title: Anti-PDL1, replicate 1, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.1n.barcodes.tsv.gz
S2.1n.features.tsv.gz
S2.1n.matrix.mtx.gz


title: HCC_008

status: Public on Dec 31 2024

type: SRA

city: Seongnam

first: Sung Hwan

last: Lee

address: 59 Yatap-ro

department: Department of Surgery

country: South Korea

institute: CHA Bundang Medical Center

library_source: transcriptomic

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2
The read count data were processed based on quantile normalization method using EdgeR within R
Gene classification was based on searches done by DAVID and Medline databases
Assembly: hg19
Supplementary files format and content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Human liver

extract_protocol:
Total RNA was isolated using Trizol reagent.
The construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit

tag: cell line origin

value: Human Hepatocarcinoma

tag: treatment

value: liver cancer tumor tissue


title: WholeBlood-Control-F-187

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

data_processing:
raw reads were trimmed with bbduk
raw reads were aligned using STAR v2.5.3a and Gencode v29 annotations
gene expression (raw counts) were quantified using HTSeq v0.11.2
Assembly: GRCh38.p12
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Venous blood passed through LeukoLOCK™ filters (Life Technologies, Ambion), followed by total RNA extraction using ethanol precipitation
libraries were prepared from 500 ng of total RNA, using poly-A capture and the QIAseq Stranded mRNA Select kit (Qiagen) in Females (F) OR the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA) in males (M)

treatment_protocol: Not applicable

tag: tissue

value: Whole blood

tag: group

value: Control

tag: Sex

value: Female


title: Th17_PSIN_empty control rep2

city: San Diego

first: Wendy

last: Huang

state: CA

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

country: USA

institute: University of California San Diego

description: RNA-seq

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM21 annotation with parameters "-p -B --ignoreDup"
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
Assembly: mm10
Supplementary files format and content: Txt files include normalized Deseq count for each gene per sample

organism: Mus musculus

source_name: Th17 72h cells

growth_protocol: All mice were raised in Specific Pathogen Free (SPF) facility on normal diet. 8-12 week old animals were used for experiments.

extract_protocol:
RNA were isolated using Qiagen Rneasy mini kit (74106)
Ribosome-depleted RNAs were used to generate the cDNA libraries using the KAPA Hyper Prep Kit (KR0961) according to the manufacturer's instructions. Briefly, DNA was end-repaired and A-tailed to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-ligation clean was used to remove the extra adapters. Then the adapter-ligated DNA was PCR amplified with Illumina primers for 8 cycles, followed with post-amplification clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq S4 following the manufacturer's protocols.

treatment_protocol: Naïve CD4+ T cells  were activated in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience). 24hrs post activation, activated T cells were transduced with retroviruses and then polarized toward Th17 in the presence of 0.3 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) for 72hrs.

tag: cell type

value: Th17 72h cells

tag: genotype

value: Cas9 transgene


title: Th17_PSIN_sgAdarb1 rep1

description: RNA-seq

value: PSIN_empty control


title: HCC_007


title: WholeBlood-Control-F-185


title: Anti-PDL1, replicate 1, lymph node, scRNA-seq

city: South San Francisco

first: Thomas

middle: D

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.1n.barcodes.tsv.gz
S2.1n.features.tsv.gz
S2.1n.matrix.mtx.gz

data_processing:
Sequencing files from Illumina assays were run through CellRanger version 6.1.1 against a transcriptome derived from ENSEMBL version 2.2.0 for the mouse genome GRCm38.  FASTQ files were generated using "cellranger mkfastq".  Gene expression (RNA-seq), ADT-seq, and CITE-seq libraries were processed using "cellranger count", providing a libraries.csv file (provided as a Supplementary File) to identify ADT-seq and CITE-seq barcodes.  TCR-seq libraries were processed using "cellranger vdj".
Assembly: GRCm38
Supplementary files format and content: For scRNA-seq, ADT-seq, and CITE-seq libraries, CellRanger version 6.1.1 files containing barcodes, features, and count matrices
Supplementary files format and content: For scTCR-seq, CellRanger 6.1.1 files containing filtered contig annotations

molecule: polyA RNA

source_name: Draining lymph node

growth_protocol: Mice were inoculated subcutaneously with 0.1 x 10^6 CT26 cells in 100 µL Hank's balanced solution (HBSS) and Matrigel (BD Biosciences, San Jose, CA).  Once tumours achieved a mean volume of 150-200 mm^3, animals were apportioned into treatment groups.

