title: EBNA3C-HT 4C-seq CDKN2A 3C On Replicate 1

description: E3C 4C-seq at CDKN2A

value: Lymphoblastoid Cell Lines

value: EBNA3C-HT Lymphoblastoid Cell Lines


title: GSC3028_shNT_Replicate2

status: Public on Dec 22 2022

type: SRA

city: La Jolla

first: Derrick

last: Lee

state: CA

address: 9500 Gilman Dr

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
The Fastq files of the RNA-seq data were processed to read quality control by running ‘FastQC’ (Galaxy version 0.72) in Galaxy (usegalaxy.org) and then to remove the adapters by running ‘Trim Galore!’ (Galaxy version 0.4.3.1). The trimmed reads were mapped to human genome 38 by ‘HISAT2’ (Galaxy version 2.1.0+galaxy 4) and the mapped reads were then counted with ‘featureCounts’ (Galaxy version 1.6.3+galaxy 2). The counts were processed to differentially expressed gene analysis with R package ‘DESeq2’ (Version 1.14.1). Volcano plots were generated using GraphPad Prism. Downregulated genes upon EYA2 knockdown were processed to GO analysis (http://geneontology.org/). Pre-ranked genes by fold change were processed to GSEA (Gene Set Enrichment Analysis; Broad institute).
Assembly: hg19
Supplementary files format and content: counts.txt
Supplementary files format and content: Counts of all RNA-seq files including replicates

molecule: total RNA

organism: Homo sapiens

growth_protocol: Xenografted tumors were dissociated using a papain dissociation system according to the manufacturer’s instructions. Cells were then cultured in Neurobasal medium supplemented with 2% B27, 1% L-glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF) for at least 6 hours to recover expression of surface antigens. Because cell surface markers are not uniformly informative for marking GSCs, we utilized a combination of functional criteria to validate GSCs. Both GSCs and DGCs were derived immediately following dissociation or following transient xenograft passage in immunocompromised NSG mice using prospective sorting followed by assays to confirm stem cell marker expression, sphere formation, and secondary tumor initiation. Cells were labeled with CD133/2(293C)-Allophycocyanin (APC) antibody kit (Miltenyi Biotec, 130098826), and the CD133+ cells were sorted and analyzed by flow cytometry. The sorted CD133+ cells were cultured in NBM-B27 medium containing 20 ng/ml of both epidermal growth factor (EGF) (R&D system, 236-EG-01M) and recombinant human FGF basic (FGF) (R&D system, 4114-TC-01M) for a short period before treatment and analyzed. GSC phenotypes were validated by expression of stem cell markers (SOX2 and OLIG2) and functional assays of self-renewal. Corresponding differentiated glioma cells were obtained by culturing the GSCs in DMEM medium supplemented with 10% FBS for at least 2 weeks.

extract_protocol:
Totoal RNA from GSCs transduced with shCONT or shKLHDC8A were collected with miRNeasy mini kit (Qiagen) and processed to library construction with TruSeq RNA library Prep Kit (illumine).
Totoal RNA from GSCs transduced with shCONT or shKLHDC8A were collected with miRNeasy mini kit (Qiagen) and processed to library construction with TruSeq RNA library Prep Kit (illumine).

treatment_protocol: Lentiviral clones expressing two or three non-overlapping shRNAs directed against human KLHDC8A (TRCN0000138219 and TRCN00000138761), or a non-targeting control shRNA were obtained from Sigma-Aldrich. 293FT cells were used to generate lentiviral particles through co-transfection of the packaging vectors pCMV-dR8.2 dvpr and pCI-VSVG using a standard calcium phosphate transfection method in DMEM plus 10% FBS. 12 hours later after transfection, medium was changed to neurobasal complete medium. Neurobasal complete medium containing lentiviral particles was collected by filtering with 0.45uM filter for immediate use or stock in -80°C.

tag: cell line

tag: cell type

value: Glioblatoma stem cells

tag: genotype

value: WT


title: GSC3028_shKLHDC8A-1_Replicate1

value: KLHDC8A knockdown


title: RNA-seq Ikzf1 rep1

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

description: Raw salmon counts/DESeq2

data_processing:
Raw CUT&RUN fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using FDR 0.5 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Bigwig tracks files for CUT&RUN conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

organism: Mus musculus

source_name: Retina

growth_protocol: RNA-seq: P0 CD1 retinas were dissociated using Accutase and transfected using the Amaxa Neural Stem Cell Kit according to the manufacturer’s protocol.  Cells were seeded into 6-well plates coated with PLL/ Laminin, and cultured as previously described (Gomes et al., 2011).  After 9 hr, cells were harvested and dissociated with Accutase followed by FAC-sorting for GFP. Control GFP condition contained 4 x105 cells per biological replicate (n=4) and Ikzf1 condition contained 3 x 105 cells per biological replicate (n=4). CUT&RUN: Whole retinas were dissected and CUT&RUN was performed as previously described (Skene et al., 2018), with a few added modifications. For Ikzf1, CAG-Ikzf1-IRES-GFP electroporated P0 retinal explants were cultured as previously described in Elliott et al. 2008.

extract_protocol:
RNA-seq: rRNA was depleted using Ribo-Zero™ Magnetic Gold Kit for rRNA depletion (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324) according to manufacturer’s guidelines. CUT&RUN: Extraction of DNA fragments was performed as described in (Skene and Henikoff, 2018) using the Qiagen Nucleotide Romoval Kit.
RNA-seq: . Libraries were diluted and pooled equimolar and then sequenced in pair end 50 cycles (PE50) on a v4 flowcell (Illumina - HiSeq PE Cluster Kit v4 cBot - PE-401-4001) of the Illumina HiSeq 2500 System. CUT&RUN: Libraries were prepared using Manufacturer's protocols using the KAPA HyperPrep Kit (Roche).

treatment_protocol: RNA-seq: Cells were sorted directly into lysis buffer and purified using the RNeasy micro kit from Qiagen. Samples quantity (RNA Integrity Number = RIN) and quality were assessed using the Agilent RNA 6000 Pico Kit (Agilent #5067-1513) on the Bioanalyzer 2100. rRNA was depleted using Ribo-Zero™ Magnetic Gold Kit for rRNA depletion (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324) according to manufacturer’s guidelines. Library preparations were done using SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories, Inc. #634836 or #634837) according to manufacturer’s guidelines. CUT&RUN: For Ikzf1, 50,000 GFP+ve cells were sorted directly into the buffer with Concanavalin-A beads. For Ikzf4, E14 and P0 retinas, 1,500,000 cells were used for each stage. The entire procedure was done in 200μl PCR tubes. 0.01% digitonin concentration was used and pAG-MNase digestion was performed for 30min on ice.

value: Retinal progenitor cells

tag: strain

tag: condition


title: 3D culture in malignant mesotheliomal cells (3D_m107)

city: Baltimore

first: Fumiya

last: Ito

state: MARYLAND

address: 725 N. Wolfe Street, 119 Hunterian

department: Cell Biology

institute: Johns Hopkins University

description: Cancer sample

data_processing:
FastQC 0.10.0
FASTQ files were trimmed for adapters and Phred score (>20) using TrimGalore! (0.6.4).
Trimmed sequenced reads were aligned to the mouse genome assembly (GRCm39 Ensembl release 103) using STAR (2.7.9a).
Aligned reads were used to quantify mRNA with HTSeq-count(version 0.12.4).
Differential gene expression analysis of paired-comparison between 2D-culture and 3D-culture was performed using edgeR package on protein-coding genes.
Assembly: GRCm39 Ensembl release 103
Supplementary files format and content: Exce l file includes RPKM values for each Sample

source_name: mesothelial cells

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

extract_protocol:
RNA was harvested using AurumTM Total RNA Mini Kit (BioRad). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were treated crocidolite or carbon nanotube by ip injection

value: mesothelial cells

tag: treatment

value: carbon nanotube

tag: growth protocol

value: 3D culture


title: SO2.IP

city: Jinzhong

first: Qing

last: Liu

address: Taigu, Shanxi Province, PR China

country: China

institute: Shanxi Agricultural university

data_processing:
Cutadapt software (v1.9.3) was used to eliminate the reads containing adaptor contaminants and low quality bases.
HISAT2 software was applied to align clean reads of all libraries to the reference genome of E. tenella
MACS software was used to identify methylated sites on RNAs (peaks),and differentially methylated sites were identified by diffReps
The m6A-enriched motifs were identified with DREME.
Assembly: ETH001 RefSeq GCF_000499545.2
Supplementary files format and content: The xlsx format sheet (named Gene Expression Profiling) showed gene_id,counts of all samples of the gene, normalized counts by edgeR, and annotation of the genes.
Supplementary files format and content: The xlsx format sheet (named Methylated_RNA_sites.mRNA) showed information about methylation sites,methylated RNA,enrichment information,and annotations.
Library strategy: MeRIP-seq

organism: Eimeria tenella

source_name: Sporulated oocysts

extract_protocol:
Input: Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA).IP:Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA), and then subjected to immunoprecipitation (IP) by using the GenSeq® m6A-IP Kit (Cloudseq Biotech, Inc., Shanghai, China) following the manufacturer’s specifications.
RNA libraries for IP and input samples were constructed with the GenSeq® Low Input Whole RNA Library Prep Kit (Cloudseq Biotech, Inc., Shanghai, China) according to the manufacture’s instructions.

