicate (mouse) 3

value: ATP6 mtDNA


title: DMSO_HTB4274_M17

description: TC-83 nsP2-4

value: DMSO


title: Rh41,shETS1,P3F

value: shRNA knockdown


title: A375, CO1 mtDNA, replicate (mouse) 1


title: A375, ATP6 mtDNA, replicate (mouse) 2


title: A375, ATP6 mtDNA, replicate (mouse) 1


title: DMSO_HTB4274_M1

description: TC-83 nsP2-4


title: C20_6 [154_P02_F08]

value: Melanoma cell line

value: HGF-tg C57BL6


title: DMSO_HTB4274_L4

description: TC-83 nsP2-4


title: C20_7 [155_P02_G08]

value: single cells sorted from homogeneous culture


title: Rh41,P3F


title: Rh41,shKDM3A,P3F


title: Rh41,shKDM3A,KDM3A


title: A375, WT mtDNA, replicate (mouse) 3

value: WT mtDNA


title: A375, WT mtDNA, replicate (mouse) 2


title: C20_5 [153_P02_E08]


title: Rh41,shETS1,KDM3A


title: DMSO_HTB4274_L14

description: TC-83 nsP2-4


title: C20_4 [152_P02_D08]


title: KOA2_SF_CD14posCD16neg

description: synovial fluid-derived immune cells

value: monocyte-macrophage lineage cells


title: A375, WT mtDNA, replicate (mouse) 1


title: DMSO_HTB4274_L1

description: TC-83 nsP2-4


title: Rh41,KDM3A


title: C20_3 [151_P02_C08]


title: FLASH_45_FGF4LY_Rep8_S29

city: Paris

first: Michel

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

description: Trimmed and de-duplicated

data_processing:
Paired-end sequences (50-85bp, using 100 cycles sequencing kits) were generated using Illumina Next-seq 2000 instrument. UMI-containing reads were sorted out using Julia 85. RNA-seq reads were aligned to the mm10 genome using STAR 79 and quantified by RSEM 86 using the RSEM-STAR pipeline with additional options ‘--calc-pme --calc-ci --estimate-rspd --paired-end’.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Embryo

growth_protocol: Embryos were obtained from timed natural matings. Noon of the day when the vaginal plugs of mated females were identified was scored as E0.5. E2.75 were culture in KSOM for 24 hours.

extract_protocol:
Extraction and library preparation were performed in one reaction (see below)
Library preparation from single ICMs was  performed according to FLASH-seq protocol (V. Hahaut et al., “Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.” Nat Biotechnol 40, 1447-1451; 2022) with modifications from Festuccia et al (Nr5a2 is essential for morula development. Biorxiv, 2023.01.16.524255) including 3’ phosphorylation of the template switching primer and addition of 7 cycles of linear enrichment PCR for UMI reads.

treatment_protocol: Zona pellucida was removed from embryos prior to immunosurgery. E2.75 morulae embryos were cultured for 24 hours with vehicle (DMSO), 10µM LY, 1µg/ml FGF4/heparin or both.

value: Embryo

tag: developmental stage

tag: date

tag: protocol

value: FLASH-seq


title: C20_2 [150_P02_B08]


title: FLASH_45_FGF4LY_Rep7_S28

description: Trimmed and de-duplicated

tag: treatment


title: Rh41,shETS1,ETS1

tag: tissue

value: cancer cell

tag: cell line

value: Rhabdomyosarcoma


title: DMSO_HTB4274_K1

description: TC-83 nsP2-4


title: C20_1 [149_P02_A08]

tag: strain


title: Rh41,Scramble,ETS1

value: control


title: C19_8 [148_P02_H07]

source_name: Clonal subline C19


title: FLASH_45_FGF4LY_Rep5_S26

description: Trimmed and de-duplicated


title: Rh41,ETS1


title: DMSO_HTB4274_I11

description: TC-83 nsP2-4


title: DMSO_HTB4274_L12

description: TC-83 nsP2-4


title: C19_7 [147_P02_G07]


title: Rh41,Scramble,KDM3A


title: DMSO_HTB4274_G9

description: TC-83 nsP2-4


title: C19_6 [146_P02_F07]


title: FLASH_45_FGF4LY_Rep3_S25

description: Trimmed and de-duplicated


title: DMSO_HTB4274_I1

description: TC-83 nsP2-4


title: Rh30,Scramble,BRG1


title: DMSO_HTB4274_G15

description: TC-83 nsP2-4


title: Rh30,BRG1


title: FLASH_45_FGF4_Rep8_S23

description: Trimmed and de-duplicated


title: C19_4 [144_P02_D07]


title: C19_5 [145_P02_E07]


title: DMSO_HTB4274_F9

description: TC-83 nsP2-4


title: Rh30,YK,P3F

value: drug


title: Rh30,DMSO,P3F


title: DMSO_HTB4274_J1

description: TC-83 nsP2-4


title: FLASH_45_FGF4LY_Rep6_S27

description: Trimmed and de-duplicated


title: C19_3 [143_P02_C07]


title: C19_2 [142_P02_B07]


title: FLASH_45_FGF4_Rep6_S21

description: Trimmed and de-duplicated


title: DMSO_HTB4274_E3

description: TC-83 nsP2-4


title: Rh30,shKDM3A,ETS1


title: DMSO_HTB4274_B13

description: TC-83 nsP2-4


title: FLASH_45_FGF4_Rep5_S20

description: Trimmed and de-duplicated


title: C19_1 [141_P02_A07]


title: DMSO_HTB4274_A7

description: TC-83 nsP2-4


title: FLASH_45_FGF4LY_Rep2_S24

description: Trimmed and de-duplicated


title: Rh30,Scramble,ETS1


title: FLASH_45_FGF4_Rep4_S19

description: Trimmed and de-duplicated


title: C18_8 [140_P02_H06]

source_name: Clonal subline C18


title: DMSO_HTB4274_A5

description: TC-83 nsP2-4


title: Rh30,ETS1


title: FLASH_45_FGF4_Rep3_S18

description: Trimmed and de-duplicated


title: Rh30,shETS1,KDM3A


title: FLASH_45_FGF4_Rep2_S17

description: Trimmed and de-duplicated


title: DMSO_HTB4274_A20

description: TC-83 nsP2-4


title: Rh30,shETS1,ETS1


title: Rh30,shKDM3A,KDM3A


title: FLASH_45_FGF4_Rep7_S22

description: Trimmed and de-duplicated


title: DMSO_HTB4274_A13

description: TC-83 nsP2-4


title: DMSO_HTB4274_A10

description: TC-83 nsP2-4


title: C18_5 [137_P02_E06]


title: FLASH_45_LY_Rep8_S15

description: Trimmed and de-duplicated

value: LY


title: FLASH_45_FGF4_Rep1_S16

description: Trimmed and de-duplicated


title: Rh30,Scramble,KDM3A


title: FLASH_45_LY_Rep7_S14

description: Trimmed and de-duplicated


title: DMSO_HTB4273_O21

description: TC-83 nsP2-4


title: C18_3 [135_P02_C06]


title: Rh30,shETS1,P3F


title: FLASH_45_LY_Rep6_S13

description: Trimmed and de-duplicated


title: C18_7 [139_P02_G06]


title: C18_2 [134_P02_B06]


title: DMSO_HTB4273_O18

description: TC-83 nsP2-4


title: Rh30,shKDM3A,P3F


title: DMSO_HTB4273_N14

description: TC-83 nsP2-4


title: Rh30,Scramble,P3F


title: FLASH_45_LY_Rep5_S12

description: Trimmed and de-duplicated


title: DMSO_HTB4273_K18

description: TC-83 nsP2-4


title: C18_6 [138_P02_F06]


title: C18_1 [133_P02_A06]


title: FLASH_45_LY_Rep4_S11

description: Trimmed and de-duplicated


title: C17_8 [132_P02_H05]

source_name: Clonal subline C17


title: DMSO_HTB4273_K14

description: TC-83 nsP2-4


title: FLASH_45_LY_Rep3_S10

description: Trimmed and de-duplicated


title: Rh30,P3F


title: Rh30,drug,1uMYK-4-279,replicate3

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq.
Quality of fastq files was accessed using FastQC (v.0.11.8) , FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to thehg38 human reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a).
Differential gene expression analysis was performed using DESeq2 (v 1.44.0).
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen), and further purified using the Qiagen MinElute column kit.
Illumina directional mRNA prep.
Per Novogene protocol for PE150 Illumina NGS.