extract_protocol:
After treatment, tumours were dissociated into single-cell suspensions using a gentleMACS dissociator and enzymatically digested in a buffer containing collagenase D (2 mg/ml) and DNAse (40 U/ml).  Single-cell suspensions of draining lymph nodes were obtained by mechanical dissociation through 40 µm cell strainers and performing red blood cell lysis as needed.  Blood was obtained by terminal cardiac puncture and collected in lavender Microtainer Blood Collection Tubes and subjected to red blood cell lysis.  Blood samples were multiplexed using 10 barcodes with a distinct pair used to identify each individual sample before pooling. Tumor and blood samples were sorted by FACS for CD90+ T cells, and draining lymph node samples were sorted for CD90+CD44+ T cells.
5' Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics).  T cells were allowed to bind to tetramers of gp70 antigen bound to associated ADT barcodes.  CITE-seq was performed using antibodies against 18 selected proteins plus 6 control immunoglobulin proteins.  A total of 14 cycles of PCR amplification were performed.

treatment_protocol: exposed to five different treatment regimens: control anti-gp120, anti-PD-L1, anti-TIGIT, combination, and combination plus FTY720, which blocks egress of T cells from lymphoid tissue.

tag: strain

value: BALB/c

tag: age

value: 6-8 weeks

tag: cell line

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, over 1 week

value: Draining lymph node

value: CD90+CD44+ T cells


title: Th17_PSIN_empty control rep1

description: RNA-seq


title: Tam-Bleo Day 60

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Library demulitplexing and FASTQ file generation was performed using Illuminas bcl2fastq (2.19.0.316).
Sequencing reads were aligned using STAR solo (2.7.9a) in the Velocyto mode to the mm10 reference genome. During the alignment UMI deduplication was performed by STAR, as well.
Downstream processing was done in Scanpy 1.6.1.
Assembly: mm10 extended by the WPRE sequence (https://www.addgene.org/22799/sequences/)
Supplementary files format and content: List of genes in TSV format.
Supplementary files format and content: List of barcodes in TSV format.
Supplementary files format and content: Expression matrix in MTX format.

source_name: Lung

extract_protocol:
FACS sorted cells were stained with SytoxTM (Thermofisher Scientific) for dead cell exclusion. 9000 sorted viable tdTomato cells per time point were loaded into 10x Genomics Chromium.
Library preparation was conducted according to the manufacturer indications (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121).

value: Lung

tag: time

value: Day 60

value: tdTomatopos cells

value: Bleomycin


title: Control, replicate 3, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.4n.barcodes.tsv.gz
S1.4n.features.tsv.gz
S1.4n.matrix.mtx.gz

library_source: other

molecule: protein

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: HCC_005

value: Human Hepatocarcinoma

value: liver cancer tumor tissue


title: HCC_006


title: WholeBlood-Control-F-184

value: Whole blood

value: Control


title: HCC_004


title: Control, replicate 3, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.4n.barcodes.tsv.gz
S1.4n.features.tsv.gz
S1.4n.matrix.mtx.gz

value: Female


title: WholeBlood-Control-F-182


title: Control, replicate 5, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.6n.barcodes.tsv.gz
S1.6n.features.tsv.gz
S1.6n.matrix.mtx.gz


title: WholeBlood-Control-F-192


title: Aortic Cells, anti-CD8 treatment, HTO [F9_2_HTO]