value: SD-01 strain

value: Sporulated oocysts


title: 3D culture in malignant mesotheliomal cells (3D_m67)

description: Cancer sample

value: crocidolite


title: GSC3028_shNT_Replicate1


title: SO2.Input


title: RNA-seq Control rep4

description: Raw salmon counts/DESeq2

value: GFP


title: GSC23_shKLHDC8A-2_Replicate2


title: UO1.IP

source_name: Unsporulated oocysts

value: Unsporulated oocysts


title: RNA-seq Control rep3

description: Raw salmon counts/DESeq2


title: 3D culture in malignant mesotheliomal cells (3D_m60)

description: Cancer sample


title: GSC23_shKLHDC8A-2_Replicate1


title: SO1.IP


title: UO1.Input


title: 3D culture in malignant mesotheliomal cells (3D_m54)

description: Cancer sample


title: RNA-seq Control rep2

description: Raw salmon counts/DESeq2


title: SO1.Input


title: GSC23_shKLHDC8A-1_Replicate2


title: SO3.IP


title: RNA-seq Control rep1

description: Raw salmon counts/DESeq2


title: 3D culture in malignant mesotheliomal cells (3D_m28)

description: Cancer sample


title: Wild-type, CD45.1+  P3/P4 macrophages 2001

city: Boston

first: Izabel

last: Patik

state: Massachusetts

address: 300 Longwood Ave

department: Division of Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

description:
WT 1
AN1

data_processing:
Reads were aligned to the mm10 mouse genome assembly and gene counts were quantified using STAR (v2.7.3a).
Gene counts were normalized using the trimmed mean of M-values (TMM) approach in edgeR (v 3.15)
Since all mice in this study were Cdcs1 knockouts, we excluded all Cdcs1 proximal genes, which might have escaped the targeted knockout. Specifically, we ignored genes found within 1Mb up and downstream of the expanded Cdcs1 locus, as defined by Bleich et al. (2010) [PMID: 19856416]
Since wildtype (WT) mice were male and mice of all other groups were female, we excluded sex dimorphic genes in all comparisons involving WT. Specifically, we ignored genes found to be sexually dimorphic in at least three cell types as reported by Lu and Mar (2020) [PMID: 33153500]
Assembly: mm10
Supplementary files format and content: log-TMM normalized gene-level expression, ignoring genes found to be sexually dimorphic in at least three cell types as reported by Lu and Mar (2020) [PMID: 33153500], and ignoring genes found within 1Mb up and downstream of the expanded Cdcs1 locus, as defined by Bleich et al. (2010) [PMID: 19856416]

source_name: sorted Ly6C- colonic lamina propria macrophages

growth_protocol: Mice were kept under SPF conditions to induce sponteneious colitis development.

extract_protocol:
Animals were euthanized by CO2 and colonic lamina propria cells were isolated. Briefly, colons and cecums were dissected and epithelial cells were stripped by 10mM EDTA in HDMI for 30 min at 37°C. Remaining tissue was transferred to 50 ml conical tubes minced and digested using Collagenase VIII (Sigma-Aldrich, C2139-5G) in HBSS (with Ca /Mg) for 30-45 min at 37°C. Cells were then filtered through 70µm cell strainer and washed twice in 1xPBS. Viability and cell numbers were determined using an automated cell counter (TECAN) and stained with the antibody cocktail and analyzed using a LSRFortessa (BioLegend, San Diego, CA, USA ). 5000-25000 P3/P4 LP macrophages from bone marrow chimeras 8 weeks following reconstitution were FACS-sorted (gated on: CD103-, Ly6G-, CD11b+, CD11cint, CD64+, Ly6C-, CD45.1+ or CD45.2+) directly into RLT buffer (Qiagen) on a FACS Aria II (BD Life Sciences) and mRNA was extracted using the RNeasy Micro kit (Qiagen).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 50bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: Recipient mice were irradiated (Gamma Cell 40, 137Cs) with a split dose of 1200 Rads 4h apart. The following day bone marrow was harvested from the hind leg bones of donor mice by flushing with sterile PBS. Bone marrow cells were counted and 4 x 106 cells/mouse were injected into irradiated recipients via retro-orbital injections in 150 µl sterile PBS. Drinking water was supplemented with trimethoprim/sulfamethoxazole (Aurobindo Pharmaceuticals) in their drinking water for 3 weeks (240 mg/ 250 ml water). Animals were euthanized 8 weeks following reconstitution.

tag: received bone_marrow's_genotype

value: Cdcs1, wild-type


title: RNA-seq Ikzf1 rep2

description: Raw salmon counts/DESeq2


title: GSC23_shKLHDC8A-1_Replicate1


title: 3D culture in malignant mesotheliomal cells (3D_m12)

description: Cancer sample


title: Sigmoid-03T

city: Nanjing

first: linlin

last: ji

state: Jiangsu

address: 305 Zhongshan East Road, Xuanwu District

institute: Nanjing University

description: GEXSCOPE®

library_source: transcriptomic single cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: colorectal cancer

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS.
Single-cell suspensions (2×105 cells/mL) with PBS  were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

tag: tissue

value: colorectal cancer

value: colon cells

value: kras(+), braf(+)

tag: Sex

value: male

tag: tumor stage

value: IIA


title: GSC23_shNT_Replicate2

value: Glioblatoma stem cells

value: WT


title: Sigmoid-03N

description: GEXSCOPE®

source_name: normal colorectal mucosa

value: normal colorectal mucosa


title: GSC23_shNT_Replicate1


title: 3D culture in malignant mesotheliomal cells (3D_m5)

description: Cancer sample

value: mesothelial cells


title: 3D culture in normal mesothelial cells (3D_meso3)

description: Processed data not provided for control (normal) sample.

value: non treatment


title: EBO4_MUT-249

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Basecalls performed using bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl GRCh38 genome assembly using STAR_2.4.2a with following parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated by featurecounts from Rsubread_1.24.0 with minFeatureOverlap 10
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw counst for each sample

source_name: HEK293 cell line

extract_protocol:
Total RNA from cell culture samples was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MRPS5 V336Y


title: 3D culture in normal mesothelial cells (3D_meso2)

value: 3D culture


title: EBO4_MUT-247


title: Cochlea_wildtype_P8_multiome_ATAC

city: Houston

first: Andrew

last: K Groves

state: Texas

address: One Baylor Plaza, Baylor College of Medicine

institute: Baylor College of Medicine

description: P8 wildtype cochlea 10x Genomics single-cell multiome ATAC

library_source: genomic

data_processing:
Raw sequencing data from both RNA and ATAC libraries in fastq format were used as input into cellranger-arc count (10x Genomics, v2.0.0) for simultaneous alignment against the mouse mm10 genome.
The cellranger- arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing, resulting in 4,882 nuclei post-filtering for the P1 dataset, and 7,049 nuclei post-filtering for the P8 dataset. ATAC peaks were called using macs2 v2.1.2. Multiome datasets were clustered based on RNA, ATAC, and weighted-nearest neighbor (Hao et al., 2021) to generate UMAPs. This resulted in 20 clusters for the P1 dataset, and 19 clusters for the P8 dataset. Clusters were assigned cell types based on known cell markers.
Representative signal tracks were visualized in IGV v2.4.14. ATAC peaks were filtered by hair cell enhancers previously identified (Tao et al., 2021), and intersected to find common, P1-specific, and P8-specific regions. Heatmaps were generated using deepTools v3.2.0 computeMatrix and plotHeatmap.
Cell barcodes from clusters of interest (P1 GER, P8 GER, P1 IPh/BC, P8 IPh, and P8 BC) were used to extract ATAC reads belonging to each respective cell type and generate a pseudobulk ATAC dataset.
Peaks were called on the pseudobulk ATAC datasets and common peaks were used as input into DESeq2 v1.34.0 to scale the signal between P1 and P8 datasets.
Assembly: mm10
Supplementary files format and content: cellranger output of aligned reads as bam files. Converted to feature-barcode matrices of gene expression from individual cells. Raw matrices contain every barcode sequence detected, including background, non-cellular barcodes, and low quality cells. filtered contains only detected cellular barcodes with quality control cutoff.
Supplementary files format and content: Count and barcode data for every ATAC fragment is stored in the atac fragments file.
Supplementary files format and content: Gene expression matrices and ATAC were loaded into Seurat to perform WNN UMAP clustering and cluster identification. The published cluster identities are contained in the cluster annotation file.

molecule: genomic DNA

source_name: Inner ear cochlea

growth_protocol: Wildtype mice in a mixed background of CD1 and FVB/NJ, and C57BL/6 were bred.

extract_protocol:
Cochlear tissue was dissected from P1 and P8 mice and enzymatically dissociated with a cocktail of 400µl of 0.25% Trypsin, 50µl of 1 mg/ml Dispase, and 50µl of 1 mg/ml collagenase for 20 minutes at 37°C. After incubation, the digested tissue was titurated 100 times using a small-bore 200µl pipette and centrifuged at 500x g for 5 minutes at 4°C. After centrifugation, the sample was processed according to the 10x Genomics protocol “Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing” (CG000375, Rev B). Briefly, the supernatant was decanted, and the cell pellet was resuspended in 1ml of NP-40 Lysis Buffer and incubated for 5 min on ice.
Nuclei were filtered through a 40 micron cell strainer, and centrifuged at 500x g for 5 minutes at 4°C. The supernatant was decanted, and nuclei were resuspended in 1ml of PBS + 2% BSA and incubated for 5 min at 4C. Nuclei were centrifuged at 500x g for 5 minutes at 4°C, resuspended in 100ul of 0.1x Lysis Buffer, and mixed with a pipet. Nuclei were incubated for 2 minutes on ice, followed by the addition of 1ml Wash Buffer, mixed and centrifuged at 500x g for 5 minutes at 4°C, and resuspended in the appropriate volume of Diluted Nuclei Buffer for input into the Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics). For the P1 cochlea, 6,065 nuclei were loaded. For the P8 cochlea, 9,645 nuclei were loaded.
scMultiome ATAC + Gene Expression protocol (10x Genomics).

treatment_protocol: No treatment.

value: Inner ear cochlea

tag: developmental stage

value: mixed (CD1, FVB/NJ, C57BL/6)

value: wildtype

value: no treatment


title: 3D culture in normal mesothelial cells (3D_meso1)


title: Cochlea_wildtype_P1_multiome_ATAC

description: P1 wildtype cochlea 10x Genomics single-cell multiome ATAC


title: Cochlea_wildtype_P8_multiome_RNA

description:
P8 wildtype cochlea 10x Genomics single-cell multiome RNA
nuclear RNA


title: EBO4_MUT-246


title: 2D culture in malignant mesotheliomal cells (2D_m107)

description: Cancer sample

value: carbon nanotube

value: 2D culture


title: 2D culture in malignant mesotheliomal cells (2D_m67)

description: Cancer sample

value: crocidolite


title: CD4+ T cell, juvenile, DMSO treated control, RNA-Seq, rep4

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Reads demultiplexed to fastq using BCL2FASTQ v2.17.1.14 with default parameters
Samples trimmed, filtered, aligned, and quantified using nf-core/rnaseq pipeline v. 3.8.1
Differential gene expression testing was performed using DESeq2
Assembly: mm10
Supplementary files format and content: DESeq_rlog_transformed_counts.csv, a CSV-formatted file containing rlog-transformed (normalized) gene counts
Supplementary files format and content: mRNAseq_raw_counts_matrix.tsv, a TSV-formatted file containing raw gene counts

source_name: lung

extract_protocol:
Mouse lungs were minced and dissociated into a single-cell suspension. CD4+ cells were selected by MACS. CD4+ T cells were then sorted from the CD4+ population by FACS before lysis and mRNA extraction.
Bulk RNA-seq libraries prepared using QIAGEN AllPrep DNA/RNA micro kit and the TAKARA SMARTer Stranded Total RNA-seq Kit v2.