treatment_protocol: Cells were treated with vehicle (DMSO) or drug (1 uM YK-4-279, in DMSO) for 24 hours.


title: C17_7 [131_P02_G05]


title: DMSO_HTB4273_J9

description: TC-83 nsP2-4


title: Rh30,KDM3A


title: C18_4 [136_P02_D06]


title: FLASH_45_CT_Rep8_S7

description: Trimmed and de-duplicated


title: Rh30,drug,1uMYK-4-279,replicate2


title: C17_5 [129_P02_E05]


title: FLASH_45_LY_Rep2_S9

description: Trimmed and de-duplicated


title: C17_4 [128_P02_D05]


title: C17_6 [130_P02_F05]


title: FLASH_45_CT_Rep9_S8

description: Trimmed and de-duplicated


title: FLASH_45_CT_Rep7_S6

description: Trimmed and de-duplicated


title: Rh30,vehicle,DMSO,control,replicate2


title: C17_3 [127_P02_C05]


title: Rh30,vehicle,DMSO,control,replicate3


title: DMSO_HTB4273_H6

description: TC-83 nsP2-4


title: DMSO_HTB4273_G1

description: TC-83 nsP2-4


title: FLASH_45_CT_Rep3_S3

description: Trimmed and de-duplicated


title: Rh30,drug,1uMYK-4-279,replicate1


title: FLASH_45_CT_Rep6_S5

description: Trimmed and de-duplicated


title: DMSO_HTB4273_I24

description: TC-83 nsP2-4


title: C17_2 [126_P02_B05]


title: Rh30,vehicle,DMSO,control,replicate1


title: C17_1 [125_P02_A05]


title: DMSO_HTB4273_F5

description: TC-83 nsP2-4


title: HSC, Activated, P3, rep3

city: Jette

first: Leo

middle: A.

last: van Grunsven

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
fastq.gzC followed by trimming using AfterQC
Mapping with STAR
assembly with StringTie
Assembly: hg38
Supplementary files format and content: comma seperated file with raw counts for each sample

source_name: Hepatic stellate cell

growth_protocol: DMEM 10% FBS

extract_protocol:
ReliaPrep RNA Cell Miniprep System
QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen)

value: Activated

tag: time point

value: Hepatic stellate cell


title: DMSO_HTB4273_F24

description: TC-83 nsP2-4


title: neuM22_Mock

city: Winnipeg

first: Jessy

middle: Andrew

last: Slota

state: Manitoba

address: 1015 Arlington St.

department: One Health Division

country: Canada

institute: National Microbiology Laboratory; Public Health Agency of Canada

description: 10x Genomics 3' v3

data_processing:
Sequencing data was processed with cellranger v6.1.2
Assembly: mm10
Supplementary files format and content: raw read counts for each library are provided as sparse matrix files (matrix.mtx), with matching files that contain genes (features.tsv), and barcodes (barcodes.tsv)

source_name: Telencephalon

extract_protocol:
Cerebral brain tissues were dissected in a glass petri dish, minced with a scalpel, and dissociated in 5 mL Hibernate e minus calcium with 20 units/mL papain and 0.005% DNase I for 40 min at 37 °C. To promote dissociation, tissues were gently triturated through a wide-bore (~5 mm) serum-coated plastic Pasteur pipette every 10 min. After the 40 min incubation, the tissue was triturated 10 times with a serum-coated standard p1000 pipette tip and single-cell suspension was diluted with 35 mL of loading buffer. Large debris was initially removed by passing the single-cell suspension through a 70 µm MACS strainer (Miltenyi), after which cells were pelleted by centrifuging at 300 xg for 5 min at 4 °C. Debris was removed from the cell pellet using the debris removal solution from Miltenyi. Neurons were enriched from the debris-liberated cell suspension using the mouse neuron isolation kit (Miltenyi) according to manufacturer’s instructions.
Live single-cell suspensions were processing into sequencing libraries the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Dual Index) from 10× Genomics according to manufacturer's instructions.

treatment_protocol: Wildtype CD1 mice were intraperitoneally inoculated with 200 µL of 2% brain homogenate from either Rocky Mountain Laboratory Scrapie-infected (RML) or non-infected (Mock) mice.

tag: mouse no.

value: Telencephalon

tag: Sex

value: female

value: Mock

tag: disease status

value: Normal

tag: disease stage

value: endpoint

tag: days post_infection


title: C16_7 [123_P02_G04]

source_name: Clonal subline C16

value: Melanoma cell line

value: HGF-tg C57BL6

tag: microbiota status

tag: sorting strategy

value: single cells sorted from homogeneous culture


title: DMSO_HTB4273_H1

description: TC-83 nsP2-4

value: DMSO


title: C16_8 [124_P02_H04]

tag: cell type


title: neuM21_Mock

description: 10x Genomics 3' v3

tag: genotype


title: HSC, Activated, P1, rep3

tag: group


title: DMSO_HTB4273_I18

description: TC-83 nsP2-4


title: HSC, Activated, P3, rep2


title: DMSO_HTB4273_F1

description: TC-83 nsP2-4


title: DMSO_HTB4273_E1

description: TC-83 nsP2-4


title: C16_6 [122_P02_F04]


title: neuM19_Mock

description: 10x Genomics 3' v3


title: DMSO_HTB4273_D21

description: TC-83 nsP2-4


title: HSC, Activated, P3, rep1


title: C16_5 [121_P02_E04]


title: neuM18_Mock

description: 10x Genomics 3' v3


title: C16_4 [120_P02_D04]


title: HSC, Activated, P1, rep2


title: HSC, Activated, P1, rep1


title: DMSO_HTB4273_D1

description: TC-83 nsP2-4


title: HSC, quiescent, 0h, rep4

value: quiescent


title: DMSO_HTB4273_C3

description: TC-83 nsP2-4


title: neuM17_Mock

description: 10x Genomics 3' v3


title: DMSO_HTB4273_C1

description: TC-83 nsP2-4


title: neuM16_Mock

description: 10x Genomics 3' v3


title: DMSO_HTB4273_B1

description: TC-83 nsP2-4


title: neuM15_Mock

description: 10x Genomics 3' v3


title: DMSO_HTB4273_A20

description: TC-83 nsP2-4


title: C15_8 [116_P02_H03]

source_name: Clonal subline C15


title: neuM14_RML

description: 10x Genomics 3' v3

value: RML

value: Prion


title: C16_1 [117_P02_A04]


title: C16_2 [118_P02_B04]


title: HSC, quiescent, 0h, rep1


title: C16_3 [119_P02_C04]


title: neuM20_Mock

description: 10x Genomics 3' v3


title: HSC, quiescent, 0h, rep2


title: HSC, quiescent, 0h, rep3


title: neuM13_RML

description: 10x Genomics 3' v3


title: neuM12_RML

description: 10x Genomics 3' v3


title: C15_6 [114_P02_F03]


title: DMSO_HTB4273_A1

description: TC-83 nsP2-4


title: DMSO_HTB4272_P1

description: TC-83 nsP2-4


title: neuM11_RML

description: 10x Genomics 3' v3


title: C15_4 [112_P02_D03]


title: DMSO_HTB4272_O14

description: TC-83 nsP2-4


title: DMSO_HTB4272_O21

description: TC-83 nsP2-4


title: C15_5 [113_P02_E03]


title: neuM10_RML

description: 10x Genomics 3' v3


title: C15_3 [111_P02_C03]


title: neuM09_RML

description: 10x Genomics 3' v3


title: DMSO_HTB4272_O1

description: TC-83 nsP2-4


title: C15_2 [110_P02_B03]