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads (HTO6= anti-CD8 Aortas 1, HTO7= anti-CD8 Aortas 2, HTO8= anti-CD8 Aortas 3, HTO9= anti-CD8 Aortas 4 and HTO10= anti-CD8 Aortas 5)
Hashtag-derived oligonucleotide (HTO)
barcodes.tsv
features.tsv
matrix.mtx
feature_F9_2.csv

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
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 (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Aorta

extract_protocol:
Aortas were collected from Ldlr-/- mice fed with a high fat, high cholesterol diet (Altromin, 15% milk fat, 1.25% cholesterol) for 13 weeks and treated for the last 4 weeks before sacrifice with 100 µg, i.p. twice weekly, of an anti-CD8 antibody (YTS156.7.7). 2 aortas were pooled to generate each sample, and n=5 pools were analyzed. To exclude circulating leukocytes from analysis, mice were injected with 2.5µg anti-CD45.2 APC (clone 104, BioLegend) intravenously 5 minutes before sacrifice to label blood borne immune cells. Aortas were enzymatically digested in RPMI medium containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) for 1 hour at 37°C with agitation, washed in PBS/1% FCS and passed through a 70µm cell strainer. Cells were labeled for 20 minutes at 37°C with CalceinViolet-AM (BioLegend 425203) according to the manufacturer’s instructions. Cells were washed and resuspended in PBS 1% FCS, plated in round bottom 96 well plates, and incubated for 10 minutes on ice with anti-CD16/32 (Biolegend, Clone 93, 10µg/ml) to block unspecific binding of antibodies to Fc receptor. Cells were subsequently labeled in a final volume of 100µl for 15 minutes at 4°C with anti-CD45.2 Alexa488 (2.5µg/ml, clone 104, BioLegend), anti-Ter119 PE-Cy7 (1µg/ml, clone TER119, BioLegend), 1:1000 Fixable Viability Dye, CITE-seq antibodies (see table), and hashtag antibodies. Each sample was labeled with a specific Hashtag antibody (Hashtag 6 to 10, final concentration 1:200, BioLegend). Cells were washed twice and all the sample were pooled. Viable Ter119negCD45.2-APC(i.v.)negCalceinAM+ cells were sorted using a BD FACS Aria III with a 100µm nozzle. The amount of sorted cells was adjusted so that ~50% of the total cells represent leukocytes (CD45-Alexa488+). Cells were sorted in PBS supplemented with 0.04% BSA, washed and counted in Trypan blue to assess viability (>85%). 18,000 cells were loaded at a concentration of 600 cells/µl in the 10x Genomics Chromium (Single Cell 3’ v3 reagents, 10x Genomics) and scRNA-seq ADT and HTO libraries were prepared.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Aorta

value: not applicable

value: Ldlr-/-


title: HCC_003


title: WholeBlood-Control-F-178


title: HCC_002


title: Control, replicate 4, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.5n.barcodes.tsv.gz
S1.5n.features.tsv.gz
S1.5n.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: Aortic Cells, anti-CD8 treatment, GEX [F9_2_GEX]

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


title: WholeBlood-Control-F-174


title: WholeBlood-Control-F-173


title: Control, replicate 4, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.5n.barcodes.tsv.gz
S1.5n.features.tsv.gz
S1.5n.matrix.mtx.gz

value: Draining lymph node


title: R6/2 GFA2, 35

city: paris

first: farah

last: CHALI

address: 47 Boulevard de l’Hôpital  75013 Paris, FRANCE

institute: AskBio

data_processing:
Poor quality sequences has been trimmed or removed with Trimmomatic / fastp software to retain only good quality paired reads
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expected counts, TPM and FPKM of genes

source_name: Striatum

growth_protocol: mice striatum were removed and stored in -80°c

extract_protocol:
Striatum were removed, RNA was extracted following the protocol of miRNeasy Tissue/Cells Advanced Mini Kit (QIAGEN)
mRNA library preparation were realized following manufacturer’s recommendations (KAPA mRNA HyperPrep Kit from ROCHE).