value: lung

value: CD4+ T cell

value: Control


title: EBO4_MUT-245


title: 2D culture in malignant mesotheliomal cells (2D_m60)

description: Cancer sample


title: EBO4_MUT-243


title: Cochlea_wildtype_P1_multiome_RNA

description:
P1 wildtype cochlea 10x Genomics single-cell multiome RNA
nuclear RNA


title: CD4+ T cell, juvenile, DMSO treated control, RNA-Seq, rep3


title: 2D culture in malignant mesotheliomal cells (2D_m54)

description: Cancer sample


title: CD4+ T cell, juvenile, DMSO treated control, RNA-Seq, rep2


title: EBO1_MUT-307

value: MRPS5 G313R


title: 2D culture in malignant mesotheliomal cells (2D_m28)

description: Cancer sample


title: EBO1_MUT-306


title: CD4+ T cell, juvenile, DMSO treated control, RNA-Seq, rep1


title: CD4+ T cell, juvenile, DAC treated, RNA-Seq, rep4

value: DAC


title: EBO1_MUT-305


title: EBO1_MUT-304


title: 2D culture in malignant mesotheliomal cells (2D_m5)

description: Cancer sample


title: EBO1_MUT-240


title: CD4+ T cell, juvenile, DAC treated, RNA-Seq, rep2


title: 2D culture in normal mesothelial cells (2D_meso3)

value: WT


title: EBO1_4_WT-260

value: MRPS5 WT


title: 2D culture in normal mesothelial cells (2D_meso1)

value: mesothelial cells

value: non treatment


title: 2D culture in malignant mesotheliomal cells (2D_m12)

description: Cancer sample


title: EBO1_4_WT-238


title: Anti CTLA4 treated AB12 mouse tumor sample collected at day 14 rep3

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
FASTQ files were aligned to the mouse reference genome GRCm38/mm10 using TopHat2 (v2.0.14)
Uniquely mapped reads were kept and BAM files were indexed and sorted using Sambamba (v0.6.5)
We used HTSeq to obtain the number of reads associated with each gene in the Gencode vM22 transcriptome indexes.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file includes count matrix values for each sample

source_name: Peritoneal tumor sample

growth_protocol: AB12 cells (10^5) were injected to the peritoneum of BALB/c mice

extract_protocol:
Total RNA from tumor was isolated using TRIzol reagent according to the manufacturer's protocol, followed by Direct zol
Libraries were prepared using the KAPA RNA HyperPrep kit (Roche), according to the manufacturer instructions.

treatment_protocol: 200 µg of anti-CTLA4 (clone 9D9) were injected to the peritoneum of tumor bearing mice at the indicated time points. The treatment protocol consisted of four injections, two injections per week for two weeks.

value: mesothelioma

value: BALB/c

value: anti-CTLA4 (clone 9D9)

tag: disease state

value: 14 days after AB12 cell injection


title: CD4+ T cell, neonatal, DMSO treated control, RNA-Seq, rep3


title: CD4+ T cell, juvenile, DAC treated, RNA-Seq, rep1


title: EBO1_4_WT-237


title: Anti CTLA4 treated AB12 mouse tumor sample collected at day 14 rep2


title: CD4+ T cell, neonatal, DMSO treated control, RNA-Seq, rep2


title: CD4+ T cell, neonatal, DMSO treated control, RNA-Seq, rep4


title: Anti CTLA4 treated AB12 mouse tumor sample collected at day 14 rep1


title: EBO1_4_WT-236


title: CD4+ T cell, juvenile, DAC treated, RNA-Seq, rep3


title: 2D culture in normal mesothelial cells (2D_meso2)


title: CD4+ T cell, neonatal, DMSO treated control, RNA-Seq, rep1


title: Anti CTLA4 treated AB12 mouse tumor sample collected at day 10 rep3

value: 10 days after AB12 cell injection


title: EBO1_4_WT-259


title: EBO1_4_WT-235


title: CD4+ T cell, neonatal, DAC treated, RNA-Seq, rep4


title: EBO1_4_WT-233


title: Anti CTLA4 treated AB12 mouse tumor sample collected at day 10 rep2


title: Genomic DNA of AZA-untreated HD-MSCs S25

type: genomic

city: Guangzhou

first: Ruohao

last: Xu

state: Guangdong

address: Zhongshan Second Road, Guangzhou, China

department: Hematology

institute: Guangdong Provincial People's Hospital

description: bone marrow MSCs from healthy donor (HD)

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

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

data_processing: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

label: Cy3 and Cy5

source_name: AZA-untreated HD-MSCs

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from ex vivo expanded MSC samples  using Qiagen DNeasy Kit according to standard instructions

value: bone marrow MSCs at P2


title: untreated AB12 mouse tumor sample collected at day 14 rep3

value: untreated


title: 747495 WT-PEPD-mix_CITE-TSA

city: London

first: Rose

last: Hodgson

address: 2 Monnery Road

country: United Kingdom

institute: MiNA Therapeutics

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
metadata.tsv
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz
seurat.rds

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.1) and aligning to the mm10-1.2.0 genome build.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: spleen

extract_protocol:
All mice are on a C57BL/6 background. 10% WT CD45.1+ splenic cells were spiked into 1 WT CD45.2+ and 1 Pepd-/- CD45.2+ sample, and 10% WT CD45.1+CD45.2+ splenic cells were spiked into 1 WT CD45.2+ and 1 Pepd-/- CD45.2+ sample. Total T cells from the 4 samples described above and 1 WT CD45.2+ and 1 Pepd-/- CD45.2+ splenic samples were isolated by magnetic sorting, and then the 6 samples were multiplexed using Biolegend TotalSeq-B hashing antibodies by protocol (B0301 #155831, B0302 #155833, B0303 #155835, B0304 #155837, B0305 #155839, B0306 #155841). Pooled hashtagged cells were labelled with TotalSeq-A antibodies by protocol (anti-CD4 #100569, anti-CD8a #100773, anti-CD279 (PD-1) #109123, anti-CD44 #103063, anti-CD62L #104451, anti-CD25 #102055, anti-CD127 (IL7R), #135045, anti-ICOS #313555, anti-CD69 #104546, anti-CD27 #124235, anti-CD5 #100637, anti-KLRG1 #138431, anti-CD95 #152614, anti-CD45.1 #110753 and anti-CD45.2 #109853). After washing, cells were loaded into the chromium controller (10X-Genomics) chip and sequenced as previously described (16). Reads for TotalSeq anti-CD45.1 and anti-CD45.2 alone could not be detected, thus the CD45.1+ and CD45.1+/CD45+ populations could not be separated from the CD45.2 in this scRNAseq experiment dataset.
Cells were loaded into the chromium controller (10×-Genomics) chip following the standard protocol for the chromium single cell 3’ kit. (Multi-omic single cell analysis resolves novel stromal cell populations in healthy and diseased human tendon., Kendel et al. Scientific Reports., 2020)
Total-Seq-A ADT and Total-Seq-B Hashtag-seq as previously described following biolegend protocols (Multi-omic single cell analysis resolves novel stromal cell populations in healthy and diseased human tendon., Kendel et al. Scientific Reports., 2020)

value: spleen

value: T cells

tag: library type

value: ADT

tag: antibodies/tags


title: Anti CTLA4 treated AB12 mouse tumor sample collected at day 10 rep1


title: 747495 WT-PEPD-mix_HTO-TSB

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
metadata.tsv
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz
seurat.rds

source_name: Spleen

value: Spleen

value: HTO


title: CD4+ T cell, neonatal, DAC treated, RNA-Seq, rep3

value: lung

value: CD4+ T cell

value: DAC


title: Genomic DNA of AZA-treated HD-MSCs S26

source_name: AZA-treated HD-MSCs


title: CD4+ T cell, neonatal, DAC treated, RNA-Seq, rep2


title: Genomic DNA of AZA-treated HD-MSCs S28


title: Genomic DNA of AZA-treated HD-MSCs S29

value: bone marrow MSCs at P3


title: Genomic DNA of AZA-untreated HD-MSCs S24


title: Genomic DNA of AZA-treated CMML-MSCs S19

description: bone marrow MSCs from patient with CMML

source_name: AZA-treated CMML-MSCs


title: Genomic DNA of AZA-untreated HD-MSCs S23


title: Genomic DNA of AZA-treated CMML-MSCs S16

description: bone marrow MSCs from patient with CMML


title: Genomic DNA of AZA-treated CMML-MSCs S18

description: bone marrow MSCs from patient with CMML


title: Genomic DNA of AZA-treated HD-MSCs S27


title: Genomic DNA of AZA-treated CMML-MSCs S17

description: bone marrow MSCs from patient with CMML


title: Genomic DNA of AZA-treated HD-MSCs S25


title: 747495 WT-PEPD-mix_GEX-v3.1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
metadata.tsv
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz
seurat.rds

value: mRNA


title: untreated AB12 mouse tumor sample collected at day 10 rep5

value: mesothelioma


title: untreated AB12 mouse tumor sample collected at day 14 rep1

value: BALB/c


title: CD4+ T cell, juvenile, DMSO treated control, rep3

data_processing:
Reads demultiplexed to fastq using BCL2FASTQ v2.17.1.14 with default parameters
Reads were trimmed and filtered using TrimGalore! v0.4.3
Reads were aligned to the mm10 genome and methylation status was extracted using Bismark v0.16.3
Statistical analysis of differential methylation was performed using the R package DSS
Assembly: mm10
Supplementary files format and content: bismark.cov.gz files, methylation calling output from Bismark after alignment, used as direct input to DSS
Supplementary files format and content: DMLtest files, CSV files containing the results of the DMLtest function from DSS, filtered by FDR and annotated with HOMER

extract_protocol:
Mouse lungs were minced and dissociated into a single-cell suspension. CD4+ cells were selected by MACS. CD4+ T cells were then sorted from the CD45+ population by FACS before lysis and mRNA extraction.
Bulk mRRBS libraries prepared using QIAGEN AllPrep DNA/RNA micro kit, disgested with the endonuclease MspI, size-selected using SPRI beads, and subjected to bisulfite conversion using the Zymo Research EZ DNA Methylation-Lightning kit. Libraries were constructed with the Zymo Research Pico Methyl-Seq Library Prep Kit with Illumina TruSeq DNA methylation indices.