title: DMSO_HTB4272_N20

description: TC-83 nsP2-4


title: DMSO_HTB4272_N1

description: TC-83 nsP2-4


title: neuM07_RML

description: 10x Genomics 3' v3


title: C14_7 [107_P02_G02]

source_name: Clonal subline C14


title: C15_1 [109_P02_A03]


title: neuM06_Mock

description: 10x Genomics 3' v3


title: neuM08_RML

description: 10x Genomics 3' v3


title: DMSO_HTB4272_M1

description: TC-83 nsP2-4


title: DMSO_HTB4272_L1

description: TC-83 nsP2-4


title: C14_8 [108_P02_H02]


title: C14_6 [106_P02_F02]


title: DMSO_HTB4272_L9

description: TC-83 nsP2-4


title: neuM04_RML

description: 10x Genomics 3' v3


title: neuM03_RML

description: 10x Genomics 3' v3


title: C14_5 [105_P02_E02]


title: DMSO_HTB4272_K1

description: TC-83 nsP2-4


title: C14_4 [104_P02_D02]


title: DMSO_HTB4272_J23

description: TC-83 nsP2-4


title: C14_3 [103_P02_C02]


title: neuM02_Mock

description: 10x Genomics 3' v3


title: C14_2 [102_P02_B02]


title: DMSO_HTB4272_J1

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Swap1-Day10_rep1

data_processing:
Sequence reads were trimmed for adaptor sequence using Trim Galore.
Fastp v0.21.0 was used to remove potential adapters and low-quality reads (parameter: fastp -w 10)
HISAT2 v2.0.4 was applied to map the clean reads to GRCh38
Gene counts and the normalized expression value (TPM, transcripts per kilobase million) were computed by StringTie v2.1.4
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw gene counts and transcript counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: HCT116 cells with LNP-mSTELLA-Swap1 treatment at Day 10

growth_protocol: BeWo cells were maintained in Ham‘s F-12K complete medium.  NCCIT cells were maintained in RPMI 1640 complete medium. HCT116 and HCT116-UHRF1+/- cells (HCT116_UHRF1_def ) cells were maintained in McCoy's 5A complete medium. RKO cells were maintained in MEM complete medium.

extract_protocol:
Total RNA was isolated from cell pallets using RNAiso Plus reagent (Takara) and 1 μg total RNA was used to generate cDNA with the PrimeScript™ RT Master Mix (Takara). RNA was quantified with NanoDrop followed by integrity evaluation via Agilent 4200 TapeStation analysis according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using mRNA-Seq library kit following manufacturer's protocol.

treatment_protocol: BeWo and NCCIT cells were transduced by lentivirus expressing Cas9/sgRNA targeting hSTELLA. The single-cell clones were subsequently selected through serial dilution of these transduced cells, and verified by western blot and sequencing. CRC cells (HCT116, HCT116-UHRF1+/- and RKO cells) with lentivirus-mediated stable overexpression of STELLA orthologs were harvested on Day 9 post virus-transduction. HCT116 cells treated with LNP-mRNA or vehicle control were harvested on Days 2, 6 and 10.

value: Colon

value: colorectal carcinoma

value: LNP delivery of mSTELLA-Swap1 mRNA

value: LNP-mSTELLA-Swap1 treatment at Day 10


title: C14_1 [101_P02_A02]


title: DMSO_HTB4272_I12

description: TC-83 nsP2-4

data_processing:
Basecalling was done using Nanopore Guppy (ver. 5.1.12)
Sequencing reads were checked for read quality and de-multiplexed using 9 nt-long barcode sequence plus adjacent 10 nt primer sequence
Reads were aligned to Venezuelan equine encephalitis virus genome L01443.1 using Minimap2 (version 2.17-r941)
VCF for each sample was generated by SAMtools mpileup function using mapped BAM file.
Assembly: L01443.1
Supplementary files format and content: vcf format


title: C13_8 [100_P02_H01]

source_name: Clonal subline C13


title: HCT116_LNP-mSTELLA-Day10_rep1

source_name: HCT116 cells with LNP-mSTELLA treatment at Day 10

value: LNP delivery of mSTELLA mRNA

value: LNP-mSTELLA treatment at Day 10


title: C13_7 [99_P02_G01]


title: neuM05_Mock

description: 10x Genomics 3' v3

value: Telencephalon

value: female


title: DMSO_HTB4272_I10

description: TC-83 nsP2-4


title: HCT116_LNP-Day10_rep1

source_name: HCT116 cells with LNP treatment at Day 10

value: WT

value: LNP treatment at Day 10


title: DMSO_HTB4272_I1

description: TC-83 nsP2-4


title: DMSO_HTB4272_G21

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Swap1-Day6_rep2

source_name: HCT116 cells with LNP-mSTELLA-Swap1 treatment at Day 6

value: LNP-mSTELLA-Swap1 treatment at Day 6


title: HCT116_LNP-Day10_rep2


title: DMSO_HTB4272_D19

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Swap1-Day6_rep1


title: C13_4 [96_P02_D01]

value: Melanoma cell line

value: HGF-tg C57BL6


title: C13_5 [97_P02_E01]

value: single cells sorted from homogeneous culture


title: HCT116_LNP-mSTELLA-Day10_rep2


title: C13_3 [95_P02_C01]


title: DMSO_HTB4272_B14

description: TC-83 nsP2-4

value: DMSO


title: DMSO_HTB4272_I17

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Day6_rep1

source_name: HCT116 cells with LNP-mSTELLA treatment at Day 6

value: LNP-mSTELLA treatment at Day 6


title: HCT116_LNP-mSTELLA-Swap1-Day10_rep2


title: C15_7 [115_P02_G03]


title: DMSO_HTB4272_A5

description: TC-83 nsP2-4


title: C13_6 [98_P02_F01]


title: HCT116_LNP-mSTELLA-Day6_rep2


title: DMSO_HTB4272_A10

description: TC-83 nsP2-4


title: HCT116_LNP-Day6_rep1

source_name: HCT116 cells with LNP treatment at Day 6

value: LNP treatment at Day 6


title: C13_1 [93_P02_A01]


title: C12_8 [92_P01_H12]

source_name: Clonal subline C12


title: DMSO_HTB4271_P23

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Swap1-Day2_rep2

source_name: HCT116 cells with LNP-mSTELLA-Swap1 treatment at Day 2

value: Colon

value: LNP-mSTELLA-Swap1 treatment at Day 2


title: C12_7 [91_P01_G12]


title: C12_6 [90_P01_F12]


title: DMSO_HTB4271_P19

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Day2_rep2

source_name: HCT116 cells with LNP-mSTELLA treatment at Day 2

value: colorectal carcinoma

value: LNP-mSTELLA treatment at Day 2


title: HCT116_LNP-mSTELLA-Swap1-Day2_rep1

value: LNP delivery of mSTELLA-Swap1 mRNA


title: DMSO_HTB4271_P16

description: TC-83 nsP2-4


title: DMSO_HTB4271_N14

description: TC-83 nsP2-4


title: DMSO_HTB4271_N12

description: TC-83 nsP2-4


title: C12_5 [89_P01_E12]


title: DMSO_HTB4272_D11

description: TC-83 nsP2-4


title: HCT116_LNP-Day2_rep2

source_name: HCT116 cells with LNP treatment at Day 2

value: LNP treatment at Day 2


title: HCT116_LNP-mSTELLA-Day2_rep1

value: LNP delivery of mSTELLA mRNA


title: C13_2 [94_P02_B01]


title: DMSO_HTB4271_M21

description: TC-83 nsP2-4


title: HCT116_LNP-Day6_rep2


title: HCT116_LNP-Day2_rep1


title: C12_1 [85_P01_A12]


title: HCT116_UHRF1_def_mSTELLA-Swap2_rep1

source_name: HCT116-UHRF1+/- cells (HCT116_UHRF1_def ) stably expressing mSTELLA-Swap2

value: mSTELLA-Swap2 stable overexpression and UHRF1+/-

value: stably expressing mSTELLA-Swap2


title: DMSO_HTB4271_J13

description: TC-83 nsP2-4


title: DMSO_HTB4271_L7

description: TC-83 nsP2-4


title: HCT116_UHRF1_def_mSTELLA-Swap2_rep2


title: C11_8 [84_P01_H11]