value: Striatum

tag: disease state

value: mouse model of HD

value: CYP46A1 GFA2


title: HCC_001


title: R6/2 GFA2, 37


title: WholeBlood-Control-F-172


title: Breast cancer cell line, scATAC-seq, T47D_ATAC

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

library_source: genomic single cell

data_processing:
scRNA-seq: The Cell Ranger Software Suite (version 3.1.0) was used for demultiplexing BCL files, alignment, barcode counting, and UMI counting for scRNA-seq libraries. GRCh38-3.0.0 was used as a reference transcriptome. Specific details and instructions for running Cell Ranger can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger scATAC-seq: The Cell Ranger ATAC Software Suite (version 1.2.0) was used for demultiplexing BCL files, alignment, barcode counting, and generating fragments.tsv.gz files for scATAC-seq libraries. refdata-cellranger-atac-GRCh38-1.2.0 was used as a genomic reference. Specific details and instructions for running Cell Ranger ATAC can be found at: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
Assembly: hg38
Supplementary files format and content: Cell Ranger scRNA filtered feature barcode matrices contain gene counts for cellular barcodes. Cell Ranger scATAC fragments files list unique ATAC fragments per barcode sequence.

molecule: genomic DNA

source_name: breast cancer cell line

extract_protocol:
Tissue specimens were minced and digested overnight in DMEM/F12 + 5% FBS, 15mM HEPES (Gibco), 1x Glutamax (Gibco), 1x Collagenase/Hyaluronidase (Stem Cell Technologies, 07912), 1% Penicillin/Streptomycin (Corning), and 0.48 µg/mL Hydrocortisone (Stem Cell Technologies, 74144) on a stir plate at 37C and 180 rpm. Some tissues were dissociated with Gentle Collagenase/Hyaluronidase (Stem Cell Technologies, 07919) instead of Collagenase/Hyaluronidase. After digestion, cells were washed twice with cold PBS + 2% FBS and 10mM HEPES (PBS-HF) and centrifuged. To remove red blood cells, the cell pellet was treated with cold Ammonium Chloride Solution (Stem Cell Technologies, 07850) and PBS-HF (ratio 1 Ammonium Chloride: 4 PBS-HF), for 1 minute, then centrifuged. The volume of Ammonium Chloride Solution added was determined by the size of the cell pellet and visual assessment of pink or red color of the pellet. Red blood cell removal was repeated a second time if the pellet still exhibited a pink color after the first treatment. Next, cell pellets were resuspended in 0.05% Trypsin-EDTA (Gibco) and the suspension was gently pipetted up and down for 1 min. Trypsin was then inactivated by adding 10mL PBS-HF solution and the suspension was centrifuged. If cell suspensions were still clumpy after trypsin treatment, cells were resuspended with 1-2 mL Dispase (Stem Cell Technologies, 07923) and 200 µL 1mg/mL DNase I (Stem Cell Technologies, 07900) for 1 min, then inactivated with 10 mL PBS-HF. If the Dispase step was not necessary, cells were treated with DNase I during the trypsinization step. Cells were again centrifuged, then washed in PBS-HF and filtered through a 100µm cell strainer and washed again. The cell pellet was resuspended in DMEM/F12 + 5% FBS using a volume based on the final pellet size and filtered using a 40µm cell strainer. Single-cell suspension concentration and cell viability was measured with the Countess II Automated Cell Counter (Thermo Fisher, AMQAX1000). Cell viability varied between 43% and 94% across all samples, with the majority of suspensions having over 70% viability.
Cell suspensions were used for scRNA-seq and scATAC-seq library prep. For scRNA-seq, cell suspensions were diluted to 1200 cells/µL and 10,000 cells were used in library generation with the following 10x Genomics Single Cell 3’ kits: Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (PN-1000075), Chromium Chip B Single Cell Kit (PN-10000153), and Chromium i7 Multiplex Kit (PN-120262) following the manufacturer’s protocol.  For scATAC-seq, 500,000 cells were used in nuclei isolation following the Nuclei Isolation for Single Cell ATAC Sequencing protocol from 10x Genomics. For the lysis step, cells were lysed for 4 min. For the resuspension step, nuclei were resuspended in 50 µL 1x Nuclei Buffer. Nuclei were counted with the Countess II Automated Cell Counter. 10,000 nuclei were used in library preparation using the following 10x Genomics Single Cell ATAC Kits: Chromium Single Cell ATAC Library & Gel Bead Kit v1 (PN-1000110), Chromium Chip E Single Cell ATAC Kit (PN-1000082), and Chromium i7 Multiplex Kit N, Set A (PN-1000084) following the manufacturer’s protocol.  All libraries were sequenced using the 10X Genomics suggested sequencing parameters on an Illumina NextSeq 500 instrument.