value: Control


title: Genomic DNA of AZA-treated CMML-MSCs S20

description: bone marrow MSCs from patient with CMML


title: CD4+ T cell, neonatal, DAC treated, RNA-Seq, rep1


title: CD4+ T cell, juvenile, DMSO treated control, rep2


title: untreated AB12 mouse tumor sample collected at day 10 rep4


title: untreated AB12 mouse tumor sample collected at day 14 rep2

value: 14 days after AB12 cell injection


title: Genomic DNA of AZA-untreated HD-MSCs S22


title: CD4+ T cell, juvenile, DMSO treated control, rep1


title: ATACseq.E0771GFP-ZBTB18OE_3

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

data_processing:
100 bp paired-end reads obtained from all samples. Next, Trim_Galore(v0.4.4) was used to quality trim 3’ adapters from raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used. The first 15bp of each reads were also clipped to reduce the GC bias. Next reads were aligned to mouse mm10 genome by BWA (version 0.7.17-r1198), and convert to bam file (a binary version of sam file) by samtools (v1.2, PMID: 19505943). biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) were used to mark duplicated reads and only non-duplicated proper paired reads were chosen by samtools (parameter “-q 1 -F 1804” version 1.2).
We adjust Tn5 shift (reads were offset by +4 bp for the sense strand and -5 bp for the antisense strand) and separated reads into nucleosome free, mononucleosome, dinucleosome, and trinucleosome by fragment size. We generated bigwig files by using the center 80bp of fragments and scale to 20 million nucleosome free reads. We confirmed nucleosome tracks surrounded nucleosome free tracks, and provided nucleosome free tracks here.
Nucleosome free fragments (fragment size < 100bp) were extracted with bedtools (v2.24.0, PMID: 20110278).
Genome_build: mm10 (Gencode M22)
Supplementary_files_format_and_content: bigwig

source_name: E0771 cells (CH3 BioSystems cat. #94A001)

growth_protocol: Cells were maintained in RPMI 1640 (Thermo Fisher) supplemented with 10% calf serum with iron (Hyclone) and 1% penicillin/streptomycin.

extract_protocol:
Transposition was performed using the Nextera DNA Library Prep Kit (Illumina, #20034197) with nuclei from 50,000 cells.
DNA was purified with the DNA Clean & ConcentratorTM-5 kit (Zymoresearch, #D4013) and the libraries were amplified by PCR using the NEBNext HiFi 2x PCR Master Mix (NEB, #M0541S). PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined with the Agilent High Sensitive DNA Kit and Bioanalyzer, respectively. ATAC-seq libraries were sequenced with an Illumina HiSeq Platform with 100-bp paired-end reads in triplicates.

tag: genotype/variation

value: E0771GFP cells (ZBTB18 overexpression)

value: breast cancer cells


title: Old_TBI_rep3

city: Charlottesville

first: Daniel

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

department: Neuroscience

institute: University of Virginia School of Medicine

data_processing:
All code used for analysis is available at [https://github.com/danielshapiro1/MeningealTransciptome]
The raw sequencing reads (FASTQ files) were aligned to the UCSC mm10 mouse genome build using the splice-aware read aligner HISAT2.
Samtools was used for quality control filtering/ PCR duplicate removal.
Reads were sorted into features with HTSeq, produing the processed .txt files.
Assembly: mm10
Supplementary files format and content: Microsoft Excel Open XML Spreadsheet include RPKM values for each Sample

source_name: Male dorsal  meninges

extract_protocol:
Meninges were removed, flash frozen on dry ice in 500ul of trizol, homogenized and processed for RNA extraction
RNA libraries were prepared for sequencing by GENEWIZ

treatment_protocol: We performed bulk RNA sequencing on the meningeal tissue at 1.5 months post TBI or Sham treatment in both young (10 weeks of age) and aged (20 months of age)

value: Male dorsal  meninges

value: RNA from whole meninges, 1.5mo after injury or sham, aged mice are 20-24mo of age

value: Mild traumatic brain injury

tag: time

value: 1.5 months prior to harvest


title: Genomic DNA of AZA-treated CMML-MSCs S15

description: bone marrow MSCs from patient with CMML

value: bone marrow MSCs at P2


title: CD4+ T cell, juvenile, DAC treated, rep4


title: Old_TBI_rep2

tag: cell line


title: 738890 WT-PEPD-mix_CITE-TSA

value: Spleen

tag: cell type

value: T cells

value: ADT


title: ATACseq.E0771GFP-ZBTB18OE_2

description: Transposition was performed using the Nextera DNA Library Prep Kit (Illumina, #20034197) with nuclei from 50,000 cells.


title: CD4+ T cell, juvenile, DAC treated, rep3

value: lung

value: CD4+ T cell

tag: genotype

value: DAC


title: Old_TBI_rep1


title: CD4+ T cell, juvenile, DMSO treated control, rep4


title: ATACseq.E0771GFP-ZBTB18OE_1


title: Old_Sham_rep3

value: Sham


title: Genomic DNA of AZA-untreated HD-MSCs S21


title: CD4+ T cell, juvenile, DAC treated, rep2


title: 738890 WT-PEPD-mix_HTO-TSB

value: spleen

value: HTO


title: CD4+ T cell, juvenile, DAC treated, rep1


title: ATACseq.E0771GFP-EV_2

value: E0771GFP cells (empty vector)


title: CD4+ T cell, neonatal, DMSO treated control, rep4

value: Control


title: Old_Sham_rep2


title: Genomic DNA of AZA-treated CMML-MSCs S11

description: bone marrow MSCs from patient with CMML


title: CD4+ T cell, neonatal, DMSO treated control, rep3


title: ATACseq.E0771GFP-EV_1

value: breast cancer cells


title: Young_TBI_rep3

value: Male dorsal  meninges

value: RNA from whole meninges, 1.5mo after injury or sham, young mice are 10 weeks of age


title: MTm4h

city: Lanzhou

first: Wei

last: Wei

state: Gansu Province

address: No. 222 South Tianshui Road

department: School of Life Sciences

institute: Lanzhou University

description:
GM
MTm4h

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequencing data were filtered with Cutadapt (v1.15) to get Clean Data, then the filtered Reads were mapping to the reference genome using the HISAT2, the upgraded version of TopHat2 (version 2.1.0)(http://ccb.jhu.edu/software/hisat2/index.shtml). The parameters were -q -p 1 -e 70 -f -v 1 -a -m 10 --best --strata.
HisSeq (0.9.1) was used to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
FPKM (Fragments Per Kilobase Million), which is the number of Reads per kilobase length from a gene per million Reads, is a commonly used method for normalizing gene expression that takes into account the effects of both sequencing depth and gene length on gene expression counts.
Genome_build: Ensembl
Supplementary_files_format_and_content: text files include FPKM values for each Samples

source_name: M-BMDM treated with Tm for 4 h

extract_protocol:
Total RNAs were extracted using Trizol reagent (Invitrogen Life Technologies). After the sequencing libraries were generated, the library fragments were purified using the AMPure XP system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow-derived macrophage

tag: strain

value: bone marrow

value: 4 h Tm treatment M-BMDM


title: Genomic DNA of AZA-treated CMML-MSCs S12

description: bone marrow MSCs from patient with CMML

value: bone marrow MSCs at P3


title: Genomic DNA of AZA-untreated CMML-MSCs S9

description: bone marrow MSCs from patient with CMML

source_name: AZA-untreated CMML-MSCs


title: CD4+ T cell, neonatal, DMSO treated control, rep2


title: Genomic DNA of AZA-treated CMML-MSCs S14

description: bone marrow MSCs from patient with CMML


title: Young_TBI_rep2

value: Mild traumatic brain injury

value: 1.5 months prior to harvest


title: CD4+ T cell, neonatal, DMSO treated control, rep1

value: lung


title: multidrug-resistant tuberculosis patient-78

type: RNA

city: Hangzhou

first: Zhi-Bin

last: Li

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

hyb_protocol: The labeled cDNA was hybridized with the on-chip probes after purification.

scan_protocol: After the hybridization was completed, the chip was scanned using an Agilent Microarray Scanner (Agilent p/n G2565BA) to obtain the fluorescence intensity information.

data_processing: The fluorescence intensity information was analyzed and converted to quantified values using Agilent Feature Extraction software (version 11.0.1.1). Data were normalized using GeneSpring GX v12.1 software (Agilent Technologies).

source_name: Plasma

label_protocol: The tested total RNA was reverse-transcribed using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190–0442) to obtain a labeled cDNA.

extract_protocol: Prior to lncRNA microarray detection, total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies) and purified using the RNeasy Mini Kit (Qiagen p/n 74104), and then tested for purity and  concentration using NanoDrop ND-1000.

treatment_protocol: Fasting blood samples were collected from all subjects in the morning.Peripheral blood (10 ml) was drawn into a disposable ethylenediaminetetraacetic acid (EDTA) anticoagulant vacuum blood collection tube.The plasma was separated within 4 h after blood collection and after centrifugation at 4℃ and 3000 g for 10 min. Plasma samples were dispensed into RNase-free tubes and stored at -80℃.

tag: gender

value: male

tag: age

value: 67 years old

value: Plasma


title: GTm4h

description:
GM
GTm4h

source_name: GM-BMDM treated with Tm for 4 h

tag: treatment

value: 4 h Tm treatment GM-BMDM


title: M0

description:
GM
M0

source_name: M-BMDM in normal condition

value: M-BMDM


title: Genomic DNA of AZA-treated CMML-MSCs S13

description: bone marrow MSCs from patient with CMML


title: Young_TBI_rep1


title: ATACseq.E0771GFP-EV_3

value: E0771GFP cells (empty vector)


title: CD4+ T cell, neonatal, DAC treated, rep4

value: CD4+ T cell

value: DAC


title: Young_Sham_rep3

value: Male dorsal  meninges

value: Sham


title: cured tuberculosis subject-102

value: cured tuberculosis subject

value: 25 years old


title: Genomic DNA of AZA-untreated CMML-MSCs S10

description: bone marrow MSCs from patient with CMML


title: Young_Sham_rep2

value: RNA from whole meninges, 1.5mo after injury or sham, young mice are 10 weeks of age