source_name: Clonal subline C11


title: HCT116_UHRF1_def_mSTELLA-Swap1_rep2

source_name: HCT116-UHRF1+/- cells (HCT116_UHRF1_def ) stably expressing mSTELLA-Swap1

value: mSTELLA-Swap1 stable overexpression and UHRF1+/-

value: stably expressing mSTELLA-Swap1


title: DMSO_HTB4271_H20

description: TC-83 nsP2-4


title: C11_7 [83_P01_G11]

value: Melanoma cell line


title: DMSO_HTB4271_H16

description: TC-83 nsP2-4


title: HCT116_UHRF1_def_mSTELLA-Swap1_rep1


title: C12_4 [88_P01_D12]

value: HGF-tg C57BL6


title: DMSO_HTB4271_H1

description: TC-83 nsP2-4


title: HCT116_UHRF1_def_mSTELLA_rep2

source_name: HCT116-UHRF1+/- cells (HCT116_UHRF1_def ) stably expressing mSTELLA

value: mSTELLA stable overexpression and UHRF1+/-

value: stably expressing mSTELLA


title: HCT116_UHRF1_def_mSTELLA_rep1


title: C11_4 [80_P01_D11]

value: single cells sorted from homogeneous culture


title: C11_5 [81_P01_E11]


title: C11_6 [82_P01_F11]


title: HCT116_UHRF1_def_hSTELLA_rep2

source_name: HCT116-UHRF1+/- cells (HCT116_UHRF1_def ) stably expressing hSTELLA

value: hSTELLA stable overexpression and UHRF1+/-

value: stably expressing hSTELLA


title: DMSO_HTB4271_G23

description: TC-83 nsP2-4

value: DMSO


title: C12_2 [86_P01_B12]


title: C12_3 [87_P01_C12]


title: C11_2 [78_P01_B11]


title: C11_3 [79_P01_C11]


title: HCT116_UHRF1_def_hSTELLA_rep1

value: Colon

value: colorectal carcinoma


title: DMSO_HTB4271_G1

description: TC-83 nsP2-4


title: C11_1 [77_P01_A11]


title: DMSO_HTB4271_F1

description: TC-83 nsP2-4


title: HCT116_UHRF1_def_EV_rep2

source_name: HCT116-UHRF1+/- cells (HCT116_UHRF1_def ) stably expressing empty vector

value: stably expressing empty vector


title: DMSO_HTB4271_D21

description: TC-83 nsP2-4


title: C10_8 [76_P01_H10]

source_name: Clonal subline C10


title: HCT116_UHRF1_def_EV_rep1


title: RKO_mSTELLA-OE_rep2

source_name: RKO cells stably expressing mSTELLA

value: RKO

value: mSTELLA stable overexpression


title: DMSO_HTB4271_E1

description: TC-83 nsP2-4


title: C10_7 [75_P01_G10]


title: RKO_mSTELLA-OE_rep1


title: C10_6 [74_P01_F10]


title: DMSO_HTB4271_D1

description: TC-83 nsP2-4


title: RKO_hSTELLA-OE_rep2

source_name: RKO cells stably expressing hSTELLA

value: hSTELLA stable overexpression


title: PANC1 cells, 1 hr 10 ng/ml TNF + 1 µg/ml dox treatment

city: London

first: Chris

last: Bakal

address: 237 Fulham Road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
Basecalling - Illumina bcl2fastq2 (v2.20)
Alignment - STAR (v2.7.6a)
Feature counts - HTSeq v0.12.4 (option HTSeq-count)
Assembly: Hg38 release GRCh38.92
Supplementary files format and content: tab-delimited text file includes raw counts and library names for all samples

source_name: Pancreatic

growth_protocol: MIA Paca2 and PANC1 cells were maintained at 37 °C and 5 % CO2 in Dulbecco’s Modified Eagle Medium supplemented with 10 % heat-inactivated Fetal Bovine Serum and 1 % Penicillin/Streptomycin.

extract_protocol:
RNA was extracted using RNeasy Plus mini kit (Qiagen).
DNase Treatment using TURBO DNAse (Thermo Fisher), PolyA selection using NEBNext PolyA mRNA  Magnetic Isolation Module (NEB) and Library Preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: Cells were seeded in t25s to attain 30 % confluence the following day. 24 hr after seeding, cells were treated with 1 µg/ml dox or DMSO. After 48 hr dox, cells were treated with TNFα at a final concentration of 0.01 ng/ml, 0.1 ng/ml or 10 ng/ml, or with a BSA/PBS control for 1 hr or 5 hr.

value: Pancreatic

value: Pancreatic ductal adenocarcinoma

tag: genetic information

value: Doxycycline-inducible lentiviral IκB-SR

value: 10 ng/ml TNF + 1 µg/ml dox

tag: time

value: 1 hr


title: DMSO_HTB4271_C20

description: TC-83 nsP2-4

tag: treatment


title: C10_5 [73_P01_E10]

value: Melanoma cell line

value: HGF-tg C57BL6


title: DMSO_HTB4271_C1

description: TC-83 nsP2-4


title: RKO_EV_rep2

source_name: RKO cells stably expressing empty vector

tag: tissue

value: WT


title: PANC1 cells, 1 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment

tag: cell line

value: 0.1 ng/ml TNF + 1 µg/ml dox


title: C10_4 [72_P01_D10]

tag: strain

value: single cells sorted from homogeneous culture


title: DMSO_HTB4271_G9

description: TC-83 nsP2-4

value: DMSO


title: DMSO_HTB4271_B19

description: TC-83 nsP2-4


title: RKO_EV_rep1

value: Colon


title: PANC1 cells, 5 hr DMSO + 1 µg/ml dox treatment

value: DMSO + 1 µg/ml dox

value: 5 hr


title: C10_2 [70_P01_B10]


title: C10_3 [71_P01_C10]


title: PANC1 cells, 1 hr DMSO + 1 µg/ml dox treatment


title: DMSO_HTB4271_B1

description: TC-83 nsP2-4


title: C10_1 [69_P01_A10]


title: DMSO_HTB4271_A21

description: TC-83 nsP2-4


title: PANC1 cells, 5 hr 10 ng/ml TNF treatment

value: 10 ng/ml TNF


title: HCT116_mSTELLA-OE_rep2

source_name: HCT116 cells stably expressing mSTELLA

value: colorectal carcinoma

value: mSTELLA stable overexpression

value: HCT116 cells stably expressing mSTELLA


title: HCT116_mSTELLA-OE_rep1


title: PANC1 cells, 5 hr 10 ng/ml TNF + 1 µg/ml dox treatment

value: Pancreatic

value: Pancreatic ductal adenocarcinoma


title: DMSO_HTB4271_C6

description: TC-83 nsP2-4


title: DMSO_HTB4271_A11

description: TC-83 nsP2-4


title: PANC1 cells, 5 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment

value: Doxycycline-inducible lentiviral IκB-SR


title: HCT116_hSTELLA-OE_rep2

source_name: HCT116 cells stably expressing hSTELLA

value: hSTELLA stable overexpression

value: HCT116 cells stably expressing hSTELLA


title: RKO_hSTELLA-OE_rep1

value: RKO

value: stably expressing hSTELLA


title: PANC1 cells, 1 hr 10 ng/ml TNF treatment

value: 1 hr


title: C9_8 [68_P01_H09]

source_name: Clonal subline C9

value: Melanoma cell line

value: HGF-tg C57BL6

value: single cells sorted from homogeneous culture


title: PANC1 cells, 5 hr 0.1 ng/ml TNF treatment

value: 0.1 ng/ml TNF


title: DMSO_HTB4271_A1

description: TC-83 nsP2-4

value: DMSO


title: HCT116_hSTELLA-OE_rep1

value: Colon


title: C9_6 [66_P01_F09]


