title: GBM-6425_B.1B05, single cell DNA methylation

description: Library name: GBM-6425_B.1B05


title: Fish102

status: Public on Apr 01 2025

type: SRA

city: Ås

first: Linn

middle: Haug

last: Eide

address: Oluf Thesens vei 6

country: Norway

institute: Norwegian University of Life Sciences

library_source: transcriptomic

data_processing:
Raw reads cleaned by BBDuk (v34.56) to trim low quality reads, adapter sequences and PhiX (Illumina spike-in).
Fragments counted using featureCounts (c1.4.6-pl)
Differentially expressed genes (DEGs) estimated using SARTools R package (v1.7.3).
DEGs were used in an enrichment analysis by CLueGo with term fusion in Cytoscape v.3.8.2.
Gene ontology databases for Atlantic salmon (biological process, cellular component, molecular function and immune system process were used to compare DEGs results, genes included in final results if 10 % of genes in each term were covered.
Assembly: Cleaned reads aligned to Salmo salar genome SSAL_v3.1 (GenBank assembly accession GCA_905237065.2
Supplementary files format and content: .counts files

molecule: total RNA

organism: Salmo salar

source_name: distal intestine

extract_protocol:
RNA was isolated with 900 µL QIAzol lysis reagent (Qiagen, Hilden, Germany, cat. No. 79306) and a 5 mm  stainless steel bead (Qiagen, cat. No. 69989). The tissues were lysed with a Qiagen TissueLyser bead mill  (Retsch, Haan, Germany, cat. no. 85220)  at 20 Hz for 2 min (twice). 180 µL chloroform was added before  vortexing. Tubes were centrifuged at 12 000 rpm (4 °C) The upper phase containing RNA and water was  transferred to new tubes, and 450 µL isopropanol was added. Tubes were shaken by hand and incubated  for 10 min at room temperature, before centrifugation for 15 min. Excess liquid was removed and 200 µL  70 % ethanol was added before centrifugation at 10 min. The supernatant was removed, and the samples  were centrifugated for 3 min. With the lids open, the pellets dried for 5-10 min. The RNA was then  dissolved in 40 μL RNAse-free water, followed by a 10 min incubation at 55 °C. 20 ng/ul.
Poly A enrichment  and reverse transcription of cDNA.

tag: tissue

value: distal intestine

tag: treatment


title: Fish101


title: Fish105


title: wild type, mouse 1

city: Utrecht

first: Akashdip

last: Singh

address: Lundlaan 6

country: Netherlands

institute: UMC Utrecht

data_processing:
Read 1 was used to identify the Illumina library index and CEL-seq sample barcode.
Read 2 was aligned to the mouse mm10 reference transcriptome using BWA MEM
Reads that mapped equally well to multiple locations were discarded.
Mapping and generation of count tables was done using the MapAndGo script.
Assembly: mm10
Supplementary files format and content: tsv file with count tables for genes per sample

organism: Mus musculus

source_name: naive CD8 T cells

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol
Sequencing libraries were prepared with Illumina Truseq small RNA primers

treatment_protocol: For RNA sequencing of naïve CD8+ T cells, spleens were isolated from 3 Lair1+/+ mice and 3 Lair1-/- mice, processed to single cell suspensions, followed by red blood cell lysis and multiple washing steps. Cells were then stained for 30 minutes on ice, washed and resuspended in FB. Afterwards, 100.000 CD45+CD3+CD8+CD62L+CD44- cells each were sorted on FACSAriaIII (BD). Cells were then spun down at 300xg, and resuspended in TRIzol (Invitrogen).

tag: cell type

value: naive CD8 T cells

tag: genotype

value: wild type


title: fat, control 4

city: Vienna

first: Clemens

last: Fürnsinn

address: Währinger Gürtel 18-20

department: Department of Medicine III

country: Austria

institute: Medical University Vienna

description: read length 1x75bp

data_processing:
fastq generation, bcl2fastq via Basespace
alignment and extraction of counts/gene, Tophat (version 2.1.0) and Bowtie2 (version 2.2.6) aligners via Basespace,
differential gene expression analysis, DESeq2 (1.6.3) via Basespace
Assembly: UCSC mm10
Supplementary files format and content: plain text, mouse gene symbols and raw counts per gene, one file per sample

source_name: white adipose tissue (epidydimal)

extract_protocol:
RNA was extracted from gastrocnemius muscle, liver, and epidydimal adipose tissue derived from hypoxia-exposed mice and their weight-matched controls (n=4 per group) using TRIzol®.
NEB Next Ultra Directional RNA Library Prep Kit for  Illumina

treatment_protocol: After 3 months on a high fat diet, male obese mice were kept for another three months in a chamber equipped with oxygen sensors and controllers, which allowed the maintenance of the target oxygen concentration (10%) by controlled inflow of nitrogen. To account for the hypoxia-induced reduction of food intake the control group, which was maintained at normal air (20-21% O2), was fed restrictedly with one portion of food per day, so to obtain a mean weight curve as similar as possible to the curve of their treated counterparts. Tissue samples  were collected approximately 4 h after opening the hypoxia chamber, i.e. after 4 h of breathing normal air.

value: white adipose tissue (epidydimal)

tag: strain

value: Control


title: GBM-6425_B.1B02, single cell DNA methylation

city: Toronto

first: Federico

last: Gaiti

state: Ontario

address: 101 college street

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: GBM-6425_B.1B02

library_source: genomic

data_processing:
The single-cell DNA methylation sequencing data from Scale Biosciences was processed using the ScaleBio Seq Suite: Methylation Workflow (v1.1.0 pre-release) under default parameters.
Assembly: hg38
Supplementary files format and content: h5 files with matrices of DNA methylation status for each cell
Library strategy: sciMet

molecule: genomic DNA

organism: Homo sapiens

source_name: GBM patient brain tissue

extract_protocol:
Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. Nuclei were fixed with 16% formaldehyde followed by nucleosome disruption. After gently mixing nucleosome disruption solution with nuclei suspension, nuclei were centrifuged with pellet resuspended for each biological sample. Nuclei inputs were normalized across samples, and the tagmentation-nuclei mix was prepared for each biological sample based on the number of reactions. Nuclei were distributed across the three 96-well Met Tagment Barcode Plates, using a total of 288 unique barcodes for nuclei tagmentation. Tagmented nuclei were gated for positive DNA staining and sorted for 24 nuclei per well on the sorting plate. Bisulfite Conversion Solution was added to each well to convert unmethylated cytosines to uracil and the post-reaction product was cleaned up through elution.
The sequencing library was prepared by adding amplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.

value: GBM patient brain tissue


title: DOG 065

city: Chapel Hill

first: Liubov

last: Arbeeva

state: North Carolina

address: 3300 Thurston Bldg., CB# 7280

country: USA

institute: UNC

description: Library name: R065-268002

data_processing:
Sequencing output was converted to fastq format and demultiplexed using Illumina bclconvert ver 4.2.4.
The resulting paired-end reads were processed with the QIIME ver.2.2022.2 wrapper for DADA2 including merging paired ends, quality filtering, error correction, and chimera detection.
Amplicon sequencing units from DADA2 were assigned taxonomic identifiers using the Silva 138 database.
Alpha diversities with respect to Shannon index, Phylogenetic Diversity, and Pielou’s Evenness index were estimated using QIIME2 at a rarefaction depth of 5,000 sequences per subsample.
Beta diversity estimates were calculated within QIIME2 using Weighted UNIFrac distance and Bray Curtis dissimilarity between samples at a subsampling depth of 5,000.
Assembly: Silva 138
Supplementary files format and content: feature-table.biom
Library strategy: 16S rRNA-seq

organism: Canis lupus familiaris

source_name: stool in ethanol

extract_protocol:
Samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA).
Mechanical lysis was performed for 20 minutes on a digital vortex mixer.
After 5 min centrifugation, 0.45 ml of supernatants were aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution.
The suspension was incubated at 4°C overnight.
After 5 min centrifugation, the supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads.
DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase-free water.
12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene.
Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with the Illumina sequencing platform
The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer, and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by cycling of denaturing at 95°C for 30 seconds, annealing at 55°C for 30 seconds, and a 30-second extension at 72°C (25 cycles), a 5-minute extension at 72°C and a final hold at 4°C.
Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN). In the next step, each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30-second extension at 72°C (8 cycles), a 5-minute extension at 72°C and a final hold at 4°C.
The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified, and normalized before pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer, and heat-denatured before loading on the MiSeq reagent cartridge (Illumina) and the MiSeq instrument (Illumina). Automated cluster generation and paired–end sequencing with dual reads were performed according to the manufacturer’s instruction

value: stool in ethanol

tag: age

tag: body composition_score

tag: mjoa

value: NO


title: DOG 056

description: Library name: R056-491410


title: Fish100


title: muscle, control 4

description: read length 1x75bp

source_name: skeletal muscle (gastrocnemius)

value: skeletal muscle (gastrocnemius)