title: CD4+ T cell, neonatal, DAC treated, rep2


title: cured tuberculosis subject-99

value: 60 years old


title: CM_G12

description:
LLC
D

source_name: LLC incubated with conditioned media from 12 h Tm treatment GM-BMDM

value: Lewis lung carcinoma cells

value: 12 h Tm stimulated CM_GM treatment LLC


title: CD4+ T cell, neonatal, DAC treated, rep1

value: lung


title: CM_M0

description:
LLC
C

source_name: LLC incubated with conditioned media from M-BMDM

value: 0 h Tm stimulated CM_M treatment LLC


title: Genomic DNA of AZA-untreated CMML-MSCs S6

description: bone marrow MSCs from patient with CMML

value: bone marrow MSCs at P3


title: cured tuberculosis subject-93

value: male

value: 24 years old

value: Plasma


title: multidrug-resistant tuberculosis patient-75


title: Genomic DNA of AZA-untreated CMML-MSCs S5

description: bone marrow MSCs from patient with CMML


title: Rag1-/-NE1-/- pro-B cells-rep_1

city: Chicago

first: Hammad

last: Farooq

state: IL

address: 835 S Wolcot

department: Microbiology and Immunology

institute: University of Illinois Chicago, College of Medicine

description: In situ Hi-C

data_processing:
Hi-C data was processed using the Juicer pipeline (v.1.5), CPU version. The pipeline was set up with BWA (0.7.15- r1140) [2] to map each read end separately to the mm10 reference genome (GRCm38).
Duplicate and near-duplicate reads, as well as reads that map to the same fragment were removed. Among the remaining reads, those with mapping quality score (MAPQ) < 30 are retained. Arima-HiC-specific restriction sites (mm10_GATC_GANTC.txt) were obtained from ftp://ftp-arimagenomics.sdsc. edu/pub/JUICER CUTSITE FILES.
Both individual replicates and merged Hi-C reads of pro-B cells were processed using the Juicer pipeline. For individual replicates, raw reads from each sample were mapped separately to the reference genome, and then filtered by the MAPQ score. For merged replicates of each sample, valid read pairs from both replicates were merged, mapped to the reference genome, and then filtered by the MAPQ score.
Hi-C contact matrices were extracted from .hic files using the Dump command provided by a java-based program in the juicer tools. Hi-C maps were then normalized with the Knight and Ruiz (KR) matrix balancing method.
Assembly: mm10
Supplementary files format and content: hic files were generated

source_name: Pro-B cells

growth_protocol: In situ Hi-C was performed in mouse bone marrow pro-B cells using the Arima genome-wide Hi-C kit. CD19+ pro-B cells were isolated and grown in IL7 for 5 days.

extract_protocol: After shearing DNA and biotin pull down adapters were added by ligation and Hi-C library was PCR amplified followed by paired-end sequencing.

treatment_protocol: The cells were then formaldyhyde crosslinked and digested with the Arima RE Cocktail.  The 5' overhangs were filled-in, tagged with biotin and ligated. DNA was sheared, pulled down and adapters were ligated for NGS.

value: pro-B cells


title: TBI_rep1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
RStudio (v1.2.5033) was used for all downstream analyses and Seurat (v.3.9.9) was used for filtering out low-quality cells, normalization of the data, determination of cluster defining markers and graphing of the data on UMAP (53, 54).
Low-quality cells were excluded in an initial quality-control (QC) step by removing cells with fewer than 150 unique genes and cells expressing more than 5,000 unique genes in effort to remove doublets and triplets
Cells with transcriptomes that were more than 20% mitochondrial-derived were removed and cells with more than 5% hemoglobin among their expressed genes were also removed.
Using Seurat, genes with high variance were selected using the FindVariableGenes() function, then the dimensionality of the data was reduced by principle component analysis (PCA) and identified by random sampling of 20 significant principal components (PCs) for each sample with the PCElbowPlot() function. Cells were clustered with Seurat’s FindClusters() function.
Next, differential gene expression analysis was performed within the clusters using the ZINB-WaVE (v1.12.0) and DESeq2 (v1.30.0) packages
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: single cell RNA from whole meninges, 1 week after injury, mice are 10 weeks of age. The meninges from 5 mice that had received TBI 1 week prior were pooled as one biological replicate.

extract_protocol:
Singe cell suspension was provided to the UVA genomics core. Approximately 4,000 cells per sample were loaded onto a 10X Genomics Chromium platform to generate cDNAs carrying cell- and transcript-specific barcodes and sequencing libraries constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit 2.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
We subjected mice to a mild closed-skull injury and then performed scRNAseq on whole dorsal meningeal tissue one week post injury. The meninges from 5 mice that had received TBI 1 week prior were pooled as one biological replicate. The meninges from 5 mice that had received a Sham procedure 1 week prior were pooled as one biological replicate.
Meninges were then digested for 15 minutes at 37°C with constant agitation using 1 mL of pre-warmed digestion buffer (DMEM, with 2% FBS, 1 mg/mL collagenase VIII (Sigma Aldrich), and 0.5 mg/mL DNase I (Sigma Aldrich)). The enzymes were neutralized with 1 mL of complete medium (DMEM with 10% FBS) and meninges were then filtered through a 70 μm cell strainer. An additional 2 mL of FACS buffer was added, samples were centrifuged at 400 xg for five minutes, and samples were resuspended in FACS buffer. After 2 washes, cells were resuspended in FACS buffer with DAPI (0.2 μg/mL). Singlet gates were selected using pulse width of the side scatter and forward scatter. Live cells were selected based on the lack of DAPI staining. Cells were sorted into 1.5 mL tubes with ice cold DMEM. Following sorting, cells were centrifuged again at 450 xg for 4 mins and the media was aspirated. Cells were resuspended in 200 μL 0.04% BSA in PBS (0.04% non-acetylated BSA) and centrifuged again. Cells were counted in 20 μL of 0.04% BSA in PBS using trypan blue.

value: 10-12 weeks old


title: cured tuberculosis subject-92

value: female

value: 22 years old


title: Genomic DNA of AZA-untreated CMML-MSCs S4

description: bone marrow MSCs from patient with CMML

value: bone marrow MSCs at P2


title: CM_G0

description:
LLC
B

source_name: LLC incubated with conditioned media from GM-BMDM

value: 0 h Tm stimulated CM_GM treatment LLC


title: Young_Sham_rep1

value: Male dorsal  meninges

value: Sham

value: 1.5 months prior to harvest


title: Genomic DNA of AZA-untreated CMML-MSCs S7

description: bone marrow MSCs from patient with CMML


title: Sham_rep1

description: 10x Genomics

source_name: single cell RNA from whole meninges, 1 week after sham, mice are 10 weeks of age. The meninges from 5 mice that had received Sham 1 week prior were pooled as one biological replicate.


title: active tuberculosis patient-345

value: active tuberculosis patient

value: 32 years old


title: multidrug-resistant tuberculosis patient-79

value: 36 years old


title: Genomic DNA of AZA-untreated CMML-MSCs S3

description: bone marrow MSCs from patient with CMML


title: Rag1-/- pro-B cells-rep_2

description: In situ Hi-C


title: NT

description:
LLC
A

source_name: normal condition LLC

value: Lewis lung carcinoma cells

value: lung

value: LLC control


title: untreated AB12 mouse tumor sample collected at day 10 rep3

source_name: Peritoneal tumor sample

value: mesothelioma

value: BALB/c

value: untreated

value: 10 days after AB12 cell injection


title: 738890 WT-PEPD-mix_GEX-v3.1

source_name: spleen

value: spleen

value: T cells

value: mRNA


title: untreated AB12 mouse tumor sample collected at day 10 rep2


title: active tuberculosis patient-340

value: male

value: 30 years old

value: Plasma


title: Genomic DNA of AZA-untreated CMML-MSCs S8

description: bone marrow MSCs from patient with CMML

value: bone marrow MSCs at P2


title: pro-B NE1KO2

first: Amy

last: Kenter

address: 835 S Wolcott

institute: UIC

description: VDJ-seq library

data_processing:
The MiXCR pipeline was used to identify and group clonotypes by their CDRs to determine V gene usage.
Tables of unique CDR3 identified for each sample are provided as processed files. Tables include read counts, fraction, and sequence quality for each unique CDR3 region as well as the possible IGHV, IGHD and IGHJ gene names, scores, and sequence.
Assembly: mm9
Library strategy: VDJ-Seq

organism: Mus

source_name: BM derived NE1-/- pro-B cells

growth_protocol: Bone marrow derived primary pro-B cells were FACS purified from WT (C57Bl/6), NE1-/- and Site I.3Pr-/- mice.

extract_protocol:
Genomic DNA (gDNA) was isolated from purified CD19+ pro-B cells.
The V(D)J-seq protocol using gDNA was performed while omitting the negative depletion step and using custom JH primers. GDNA was sonicated to a range of 500 bp to 1000 bp using a Covaris S2 (Covaris).  Library barcoding was carried out using NEBNext Multiplex Oligos for Illumina (E7600S).

treatment_protocol: CD19+ cells were isolated using anti-CD19 conjugated MACS beads, pre-incubated with CD16/32 Fc Block and FACS purified using antibodies for CD19-BB515, CD93-PE/Cy7, IgM Fab-AF647, CD2-PE, CD43-BV421.

value: pro-B


title: untreated AB12 mouse tumor sample collected at day 10 rep1


title: CUT&RUN IgG P0

first: Awais

last: Javed

address: 110 Avenue des Pins

institute: IRCM

description: Bamcoverage .bigwig file/MACS2 peak calling .bed file

data_processing:
Library strategy: CUT&RUN
Raw CUT&RUN fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using FDR 0.5 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Bigwig tracks files for CUT&RUN conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

source_name: Retina

extract_protocol:
RNA-seq: rRNA was depleted using Ribo-Zero™ Magnetic Gold Kit for rRNA depletion (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324) according to manufacturer’s guidelines. CUT&RUN: Extraction of DNA fragments was performed as described in (Skene and Henikoff, 2018) using the Qiagen Nucleotide Romoval Kit.
RNA-seq: . Libraries were diluted and pooled equimolar and then sequenced in pair end 50 cycles (PE50) on a v4 flowcell (Illumina - HiSeq PE Cluster Kit v4 cBot - PE-401-4001) of the Illumina HiSeq 2500 System. CUT&RUN: Libraries were prepared using Manufacturer's protocols using the KAPA HyperPrep Kit (Roche).