title: PANC1 cells, 1 hr 0.1 ng/ml TNF treatment


title: HCT116_EV_rep2

source_name: HCT116 cells stably expressing empty vector

value: colorectal carcinoma

value: WT


title: ML336_EIDD1931_1uM_1_HTB7391_K5

description: TC-83 nsP2-4


title: ML336_EIDD1931_1uM_1_HTB7391_F15

description: TC-83 nsP2-4


title: C9_5 [65_P01_E09]


title: HCT116_EV_rep1

value: HCT116 cells stably expressing empty vector


title: ML336_EIDD1931_1uM_1_HTB7391_A7

description: TC-83 nsP2-4


title: C9_4 [64_P01_D09]


title: PANC1 cells, 5 hr 0.01 ng/ml TNF treatment

value: Pancreatic

value: 0.01 ng/ml TNF

value: 5 hr


title: PANC1 cells, 1 hr 0.01 ng/ml TNF treatment

value: Pancreatic ductal adenocarcinoma

value: Doxycycline-inducible lentiviral IκB-SR


title: C9_3 [63_P01_C09]


title: ML336_EIDD1931_1uM_1_HTB7391_A16

description: TC-83 nsP2-4


title: NCCIT_hSTELLA-KO-c1

source_name: Clone 1 from hSTELLA-targeting sgRNA transduced NCCIT cells

value: Mediastinum

value: NCCIT

value: embryonalcarcinoma

value: hSTELLA knock-out


title: NCCIT_hSTELLA-KO-c2

source_name: Clone 2 from hSTELLA-targeting sgRNA transduced NCCIT cells


title: C9_1 [61_P01_A09]

value: Melanoma cell line

value: HGF-tg C57BL6


title: C9_2 [62_P01_B09]

value: single cells sorted from homogeneous culture


title: NCCIT_SCR-c2

source_name: Clone 2 from sgSCR transduced NCCIT cells

value: Clone 2 from sgSCR transduced


title: C8_6 [60_P01_H08]

source_name: Clonal subline C8


title: ML336_EIDD1931_1uM_1_HTB7384_P4

description: TC-83 nsP2-4


title: MIA PaCa2 cells, 1 hr 10 ng/ml TNF + 1 µg/ml dox treatment

value: MIA PaCa2

value: 10 ng/ml TNF + 1 µg/ml dox

value: 1 hr


title: ML336_EIDD1931_1uM_1_HTB7384_M21

description: TC-83 nsP2-4


title: C9_7 [67_P01_G09]


title: C8_5 [59_P01_G08]


title: NCCIT_SCR-c1

source_name: Clone 1 from sgSCR transduced NCCIT cells

value: WT

value: Clone 1 from sgSCR transduced


title: ML336_EIDD1931_1uM_1_HTB7384_J22

description: TC-83 nsP2-4


title: ML336_EIDD1931_1uM_1_HTB7384_P23

description: TC-83 nsP2-4


title: BeWo_hSTELLA-KO-c3

source_name: Clone 3 from hSTELLA-targeting sgRNA transduced BeWo cells

value: Placenta

value: BeWo

value: choriocarcinoma


title: PANC1 cells, 1 hr DMSO treatment

value: Pancreatic

value: Pancreatic ductal adenocarcinoma

value: Doxycycline-inducible lentiviral IκB-SR

value: DMSO


title: ML336_EIDD1931_1uM_1_HTB7384_I3

description: TC-83 nsP2-4


title: MIA PaCa2 cells, 1 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment

value: 0.1 ng/ml TNF + 1 µg/ml dox


title: MIA PaCa2 cells, 5 hr DMSO + 1 µg/ml dox treatment

value: DMSO + 1 µg/ml dox

value: 5 hr


title: PANC1 cells, 5 hr DMSO treatment


title: BeWo_hSTELLA-KO-c1

source_name: Clone 1 from hSTELLA-targeting sgRNA transduced BeWo cells

value: hSTELLA knock-out


title: NCCIT_hSTELLA-KO-c3

source_name: Clone 3 from hSTELLA-targeting sgRNA transduced NCCIT cells

value: Mediastinum

value: NCCIT

value: embryonalcarcinoma


title: MIA PaCa2 cells, 5 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment

value: MIA PaCa2


title: C8_4 [58_P01_F08]

value: Melanoma cell line

value: HGF-tg C57BL6

value: single cells sorted from homogeneous culture


title: ML336_EIDD1931_1uM_1_HTB7384_G11

description: TC-83 nsP2-4


title: C8_2 [56_P01_B08]


title: BeWo_hSTELLA-KO-c2

source_name: Clone 2 from hSTELLA-targeting sgRNA transduced BeWo cells

value: Placenta

value: BeWo


title: C8_3 [57_P01_E08]


title: ML336_EIDD1931_1uM_1_HTB7384_A3

description: TC-83 nsP2-4


title: MIA PaCa2 cells, 1 hr DMSO + 1 µg/ml dox treatment

value: Pancreatic

value: 1 hr


title: MIA PaCa2 cells, 5 hr 10 ng/ml TNF + 1 µg/ml dox treatment

value: Pancreatic ductal adenocarcinoma

value: Doxycycline-inducible lentiviral IκB-SR

value: 10 ng/ml TNF + 1 µg/ml dox


title: ML336_EIDD1931_1uM_1_HTB7383_P19

description: TC-83 nsP2-4


title: MIA PaCa2 cells, 5 hr 10 ng/ml TNF treatment

value: 10 ng/ml TNF


title: MIA PaCa2 cells, 1 hr 10 ng/ml TNF treatment


title: C7_8 [54_P01_H07]

source_name: Clonal subline C7


title: BeWo_SCR-c1

source_name: Clone 1 from sgSCR transduced BeWo cells

value: choriocarcinoma

value: WT

value: Clone 1 from sgSCR transduced


title: ML336_EIDD1931_1uM_1_HTB7383_O4

description: TC-83 nsP2-4


title: ML336_EIDD1931_1uM_1_HTB7383_F9

description: TC-83 nsP2-4


title: MIA PaCa2 cells, 5 hr 0.1 ng/ml TNF treatment

source_name: Pancreatic

value: 0.1 ng/ml TNF

value: 5 hr


title: ML336_EIDD1931_1uM_1_HTB7383_D5

description: TC-83 nsP2-4


title: C7_5 [51_P01_E07]


title: ML336_EIDD1931_1uM_1_HTB7383_C15

description: TC-83 nsP2-4


title: MIA PaCa2 cells, 1 hr 0.1 ng/ml TNF treatment

value: MIA PaCa2


title: KO, CD-fed, infertile, rep3

city: Tokyo

first: Yoshihide

last: Yamanashi

address: 7-3-1 Hongo, Bunkyo-ku

department: Pharmacy

country: Japan

institute: The University of Tokyo Hospital

description: Sample 7

data_processing:
RaNA-seq (an online bioinformatics tool for the analysis of RNA-seq data, https://ranaseq.eu/index.php)
Assembly: GRCm38
Supplementary files format and content: Excel file (RNAseq_TPMs.xlsx) includes TPM values for each sample

source_name: Ovary

extract_protocol:
Ovaries were collected from 8- to 12-week-old female mice. Each ovary was then homogenized in 200 µL RNAiso Plus (TaKaRa, Osaka, Japan) (1 ovary/200 µL RNAiso Plus), incubated at room temperature for 5 min, centrifuged at 12,000 × g for 5 min, and the supernatant was collected. Then, 40 µL chloroform was added to the collected supernatant, shaken vigorously, incubated at room temperature for 5 min, centrifuged at 12,000 × g for 15 min, and the top layer was collected. To the collected top layer, 200 µL isopropanol was added, mixed by inversion, incubated at room temperature for 10 min, centrifuged at 12,000 × g for 10 min, and the supernatant was removed. Next, 200 µL of ice-cold 75% ethanol was added to the pellet, centrifuged at 7,500 × g for 5 min, and the supernatant was removed. After the pellet was air-dried, it was redissolved in 16 µL of diethylpyrocarbonate-treated water, incubated at 65°C for 5 min, and rapidly cooled on ice. The resulting RNA extract was purified using the PicoPure® RNA Isolation Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions.
Outsourced to Eurofins Genomics (Tokyo, Japan)