title: muscle, control 3

description: read length 1x75bp


title: DOG 054

description: Library name: R054-226152


title: DOG 059

description: Library name: R059-491590


title: Fish99


title: GBM-6425_B.1B01, single cell DNA methylation

description: Library name: GBM-6425_B.1B01


title: GBM-6425_B.1A12, single cell DNA methylation

description: Library name: GBM-6425_B.1A12


title: DOG 058

description: Library name: R058-491416


title: muscle, control 2

description: read length 1x75bp


title: Fish98


title: GBM-6425_B.1A11, single cell DNA methylation

description: Library name: GBM-6425_B.1A11


title: DOG 052

description: Library name: R052-490940


title: Fish97


title: muscle, control 1

description: read length 1x75bp


title: DOG 049

description: Library name: R049-230416


title: GBM-6425_B.1A10, single cell DNA methylation

description: Library name: GBM-6425_B.1A10


title: Fish96


title: muscle, hypoxia 3

description: read length 1x75bp

value: Hypoxia 3 months


title: DOG 048

description: Library name: R048-240898


title: GBM-6425_B.1A08, single cell DNA methylation

description: Library name: GBM-6425_B.1A08


title: muscle, hypoxia 2

description: read length 1x75bp


title: GBM-6425_B.1A09, single cell DNA methylation

description: Library name: GBM-6425_B.1A09


title: liver, control 1

description: read length 1x75bp

source_name: liver

value: liver


title: DOG 045

description: Library name: R045-242237


title: GBM-6425_B.1A07, single cell DNA methylation

description: Library name: GBM-6425_B.1A07


title: Fish94


title: liver, hypoxia 4

description: read length 1x75bp


title: DOG 044

description: Library name: R044-490182


title: GBM-6425_B.1A06, single cell DNA methylation

description: Library name: GBM-6425_B.1A06


title: Fish93


title: GBM-6425_B.1A05, single cell DNA methylation

description: Library name: GBM-6425_B.1A05


title: Fish95


title: Fish91


title: liver, hypoxia 1

description: read length 1x75bp


title: liver, hypoxia 3

description: read length 1x75bp


title: Fish92


title: GBM-6425_B.1A04, single cell DNA methylation

description: Library name: GBM-6425_B.1A04


title: DOG 039

description: Library name: R039-489573

value: YES


title: liver, control 4

description: read length 1x75bp


title: GBM-6425_B.1A03, single cell DNA methylation

description: Library name: GBM-6425_B.1A03


title: DOG 037

description: Library name: R037-258410


title: Fish30


title: muscle, hypoxia 4

description: read length 1x75bp


title: GBM-6425_B.1A02, single cell DNA methylation

description: Library name: GBM-6425_B.1A02


title: liver, control 3

description: read length 1x75bp


title: DOG 035

description: Library name: R035-255769


title: liver, hypoxia 2

description: read length 1x75bp


title: DOG 043

description: Library name: R043-239792


title: DOG 041

description: Library name: R041-487662


title: liver, control 2

description: read length 1x75bp


title: DOG 032

description: Library name: R032-488735


title: 6425_A, Spatial transcriptomics

description: Library name: 6425_A

data_processing:
The spatial transcriptomic data from 10x Genomics Visium HD was processed using Space Ranger (v3.0.0)
Assembly: hg38
Supplementary files format and content: Matrix files and comma-separated value file
Library strategy: Spatial transcriptomics

extract_protocol:
Region of interest was selected by consulted a pathologist to confirm the presence of malignant cells to ensure their inclusion within the Visium HD capture area. FFPE tissue blocks were sectioned at 5 μm thickness and placed on blanks slides following Visium HD FFPE Tissue Preparation Handbook (10x Genomics; CG000684). Slides were deparaffinized for H&E staining and imaging by incubating the slides for 2 hours at 60°C followed by xylene washes, destained, and de-crosslinked for downstream spatial transcriptomics library construction.
Following Visium HD Spatial Gene Expression Reagent Kits User Guide (10x Genomics; CG000685), human whole transcriptome probe panel was used for probe hybridization, probe ligation, slide preparation, probe release and extension, and probe-based library construction.


title: Fish28


title: GBM-6425_B.1A01, single cell DNA methylation

description: Library name: GBM-6425_B.1A01


title: DOG 033

description: Library name: R033-213054


title: Fish25


title: fat, control 3

description: read length 1x75bp


title: fat, hypoxia 1

description: read length 1x75bp


title: Fish27


title: Fish26


title: mycelia - GFP_JMJ1-rsc1_rep2_IP

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

country: China

institute: mengtingxu

description: Library name: Sample 3

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012)
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Assembly: MG8
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph

organism: Pyricularia oryzae

growth_protocol: The Pyricularia oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) or anti-H3K4ac (Active Motif, 39381) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.

tag: cell line

value: mycelia


title: mycelia - GFP_JMJ1-rsc1_rep1_IP

description: Library name: Sample 2


title: Fish24


title: DOG 031

description: Library name: R031-483339


title: Fish23


title: fat, control 2

description: read length 1x75bp


title: Fish29


title: DOG 036

description: Library name: R036-246259


title: fat, hypoxia 4

description: read length 1x75bp


title: DOG 029

description: Library name: R029-486865


title: Fish22


title: 6425_B, Spatial transcriptomics

description: Library name: 6425_B


title: DOG 028

description: Library name: R028-488160


title: DOG 027

description: Library name: R027-487945


title: fat, control 1

description: read length 1x75bp


title: DOG 030

description: Library name: R030-487941


title: Fish21


title: DOG 026

description: Library name: R026-487943


title: DOG 025

description: Library name: R025-199836


title: fat, hypoxia 3

description: read length 1x75bp


title: Fish19


title: DOG 022

description: Library name: R022-487689


title: fat, hypoxia 2

description: read length 1x75bp


title: Severe leptospirosis_08

type: RNA

city: Bangkok

first: Umaporn

last: Limothai

state: Thailand

address: 1873 Rama IV Rd, Pathum Wan, Pathum Wan District, Faculty of Medicine, Chulalongkorn University

country: Thailand

institute: Chulalongkorn University, Faculty of Medicine

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Gene Expression RNA CodeSet Hybridization Protocol MAN-10056).

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (280 fields of view).

data_processing: Raw count data were managed in nSolver software (v4.0; NanoString). Negative controls were used for background thresholding, all raw counts below average of the negative controls will be adjusted to it. Profiling data were then normalized by the average (geometric mean) of positive controls and the best subset of the housekeeping gene included in the panel, as determined by geNorm

label: not provided

source_name: Whole blood

label_protocol: Labeling was performed according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from 200 μL of whole blood using Trizol reagent (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s protocol.

tag: condition

value: Severe leptospirosis

tag: sample type

value: Whole blood


title: DOG 021

description: Library name: R021-267358


title: Fish18


title: NORM.P14.CD31.WT.S129_Joyal_r2

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

description: Drop-Seq

library_source: transcriptomic single cell

data_processing:
Unique molecular identifier (UMI) counts for WT and/or Sirt3–/– scRNAseq replicates were compiled into Digital Gene Expression (DGE) matrices using Dropseq tools (V1.13) and processed using the "Seurat" package (V3).
Assembly: mm10
Supplementary files format and content: Tab-separated values files (Digital GeneExpression matrix)

source_name: Retina

growth_protocol: Animal procedures were performed in compliance with the Animal Care Committee of CHU Sainte-Justine, following the principles of the Guide for the Care and Use of Experimental Animals developed by the Canadian Council on Animal Care. All in vivo work adhered to the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Vision Research. S129 (#002448) and mutant mice with Sirt3 deletion (129-Sirt3tm1.1Fwa/J, #012755) were obtained from The Jackson Laboratory. All colonies were maintained and bred in identical lighting conditions at the CHU Sainte-Justine mice facility. Pups weighing less than 6 grams or more than 8 grams on postnatal (P) day 14 or 17 (P14, P17) were excluded. Both littermate females and males were used. All animals were sacrificed by lethal pentobarbital intraperitoneal (i.p.) injections at P12, P14, or P17 for analyses.

extract_protocol:
Drop-seq procedure was done on endothelial enriched cell suspension isolated from mouse retina. Briefly, single-cell suspensions were prepared from P14 and P17 retina, as reported by Macosko et al,  through successive steps of digestion (using papain solution; Worthington, LK003150), trituration and filtration to obtain a final concentration of 120 cells/μl. Endothelial cells were enriched using CD31 microbeads (Miltenyi Biotech, 130-097-418) according to the manufacturer’s protocol.
Droplet generation and cDNA libraries were performed as described in the Drop-seq procedure (Macosko et al, Cell 2015), and sequencing was done on Illumina NextSeq 500.
Resulting, quality-controlled libraries were sequenced on Illumina NextSeq 500.

treatment_protocol: WT and Sirt3 KO mice pups and their adoptive lactating S129 mother were exposed to 75% oxygen from P7 to P12. Mice were returned to room air at P12 until used for experimentation.

value: Retina

value: CD31-enriched cell

value: WT

value: Normoxia

tag: endpoint


title: Severe leptospirosis_07


title: muscle, hypoxia 1

description: read length 1x75bp

value: wild type


title: Fish17

value: distal intestine


title: NORM.P14.CD31.WT.S129_Joyal_r1

description: Drop-Seq


title: Severe leptospirosis_05


title: Severe leptospirosis_04


title: Fish20


title: OIR.P14.CD31.Sirt3KO.S129_Joyal_r2

description: Drop-Seq

value: Sirt3 KO

value: Oxygen-induced retinopathy


title: DOG 020

description: Library name: R020-269007

value: stool in ethanol


title: Fish15


title: Severe leptospirosis_02


title: mycelia - GFP_JMJ1-rsc1_Input

description: Library name: Sample 1


title: Fish16


title: Severe leptospirosis_03


title: Fish14


title: Severe leptospirosis_01


title: DOG 018

description: Library name: R018-215510


title: Severe leptospirosis_06


title: DOG 019

description: Library name: R019-485406

value: NO


title: DOG 015

description: Library name: R015-248332


title: Fish13


title: OIR.P14.CD31.WT.S129_Joyal_r1

description: Drop-Seq


title: DOG 012

description: Library name: R012-486611


title: Fish11


title: Fish12


title: DOG 013

description: Library name: R013-241201


title: OIR.P17.CD31.Sirt3KO.S129_Joyal_r3

description: Drop-Seq


title: 2913_WT_Rep3_PlusDox

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main Street

department: Department of Microbiology and Immunology

institute: University at Buffalo

data_processing:
Reads were mapped to the Trypanosoma brucei TREU927 build with HISAT2 (v2.1.0), reads aligned to the TREU927 build were quanitifed with featureCounts (v1.5.0), which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location, DESeq2 (v.1.42.1) was used to normalize the read counts and derive TPM values
Assembly: Trypanosoma brucei brucei TREU927
Supplementary files format and content: 2913_WT_RF_RK_RNAseq_counts.csv
Supplementary files format and content: featureCounts output from RNA-seq experiment

organism: Trypanosoma brucei

source_name: 29-13-derived PF

growth_protocol: Procyclic form (PF) T. brucei strain 29-13, derivatives were used in this study, which includes doxycycline-inducible N-terminal MYC tagged DRBD18 over-expression, and over-expression of its methyl mutants (Triple R to F and triple R to K mutant) generated by site-directed mutagenesis. Cells were grown in standard conditions at 27ºC in SDM-79 medium supplemented with 10% fetal bovine serum and 10U/ml of penicillin/streptomycin. Drug concentrations used in this work were 15 µg/ml of hygromycin (Sigma), 15 µg/ml of neomycin (Sigma), 50 µg/ml of puromycin (Invivogen) and 1 µg/ml of doxycycline (Sigma).

extract_protocol:
For RNA isolation, doxycycline-induced and uninduced cells were harvested, Trizol reagent (Invitrogen) was added and this suspension was frozen at −80℃. Total RNA was isolated using Trizol reagent and phenol–chloroform extraction followed by DNase-I treatment (DNA-free DNase kit; Ambion). The RNA was further purified using phenol–chloroform extraction and the purity and quality of the RNA were measured using Nanodrop 1000, and the 260/280 ratio was ~2.
RNAseq was done using the PolyA mRNA magentic isolation beads (E7490) and the NEBNext Ultra II directional RNA kit (E7760) from NEB.  Samples were sequenced on a NextSeq2000, PE100,  P3 flow cell.