value: All retinal cells

tag: condition

value: IgG


title: Old_Sham_rep1

source_name: Male dorsal  meninges

value: Male dorsal  meninges

value: RNA from whole meninges, 1.5mo after injury or sham, aged mice are 20-24mo of age

value: Sham

value: 1.5 months prior to harvest


title: Genomic DNA of AZA-untreated CMML-MSCs S1

description: bone marrow MSCs from patient with CMML

tag: tissue


title: untreated AB12 mouse tumor sample collected at day 6 rep3

value: mesothelioma

value: BALB/c

value: 6 days after AB12 cell injection


title: CUT&RUN Ikzf4 P0 rep2


title: Rag1-/- pro-B cells-rep_1

description: In situ Hi-C

value: pro-B cells


title: pro-B NE1KO1

description: VDJ-seq library


title: CUT&RUN Ikzf4 P0 rep1


title: pro-B Wt2

description: VDJ-seq library

source_name: BM derived WT pro-B cells

value: WT


title: CUT&RUN Ikzf1 P0+9hours

value: Electroporated retinal cells


title: active tuberculosis patient-338

value: active tuberculosis patient

value: male

value: 21 years old


title: Rag1-/-NE1-/- pro-B cells-rep_2

description: In situ Hi-C


title: active tuberculosis patient-335

value: 28 years old

value: Plasma


title: healthy control-69

value: healthy control

value: 39 years old


title: healthy control-42

value: 60 years old


title: untreated AB12 mouse tumor sample collected at day 6 rep2

value: untreated


title: pro-B Wt1

description: VDJ-seq library

value: pro-B


title: CD4+ T cell, neonatal, DAC treated, rep3

source_name: lung

value: lung

value: CD4+ T cell

value: DAC


title: CUT&RUN Ikzf4 E14

value: All retinal cells


title: Input-T-2

status: Public on Dec 21 2022

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

country: Japan

institute: Tohoku university school of medicine

data_processing:
After removing Adaptor sequences and low quality sequences using cutadapt ver. 1.9.1, paired reads with a quality score of less than 20 or 40 bases were removed using sickle ver. 1.33.
Reads were mapped to the GRCh38.p13 reference sequence using hisat2 ver. 2.2.0.
Reads mapped to reference sequences were counted using featureCounts ver. 2.0.0.
Assembly: GRCh38
Supplementary files format and content: read count data text file

source_name: HeLa cell line

growth_protocol: Cells were cultured in DMEM media containing 4.5 g/l of glucose (08458-16, Nacalai Tesque, Kyoto, Japan) supplemented with 10% FBS (26140079, Thermo Fisher Scientific).

extract_protocol:
Cells were lysed in hypotonic lysis buffer. Total RNA was extracted from clarified lysate and polysone bound RNA was extracted from sucrose gradient fraction by ethanol precipitation in presence of guanidine hydrochloride.
The library was prepared from 300 ng of total RNA using an MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd. Shenzhen Shi, China) with the protocol described in the manufacturer’s manual. The library quality was confirmed with Fragment Analyzer using a dsDNA 915 Reagent Kit (Advanced Analytical Technologies, Ankeny, IA). The circularized DNA was prepared using an MGIEasy Circularization Kit (MGI Tech Co., Ltd.) with the manufacturer’s guideline. DNA nanoball (DNB) was made manually by using the DNBSEQ-G400RS High-throughput Sequencing Kit (MGI Tech Co., Ltd.).

treatment_protocol: In the treatment group cells were treated with 30 mM MAT2 inhibitor, Cycloleucine (cLEU) for 6 hr

value: HeLa cell line

value: MAT2 inhibitor (Cycloleucine)

tag: sample rna type

value: Total RNA


title: healthy control-29

source_name: Plasma

value: 37 years old


title: multidrug-resistant tuberculosis patient-69

value: female


title: untreated AB12 mouse tumor sample collected at day 6 rep1

value: mesothelioma

value: BALB/c

value: 6 days after AB12 cell injection


title: Polysome-C-2

value: No drug

value: Polysome bound RNA


title: Input-T-1


title: Polysome-T-1


title: Polysome-C-1


title: Input-C-2


title: Input-C-1


title: NIH3T3_click_protease_ 1

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.8 with default parameter.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1
Assembly: mm9
Supplementary files format and content: Excel with raw FPKM for every gene and every sample

growth_protocol: NIH3T3 cells were maintained in DMEM minimal medium with 10% FBS .mESCs were cultured in DMEM/F12 medium supplemented with 20% Knockout serum replacement, 2 mM L-glutamine, 1mM sodium pyruvate, 0.1 mM β-mercaptoethanol , 1% non-essential amino acids  and 1000 units/mL mouse leukemia inhibitory factor (LIF) .

extract_protocol:
In order to harvest enough S phase cells, NIH3T3 cells were synchronized by 2 mM thymidine for 15 hours, followed by fresh medium culture for 2.5 hours. For each sample, 108 synchronized NIH3T3 or normal cultured mESCs were incubated with 10 mM EdU for 10 minutes, followed by PBS wash and hydroxyurea (HU) treatment.Next, the cells were fixed with 1% formaldehyde and then quenched with 0.125 M glycine. The cells were scraped, and permeabilized by ice-cold 0.25% Triton X-100/PBS for 30 minutes at room temperature. After washing with 0.5% BSA/PBS, the cells were re-suspended in click reaction buffer including 10 μM Biotin-azide or DMSO (negative control) for 1 hour at room temperature. After the click reaction, cells were washed with 0.5% BSA/PBS for three times, and re-suspended in lysis buffer (50 mM Tris-HCl, pH 8.0; 1% SDS; 1 μg/mL aprotinin; 1 μg/mL leupeptin) for sonication (30 seconds pulse/30 seconds pause, 60 cycles) using BioruptorTM UCD-200 machine. Finally, samples were centrifuged at 10000×g for 10 minutes at 4°C to remove the precipitate. The samples were incubated with streptavidin magnetic beads to purify replicaiton fork components. then the replicaiton fork components RNA was harvested using Trizol reagent.To avoid RNA degradation, all the buffers and reagents were prepared using DEPC-treated ddH2O and RNase inhibitors in the whole procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HU samples were treatment with 4 mM hydroxyurea(HU) for 4 h.

value: hydroxyurea

value: wild-type


title: NIH3T3_click_protease_ 2


title: NIH3T3_click_chase_2


title: Genomic DNA of AZA-untreated CMML-MSCs S2

description: bone marrow MSCs from patient with CMML

source_name: AZA-untreated CMML-MSCs

value: bone marrow MSCs at P2


title: NIH3T3_click_chase_1


title: NIH3T3_click_normal_ 2


title: NIH3T3_click_HU_ 1


title: healthy control-17

value: healthy control

value: 35 years old

value: Plasma


title: NIH3T3_no_click 2


title: NIH3T3_no_click 1


title: NIH3T3_click_normal_ 1


title: ESC_click_protease_ 2

source_name: embryonic stem cells

value: embryonic stem cells


title: ESC_click_protease_ 1


title: G0

description:
GM
G0

source_name: GM-BMDM in normal condition

value: Bone marrow-derived macrophage

value: bone marrow

value: GM-BMDM


title: ESC_click_HU_ 2


title: ESC_click_normal_ 2


title: NIH3T3_click_HU_ 2


title: ESC_click_HU_ 1


title: ESC_click_chase 1


title: ESC_click_normal_ 1


title: ESC_no_click 2


title: GTML_8

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

data_processing:
All RNA sequence reads were mapped against the human genome assembly GRCh37/hg19 using STAR v2.4.0 in a two step aproach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016
Unmapped reads were realigned using Bowtie2 v2.2 and default parameters
Duplicate reads were removed with Piccard v1.127 and default parameters
Counts were measured using Subread v1.5.2
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file include transcript names and counts.

source_name: tumor biopsy

extract_protocol:
RNA from fresh-frozen tumor biospy was extracted according to QUIAGEN RNEasy extraction protocol
RNA-Seq were prepared for sequencing using standard Ion-Torrent protocols.

tag: model

value: GTML

tag: sample type

value: brain tumor biopsy

value: tumor


title: GTML_3


title: GTML_7


title: GTML_6


title: Polysome-T-2

value: HeLa cell line

value: MAT2 inhibitor (Cycloleucine)


title: GMYC_6

value: GMYC


title: GMYC_5


title: GTML_2


title: GTML_4


title: GMYC_4


title: GTML_1


title: ESC_click_chase 2


title: GMYC_2


title: GMYC_1


title: dTAGSET1AB_ZC3H4_TTseq_Rep3_2hr

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

institute: University of Oxford

data_processing:
Library strategy: TT-seq
Reads that aligned to the mm10 and dm6 rDNA genomic sequences (GenBank: BK000964.3 and M21017.1) were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the concatenated mm10 and dm6 genomes using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
To internally calibrate TT-seq, we spiked-in a fixed number of Drosophila SG4 to each experimental sample. For data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample.
Read counts from biological triplicates were determined using custom scripts utilising SAMTools for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered to remove very short genes with poor sequence mappability and highly similar transcripts which resulted in the final set of 20,633 genes. Raw mm10 reads prior to spike-in normalisation were used for read counts quantitation for differential expression analysis.
The final set of 20,633 genes were used for differential analysis using a custom R script adapting DESeq2 (Love et al., 2014) for spike-in calibrated TT-seq data. To incorporate spike-in calibration into this analysis, read counts for the spike-in genome at a control set of intervals were supplied to calculate DESeq2 size factors which were then used for DESeq2 normalisation of raw mm10 read counts. A set of unique dm6 refGene genes was used for spike-in normalisation of TT-seq. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: mm10, dm6
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for a non-redundant set of mm10 refGene genes.

organism:
Drosophila melanogaster
Mus musculus

source_name: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, dTAG-SET1A/B/ZC3H4 cells depleted of dTAG-SET1A, dTAG-SET1B and ZC3H4-dTAG

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
cTT-seq was performed largely as described previously (Gregersen et al., 2020). In brief, 9 million ESCs and 3 million Drosophila SG4 cells were labelled with 500 µM 4-thiouridine (4sU, Glentham Life Sciences) for 15 min and harvested into TRIzol reagent. 4sU-labelled mouse and Drosophila cells were mixed and RNA was extracted using the Direct-zol DNA/RNA Miniprep kit (Zymo Research) as per the manufacturer’s protocol. gDNA was depleted using the TURBO DNA-free Kit (Thermo Fisher Scientific). An equal quantity of RNA (60-80 µg) was taken into 100 µl nuclease free water and fragmented on ice with 20 µl 1M NaOH for 20 min. Fragmentation was stopped with 80 μl 1 M Tris, pH 6.8 and the RNA was cleaned up with Micro Bio-Spin P-30 gel columns (Biorad). RNA was biotin-labelled with 50 μl 0.1 mg/ml MTSEA biotin-XX linker (Biotium) with 3 μl biotin buffer (833 mM Tris HCl, pH 7.4, 83.3 mM EDTA) for 30 min at RT. Biotin-labelled RNA was purified with a 1:1 ratio of Phenol/Chloroform/Isoamyl alcohol (Thermo Fisher Scientific). Streptavidin pull-down was performed with the μMACS Streptavidin Kit (Miltenyi Biotec), washing the columns three times with 55°C pull-down wash buffer (100 mM Tris HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween 20) and 3x RT pull down wash buffer. Biotin-labelled RNA was eluted with 100 μl elution buffer (100 mM DTT in nuclease-free water) and cleaned up with the RNeasy MinElute Cleanup kit (QIAGEN), adjusting the amount of ethanol to capture RNA < 200 nucleotides in length. RNA was quantified using the Qubit RNA HS assay kit.
RNA libraries were prepared from 20-50 ng RNA with the Ultra II Directional RNA library prep kit, as per the manufacturer’s guidelines for rRNA depleted and FFPE RNA (NEB).