value: Ovary

value: Abcg5/g8 KO

value: CD-fed


title: KO, VOFD-fed, fertile, rep2

description: Sample 6

value: VOFD-fed


title: MIA PaCa2 cells, 5 hr 0.01 ng/ml TNF treatment

value: 0.01 ng/ml TNF


title: C7_4 [50_P01_D07]

value: Melanoma cell line

value: HGF-tg C57BL6

value: single cells sorted from homogeneous culture


title: KO, CD-fed, infertile, rep2

description: Sample 5


title: C7_3 [49_P01_C07]


title: WT, CD-fed, fertile, rep2

description: Sample 4


title: MIA PaCa2 cells, 1 hr 0.01 ng/ml TNF treatment

value: Pancreatic

value: Pancreatic ductal adenocarcinoma

value: Doxycycline-inducible lentiviral IκB-SR

value: 1 hr


title: BeWo_SCR-c3

source_name: Clone 3 from sgSCR transduced BeWo cells

value: Placenta

value: BeWo

value: choriocarcinoma

value: WT

value: Clone 3 from sgSCR transduced


title: BeWo_SCR-c2

source_name: Clone 2 from sgSCR transduced BeWo cells

value: Clone 2 from sgSCR transduced


title: KO, VOFD-fed, fertile, rep1

description: Sample 3

value: Ovary

value: Abcg5/g8 KO


title: ML336_EIDD1931_1uM_1_HTB7383_A14

description: TC-83 nsP2-4

extract_protocol:
VEEV TC-83 nsP234 region is PCR-amplified from cDNA synthesized from viral RNA.
For samples sequenced with Nanopore MinION, Nanopore ligation-based sequencing kit was used. For samples sequenced with PacBio Sequel IIe, samples were prepared into SMRTbell template libraries.


title: MIA PaCa2 cells, 1 hr DMSO treatment

value: MIA PaCa2

value: DMSO


title: MIA PaCa2 cells, 5 hr DMSO treatment

value: 5 hr


title: C7_6 [52_P01_F07]

value: Melanoma cell line

value: HGF-tg C57BL6


title: C7_2 [48_P01_B07]

value: single cells sorted from homogeneous culture


title: ML336_EIDD1931_1uM_1_HTB7382_M8

description: TC-83 nsP2-4


title: ML336_EIDD1931_1uM_1_HTB7382_M19

description: TC-83 nsP2-4


title: C7_1 [47_P01_A07]


title: input_SOX3

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Reads were trimmed to remove NEBNext Ultra II DNA (TruSeq) adaptors with bclconvert (v 00.000.000.3.9.3).
Mapping and peak calling were perfromed with BWA and MACS2 (nf-core/chipseq version 2.0.0) on the human genome hg38 with the following parameters: macs_gsize = 2.7e9, macs_fdr = 0.05, narrow_peak = true, all other parameters were left to default.
Peak calling was performed with MACS2 on pooled replicates.
Assembly: hg38
Supplementary files format and content: bedgragh, narrowPeak (except for input samples)

growth_protocol: MB157 cells were obtained from the American Type Culture Collection and were cultured in DMEM supplemented with 10% foetal bovine serum and antibiotics at 37°C in a 5% CO2humidified atmosphere. MB157R are GSI-resistant MB157. Drug resistant cells were generated by treating the MB157 cells for 25 weeks with 1µM GSI (Spirochem, LY3039478), replenishing the inhibitor every 3-4 days. Cells were maintained at a minimal density of 2.5-3 × 106 cells/10-cm dish.

extract_protocol:
Adherent cells were directly fixed into the dishes with 2mM DSG (Santa Cruz, Cat# sc-285455) + 1mM MgCl2 in 8ml 1X PBS for 45min at room temperature. Then cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies, Cat# 28906) and quenched with 0.125 M glycine. Cells were lysed with lysis buffer LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100, Protease inhibitor cocktail (Sigma, Cat # P8340)) twice during 10 minutes at 4 °C. Nuclear lysis was performed using LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, Protease inhibitor cocktail (Sigma, Cat # P8340)) for 10 minutes at 4°C. The cell pellet was rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS, Protease inhibitor cocktail), resuspended in 1ml SDS shearing buffer and transferred to a milliTUBE 1 ml AFA fiber. Chromatin was sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 18 min, 200 cycles, 5% duty, 140W. The IP reactions were performed following the protocols of the Diagenode iDeal ChIP-seq kit for Transcription Factors (Diagenode, Cat# C01010170). For each IP reaction, 4 million cells were used. Sheared chromatin was immunoprecipitated overnight at 4°C with HA (Abcam Cat #ab9110, 2µg), RBPJ (CST Cat #5313, 1:50) or SOX2 (CST Cat #23064, 1:50) antibodies. Eluted DNA was quantified with Qubit (Thermo Fisher) and Agilent Fragment Analyzer (Advanced Analytical).
We performed a "NEBNext Ultra II DNA" library prep starting from 3 ng of DNA for 'Chip' samples and 10ng of DNA for 'input' samples (see table below), according to New England Biolabs' protocol NEBNext Ultra™ II DNA Library Prep Kit, Version 6.1_5/20 (internal exp code RPX030). We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation TS4200.

treatment_protocol: Expression of SOX2-HA or N1-ICD was induced with 1µg/ml doxycycline (Merck, Cat #D9891) for 72h.

value: Triple Negative Breast Cancer

value: Wild type


title: input_SOX2


title: ML336_EIDD1931_1uM_1_HTB7382_L15

description: TC-83 nsP2-4


title: C8_1 [55_P01_A08]


title: C6_7 [45_P01_G06]

source_name: Clonal subline C6


title: input_SOX1


title: ML336_EIDD1931_1uM_1_HTB7382_A21

description: TC-83 nsP2-4


title: C6_6 [44_P01_F06]


title: ML336_EIDD1931_1uM_1_HTB7382_D22

description: TC-83 nsP2-4


title: input_Px3

value: GSI-resistant MB157R

value: Dox-EV


title: Colchicine treated3

city: Hefei

first: Yaping

last: Zhao

address: No. 443 Huangshan Road

institute: University of Science and Technology of China

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: aorta

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qisagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: aorta


title: C6_5 [43_P01_E06]


title: ML336_EIDD1931_1uM_1_HTB7383_A20

city: Louisville

first: Jae Yeon

institute: University of Louisville

description: TC-83 nsP2-4


title: KO, CD-fed, infertile, rep1

description: Sample 2

value: CD-fed


title: ML336_EIDD1931_1uM_1_HTB7381_P20

description: TC-83 nsP2-4


title: input_Px1


title: input_Px2


title: ML336_EIDD1931_1uM_1_HTB7382_A16

description: TC-83 nsP2-4


title: Vehicle control4


title: WT, CD-fed, fertile, rep1

description: Sample 1

value: WT


title: C6_3 [41_P01_C06]


title: C6_8 [46_P01_H06]


title: Colchicine treated4


title: Colchicine treated1


title: C7_7 [53_P01_G07]


title: ML336_EIDD1931_1uM_1_HTB7381_N16

description: TC-83 nsP2-4


title: Colchicine treated2


title: Vehicle control3


title: C6_2 [40_P01_B06]


title: input_N3

value: Dox-NICD


title: ML336_EIDD1931_1uM_1_HTB7381_J20

description: TC-83 nsP2-4


title: C6_1 [39_P01_A06]


title: input_N2


title: input_N1


title: C6_4 [42_P01_D06]


title: Vehicle control2


title: ML336_EIDD1931_1uM_1_HTB7381_J15

description: TC-83 nsP2-4


title: ML336_EIDD1931_1uM_1_HTB7381_J11

description: TC-83 nsP2-4


title: C5_8 [38_P01_H05]

source_name: Clonal subline C5


title: Vehicle control1


title: C5_7 [37_P01_G05]