treatment_protocol: Three biological replicates of the cells harbouring either N2MYC-DRBD18(WT), N2MYC-DRBD18(R->F), or MHT-DRBD18(R->K) were grown in the presence and absence of 1 µg/ml doxycycline for 36 hrs.

value: 29-13-derived PF

value: procyclic form

value: DRBD18 WT Overexpression

value: 1 ug/ml doxycycline


title: DOG 011

description: Library name: R011-473822


title: Fish10


title: DOG 010

description: Library name: R010-486287


title: Fish9


title: Fish8


title: Non-severe leptospirosis_02

value: Non-severe leptospirosis


title: Non-severe leptospirosis_03


title: OIR.P17.CD31.WT.S129_Joyal_r2

description: Drop-Seq


title: OIR.P17.CD31.WT.S129_Joyal_r3

description: Drop-Seq


title: OIR.P14.CD31.WT.S129_Joyal_r2

description: Drop-Seq


title: 2913_WT_Rep3_MinusDox

value: No Dox


title: OIR.P17.CD31.Sirt3KO.S129_Joyal_r2

description: Drop-Seq


title: OIR.P14.CD31.Sirt3KO.S129_Joyal_r1

description: Drop-Seq


title: DOG 009

description: Library name: R009-265355

value: YES


title: NORM.P17.CD31.WT.S129_Joyal_r2

description: Drop-Seq

value: Retina


title: Non-severe leptospirosis_04

value: Whole blood


title: 2913_WT_Rep2_MinusDox


title: DOG 007

description: Library name: R007-483868


title: 2913_WT_Rep2_PlusDox


title: NORM.P17.CD31.WT.S129_Joyal_r1

description: Drop-Seq

value: CD31-enriched cell

value: WT


title: Fish7


title: 2913_WT_Rep1_PlusDox


title: DOG 006

description: Library name: R006-485707


title: Non-severe leptospirosis_01


title: OIR.P17.CD31.Sirt3KO.S129_Joyal_r1

description: Drop-Seq


title: Fish4


title: Fish5


title: OIR.P17.CD31.WT.S129_Joyal_r1

description: Drop-Seq


title: DOG 003

description: Library name: R003-265911


title: 2913_RK_Rep3_MinusDox

value: DRBD18 methyl mutant


title: Fish3

value: distal intestine


title: 2913_RK_Rep3_PlusDox


title: EMM_24h_rep1 (ATAC-seq)

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
peaks were called using MACS2 (narrow)
Genome_build: mm10
Supplementary_files_format_and_content: MACS PEAK BED

growth_protocol: Cells were grown in standard ESC medium supplemented with LIF

extract_protocol:
Nuclei were purified by incubation with 10mM TrisHCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.3% Igepal. Open DNA was tagged using the tn5 transposase kit (Illumina)
Fragments were indexed and amplidied using standard Illumina barcodes

treatment_protocol: See description above, cells cultured in EMM for 3h, 9h or 24h (or Serum/LIF media for 24h) before RNA was collected.

value: Mouse Embryonic Stem Cells

value: EMM

tag: time


title: Fish2


title: 2913_RK_Rep2_PlusDox


title: TNBC

city: Houston

first: Tu N

last: Tran

state: Texas

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

data_processing: Slides were profiled using Xenium Analyzer (10x Genomics). Following analysis, Xenium slides were processed for Hematoxylin & Eosin (H&E) staining using 10x Genomics protocol # CG000613. H&E slides were imagined using Akoya Bioscience Phenocycler Fusion.

extract_protocol: The triple-negative breast cancer patient-derived xenograft sample was snap freeze using 10x Genomics protocol # CG000663. Frozen OCT tumors were sectioned using cryostat as per 10x Genomics protocol # CG000579 (Rev E) and mounted directly on the Xenium slide. Next, sections on Xenium slides were processed as per 10x Genomics protocol # CG000613 (Rev B). For the probes, we used a 10x pre-designed human breast panel that has 280 genes on the panel.

value: breast


title: RNA-seq, round sperm, Daxx knockdown, biol rep3

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

description: Library name: Sample 12

data_processing:
For analysis of differentially expressed genes , raw sequence reads were trimmed using Trim Galore (0.6.10, parameters:–paired–length 25--stringency 4--clip_R1 12 --clip_R2 12 ). Then, clean sequence reads were mapped to the UCSC mm39 genome  with default parameters using HISAT2(2.2.1) , mapped reads per gene were counted with FeatureCount (1.5.3), providing a GTF file, and differential expression analysis was performed by DESeq2(1.46.0). For analysis of differentially expressed TEs, similar to the analysis mentioned above, and the GTF file was acquired from Gale-Hammell lab(https://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/ mm39_rmsk_TE.gtf.gz).
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample(gene counts and TEs counts)

molecule: polyA RNA

source_name: testis

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA concentration and purity was measured using NanoDrop 2000                                                                                (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: testis

value: round sperm

value: DAXX knockdown


title: Fish1


title: 2913_RK_Rep2_MinusDox

value: 29-13-derived PF

value: procyclic form


title: EMM_9h_rep1 (ATAC-seq)


title: RNA-seq, round sperm, Daxx knockdown, biol rep2

description: Library name: Sample 11


title: EMM_9h_rep2 (ATAC-seq)


title: 3380-Phet

city: Beijing

first: Lin

last: Yuan

address: You'anmenwai,Fengtai District

institute: Capital Medical University

data_processing:
RNA-seq reads were trimmed using Trimmomatic v0.39.
RNA-seq reads were aligned to the UCSC mm10 genome using HISAT2 version  2.1.0.
the read is counted by HTSeq version 0.6.1.
Read count normalization and Differential Expression Analysis were performed using DEseq2 version 1.26.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: prefrontal cortex

extract_protocol:
Preforntal coretex of 8 weeks mouse was removed,flash frozen on dry ice,and RNA was harvested using Trizol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations .

value: prefrontal cortex

tag: development stage

value: 8 week

tag: Sex

value: male


title: EMM_3h_rep2 (ATAC-seq)


title: DOG 005

description: Library name: R005-479901

value: stool in ethanol

value: YES


title: 2913_RK_Rep1_PlusDox

value: 1 ug/ml doxycycline


title: 3445-Phet


title: RNA-seq, round sperm, Daxx knockdown, biol rep1

description: Library name: Sample 10


title: 2913_RK_Rep1_MinusDox

value: No Dox


title: 3440-Phet


title: 2913_WT_Rep1_MinusDox

value: DRBD18 WT Overexpression


title: Serum_LIF_rep2 (ATAC-seq)

value: control


title: 3439-Phet


title: EMM_24h_rep2 (ATAC-seq)

value: Mouse Embryonic Stem Cells


title: 2913_RF_Rep3_PlusDox

value: DRBD18 methyl mimic


title: RNA-seq, round sperm, Wild type, biol rep3

description: Library name: Sample 9

value: WT


title: Fish6

value: distal intestine


title: DOG 001

description: Library name: R001-242236

value: NO


title: RNA-seq, round sperm, Wild type, biol rep2

description: Library name: Sample 8

value: testis

value: round sperm


title: Serum_LIF_rep1 (ATAC-seq)


title: 2913_RF_Rep3_MinusDox

value: 29-13-derived PF

value: procyclic form


title: RNA-seq, round sperm, Wild type, biol rep1

description: Library name: Sample 7


title: EMM_24h_rep3 (RNA-seq)

data_processing:
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using featureCounts
fold change vaues were determined using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.tsv (raw count matrix)

extract_protocol:
Total RNA was collected using the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen).
Libraries were prepared using the NEB Next Ultra 2 kit.

value: EMM


title: 3447-Pwt

value: prefrontal cortex

value: wt

value: 8 week

value: male


title: 2913_RF_Rep2_MinusDox

value: No Dox


title: RNA-seq, meiotic cells, Daxx knockdown, biol rep2

description: Library name: Sample 5

value: meiotic cells

value: DAXX knockdown


title: EMM_24h_rep2 (RNA-seq)

value: Mouse Embryonic Stem Cells


title: RNA-seq, meiotic cells, Daxx knockdown, biol rep3

description: Library name: Sample 6


title: 2913_RF_Rep1_PlusDox

value: DRBD18 methyl mimic

value: 1 ug/ml doxycycline


title: 2P_WT


title: EMM_24h_rep1 (RNA-seq)


title: 776_R1_001 ,776_R2_001

city: NY

first: Yoshinobu

last: Nakayama

address: 160 Convent Ave

institute: City College of New York

data_processing:
The trimmed reads were mapped to the mus musculus GRCm38 reference genome available on ENSEMBL using STAR ultrafast universal RNA-seq aligner.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The differential expression analysis was performed by DESeq2
The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: heart

growth_protocol: In vivo tissues

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep kit, according to the manufacturer’s instructions.

treatment_protocol: MerCreMer, 4-hydroxytamoxifen treatment

tag: background strain

value: conditional knock-in

value: Txnip PPXY to AAXA mutant


title: 2913_RF_Rep1_MinusDox


title: RNA-seq, meiotic cells, Daxx knockdown, biol rep1

description: Library name: Sample 4

value: testis


title: EMM_9h_rep3 (RNA-seq)


title: 775_R1_001 ,775_R2_001


title: RNA-seq, meiotic cells, Wild type, biol rep3

description: Library name: Sample 3

value: WT


title: EMM_9h_rep2 (RNA-seq)


title: 773_R1_001 ,773_R2_001


title: EMM_9h_rep1 (RNA-seq)


title: RNA-seq, meiotic cells, Wild type, biol rep2

description: Library name: Sample 2


title: 762_R1_001 ,762_R2_001

value: wild-type

value: Txnip flox


title: 3437-Pwt


title: sams1 Day 7 R1

city: Worcester

first: Amy

last: Walker

state: MA

address: 373 Plantation Street

institute: UMass Medical School

description: Library name: Sample 7

data_processing:
Nextflow (Trimmomatic 0.39, STAR 2.710b, RSEM 1.3.3, DESeq2 1.38, WormCat 2.0)
Assembly: WS289 (Wormbase)
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans were grown on agar plates on HT115 bacteria.

extract_protocol:
RNA for sequencing was purified using TriReagent, then RNAeasy columns (Qiagen).
RNA library construction was performed by BGI (Hong Kong).