treatment_protocol: Cell lines expressing dTAG fusion proteins were treated with 100 nM dTAG-13 (produced by Behnam Nabet and Nathanael Gray1 or Carole Bataille and Angela Russell) to induce protein depletion.

value: 100nM dTAG13

tag: treatment time

tag: additional treatment

value: 500 µM 4-thiouridine

tag: additional treatment time

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: protocol

value: calibrated TT-seq


title: GMYC_3


title: GTML_5


title: ESC_no_click 1

tag: cell type

value: wild-type


title: dTAGSET1AB_ZC3H4_TTseq_Rep2_2hr

tag: cell line

value: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, dTAG-SET1A/B/ZC3H4 cells depleted of dTAG-SET1A, dTAG-SET1B and ZC3H4-dTAG


title: dTAGSET1AB_ZC3H4_TTseq_Rep2_0hr

source_name: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, untreated control, dTAG-SET1A/B/ZC3H4

value: untreated


title: dTAGSET1AB_ZC3H4_TTseq_Rep1_2hr


title: dTAGSET1AB_ZC3H4_TTseq_Rep1_0hr

value: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, untreated control, dTAG-SET1A/B/ZC3H4


title: dTAGZ4_TTseq_Rep3_2hr

source_name: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, ZC3H4-dTAG cells depleted of ZC3H4-dTAG


title: dTAGZ4_TTseq_Rep2_2hr

value: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, ZC3H4-dTAG cells depleted of ZC3H4-dTAG


title: dTAGSET1AB_RNAseq_Rep3_4hr

data_processing:
Reads that aligned to the mm10 and dm6 rDNA genomic sequences (GenBank: BK000964.3 and M21017.1) were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the concatenated mm10 and dm6 genomes using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
To internally calibrate RNA-seq, we spiked-in a fixed number of Drosophila SG4 to each experimental sample. For data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample.
Read counts from biological triplicates or quadruplicates were determined using custom scripts utilising SAMTools for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered to remove very short genes with poor sequence mappability and highly similar transcripts which resulted in the final set of 20,633 genes. Raw mm10 reads prior to spike-in normalisation were used for read counts quantitation for differential expression analysis.
The final set of 20,633 genes were used for differential analysis using a custom R script adapting DESeq2 (Love et al., 2014) for spike-in calibrated RNA-seq data. To incorporate spike-in calibration into this analysis, read counts for the spike-in genome at a control set of intervals were supplied to calculate DESeq2 size factors which were then used for DESeq2 normalisation of raw mm10 read counts. A set of unique dm6 refGene genes was used for spike-in normalisation of RNA-seq. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: mm10, dm6
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for a non-redundant set of mm10 refGene genes.

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B

extract_protocol:
ESCs (~106) were counted and mixed with ¼ of the number of SG4 Drosophila cells in PBS. RNA was extracted from cells using TRIzol reagent, according to the manufacturer’s protocol (Thermo Fisher Scientific). gDNA contamination was depleted using TURBO DNA-free Kit (Thermo Fisher Scientific) and quality of RNA was assessed using 2100 Bioanalyzer RNA 6000 Pico kit (Agilent). 900 ng RNA was depleted of rRNA using the NEBNext rRNA Depletion kit (NEB).
RNA-seq libraries were prepared from an equal amount of ribo-depleted RNA using the NEBNext Ultra II Directional RNA Library Prep kit, including 2.5-4 min fragmentation at 94⁰C (NEB).

value: calibrated RNA-seq


title: dTAGSET1AB_RNAseq_Rep3_0hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control for dTAG-SET1A/B cells


title: dTAGSET1AB_TTseq_Rep3_0hr

source_name: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, untreated control, dTAG-SET1A/B


title: dTAGZ4_TTseq_Rep1_0hr

source_name: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, untreated control, ZC3H4-dTAG


title: dTAGSET1AB_TTseq_Rep2_0hr

value: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, untreated control, dTAG-SET1A/B


title: dTAGSET1AB_TTseq_Rep1_2hr

source_name: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B


title: dTAGSET1AB_TTseq_Rep2_2hr

value: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B


title: dTAGZ4_TTseq_Rep1_2hr


title: dTAGSET1AB_TTseq_Rep1_0hr


title: dTAGSET1AB_RNAseq_Rep3_24hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B


title: dTAGZ4_TTseq_Rep2_0hr

value: 4sU-labelled mouse embryonic stem cells with 4sU-labelled Drosophila SG4 cells spike-in, untreated control, ZC3H4-dTAG


title: dTAGSET1AB_TTseq_Rep3_2hr


title: dTAGSET1AB_RNAseq_Rep3_2hr


title: dTAGSET1AB_ZC3H4_TTseq_Rep3_0hr


title: dTAGSET1AB_RNAseq_Rep2_4hr


title: dTAGSET1AB_RNAseq_Rep2_0hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control for dTAG-SET1A/B cells


title: dTAGSET1AB_RNAseq_Rep2_2hr


title: dTAGSET1AB_RNAseq_Rep2_24hr


title: dTAGZ4_TTseq_Rep3_0hr


title: dTAGSET1AB_RNAseq_Rep1_4hr


title: dTAGSET1AB_RNAseq_Rep1_0hr


title: dTAGSET1AB_RNAseq_Rep1_2hr


title: dTAGSET1AB_RNAseq_Rep1_24hr


title: dTAGSET1A_RNAseq_Rep3_24hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, dTAG-SET1A cells depleted of dTAG-SET1A


title: dTAGSET1A_RNAseq_Rep3_4hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, dTAG-SET1A cells depleted of dTAG-SET1A


title: dTAGSET1A_RNAseq_Rep3_2hr


title: dTAGSET1A_RNAseq_Rep3_0hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control for dTAG-SET1A cells


title: dTAGSET1A_RNAseq_Rep2_4hr


title: dTAGSET1A_RNAseq_Rep2_24hr


title: CM_M12

description:
LLC
E

source_name: LLC incubated with conditioned media from 12 h Tm treatment M-BMDM

value: Lewis lung carcinoma cells

tag: strain

value: lung

value: 12 h Tm stimulated CM_M treatment LLC


title: dTAGSET1A_RNAseq_Rep2_2hr

value: 100nM dTAG13

value: Drosophila melanogaster


title: dTAGSET1A_RNAseq_Rep1_2hr


title: dTAGSET1A_RNAseq_Rep1_4hr


title: dTAGSET1A_RNAseq_Rep1_0hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control for dTAG-SET1A cells


title: dTAGSET1A_RNAseq_Rep2_0hr


title: dTAGSET1B_RNAseq_Rep3_24hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, dTAG-SET1B cells depleted of dTAG-SET1B


title: dTAGSET1B_RNAseq_Rep4_2hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, dTAG-SET1B cells depleted of dTAG-SET1B


title: dTAGSET1B_RNAseq_Rep4_0hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control for dTAG-SET1B cells

value: untreated


title: dTAGSET1A_RNAseq_Rep1_24hr


title: dTAGSET1B_RNAseq_Rep3_4hr


title: dTAGSET1B_RNAseq_Rep2_24hr


title: dTAGSET1B_RNAseq_Rep3_0hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control for dTAG-SET1B cells


title: dTAGSET1B_RNAseq_Rep3_2hr


title: dTAGSET1B_RNAseq_Rep2_2hr


title: dTAGSET1B_RNAseq_Rep2_4hr


title: dTAGSET1B_RNAseq_Rep4_4hr


title: dTAGSET1B_RNAseq_Rep2_0hr


title: dTAGSET1B_RNAseq_Rep4_24hr


title: dTAGSET1B_RNAseq_Rep1_24hr


title: Input_H3K4ChIP_Rep3_24hr

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+dm6 for Native cChIP and mm10+hg19 for cross-linked cChIP) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
Sequencing datasets were calibrated to the spike-in Drosophila or human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of dm6 or hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools. Biological replicates correlated well with each other and were merged for subsequent analysis. Genome coverage tracks were generated using the pileup function from MACS2.
Assembly: mm10; dm6; hg19
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

source_name: Input sample for H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 24hr.