value: breast cancer cell line

tag: er ihc

value: Not available

tag: pr ihc

tag: her2 ihc


title: Breast cancer cell line, scRNA-seq, T47D_RNA


title: R6/2 GFA2, 10


title: Breast cancer cell line, scATAC-seq, SUM149PT_ATAC


title: Control, replicate 1, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.2n.barcodes.tsv.gz
S1.2n.features.tsv.gz
S1.2n.matrix.mtx.gz

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: CD90+CD44+ T cells


title: Control, replicate 2, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.3n.barcodes.tsv.gz
S1.3n.features.tsv.gz
S1.3n.matrix.mtx.gz


title: R6/2 GFA2, 3


title: Control, replicate 2, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.3n.barcodes.tsv.gz
S1.3n.features.tsv.gz
S1.3n.matrix.mtx.gz


title: Aortic Cells, anti-CD8 treatment, ADT [F9_2_ADT]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
barcodes.tsv
features.tsv
matrix.mtx
feature_F9_2.csv


title: Breast cancer cell line, scRNA-seq, SUM149PT_RNA


title: Control, replicate 1, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.2n.barcodes.tsv.gz
S1.2n.features.tsv.gz
S1.2n.matrix.mtx.gz


title: Breast cancer cell line, scRNA-seq, MCF7_RNA


title: R6/2 GFA2, 21


title: WholeBlood-Control-F-167


title: R6/2 hSYN, 39

value: CYP46A1 hSYN


title: Control, replicate 5, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.6n.barcodes.tsv.gz
S1.6n.features.tsv.gz
S1.6n.matrix.mtx.gz


title: WholeBlood-Control-F-169

value: Whole blood


title: WholeBlood-Control-F-168

value: Control


title: WholeBlood-Control-F-180

value: Female


title: Breast cancer cell line, scATAC-seq, MCF7_ATAC


title: Combo+FTY720, replicate 4, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.7t.barcodes.tsv.gz
S5.7t.features.tsv.gz
S5.7t.matrix.mtx.gz

source_name: Tumor

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, plus anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Tumor

value: CD90+ T cells


title: WholeBlood-Control-F-165


title: R6/2 hSYN, 43


title: Breast cancer cell line, scATAC-seq, HCC1143_ATAC


title: Combo+FTY720, replicate 4, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.7t.barcodes.tsv.gz
S5.7t.features.tsv.gz
S5.7t.matrix.mtx.gz

value: BALB/c


title: WholeBlood-Control-F-161


title: R6/2 hSYN, 27


title: Combo+FTY720, replicate 3, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.5t.barcodes.tsv.gz
S5.5t.features.tsv.gz
S5.5t.matrix.mtx.gz

value: 6-8 weeks


title: R6/2 hSYN, 17


title: Breast cancer cell line, scRNA-seq, HCC1143_RNA


title: WholeBlood-Control-F-160


title: Combo+FTY720, replicate 3, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.5t.barcodes.tsv.gz
S5.5t.features.tsv.gz
S5.5t.matrix.mtx.gz