title: ML336_EIDD1931_1uM_1_HTB7381_H1

description: TC-83 nsP2-4


title: input_EV3


title: ASXL1-MT_rep3

first: Naru

last: Sato

department: Graduate School of Pharmaceutical Sciences

institute: University of Tokyo

data_processing:
TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser).
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Normalization, the removal of batch effects of the count value, and the detection of significant expression differences were done using DESeq2 (version 2.2.1; Love et al., 2014), with raw counts generated from StringTie. The normalized count was log2-transformed and Z-score scaled before performing principal component and heatmap analyses, except for hierarchical clustering.
Differentially expressed genes were analyzed by Cuffdiff. A P-value > 0.05 was considered as not significant.
Assembly: mouse reference genome mm10 (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include log2  FPKM values for each sample

source_name: aorta macrophages

growth_protocol: The aorta were dissociated using a dissection microscope and micro-dissecting tools and collected the aortic arch and the ascending, descending, thoracic, and abdominal aorta. Whole aortas were rapidly minced in 200 μL aorta dissociation buffer, pipetted with 800 μL aorta dissociation buffer (125 U/mL Collagenase Type XI; Sigma, C7667, 60 U/mL Hyaluronidase type I; Sigma, H3506, 60 U/mL DNase I, 450 U/mL Collagenase Type I; Fujifilm, 037-17603, and 20 mM HEPES in 1x Phosphate Buffered Saline (PBS)) for a total volume of 1 mL, and incubated for 1 h at 37 °C while shaking at 220 rpm. The suspensions were passed through a 40-μm cell strainer into a new tube using the rubber piston of a syringe plunger. The cells were collected by centrifugation and suspended in cold FACS Buffer containing anti-mouse CD16/CD32 Fc receptor blocking antibody and then stained with anti-CD11b antibody and anti-F4/80 antibody. CD11b+ F4/80+ aortic plaque macrophages were sorted using the FACSAria.

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
The libraries for RNA sequencing were generated from fragmented DNA with eight cycles of amplification using a NEB Next Ultra DNA Library Prep Kit (New England Biolabs), according to the manufacturer’s instructions.

treatment_protocol: The lethally irradiated Ldlr-/- mice transplanted with BMCs from ASXL1-MT KI or control mice were fed the HFHCD (Research Diets Inc., D12108C)  after reconstitution for more than 1 month.   After 12 weeks of treatment, the murine aorta-cells were dissociated using the method described.

tag: background strain

value: aorta macrophages

value: VAV1-Cre+/- ASXL1-MTfl/fl

value: High-fat/High-cholesterol diet-fed for 12 weeks


title: ASXL1-MT_rep2


title: ML336_EIDD1931_1uM_1_HTB7381_G1

last: Hwang

description: TC-83 nsP2-4


title: C5_6 [36_P01_F05]

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples


title: SOX3_RBPJ

description:
SOX_RBPJ_IP.bigWig
SOX_RBPJ_IP_peaks.narrowPeak
SOX_RBPJ_IP_treat_pileup.bdg

tag: chip antibody

value: RBPJ


title: SOX3_HA

description:
SOX_HA_SOX2_IP.bigWig
SOX_HA_SOX2_IP_peaks.narrowPeak
SOX_HA_SOX2_IP_treat_pileup.bdg

value: HA


title: ML336_EIDD1931_1uM_1_HTB7381_F1

description: TC-83 nsP2-4


title: ASXL1-MT_rep1


title: C5_4 [34_P01_D05]


title: ML336_EIDD1931_1uM_1_HTB7381_E1

description: TC-83 nsP2-4


title: C5_3 [33_P01_C05]


title: WT_rep3

value: wild-type


title: ML336_EIDD1931_1uM_1_HTB7381_D13

description: TC-83 nsP2-4


title: input_EV2


title: WT_rep2


title: SOX2_RBPJ


title: C5_2 [32_P01_B05]

value: Melanoma cell line


title: ML336_EIDD1931_1uM_1_HTB7376_P8

description: TC-83 nsP2-4


title: C5_1 [31_P01_A05]

value: HGF-tg C57BL6


title: SOX2_HA


title: WT_rep1


title: T0_REP2

description: Time Zero

data_processing:
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK, v.0.5.9.2) was used to analyse the data. Reads were trimmed of their adapters with bcl2fastq (v2.19) and quality-controlled with fastQC (v0.11.5). Read count table was obtained using the MAGeCK count command with default parameters on the Human GeCKOv2 combined library of A and B.
Gene summary table was filtered to remove non targeting controls, genes with less than 4 guide RNAs and non-annotated genes. GSI and DMSO treated samples were compared using the MAGeCK test command with default parameters, producing Robust Rank Aggretion (RRA) tables.
Assembly: Human_GeCKOv2_combined
Supplementary files format and content: tab separated

growth_protocol: CRISPR-Cas9 screens were performed using Human GeCKOv2 library (Deposited on Addgene by Feng Zhang 52, Cat#1000000048 and #1000000049). A minimum of 6x107 Cas9-expressing MB157R cells (cultured with 8µg/mL blasticidin) were transduced at an MOI of 0.3-0.4 with the sgRNA library for minimum 200-fold coverage, in the presence of 1µg/mL polybrene (Santa Cruz, Cat#sc-134220) and seeded onto 10-cm dishes. Forty-eight hours post-transduction, medium was changed and replaced with fresh DMEM media containing 8µg/mL blasticidin (resistance for Cas9 plasmid) and 1µg/mL puromycin (resistance for sgRNA plasmid).

extract_protocol:
Genomic DNA was extracted using the using ZymoResearch Quick-gDNA MidiPrep Plus Kit (Zymo Research, Cat#ZYM-D4075-25TST) according to manufacturer’s protocol.
sgRNA sequences were amplified using Herculase II Fusion DNA polymerase (Agilent Technologies, Cat#600679) in two rounds: first round by GeCKO-F1/R1; second round by NGS-Lib_Fwd/Rev 1-10. PCR products were purified (Qiagen gel purification kit, Cat#28706, and Qiagen PCR purification kit, Cat#28106), quantified by Qubit (Thermo Fisher Scientific), and profiled by Fragment Analyzer (Advanced Analytical). Samples were sequenced on an Illumina NextSeq 500 Instrument (Illumina) according to the manufacturer instructions, yielding 24 to 36 million single-end 75 nucleotide reads per sample.

treatment_protocol: After 4 days of puromycin selection, cells were combined and two T0 samples (6x107 cells per sample) were collected and stored at -80°C for later processing. Remaining cells were divided into triplicates and cultured with DMSO (AppliChem, Cat#A3672.0100) or GSI (Spirochem, LY3039478) at 10µM (Spirochem, LY3039478) for an additional 14 days. At this point cells were collected in 6x107 cell aliquots (200-fold coverage) for gDNA extraction.


title: C5_5 [35_P01_E05]

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

value: single cells sorted from homogeneous culture


title: SOX1_RBPJ

value: Triple Negative Breast Cancer


title: T0_REP1

description: Time Zero


title: ML336_EIDD1931_1uM_1_HTB7376_B20

description: TC-83 nsP2-4


title: SOX1_HA

value: Wild type


title: C4_6 [29_P01_F04]

source_name: Clonal subline C4


title: LY_REP3

description: Day 14

value: GSI-resistant MB157R

value: GSI


title: ML336_EIDD1931_1uM_1_HTB7376_B18

description: TC-83 nsP2-4


title: Px3_SOX2

description:
Px_SOX2_IP.bigWig
Px_SOX2_IP_peaks.narrowPeak
Px_SOX2_IP_treat_pileup.bdg

value: Dox-EV


title: LY_REP2

description: Day 14


title: C4_5 [28_P01_E04]


title: ML336_EIDD1931_1uM_1_HTB7376_A2

description: TC-83 nsP2-4


title: C4_3 [26_P01_C04]


title: Px3_RBPJ

description:
Px_RBPJ_IP.bigWig
Px_RBPJ_IP_peaks.narrowPeak
Px_RBPJ_IP_treat_pileup.bdg