treatment_protocol: Lysis of young adult C. elegans was performed in 0.5% SDS, 5% β-ME, 10 mM EDTA, 10 mM Tris-HCl ph7.4, 0.5 mg/ml Proteinase K

value: whole organism

value: RNAi


title: RNA-seq, meiotic cells, Wild type, biol rep1

description: Library name: Sample 1


title: 2913_RF_Rep2_PlusDox

value: 29-13-derived PF

value: procyclic form


title: sams1 Day 1 R2

description: Library name: Sample 6


title: EMM_3h_rep3 (RNA-seq)

value: EMM


title: shHELLS-1, G4-ChIP, rep2

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

data_processing:
Raw reads of ChIP-seq data were aligned to human hg38 reference genome using Bowtie2 (v2.4.5). PCR duplication was removed by Picard (v2.27.3) MarkDuplicates. Unique reads were filtered by MAPQ > 1 using samtools (1.15.1) view with parameters ‘-hb -p 1’.  Genome coverage bigwig files for Integrative Genomics Viewer visualization were generated by deeptools (v3.5.1) bamCoverage using RPGC for the normalization.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ChIP-seq library was prepared using the CUTANA Targets & Tagmentation (CUT&Tag) Kit (EpiCypher, Inc.) following the manufacturer’s instructions.
ChIP-seq library was prepared using the CUTANA Targets & Tagmentation (CUT&Tag) Kit (EpiCypher, Inc.) following the manufacturer’s instructions.
The purified DNA libraries were subsequently quantified using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on an MGI-seq 2000 instrument (BGI, China) with 100-bp paired-end sequencing.

value: Human Bone Osteosarcoma Epithelial Cells

tag: chip antibody


title: EMM_3h_rep2 (RNA-seq)


title: 759_R1_001 ,759_R2_001


title: sams1 Day 1 R1

description: Library name: Sample 5

tag: tissue


title: shHELLS-1, G4-ChIP, rep1


title: 758_R1_001, 758_R2_001

tag: treatment


title: EMM_3h_rep1 (RNA-seq)

tag: cell type


title: wild-type Day 7 R2

description: Library name: Sample 4

tag: genotype

value: Control


title: wild-type Day 7 R1

description: Library name: Sample 3


title: shCtrl, G4-ChIP, rep2


title: Serum_LIF_rep3 (RNA-seq)

value: control


title: shCtrl, G4-ChIP, rep1


title: sams1 Day 7 R2

description: Library name: Sample 8


title: wild-type Day 1 R2

description: Library name: Sample 2


title: Serum_LIF_rep2 (RNA-seq)

value: Mouse Embryonic Stem Cells


title: A slide of coronal section of forebrain, ICR mouse E17 stage

city: Tokyo

first: Yuichiro

last: Hara

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Research Center for Genome & Medical Sciences

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

data_processing:
FASTQ files were processed with Space Ranger 1.2.0 (10x Genomics Inc., USA) with default parameter settings referring to the gene annotations of the mouse mm10 genome assembly provided by 10X Genomics (refdata-gex-mm10-2020-A) resulting in a production of the matrices of gene expression profiles of the individual spots.
Read count normalization, clustering of spots, detection of marker genes, and integration of multiple datasets were performed with Seurat v3.2.3.
Assembly: mm10
Supplementary files format and content: HDF5 files
Supplementary files format and content: jpeg, png, json, and csv files

source_name: Forebrain

extract_protocol:
A 10 µm thick frozen section was placed  on the Visium Spatial Gene Expression Slide (10x Genomics, USA) and processed with the Visium Spatial Gene Expression Reagent kit (10x Genomics, USA) according to the manufacture’s protocol.
A sequence library was prepared with Library Construction Kit implemented in the Visium Spatial Gene Expression Reagent kit as well as Dual Index Kit TT Set A according to the manufacture’s protocol.
Spatial transcriptome

value: Forebrain

tag: strain

value: ICR


title: wild-type Day 1 R1

description: Library name: Sample 1


title: RAW264.7 cells-lysosome [RNA-seq]

city: 东城区

first: 张仕坤

last: Zhang

state: 北京市

address: 东单三条五号

institute: 协和医学院基础医学研究所

data_processing:
Primary sequencing data that produced by Illumina Xten, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Raw data quality control was performed by FastQC, and raw data filter was performed by scripts.
Trimmomatic and Fastx-toolkit were used to trim adaptor contamination and low quality bases.
Clean data mapped to mm10 reference genome by HISAT2.
Assemble of RNA-Seq alignments into mm10 transcripts was processed by Stringtie.
Differential expression analysis between sample 1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured and passaged in DMEM with 10% (v/v) fetal bovine serum (FBS) (Gibco). TLR3 overexpression RAW264.7 cell line was obtained by transfecting RAW264.7 cells with the plasmid: pUNO1-mTLR3-3×HA (InvivoGen)

extract_protocol:
Lysosome were extracted following manufacturer’s instructions of "Lysosome Enrichiment Kit for Tissue and Cultured Cells"(Thermo).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treamtment

tag: molecule subtype

value: RNA extracted from lysosome


title: RAW264.7 cells-early endosome [EE RNA-seq]

institute: 协和医学院基础医学研究所

growth_protocol: RAW264.7 cells were cultured and passaged in DMEM with 10% (v/v) fetal bovine serum (FBS) (Gibco).

extract_protocol:
Early endosome was were extracted following manufacturer’s instructions of "Early Endosome Extraction Kit"(Invent).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RNA extracted from early endosome


title: Serum_LIF_rep1 (RNA-seq)


title: A549 cells, shDEPDC1B, 2Days

city: 重庆市

first: 东宇

last: 王

address: 重庆市渝中区重庆医科大学

institute: 重庆医科大学

data_processing:
Bowtie2 was used to align raw data
The bam files was quantify by RSEM
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: A549 cells were cultured in DME-F12 medium containing 50 units/mL penicillin, 50 mg/mL streptomycin, and 10% (v/v) fetal bovine serum.

extract_protocol:
The DEPDC1B knockdown cells and its corresponding negative control cells were collected, total RNA was extracted, and cDNA libraries were then constructed and subjected to RNA-seq analysis
RNA libraries were prepared for sequencing using standard MGI-G400/MGI-2000 protocols

treatment_protocol: The shNC/shDEPDC1B lentivirus particles were then used to infect the A549 cells with 5μg/mL polybrene, and forty-eight hours later, cells were harvested and subjected to RNA-Seq.

value: LUAD


title: pituitary, snRNAseq

status: Public on Mar 31 2025

city: Haerbin

first: Lulu

last: Liu

address: No. 26, Hexing Road, Xiangfang District, Haerbin City, Heilongjiang Province, China

institute: Northeast Forestry University

description: 10x Genomics

data_processing:
sn-RNAseq data were processed using the Cell Ranger software v6.1.2.
Assembly: GCF_018350195.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Panthera tigris altaica

source_name: pituitary gland

extract_protocol:
The thawed pituitary tissue was carefully transferred to a new 50 mL conical tube containing Hibernate E®/B27®/GlutaMAX™ (HEB) medium until the tissue settled to the bottom of the tube. The HEB medium was then decanted into a new 50 mL conical tube, retaining only sufficient medium to cover the tissue. The retained HEB medium was reserved for subsequent experiments. The tissue was treated with 10 mL of trypsin solution and incubated at 37ºC for 20 minutes. Following incubation, the trypsin solution was removed and discarded. At this stage, the previously reserved HEB medium was added to the tissue, which was then pipetted into a silanized Pasteur pipette containing the HEB medium, and the contents were immediately returned to the conical tube. The tissue was passed through the pipette 10-15 times, after which it was allowed to settle for 1 minute. The supernatant, containing the dispersed cells, was transferred to a new conical tube, leaving the tissue fragments at the bottom. The cells were then centrifuged at 200 rcf for 2 minutes, and the supernatant was removed and discarded. The resulting cell pellet was resuspended in pre-warmed 10% FBS/DMEM medium. For nuclear isolation from the single-cell suspension, cells were centrifuged again at 300 rcf for 5 minutes. The supernatant was discarded, and Lysis Buffer was added until the cells were fully suspended. Cell lysis was continued on ice for 5 minutes before centrifuging the nuclei at 500 rcf for 5 minutes at 4°C. The supernatant was subsequently removed, and Cell Nucleus Wash and Resuspension Buffer was added, with gentle pipetting and mixing. The nuclei were then centrifuged at 500 rcf at 4°C for 5 minutes. Following this, the supernatant was removed and Nucleus Wash and Resuspension Buffer, or an appropriate volume of buffer, was added to the precipitated nuclei to achieve the target concentration of 1 nucleus/µL. Cell debris and large cellular fragments were removed using a cell filter. Nuclei concentration was determined using a Countess II FL automated cell counter, achieving a pituitary nuclei concentration of 1080 nuclei/µL. The nuclei were kept on ice, and the 10x Genomics® Single Cell protocol was performed immediately to minimize the interval between nucleus preparation and chip loading.
Library for sequencing was prepared using the 10x Genomics Chromium system with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (CG000204, 10x Genomics) and follow the User Guidelines. In summary, the library construction process was conducted in three main steps: GEM Generation & Barcoding, Post GEM-RT Cleanup & cDNA Amplification, and 3ʹ Gene Expression Library Construction. Finally, the total cDNA quantity was determined by analyzing 1 µl of the sample on an Agilent Bioanalyzer using a High Sensitivity microarray chip, following dilution of the sample with nuclease-free water at a 1:10 ratio. The expression libraries were constructed with standard Illumina paired-end structures, ultimately yielding a standard Illumina BCL data output folder.

value: pituitary gland

value: female

tag: age

value: 6 years old


title: 3dESC

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured in LIF-serum medium comprised of DMEM  high  glucose  (Hyclone)  supplemented  with  15%  ES  cell  FBS  (Gibco),  2mM  L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). EPSC were derived from ESC by culturing in EPSC media developed by (Yang et al 2017), comprising of DMEM/F12 (Invitrogen), 20% KnockOut Serum Replacement (Invitrogen), 1× GPS, 1× non-essential amino acids, 0.1 mM β-ME, 103 U ml−1 hLIF, 3 μM CHIR99021 (Tocris), 1 μM PD0325901 (Tocris), 4 μM JNK Inhibitor VIII (Tocris), 10 μM SB203580 (Tocris), 0.3 μM A-419259 (Santa Cruz) and 5 μM XAV939 (Sigma). All cultures were maintained at 37°C with 5% CO2. All cells were maintained on plates pre-coated with 0.1% gelatine (porcine).