extract_protocol:
Native cChIP-seq was performed as described previously (Fursova et al. 2019). In brief, 5 x 107 ESCs were mixed with 2 x 107 Drosophila SG4 cells and nuclei were released by resuspending in RSB (10 mM Tris HCl pH 8, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40. Nuclei were pelleted at 1500xg for 5 min and then washed and resuspended in 1 ml MNase digestion buffer (RSB with 0.25 M Sucrose, 3 mM CaCl2, 1x PIC). Each sample was incubated with 200 units of MNase (Fermentas) at 37⁰C for 5 minutes, with gentle inversion. Digestion was stopped by addition of 4 mM EDTA. Following centrifugation at 1500xg for 5 min, the supernatant (S1 fraction) was retained and the remaining pellet was resuspended in 300 μl nucleosome release buffer (10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x PIC), rotated at 4⁰C for 1 hr and then passed five times through a 27G needle using a 1 ml syringe. Following centrifugation at 1500xg for 5 min, the supernatant (S2) was combined with S1 fraction, aliquoted, snap frozen and stored at -80°C. For each IP, 100 μl S1/S2 nucleosomes were diluted to 1 ml total volume in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris HCl, pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1 % Triton-X100, 1x PIC) and immunoprecipitated with 3 µl H3K4me3 antibody (Klose Lab) overnight at 4⁰C. IPs were all set up in duplicate for each sample. 100 μl diluted chromatin was also set aside as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in native ChIP incubation buffer, overnight at 4⁰C. 40 μl slurry of pre-blocked agarose beads were used to capture antibody-bound nucleosomes at 4⁰C for 1 hr. Beads were then washed 4x with Native ChIP wash buffer (20 mM Tris HCl, pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1 % Triton-X100, 1x PIC) and 1x TE buffer, pH 8. DNA was eluted by vortexing for 30 min in elution buffer (1% SDS and 0.1 M NaHCO3) and DNA was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). For each ChIP, DNA from the matched input control (10% of the IP) was also purified. Purified DNA was analysed using ChIP-qPCR.    For double cross-linked T7-SET1A ChIP and ZC3H4-T7 ChIP, 5 x 107 ESCs were fixed with 2 mM DSG (disuccinimidyl glutarate, Thermo Fisher Scientific) for 50 min at 25⁰C and then 1% formaldehyde (methanol-free, Thermo Fisher Scientific) for 10 min. Alternatively, for single cross-linked RNA Pol II ChIP, 5 x 107 ESCs were fixed with 1% formaldehyde for 10 min at 25⁰C. Fixation was quenched using glycine added to 125 mM. Cells were then pelleted at 1000xg for 5 min and washed with PBS. Cross-linked ESCs were mixed with 1 x 105 cross-linked HEK 293T/T7-SCC1 cells (1% formaldehyde, 15 min for SET1A ChIP; a gift from Martin Houlard, Nasmyth lab) or 2 x 106 cross-linked HEK 293T cells (1% formaldehyde, 10 min for RNA Pol II ChIP). Chromatin was prepared by incubation in 1 ml FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x PIC, 1 mM AEBSF. For RNA Pol II ChIP, EDTA concentration was increased to 2 mM and 10 mM NaF was added fresh) on ice for 10 min. Chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode) at 4⁰C. Sonication was performed using 23-30 cycles of 30s on/30s off at full power, shearing genomic DNA to an average size of 0.5 kb. The sonicated material was pelleted at 20,000xg for 20 min, and the supernatant taken as sonicated chromatin. 300 μg chromatin was used per IP. Chromatin was diluted to 1 ml total volume per IP in FA-lysis buffer. An additional volume of diluted chromatin was taken to use as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in 1x TE buffer at 4⁰C for 1 hr. Chromatin was pre-cleared with agarose beads (40 μl slurry beads per ChIP) at 4⁰C for 1 - 2 hr. The input sample was taken from the pre-cleared chromatin, and the remainder was immunoprecipitated overnight at 4⁰C with the appropriate amount of antibody: T7 (Cell Signalling, D9E1X, 10µl) or RNA Pol II N-terminal domain (Cell Signalling, D8L4Y, 15µl). Antibody-bound chromatin was precipitated for 3 hr at 4⁰C using 40 μl slurry of blocked Protein A agarose beads. Washes were carried out for 5 min each at 4⁰C, using FA-lysis buffer, FA-lysis buffer with 500 mM NaCl, 1x DOC buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 1 mM EDTA (2 mM EDTA for RNA Pol II ChIP), 0.5% NP-40, 0.5% Na-deoxycholate), and 2 washes with TE buffer (1x PIC and 1 mM AEBSF were added fresh to all wash buffers. 10 mM NaF was also added for RNA Pol II ChIP). DNA was eluted by vortexing for 30 min in elution buffer (1% SDS and 0.1 M NaHCO3). Cross-links were reversed for ChIPs and inputs at 65⁰C overnight with 200 mM NaCl and 2 μl RNase A (Sigma). Samples were then incubated with 20 μg Proteinase K for 1 hr at 45⁰C. DNA for ChIPs and inputs was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). Purified DNA was analysed using ChIP-qPCR.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate on Illumina NextSeq 500 platform.

value: 100 nM dTAG13

tag: replicate

tag: type of chip

value: Native

tag: ChIP

value: Input

tag: antibody


title: WT_RNAseq_Rep1_2hr

source_name: Wild type mouse embryonic stem cells with Drosophila SG4 cells spike-in, treated with dTAG13

value: ESCs

tag: condition

tag: treatment

value: calibrated RNA-seq


title: dTAGSET1B_RNAseq_Rep1_2hr


title: Input_H3K4ChIP_Rep3_2hr

source_name: Input sample for H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 2hr.


title: dTAGSET1B_RNAseq_Rep1_4hr


title: dTAGSET1B_RNAseq_Rep1_0hr


title: Input_H3K4ChIP_Rep3_4hr

source_name: Input sample for H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 4hr.


title: WT_RNAseq_Rep3_2hr

value: Wild type mouse embryonic stem cells with Drosophila SG4 cells spike-in, treated with dTAG13


title: WT_RNAseq_Rep3_0hr

source_name: Wild type mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control


title: Input_H3K4ChIP_Rep2_0hr

source_name: Input sample for H3K4me3 ChIP-seq in untreated dTAG-SET1A/B cells.


title: WT_RNAseq_Rep1_0hr

value: Wild type mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control


title: WT_RNAseq_Rep2_0hr


title: MDA-GSC-23

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

institute: CHUV / BCF / SIB

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “minfi”. The raw pre-processing (Illumina method) was used for data normalization.

label: Cy5 and Cy3

source_name: GBM cell line MDA-GSC-23

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

tag: batch

value: Batch 2

tag: alternative name

tag: disease state

value: GBM


title: Input_H3K4ChIP_Rep1_0hr

value: Input sample for H3K4me3 ChIP-seq in untreated dTAG-SET1A/B cells.

tag: treatment time


title: Input_H3K4ChIP_Rep3_0hr


title: Input_H3K4ChIP_Rep2_4hr

value: Input sample for H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 4hr.


title: Input_H3K4ChIP_Rep2_24hr

value: Input sample for H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 24hr.


title: Input_H3K4ChIP_Rep1_24hr

value: Drosophila melanogaster


title: Input_H3K4ChIP_Rep1_4hr


title: H3K4ChIP_Rep3_2hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 2hr.

value: anti-H3K4me3  (Klose Lab)


title: H3K4ChIP_Rep3_4hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 4hr.


title: H3K4ChIP_Rep2_4hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 4hr.


title: MDA-GSC-23-luc

source_name: GBM cell line MDA-GSC-23-luc

value: Batch 1

value: RRID:CVCL_DR59 (luc)


title: WT_RNAseq_Rep2_2hr

value: 100nM dTAG13


title: H3K4ChIP_Rep2_24hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 24hr.

value: 100 nM dTAG13

value: Native


title: H3K4ChIP_Rep3_24hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 24hr.


title: H3K4ChIP_Rep3_0hr

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. Untreated control for H3K4me3 ChIP-seq in dTAG-SET1A/B cells.

value: untreated


title: H3K4ChIP_Rep1_2hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 2hr.


title: H3K4ChIP_Rep1_24hr


title: H3K4ChIP_Rep1_4hr


title: H3K4ChIP_Rep2_2hr


title: Input_H3K4ChIP_Rep1_2hr

value: Input sample for H3K4me3 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B for 2hr.

value: Input


title: H3K4ChIP_Rep2_0hr

value: Mouse embryonic stem cells with Drosophila SG4 cells spike-in. Untreated control for H3K4me3 ChIP-seq in dTAG-SET1A/B cells.


title: H3K4ChIP_Rep1_0hr


title: GSC_RA_scATAC

city: Hong Kong

first: Tin-Lap

last: Lee

address: LKSIBSB, CUHK, Shatin, Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: scATAC on GSC with RA treatment

data_processing:
Sequencing data were processed using the Bio-Rad ATAC-Seq Analysis Toolkit, which performed FASTQ debarcoding, read trimming, alignment, bead filtration, bead deconvolution, cell filtration and peak calling.
For generation of the fragments file, which contain the start and end genomic coordinates of all aligned sequenced fragments, sorted bam files were further process with “bap-frag” module of BAP
Genome_build: mm10
Supplementary_files_format_and_content: Fragments file

source_name: Cultured germline stem cells (GSCs)

growth_protocol: Oct4+/KIT- germ cells were FACS-sorted and cultured on Matrigel (feeder-free) or on MEF feeder layer in StemPro™-34 SFM supplemented with GDNF, bFGF and EGF. Cells were passged every one week.

extract_protocol:
Cell tagmentation was performed according to SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) User Guide (10000106678, Bio-Rad) and the protocol based on Omni-ATAC was followed (Corces et al. 2017). In brief, washed and pelleted cells were lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin, 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl pH 7.4 for 3 min on ice. The lysis buffer was diluted with ATAC-Tween buffer that contains 0.1% Tween-20 as a detergent. Nuclei were counted and examined under microscope to ensure successful isolation. Same number of nuclei were subjected to tagmentation with equal ratio of cells/Tn5 transposase to minimize potential batch effect. Nuclei were resuspended in tagmentation mix, buffered with 1×PBS supplemented with 0.1% BSA and agitated on a ThermoMixer for 30 min at 37 °C. Tagmented nuclei were kept on ice before encapsulation.
Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ATAC-Seq Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed with PCR amplification as follows: 37 °C for 30 min, 85 °C for 10 min, 72 °C for 5 min, 98 °C for 30 s, eight cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. Emulsions were broken and products were cleaned up using Ampure XP beads. Barcoded amplicons were further amplified for 8 cycles. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were sequenced on HiSeq 2000 with 150 bp paired-end reads.

treatment_protocol: For RA treatment, cells were treated with 0.5uM UNC0638.

tag: cell source

value: Oct4-GFP+ germ cell in vitro culture

tag: age

value: Postnatal day 5.5

value: Culture on mouse embryonic fibroblast (MEF), treated with RA


title: Control myotube sEVs 2

city: Nanjing

first: Xiaoyan

last: Shao

address: No. 22, Hankou Road

institute: Nanjing University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze  their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference. Differential expression analysis of two conditions/groups was performed using the DESeq R package (3.0.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Assembly: mus_musculus_Ensembl_97
Supplementary files format and content: excel Readcount_TPM
Supplementary files format and content: excel TPM_interval

source_name: cell line

extract_protocol:
We isolated the small extracellular vesicle (sEVs) from control myotubes and atrophic myotubes and then isolated total RNA from sEVs by  miRNeasy Kit, QIAGEN (QIAGEN, USA).RNA purity was checked using the NanoPhotometer®pectrophotometer(IMPLEN, CA,USA). RNA concentration was measured using Qubit®RNA Assay Kit in Qubit®.0Flurometer (Life Technologies,CA,USA).RNA integrity was assessed using the RNA nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies,CA,USA).
Library preparation for Small RNA sequencingNovogene Experimental Department) A total amount of 1 ug total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNextRMultiplex Small RNA Library Prep Set for Illumina(NEB.USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: tissue

value: cell line

value: mouse myoblast

tag: phenotype

value: control

value: myoblast differentiation


title: Atrophy myotube sEVs 2

tag: cell type

value: atrophy

value: myoblast differentiation and starvation


title: Control myotube sEVs 1

tag: cell line