title: ML336_EIDD1931_1uM_1_HTB7375_P21

description: TC-83 nsP2-4


title: DMSO_REP3

description: Day 14

value: DMSO


title: Px2_RBPJ


title: LY_REP1

description: Day 14


title: ML336_EIDD1931_1uM_1_HTB7376_D15

description: TC-83 nsP2-4


title: Px2_SOX2


title: ML336_EIDD1931_1uM_1_HTB7375_O17

description: TC-83 nsP2-4


title: ML336_EIDD1931_1uM_1_HTB7376_A5

description: TC-83 nsP2-4


title: C4_7 [30_P01_H04]


title: ML336_EIDD1931_1uM_1_HTB7375_N16

description: TC-83 nsP2-4


title: C4_2 [25_P01_B04]


title: DMSO_REP2

description: Day 14


title: scRNAseq_MT_rep2

description: 10x Genomics

data_processing:
Raw data files (Base call files) were demultiplexed into fastq files using Cell Ranger with mkfastq command. Then, the "cellranger count" command was used for feature counts and barcode counts with reference “refdata-gex-mm10-2020-A”. Subsequent analyses were performed using Seurat 4.1.0. Quality filtering for each feature and cell was conducted based on these criteria (min.cells = 3 & min.features = 200 & nFeature_RNA > 3 & nFeature_RNA < 6500 & percent.mt < 10). Feature counts were log-normalized with the function “NormalizeData”. Two thousand highly variable features were selected for PCA. PC 1-16 components were used for UMAP and graph-based clustering with the functions FindNeighbors (object, reduction = "pca", dims = 1:15) and FindClusters (object, resolution = 0.4). Differentially expressed genes were selected with the function “FindMarkers (object, min.pct = 0.25)”.
Mutational effects on cell abundance were statistically quantified using the previously published Preleukemic Mouse Cell Atlas pipeline.
Assembly: mouse reference genome mm10
Supplementary files format and content: tab-separated values file and matrix file

source_name: CD45+ plaque cells

extract_protocol:
The aorta were dissociated using a dissection microscope and micro-dissecting tools and collected the aortic arch and the ascending, descending, thoracic, and abdominal aorta. Whole aortas were rapidly minced in 200 μL aorta dissociation buffer, pipetted with 800 μL aorta dissociation buffer (125 U/mL Collagenase Type XI; Sigma, C7667, 60 U/mL Hyaluronidase type I; Sigma, H3506, 60 U/mL DNase I, 450 U/mL Collagenase Type I; Fujifilm, 037-17603, and 20 mM HEPES in 1x Phosphate Buffered Saline (PBS)) for a total volume of 1 mL, and incubated for 1 h at 37 °C while shaking at 220 rpm. The suspensions were passed through a 40-μm cell strainer into a new tube using the rubber piston of a syringe plunger. The cells were collected by centrifugation and suspended in cold FACS Buffer containing anti-mouse CD16/CD32 Fc receptor blocking antibody and then stained with anti-CD45 antibody. CD45+ aortic plaque cells were sorted using the FACSAria.
ScRNA-seq and data processing mRNA were isolated, and libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (11x Genomics) as per manufacturer’s instructions.

tag: Sex

value: female

value: CD45+ plaque cells


title: input_EV1


title: C4_4 [27_P01_D04]


title: ML336_EIDD1931_1uM_1_HTB7375_H9

description: TC-83 nsP2-4


title: N3_SOX2

description:
N_SOX2_IP.bigWig
N_SOX2_IP_peaks.narrowPeak
N_SOX2_IP_treat_pileup.bdg

value: Dox-NICD


title: DMSO_REP1

description: Day 14


title: Px1_RBPJ


title: Px1_SOX2


title: C3_7 [23_P01_G03]

source_name: Clonal subline C3


title: ML336_EIDD1931_1uM_1_HTB7375_H15

description: TC-83 nsP2-4


title: N3_RBPJ

description:
N_RBPJ_IP.bigWig
N_RBPJ_IP_peaks.narrowPeak
N_RBPJ_IP_treat_pileup.bdg


title: C4_1 [24_P01_A04]


title: N2_SOX2


title: ML336_EIDD1931_1uM_1_HTB7375_A20

description: TC-83 nsP2-4


title: N2_RBPJ


title: PLX Control ATACseq rep2

city: Cold Spring Harbor

first: Lucas

last: Cheadle

state: NY

address: 1 Bungtown Rd

department: Neuroscience

institute: Cold Spring Harbor Laboratory

data_processing:
Fastq files were processed using the ENCODE ATAC-seq pipeline with default parameters.
Bigwig files generated using DeepTools version 3.5.0, bin size 1, normalize CPM
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.

source_name: dLGN

growth_protocol: P27 Fn14 KO and WT littermates. C57Bl/6J P32 mice.

extract_protocol:
Fn14: Mice were euthanised and their brains flash frozen. At the time of processing, coronal sections including both the hippocampus and dLGN were dissected. PLX: dLGNs were microdissected. Fn14 & PLX: Samples were homoginsed in a dounce and tight pestel 40x with ATAC buffer (AB (in mM): 10 Tris-HCl pH 7.4, 10 NaCl, 3 MgCl2, .5 Spermidine, .15 Spermine, 1 DTT, and .1 % Igepal, 1X Phosphatase inhibitors, 1X Protease inhibitors). The samples were then spun at 500 rcf for 10 minutes. The pellet was resuspended in 1.4 mL fresh AB and dounced once again 12 times. Next, the nuclei were washed by spinning for 5 minutes and resuspending in fresh AB. 50,000 nuclei were aliquoted according to the nuclei concentration obtained using the Countess II FL Automated Cell Counter. Aliquots were spun once more at 500 rcf, and then resuspended in 20 µL of DNAse free water.
Nextera DNA Library Prep Kit

treatment_protocol: No treatment for Fn14 KO/WT mice. C57Bl/6J mice were fed either PLX5562 formulated chow to depleate microglia, or control chow manufactured in parallel from P20 until euthanasia at P32.

tag: strain background

value: Control

tag: age

tag: tissue/cell type

value: dorsal lateral geniculate nuclei (dLGNs)


title: scRNAseq_WT_rep2

description: 10x Genomics

value: High-fat/High-cholesterol diet-fed for 12 weeks


title: C3_6 [22_P01_F03]

tag: microbiota status


title: scRNAseq_MT_rep1

description: 10x Genomics

value: VAV1-Cre+/- ASXL1-MTfl/fl


title: scRNAseq_WT_rep1

description: 10x Genomics

value: wild-type


title: C3_5 [21_P01_E03]

value: Melanoma cell line

tag: sorting strategy


title: ML336_EIDD1931_1uM_1_HTB7375_F21

address: 505 S. Hancock Street

description: TC-83 nsP2-4


title: C3_3 [19_P01_C03]

tag: cell type

value: HGF-tg C57BL6


title: C3_4 [20_P01_D03]

value: single cells sorted from homogeneous culture


title: C3_2 [18_P01_B03]


title: N1_SOX2

value: Triple Negative Breast Cancer

tag: genotype


title: N1_RBPJ

value: RBPJ


title: ML336_EIDD1931_0uM_1_HTB7390_O4

description: TC-83 nsP2-4

value: 1uM ML336 + DMSO


title: C3_1 [17_P01_A03]


title: EV3_RBPJ

description:
EV_RBPJ_IP.bigWig
EV_RBPJ_IP_peaks.narrowPeak
EV_RBPJ_IP_treat_pileup.bdg

value: Wild type


title: PLX ATACseq rep2

value: PLX


title: PLX Control ATACseq rep1


title: EV1_RBPJ

value: Dox-EV


title: ML336_EIDD1931_0uM_1_HTB7390_M6

description: TC-83 nsP2-4


title: Fn14 WT ATACseq rep1

source_name: Brain (Cortex, dLGN, Hippocampus)

value: Fn14 WT

value: Brain (Cortex, dLGN, Hippocampus)


title: ML336_EIDD1931_0uM_1_HTB7386_N11

description: TC-83 nsP2-4


title: EV2_RBPJ


title: ML336_EIDD1931_0uM_1_HTB7390_M3

description: TC-83 nsP2-4


title: Fn14 WT ATACseq rep2