extract_protocol:
No extraction was performed
A total of 10,000 cells per sample were loaded into the Chromium Next GEM Chip G (10X Genomics) and processed with the Chromium controller (10X Genomics) to generate gel beads in-emulsions according to manufacturer's instructions. Libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) according to manufacturer's protocol.

treatment_protocol: EPSC was transitioned back into ESC media for 1,2, or 3 days to generate 1dESC, 2dESC, or 3dESC, respectively. 20μM diethylstilbestrol (DES) was added to the ESC media daily to generate 3dESC_plus_DES. DMSO was used as vehicle control.

value: mouse embryonic stem cells

tag: developmental stage


title: 3dESC_DMSO

value: Adding DMSO


title: A slide of coronal section of forebrain, ICR mouse P0 stage

value: WT


title: EPSC


title: 3dESC_DES

value: Adding drug DES


title: EPSC [ATAC-Seq]

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively. bigwig files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigwig

extract_protocol:
Chormatin was using Illumina tagment DNA TDE1 Enzyme and Buffer kit as per manufacturer's instructions.
Library was prepared using Nextera DNA library preparation kit as per manufacturer's instructions.

treatment_protocol: EPSC was transitioned back into ESC media for 1,2, or 3 days to generate 1dESC, 2dESC, or 3dESC, respectively. 20μM diethylstilbestrol (DES) was added to the ESC media daily to generate 3dESC_plus_DES. DMSO was used as vehicle control. 50nM siRNA was added to the ESC media to generate 3dESC_siEsrrb or 3dESC_siNT


title: 1dESC


title: EPSC_siNT [ATAC-Seq]

value: adding siNT


title: 3dESC_siNT [ATAC-Seq]


title: EPSC_DES [ATAC-Seq]


title: A549 cells, shNC, 2Days

address: 重庆市渝中区重庆医科大学

tag: cell line

value: shNC


title: EPSC_DMSO [ATAC-Seq]

value: adding DMSO


title: 3dESC_DMSO [ATAC-Seq]


title: 3dESC [ATAC-Seq]


title: 1dESC [ATAC-Seq]


title: DM1 cells, RNA >50 nt and <200 nt

city: Paris

first: Florent

last: Hubé

address: 9 quai saint Bernard

department: LBD

country: France

institute: Sorbonne Université, CNRS, Paris, France

library_source: other

data_processing:
Trimmomatic (v0.32.3)
Bowtie2 (v2.2.6.2)
Slice BAM (v2.0)
Filter BAM (v1.1.2)
MultiCovBed (v2.26.0.0)
Assembly: hg38
Supplementary files format and content: tab-delimited excel files include raw count values and RPKM

molecule: other

growth_protocol: We used pathological myoblast from myotonic dystrophy (DM). Cells were grown as previously described.

extract_protocol:
Tri Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle from patient with Myotonic Dystrophy type 1


title: DICER_KO_4

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:
The Cell Ranger Single Cell Software Suite v3.1.0 was used to perform sample demultiplexing, barcode processing, and 3’ gene counting using 10X Genomics custom annotation of murine genome assembly mm10-3.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: MC38 colon adenocarcinoma cells

growth_protocol: MC38 cells were passaged at least three times to obtain actively growing cells. The cancer cells were then resuspended in PBS at a concentration of 5 × 106 cells per ml, and 100 µl of this suspension was injected subcutaneously into the right flank of C57BL/6 Dicer-KO or DIcer-WT mice . Tumors were allowed to grow up to 1 cm³ in size. Upon reaching the endpoint tumor size, experiments could continue for an additional 48 hours, provided all health parameters detailed in a health score sheet remained normal. Tumor volume was measured using calipers, calculating the volume with the formula: tumor volume = ½ × d² × D, where D is the long diameter and d is the short diameter.

extract_protocol:
Single cells were filtrated through a 40 μm Flowmi strainer (Bel-Art), and resuspended in PBS with 0.04% BSA, checked for the absence of doublets or aggregates and loaded into a Chromium Single Cell Controller (10× Genomics, Pleasanton) in a chip together with beads, master mix reagents (containing reverse transcriptase and poly-dT primers) and oil to generate single-cell-containing droplets.
Single-cell gene expression libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v2 following the manufacturer's instruction. Quality control was performed with a TapeStation 4200 (Agilent) and QuBit dsDNA high sensitivity assay (Thermo fisher scientific) following manufacturer instructions.

treatment_protocol: We conducted single-cell RNA sequencing (scRNA-seq) of MC38 tumors obtained from either Dicer-WT or Dicer-KO mice at days 11-12 after MC38 tumor challenge.

value: MC38 colon adenocarcinoma cells

tag: replicate

value: C57BL/6 LysM-Cre Dicer1-/-

value: Dicer KO


title: DICER_KO_3


title: DICER_KO_2


title: DICER_KO_1


title: 2dESC


title: EPSC_siEsrrb [ATAC-Seq]

value: adding siRNA of Esrrb


title: 3dESC_siEsrrb [ATAC-Seq]


title: DICER_WT_3

value: C57BL/6 LysM-Cre Dicer1+/+

value: Dicer WT


title: H3K27ac_HiChIP_shEV

data_processing:
HiChIP reads were aligned to mm9 genome assembly using BWA, loops were called using FitHiChIP
Assembly: mm9
Supplementary files format and content: The cool file were the reads matrix for each Sample.
Library strategy: HiChIP

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured in LIF-serum medium comprised of DMEM  high  glucose  (Hyclone)  supplemented  with  15%  ES  cell  FBS  (Gibco),  2mM  L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). 2i cells were derived from ESC by culturing in NDiff227 basal media (TakaraBio) supplemented with 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 15 μM CHIR (Tocris) and 5 μM PD0325901 (Tocris) for at least 3 passages. EPSC were derived from ESC by culturing in EPSC media developed by (Yang et al 2017), comprising of DMEM/F12 (Invitrogen), 20% KnockOut Serum Replacement (Invitrogen), 1× GPS, 1× non-essential amino acids, 0.1 mM β-ME, 103 U ml−1hLIF, 3 μM CHIR99021 (Tocris), 1 μM PD0325901 (Tocris), 4 μM JNK Inhibitor VIII (Tocris), 10 μM SB203580 (Tocris), 0.3 μM A-419259 (Santa Cruz) and 5 μM XAV939 (Sigma). RA cells were cultured in LIF-serum medium, supplemented with 1 retinoic acid for 48 hours. All cultures were maintained at 37°C with 5% CO2. All cells were maintained on plates pre-coated with 0.1% gelatine (porcine).

extract_protocol:
HiChIP was performed according to Arima HiC+ kit protocol (document part number: A160430 v00) with some modifications. Briefly, cells were crosslinked with 2% formaldehyde in PBS at room temperature for 10min, quenched for 5min and washed once with ice-cold PBS. After HiC reactions, the chromatins were sheared using Covaris S2 instrument with intensity setting 3 (equivalent to 105W), 5% duty cycle, and 200 cycles per burst for 7min. Following shearing, the chromatins were precleared using Dynabeads™ Protein A (Thermo Fisher Scientific, 10001D) for 1h at 4°C. Subsequently, 10µg of Esrrb antibody (PPH6705, Perseus Proteomics) was added to the precleared chromatins and incubated overnight at 4°C. Following the overnight incubation, BSA-blocked Dynabeads™ Protein A were added to the antibody-bound chromatins and incubated for 4h at 4°C, washed, eluted and decrosslinked according to Arima HiC+ kit protocol.
Libraries were prepared according to Illumina's instructions with optimised rounds of PCR amplification, and finally analyzed the resulting fragments with paired-end sequencing.

treatment_protocol: Lipofectamine (Invitrogen) was used for transfection of shRNA or CRISPRi plasmids according to the manufacturer’s instructions. cells were harvested for experiments after 3 days of knockdown.

value: ESC

value: shEV


title: H3K27ac_HiChIP_Esrrb_sh1

value: pSuper Esrrb shRNA plasmid


title: 2dESC [ATAC-Seq]

value: mouse embryonic stem cells


title: donor 2, 2nd_bsp (Protein)

status: Public on Mar 28 2025

city: Cambridge

first: Hui

last: Ling

address: 220 Massachusetts Ave

institute: Novartis

description:
Library name: GX_IL_LIB_21_K259_TB_AAD647_16_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads

data_processing:
The Cell Ranger Single-Cell Software Suite (version 3.0.2) was used to perform sample demultiplexing, barcode processing and single cell 5’ gene counting. Antibody derived tags (ADTs) were quantified by supplying the information in supplementary table 1 (info availabe in uploaded file Antibody_Barcode_List_GSM-AAD647-edited_feature_reference) to Cell Ranger
Assembly: The human genome assembly (Ensembl GRCh38 release-98)
Supplementary files format and content: CellRanger output files
Library strategy: CITE-seq

molecule: protein

extract_protocol:
cells were washed once in PBS, incubated in cell staining buffer (Biolegend, Cat#420201) and Human TruStain FcX Blocking (Biolegend, Cat#422301) reagent for 10 min, then incubated for 30 min at 4°C in TotalSeq antibody cocktail (supplementary table 1). Cells were then washed 3 times in cell staining buffer, resuspended in PBS and filtered through a 40um Flowmi Cell Strainer (Bel-Art, Cat#H13680-0040). Cells were counted and diluted to 1000cells/ul for appropriate input into the 10X Chromium chip.
Samples were then processed using the Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics, Cat#1000263) to generate DNA sequencing library for Illumina and the libraries were sequenced on a NovaSeq6000 with S4-200 kit (Illumina), following 10x Genomics recommendations for loading concentration and read length.

treatment_protocol: CITEseq experiment was performed on 8 RTCC samples (4 experimental conditions applied to 2 T cell donors). T cells were put through two rounds of RTCC challenging, the first challenging for 24 h and the second for 3 h prior to being processed for CITEseq. These challenges took place under varying conditions, including the presence/absence of 2.5 nM CD3/CD20 BSP, and presence/absence of Ramos cells. On day 5, post the 3 h incubation, cells were prepared for CITEseq.

value: Ramos B lymphocyte

value: Human CD3+ pan T cells

tag: donor

value: Ramos+Tcell(challenged)+CD3/CD20 BSP

tag: library type

value: ADT

tag: adt

value: CD62L_TotalSeqC, CD8_TotalSeqC, CD22_TotalSeqC, CD27_TotalSeqC, HLA-DR_TotalSeqC, CD20_TotalSeqC, CCR6_TotalSeqC, CD57_TotalSeqC, CD69_TotalSeqC, CD25_TotalSeqC, CD4_TotalSeqC, CD49b_TotalSeqC, CD45RA_TotalSeqC, CD45RO_TotalSeqC, CD95_TotalSeqC, CD127_TotalSeqC, CD134_TotalSeqC, CD137_TotalSeqC, CD154_TotalSeqC, CD107a_TotalSeqC, CD29_TotalSeqC, CTLA4_TotalSeqC, LAG3_TotalSeqC, PD1_TotalSeqC, TIGIT_TotalSeqC, CD3_TotalSeqC, CD19_TotalSeqC, CXCR3_TotalSeqC, CCR7_TotalSeqC, mIgG1k_TotalSeqC, CD226_TotalSeqC, ICOS_TotalSeqC, CXCR5_TotalSeqC, CD28_TotalSeqC, LFA1-alpha_TotalSeqC, LFA1-beta_TotalSeqC, VLA4_TotalSeqC, ICAM1_TotalSeqC, CD40_TotalSeqC, CD2_TotalSeqC, LFA-3_TotalSeqC


title: 3dESC_DES [ATAC-Seq]

value: Adding drug DES


title: DICER_WT_1


title: donor 2, 1st_veh (Protein)

description:
Library name: GX_IL_LIB_21_K256_TB_AAD647_13_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads

value: Ramos+Tcell+vehicle


title: donor 1, 2nd_bsp (Protein)

description:
Library name: GX_IL_LIB_21_K255_TB_AAD647_12_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads

value: donor 1


title: donor 1, 2nd_veh (Protein)

description:
Library name: GX_IL_LIB_21_K254_TB_AAD647_11_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads

value: Ramos+Tcell(challenged)+vehicle


title: donor 2, 1st_bsp (Protein)

description:
Library name: GX_IL_LIB_21_K257_TB_AAD647_14_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads

value: Ramos+Tcell+CD3/CD20 BSP


title: donor 2, 2nd_veh (Protein)

description:
Library name: GX_IL_LIB_21_K258_TB_AAD647_15_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads


title: DICER_WT_4

value: MC38 colon adenocarcinoma cells


title: DICER_WT_2

value: C57BL/6 LysM-Cre Dicer1+/+


title: H3K27ac_HiChIP_Esrrb_sh2


title: donor 2, 2nd_bsp (RNA)

description:
Library name: GX_IL_LIB_21_K251_TB_AAD647_08_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence

value: mRNA


title: donor 2, 2nd_veh (RNA)

description:
Library name: GX_IL_LIB_21_K250_TB_AAD647_07_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence


title: EMM_3h_rep1 (ATAC-seq)

data_processing:
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
peaks were called using MACS2 (narrow)
Genome_build: mm10
Supplementary_files_format_and_content: MACS PEAK BED

extract_protocol:
Nuclei were purified by incubation with 10mM TrisHCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.3% Igepal. Open DNA was tagged using the tn5 transposase kit (Illumina)
Fragments were indexed and amplidied using standard Illumina barcodes

value: Mouse Embryonic Stem Cells

value: EMM

tag: time


title: donor 1, 1st_bsp (RNA)

description:
Library name: GX_IL_LIB_21_K245_TB_AAD647_02_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence


title: donor 1, 1st_bsp (Protein)

description:
Library name: GX_IL_LIB_21_K253_TB_AAD647_10_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads


title: donor 1, 2nd_bsp (RNA)

description:
Library name: GX_IL_LIB_21_K247_TB_AAD647_04_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence


title: donor 2, 1st_veh (RNA)

description:
Library name: GX_IL_LIB_21_K248_TB_AAD647_05_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence


title: donor 1, 1st_veh (Protein)

description:
Library name: GX_IL_LIB_21_K252_TB_AAD647_09_ADT
ADT library: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag reads


title: donor 1, 2nd_veh (RNA)

description:
Library name: GX_IL_LIB_21_K246_TB_AAD647_03_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence


title: donor 1, 1st_veh (RNA)

description:
Library name: GX_IL_LIB_21_K244_TB_AAD647_01_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence


title: Running-muscle_new(snRNA-seq)

status: Public on Mar 25 2025

first: Wei

last: Tao

address: No.5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

description: 10X Genomics

data_processing:
For DNBelab C of MGI, the filtered gene expression count matrix was generated using PISA (version 0.12)  aligned to mm10 reference genome. For 10x Genomics, the filtered gene expression count matrix was generated using Cell Ranger (version 6.1.2) aligned to mm10 reference genome
Seurat (version 4.1.1) was used to perform the downstream analysis
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: muscle

extract_protocol:
Fresh mouse skeletal muscle was frozen in liquid nitrogen
snRNA-seq libraries were prepared for sequencing using established protocols of BGI Genomics and 10X Genomics

value: muscle

value: WT


title: donor 2, 1st_bsp (RNA)

description:
Library name: GX_IL_LIB_21_K249_TB_AAD647_06_mRNA
5' GEX library: Read 1 contains cell barcode and UMI, and Read 2 contains cDNA sequence

value: Ramos B lymphocyte


title: Young-muscle_new(snRNA-seq)

description: 10X Genomics


title: Sedentary-muscle_new(snRNA-seq)

description: 10X Genomics


title: 293T DMSO no break rep2 CALRi2

city: New York

first: Hina

last: Shah

address: 430 East 67th Street

department: Molecular Biology

institute: Sloan Kettering Institute

description: Library name: 293T BFP 53bp1-/- DMSO no break biol rep 2 PCR CALR intron 2

data_processing:
Paired-end sequencing data were analyzed using CRISPResso2. Each sample was aligned to either the reference sequence (with the intron intact) or the intron loss sequence (with the intron deleted).
For each sample, % WID was calculated by counting the number of "intron loss" reads  and dividing by the total aligned reads (reference+intronloss). Modified reads, containing insertions and/or deletions within a 6nt window of the exon-exon junction, were removed from the "intron loss" count but included in the total.
Assembly: GRCh38
Supplementary files format and content: text file includes number of unmodified and modified reads aligning to either the reference or intron loss sequence of interest

source_name: HEK 293T

growth_protocol: HEK293T cells were routinely grown with Dulbecco’s Modified Eagle’s Medium (DMEM) media supplemented with 10% bovine calf serum, 100 U/mL Penicillin-Streptomycin, 1% non-essential amino acids, 2mM L-glutamine. Cells were grown in a 37°C and 5% CO2 air incubator.

extract_protocol:
Cells were trypsinized and genomic DNA was harvested using the Zymo Research Miniprep Kit.
2µg of gDNA was used for library preparation. Locus-specific primers were used to amplify (35 cycle) target sequences of flanking exons. PCR products were subjected to a second round of PCR (11 cycle) with unique indexing sequences (i5 and i7). Samples were run by the MSK IGO core on the Illumina NovaSeq X instrument. Sequencing was performed using a 2x150 paired-end (PE) configuration.

treatment_protocol:
For knockdown experiments, 1.0x10^6 cells were reverse transfected using RNAi max (Invitrogen) according to the manufacturer’s instructions with 30 pmol of siRNAs for REV3L (Dharmacon) or scrambled nontarget siRNA (siCtrl) (Dharmacon). Cells were cultured for 48 hours. For AZT-treated samples, cells were treated for 24 hours with 10 μM/mL of AZT (MilliporeSigma A2169).
To deliver Cas9 and the gRNA against CALR intron 2, GNAS intron 11, and IL3 intron 4, a CRISPR-Cas9 ribonucleoprotein was formed. The crRNA (IDT) and the tracrRNA (IDT) were resuspended to a final concentration of 100 mM in IDT buffer and mixed in an equimolar solution to a final concentration of 50 mM, heated at 95C for five minutes, and let cool at room temperature to form the crRNA:tracrRNA duplex. For each sample, 100 pmol of crRNA:tracrRNA duplex and 100 pmol of Cas9 enzyme (IDT) were diluted in PBS1X. The ribonucleoprotein formation reaction was incubated for 20 minutes at room temperature. 1.0x10^6 cells were electroporated using the Lonza buffer and 4D nucleofector machine. A chimera DNA/6RNA donor was included for some samples. Cells were cultured for 72 hours before DNA extraction.

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone

value: DMSO


title: 293T AZT no break rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- AZT no break biol rep 2 PCR CALR intron 2

value: AZT


title: 293T DMSO sgCALR rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- DMSO sgCALR biol rep 1 PCR CALR intron 2


title: 293T DMSO no break rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- DMSO no break biol rep 1 PCR CALR intron 2


title: iNKT PBMC Targeted Data

status: Public on Mar 22 2025

city: St. Louis

first: Melissa

last: Mavers

state: MO

address: 660 Euclid Ave

department: Pediatrics

institute: Washington University School of Medicine

description: BD Rhapsody

data_processing:
Expression tables (RSEC_MolsPerCell.csv) and sample tags (Sample_Tag_Calls.csv) were downloaded from Seven Bridges and analyzed using Seurat (v4.4.0). First, separate assays were created using the CreateSeuratObject function and percent mitochondrial DNA, nCount_RNA and nFeature_RNA were evaluated for each cell. Cells were maintained for downstream processing if they met the following criteria: nFeature_RNA > 200; nFeature_RNA < 4000; nCount_RNA < 20000; percent.mito < 20. Cells with sample tags labeled “Undetermined” or “Multiplets” were filtered out. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c("nCount_RNA"), dims = 1:20). Any merged analysis or subsequent subsetting of cells/samples underwent the same scaling and normalization method. Cells were clustered using the original Louvain algorithm and top 10 PCA dimensions via ‘FindNeighbors’ and ‘FindClusters’ (with parameters: resolution = 0.5) functions. After initial subsetting and clustering, a clear population of infiltrating macrophages were identified exhibiting higher expression of FCGR3A, LYN, FCR1G, IL1B. The macrophage cluster was filtered out and we subsequently used Harmony (group.by.vars = "Sample_Tag", reduction = "pca", assay.use = "SCT") before rerunning RunUMAP, FindNeighbors and FindClusters to annotate final object (dims=1:20). The resulting merged and normalized matrix was used for the subsequent analysis. To evaluate cluster resolution we utilized clustree before settling on cluster assignment. ADT data was normalized using NormalizeData command with method = “CLR” and a margin of 2.
Assembly: GRCh38
Supplementary files format and content: gene expression matrices, genes and barcodes files

source_name: PBMC

growth_protocol: Isolated iNKTs

extract_protocol:
Human iNKT cells were enriched by magnetic bead-based positive selection (Stem Cell Technologies EasySep™ Release Human PE Positive Selection Kit) utilizing PE-conjugated anti-V11 antibody (Beckman Coulter, C21), followed by bead release, additional staining with fluorochrome-conjugated and oligomer-conjugated antibodies, and fluorescence activated cell sorting for CD24-CD3+V11+V24+ cells. Antibodies included APC-H7 CD14 (BD Biosciences, MoP9), APC-Cy7 CD19 (BD Biosciences, SJ25C1), APC-Cy7-CD24 (Biolegend, ML5), PerCP-Cy5.5 CD3 (Biolegend, UCHT1), FITC V24 (Beckman Coulter, C15), PE V11 (Beckman Coulter, C21), Oligo-CD4 (BD AbSeq, SK3), Oligo-CD8 (BD AbSeq, RPAT8), Oligo-CD45RA (BD AbSeq, HI100), and Oligo-CD45RO (BD AbSeq, UCHL1). Samples were sorted individually, cell counts roughly normalized, and then pooled for sequencing.
Refer to BD Rhapsody for library construction parameters

value: PBMC

value: iNKT


title: 293T AZT sgCALR rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- AZT sgCALR biol rep 2 PCR CALR intron 2


title: Aging-muscle_new(snRNA-seq)

description: 10X Genomics


title: 11991-JF-8

status: Public on Mar 21 2025

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 11991-JF-8

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: mm10
Supplementary files format and content: cell ranger output format

source_name: aorta

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: aorta

value: mixed (single cell)

value: mouse aortic


title: 11991-JF-7

description: Library name: 11991-JF-7


title: 293T DMSO sgCALR rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- DMSO sgCALR biol rep 2 PCR CALR intron 2


title: 11991-JF-5

description: Library name: 11991-JF-5


title: 293T AZT no break rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- AZT no break biol rep 1 PCR CALR intron 2


title: 11991-JF-4

description: Library name: 11991-JF-4


title: A2780cis FLYWCH1 R2

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

data_processing:
Sequencing was performed on an Illumina NovaSeq 600 deep sequencer acquiring 2 x 150 bp paired end reads.
Adapter sequences were removed from reads using TrimGalore. Reads were then mapped to the human reference genome T2T-CHM13v2.0 (hs1) using HISAT2 for gene expression analysis and using STAR with multimapping settings (--outFilterMultimapNmax 100) for repeat expression analysis.
Gene/repeat count was determined using feature count. For repeat count, multiple and overlapping featured were allowed during counting (setting -O, -M).
Assembly: T2T-CHM13v2.0 (hs1)
Supplementary files format and content: feature count table for genes and repeats.

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Plus Mini Kit (Qiagen).
100 ng of RNA were used for RNAseq preparation using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® and sequences at Novogene.

value: human epithelial ovarian cancer

value: 1 week FLYWCH1 overexpression and cisplatin treatment


title: 11991-JF-3

description: Library name: 11991-JF-3


title: 11991-JF-2

description: Library name: 11991-JF-2


title: 11991-JF-1

description: Library name: 11991-JF-1


title: A2780cis FLYWCH1 R1


title: genomic DNA from CD34+_CTRL_a

type: genomic

city: Rionero in Vulture

first: Ilaria

last: Laurenzana

address: via Padre Pio, 1

country: Italy

institute: IRCCS CROB, Centro di Riferimento Oncologico della Basilicata

description:
replicate_a
CD34+_CTRL_a

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina HiScanSQ system, using standard recommended Illumina scanner setting

data_processing: R/Bioconductor environment, SWAN normalization

label: Cy5 and Cy3

source_name: Umbilical cord blood CD34+ cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: primary CD34+ cells

tag: agent

value: CTRL


title: 293T AZT sgCALR rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- AZT sgCALR biol rep 1 PCR CALR intron 2


title: genomic DNA from CD34+_Evs_c

description:
replicate_c
CD34+_EVs_c

value: EVs


title: 11991-JF-6

description: Library name: 11991-JF-6


title: A2780 shRen.660+cPt

value: 7 weeks control knockdown and 6 weeks cisplatin treatment


title: A2780 shRen.660

value: 7 weeks control knockdown


title: A2780 shFLYWCH1.2446

value: 7 weeks FLYWCH1 knockdown


title: A2780 shFLYWCH1.2446+cPt input

data_processing:
Sequencing was performed on an Illumina NovaSeq 600 deep sequencer acquiring 2 x 150 bp paired end reads.
Adapter sequences were removed from reads using BBTools: BBduk and reads were trimmed to remove low quality bases using Trimmomatic. Reads were then mapped to the human reference genome T2T-CHM13v2.0 (hs1) using HISAT2.
The ChIP-seq data was quantile normalized and peaks were identified using the MACS2 peak calling algorithm.
For peak calling, noise reduction was performed by comparing the input (control) samples to the IP samples using MACS2 bdgcmp.
Broad peaks were then called from the bedGraph datasets using MACS2 bdgbroadcall. For all A2780 and A2780cis ChIP-seq data 850 was used as a cutoff for peaks and 425 as a cutoff for linking regions. For ChIP-seq data from knockdown cells a cutoff for peaks of 1000 was used and 500 as a cutoff for linking regions.
Assembly: T2T-CHM13v2.0 (hs1)
Supplementary files format and content: bigWig of samples after quantile normalisationfiles and bed files containing called peaks

extract_protocol:
Mononucleosomes were prepared from lysates by Mnase digest and supplemented with spike-in control (5% of total, mononucleosomes, D. melanogaster). Histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina and sequenced at Novogene.

value: 7 weeks FLYWCH1 knockdown and 6 weeks cisplatin treatment


title: A2780 shFLYWCH1.2446+cPt


title: A2780cis 3xFLAG R2

value: 1 week FLAG overexpression and cisplatin treatment


title: A2780 shFLYWCH1.2404+cPt H3K9me3

value: H3K9me3 (C15200146, Diagenode)


title: genomic DNA from CD34+_CTRL_c

description:
replicate_c
CD34+_CTRL_c


title: A2780 shFLYWCH1.2404+cPt


title: A2780 shRen.660+cPt input


title: A2780 shLuci.1309+cPt


title: A2780 shFLYWCH1.2404+cPt input


title: A2780 shFLYWCH1.2446 input


title: A2780 shFLYWCH1.2446+cPt H3K9me3


title: A2780 shLuci.1309


title: A2780 shRen.660+cPt H3K9me3


title: A2780 shFLYWCH1.2404 input


title: A2780 shFLYWCH1.2446 H3K9me3


title: A2780 shFLYWCH1.2404 H3K9me3


title: genomic DNA from CD34+_CTRL_b

description:
replicate_b
CD34+_CTRL_b


title: A2780cis input

value: Cisplatin treated


title: A2780cis H3K9me3


title: A2780 input


title: HEK293T_bisulfite_rep2

status: Public on Mar 18 2025

city: Guangzhou

first: Ying

middle: liang

last: Sheng

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

data_processing:
The reads generated by RIAN-seq were aligned to the human (hg38) reference genome using Bowtie2.
Reads of low mapping quality were filtered out utilizing SAMtools with the parameters ‘-F 1804 -f 2 -q 20’. potential PCR duplicates were eliminated using Sambamba.
The Bigwig files were generated by DeepTools with the parameter ‘-normalizeUsing RPKM -binSize 1 --extendReads 200’.
For Bisulfite data, the raw sequencing data underwent rigorous quality control using FastQC (version 0.11.9) to evaluate the quality of the sequencing reads. Following quality control, the reads were processed using Trim_galore (version 0.6.7) for adapter trimming and removal of low-quality bases. To further refine the data, customized adapter trimming rules were applied to the reads. For read pairs, the sequence "TTGTTTTTTATATATA" was removed from the first pair, while the sequence "TCTCTTATACATCT" was removed from the second pair. Additionally, the first 40 bases from the 5' end and the last 5 bases from the 3' end were trimmed from the reads. Subsequently, the processed reads were mapped to the hg38 genome using bwa-meth (arxiv.org/abs/1401.1129) and CT conversion sites were extracted using MethylDackel. Bigwig files are generated from BAM files without extracted information.
For yeast data, the reads generated by RIAN-seq were aligned to the yeast (SacCer3) reference genome using Bowtie2, MACS2 was employed with the parameters "--broad --broad-cutoff 1e-3 -q 1e-3".
Assembly: hg38, SacCer3
Supplementary files format and content: bigWig
Supplementary files format and content: bed

extract_protocol:
The genomic DNA was purified from HEK293T or mES cells via phenol/chloroform extraction and ethanol precipitation, or genomic DNA extraction kit.
1 µg DNA was incubated with NEB restriction enzyme mix (Alu I, Mbo I, Mse I, Dde I), Nuclease P1, T5 exonuclease, Lambda exonuclease at 4 °C for 2 hr. As controls, RNase H (NEB, M0297S) was added during the incubation stage. 0.2 µL of Proteinase (Thermo Scientific, EO0491) was added before incubation at 55 °C for 30 min and 70 °C for 30 min. 0.3 µL 1M Tris-HCl (pH 8.0), 0.15 µL 1M MgCl2, 1.5 µL PEG200, 4.8 µL 50% PEG8000 and 1 µL transposase (Vazyme, TD501) were added and incubated at 55 °C for 10 min. The transposition was stopped by the addition of 5 µL 0.25% SDS and incubation for 5 min at room temperature. Transposed DNA was gap-filled by addition of 2 µL Bst3.0 DNA polymerase (NEB, M0374S) and 25 µL NEBNext Q5 HotStart HiFi PCR Master Mix (NEB, M0543S). The mixture was incubated at 72 °C for 15 min and 80 °C for 10 min. For library amplification, the mixture was mixed with a barcoded i5 primer and a barcoded i7 primer PCR was performed to amplify the libraries using the following PCR conditions: 98 °C for 45 s; thermocycling for 10 cycles at 98 °C for 15 s, 65 °C for 75 s; followed by 65 °C for 5 min. The final libraries were purified with the 1× AMPure beads (Beckman, A63882) size selection and were subjected to next-generation sequencing.

value: Human embryonic kidney

value: WT


title: A2780 shRen.660 input


title: A2780 shFLYWCH1.2404


title: A2780 H3K9me3


title: A2780 shRen.660 H3K9me3


title: genomic DNA from CD34+_Evs_b

description:
replicate_b
CD34+_EVs_b


title: HeLa_WT_rep1

source_name: HeLa

value: HeLa

value: Human cervical cancer cell lines


title: genomic DNA from CD34+_Evs_a

description:
replicate_a
CD34+_EVs_a


title: HEK293T_bisulfite_rep1


title: HEK293T_siSETX_ctrl_rep2

value: siCtrl


title: HEK293T_PlaB_rep1

value: PlaB


title: HEK293T_CPT_rep1

value: CPT


title: HEK293T_RNASET1_rep2


title: HEK293T_RNASET1_ctrl


title: HeLa_RNASEH

value: RNASEH


title: Yeast_RNASEH

organism: Saccharomyces cerevisiae S288C

source_name: yeast

value: yeast


title: HEK293T_PlaB_rep2


title: Yeast_rep1


title: HEK293T_PlaB_ctrl_rep2

value: DMSO


title: HEK293T_siSETX_ctrl_rep1


title: HEK293T_CPT_rep2


title: HeLa_WT_rep2


title: P1 Human Colon Cancer

status: Public on Mar 17 2025

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing:
Space Ranger v3.0 (10x Genomics) was used to map FASTQ files to the human reference, detect the tissue section, align the sequencing data to the microscope image and the CytAssist image, and output gene-barcode matrices for further analysis.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: UMI count matrix in h5 format (8 micron bin)
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots (8 micron bin)
Supplementary files format and content: scalefactors_json.json: Relative scales of the user-supplied image, the images in the spatial outs and the Visium array (8 micron bin)
Supplementary files format and content: tissue_lowres_image.png: Downsampled version of the original, full-resolution image
Supplementary files format and content: probe_set.csv: Visium assay targeted probeset
Supplementary files format and content: image.tif: CytAssist Image
Supplementary files format and content: tissue_image.btf: Microscrope Image
Supplementary files format and content: alignment_file.json: Image alignment file
Supplementary files format and content: slide.vlf: Slide information file
Supplementary files format and content: Metadata.parquet: Parquet file with additional metadata values including deconvolution and unsupervised clustering results.
Library strategy: Spatial Transcriptomics

source_name: Colon Cancer

extract_protocol:
5 µm sections were taken from the FFPE tissue blocks with a microtome (Epredia HM355S). Sections were adjacent or near-adjacent (within 5-10 µm of each other). Sectioning followed the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide (CG000518, Rev C).
We placed FFPE tissue sections on plain glass slides for deparaffinization, H&E staining and imaging following the Visium HD FFPE Tissue Preparation Handbook (CG000684). Probe hybridization, probe ligation, slide preparation, probe release, extension, library construction, and sequencing followed the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG000685). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end reads (43 cycles Read 1, 10 cycles i7, 10 cycles i5, 50 cycles Read 2).

value: Colon Cancer


title: HEK293T_CPT_ctrl_rep2


title: HEK293T_RNASET1_rep1


title: P2 Human Colon Cancer.


title: Yeast_rep2


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice1 seq4

status: Public on Mar 16 2025

city: Shanghai

first: Zhenyu

last: Xu

state: 枫林校区

address: Dongan Road

institute: Shanghai Medical College, Fudan University

description: Library name: OB1 seq4

data_processing:
Raw reads were demultiplexed and mapped to the mm10 reference genome by 10× Genomics Cell Ranger pipeline（v6.1.2） using default parameters in Linux. Downstream single-cell analyses were performed using Seurat package(v4.3.0.1) on Rstudio.Cells were first filtered to have >200 detected genes(a gene with expression in more than 3 cells was considered as expressed) and less than 5% of total UMIs mapping to the mitochondrial genome.Then,each individual dataset was log-normalized, scaled, and corrected for dataset-specific batch effects using Harmony(v1.2.0).A union set of top 3000 highly variable genes from each dataset expressed in all samples was used by Seurat multicanonical correlation analysis to further correct for dataset-specific batch effects32. The informative number of correlated components was examined by the elbow plot. The top 30 aligned correlated components were used as input for uMAP dimension reduction and subsequent clustering analysis.Clusters were identified using Seurat FindClusters function using default parameters plus a resolution of 0.1.Then,Seurat FindAllmarkers function with the Wilcox test was used to identify conserved markers which were specificly highly expressed in each clusters versus all other clusters(logFC≥0.6 plus adjust P-value < 0.05).
Violin plots, heatmaps, and individual uMAP plots for the given genes were generated by using the Seurat toolkit VlnPlot, DoHeatmap, and FeaturePlot functions, respectively
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: subcutaneous adipose tissue

extract_protocol:
ADSC was isolated from adult male mice. The mice were anesthetized and the subcutaneous adipose tissue was taken and rinsed in PBS for 3 times. The adipose tissue was cut into small pieces and digested at 37℃ for 40min with 0.075% Type Ⅷ collagenase. The cell suspension was filtered through a 100um filter and centrifuged at 1700rpm for 5min. After red blood cell lysis with 1×lysis buffer, cells were centrifuged and resuspended in growth medium (DMEM/F12 1:1 containing 1% Penicillin and streptomycin and 10% FBS)
SVCs were loaded onto a GemCode instrument (10× Genomics) to generate single-cell barcoded droplets according to the manufacturer’s protocol with the 10× single-cell 3’ v2 chemistry

value: subcutaneous adipose tissue

value: primary

value: stromal

value: ob/ob


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice1 add seq4

description: Library name: OB1 add seq4


title: P3 Human Colon Normal Adjacent

source_name: Colon Normal Adjacent

value: Colon Normal Adjacent


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice1 seq3

description: Library name: OB1 seq3


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice2 seq4

description: Library name: OB2 seq4


title: P5 Human Colon Normal Adjacent


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice2 seq2

description: Library name: OB2 seq2


title: P5 Human Colon Cancer


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice1 add seq3

description: Library name: OB1 add seq3


title: SVCs extracted from subcutaneous adipose tissue of wild type mice2 seq4

description: Library name: WT2 seq4

value: wild type


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice1 seq1

description: Library name: OB1 seq1


title: SVCs extracted from subcutaneous adipose tissue of wild type mice2 seq1

description: Library name: WT2 seq1


title: A2780cis 3xFLAG R1

value: human epithelial ovarian cancer

value: 1 week FLAG overexpression and cisplatin treatment


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice2 seq1

description: Library name: OB2 seq1


title: HEK293T_siSETX_rep1

value: Human embryonic kidney

value: siSETX


title: HEK293T_siSETX_rep2


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 add seq2

description: Library name: WT1 add seq2


title: HEK293T_CPT_ctrl_rep1


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1  add seq4

description: Library name: WT1 add seq4


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice1 add seq1

description: Library name: OB1 add seq1


title: SVCs extracted from subcutaneous adipose tissue of wild type mice2 seq3

description: Library name: WT2 seq3


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 seq4

description: Library name: WT1 seq4


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 seq2

description: Library name: WT1 seq2


title: SVCs extracted from subcutaneous adipose tissue of ob/ob mice2 seq3

description: Library name: OB2 seq3


title: HEK293T_PlaB_ctrl_rep1


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 add seq3

description: Library name: WT1 add seq3


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 add seq1

description: Library name: WT1 add seq1


title: Huwe1_cKO_rep2

city: Brisbane

first: Lachlan

middle: Ian

last: Harris

state: QLD

address: 300 Herston Road

department: Cancer Research Program

country: Australia

institute: QIMR Berghofer MRI

data_processing:
scRNA-seq: CellRanger Count (Ver. 7.0.1) CUT&RUN The nf-core/cutandrun pipeline was used (v3.2). The uniquely mapped reads were aligned to the mm10 reference genome using Bowtie2. Peak calling was performed using SEACR with 0.01 seacr_peak_threshold. The BigWig file was visualized using the Integrative Genomics Viewer (IGV).
Assembly: scRNA-seq: refdata-gex-mm10-2020-A or Mycn data was mapped to a custom version of this genome, which had the Mycn gene deleted and replaced with two new contigs, corresponding to exon1 of the Mycn gene (Mycnex1) and exon 2/3 (Mycnex3). The gene encoding eGFP was also added to the custom genome. The genome was made with the cellRanger mkref command. CUT&RUN: mm10.
Supplementary files format and content: scRNA-seq: output from CellRanger Count (Ver. 7.0.1). CUT&RUN: bigWig files.

source_name: hippocampal neural stem cells (FLOW-enriched)

extract_protocol:
scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions (10x Genomics Chemistry, Single Cell version 3.0.1).  CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000  cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C  for 10 min. DNA was then purified using a DNA cleanup kit.
scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100.


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 seq1

description: Library name: WT1 seq1


title: Huwe1_control_rep2

value: hippocampal neural stem cells (FLOW-enriched)


title: Ascl1_control_rep3


title: Ascl1_sample1_rep2_demultiplex_required


title: Ascl1_cKO_rep3


title: Mycn_control_rep2


title: SVCs extracted from subcutaneous adipose tissue of wild type mice1 seq3

description: Library name: WT1 seq3


title: Huwe1_control_rep1


title: Mycn_control_rep1


title: Ascl1_control_rep1


title: SVCs extracted from subcutaneous adipose tissue of wild type mice2 seq2

description: Library name: WT2 seq2


title: Mycn_cKO_rep1


title: MDX594OR Olaparib

status: Public on Mar 03 2025

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

description:
Library name: MDX594OR Olaparib
10x Genomics

data_processing:
Single-cell RNA-seq (scRNA-seq) data were analyzed through the CellRanger Single-Cell Software Suite (v6.0.1).
Assembly: Sequencing reads from mouse  cells were mapped with the genome references for mouse (gex-mm10).
Supplementary files format and content: Cell Ranger output: matrix, barcodes and features

source_name: Breast cancer Mouse Derived Allograft

extract_protocol:
Single-cells were loaded to the 10×Genomics Chromium Controller to be partitioned into Gel Beads-in-emulsion (GEMs). The cDNA sequencing libraries were prepared using the Chromium Single Cell 5´ Library and Gel Bead Kit (10X Genomics, Cat. N. 1000006) following manufacturer's instructions. Briefly, after GEM generation and reverse transcription (RT), GEM-RT were cleaned up and cDNA was amplified during 13 cycles to be subjected to quality control and quantification on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies).
To construct the Gene expression (GEX) library, 25-50 ng of the amplified cDNA were fragmented, end repaired, A-tailed, and sample indexed using the Chromium Single Cell 5’ Library Construction Kit (10x genomics, 1000020).

value: Breast cancer Mouse Derived Allograft

value: Olaparib (PARPi) resistant

value: Olaparib (PARPi)


title: Ascl1_cKO_rep1


title: MDX594OR Vehicle

description:
Library name: MDX594OR Vehicle
10x Genomics

value: Vehicle


title: MDX594 Vehicle

description:
Library name: MDX594 Vehicle
10x Genomics

value: Olaparib (PARPi) sensitive