title: WholeBlood-Control-F-159


title: R6/2 hSYN, 26


title: Primary breast tumor, scRNA-seq, Patient_6_4C2E5L_RNA

source_name: primary breast tumor

value: primary breast tumor

value: ER-negative

value: PR-negative


title: Combo+FTY720, replicate 2, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.3t.barcodes.tsv.gz
S5.3t.features.tsv.gz
S5.3t.matrix.mtx.gz


title: Primary breast tumor, scATAC-seq, Patient_6_4C2E5L_ATAC


title: Combo+FTY720, replicate 2, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.3t.barcodes.tsv.gz
S5.3t.features.tsv.gz
S5.3t.matrix.mtx.gz


title: R6/2 CAG, 23

value: Striatum

value: mouse model of HD

value: CYP46A1 CAG


title: WholeBlood-Control-F-157


title: Normal breast tissue, scRNA-seq, Patient_4_4B146L_RNA

source_name: normal breast tissue

value: normal breast tissue

value: Not available


title: Combo+FTY720, replicate 1, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.2t.barcodes.tsv.gz
S5.2t.features.tsv.gz
S5.2t.matrix.mtx.gz


title: WholeBlood-Control-F-158


title: Normal breast tissue, scATAC-seq, Patient_4_4B146L_ATAC


title: Normal breast tissue, scRNA-seq, Patient_3_4AF75L_RNA


title: WholeBlood-Control-F-156


title: Combo, replicate 4, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.6t.barcodes.tsv.gz
S4.6t.features.tsv.gz
S4.6t.matrix.mtx.gz


title: WholeBlood-Control-F-151


title: WholeBlood-Control-F-155


title: Normal breast tissue, scATAC-seq, Patient_3_4AF75L_ATAC


title: Combo, replicate 4, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.6t.barcodes.tsv.gz
S4.6t.features.tsv.gz
S4.6t.matrix.mtx.gz


title: R6/2 CAG, 12


title: WholeBlood-Control-F-150


title: WholeBlood-Control-F-145


title: Normal breast tissue, scRNA-seq, Patient_2_49CFCL_RNA


title: Combo, replicate 3, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.5t.barcodes.tsv.gz
S4.5t.features.tsv.gz
S4.5t.matrix.mtx.gz


title: WT Stuffler, 15

value: WT

value: control

value: CYP46A1 stuffler


title: Normal breast tissue, scATAC-seq, Patient_2_49CFCL_ATAC


title: WT Stuffler, 5


title: Combo, replicate 3, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.5t.barcodes.tsv.gz
S4.5t.features.tsv.gz
S4.5t.matrix.mtx.gz

value: Female


title: WholeBlood-Control-F-141

value: Whole blood

value: Control


title: Normal breast tissue, scRNA-seq, Patient_1_49758L_RNA


title: R6/2 CAG, 18


title: R6/2 CAG, 20


title: Normal breast tissue, scATAC-seq, Patient_1_49758L_ATAC


title: Combo+FTY720, replicate 1, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.2t.barcodes.tsv.gz
S5.2t.features.tsv.gz
S5.2t.matrix.mtx.gz

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, plus anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Tumor

value: CD90+ T cells


title: Combo, replicate 2, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.3t.barcodes.tsv.gz
S4.3t.features.tsv.gz
S4.3t.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: R6/2 CAG, 33


title: WT Stuffler, 24


title: WholeBlood-Control-F-139


title: WholeBlood-Control-F-137


title: Primary breast tumor, scRNA-seq, Patient_15_45CB0L_RNA

value: primary breast tumor

value: ER-positive

value: PR-positive


title: WholeBlood-Control-F-136


title: R6/2 Stuffler, 7

value: Striatum

value: mouse model of HD


title: Combo, replicate 1, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.2t.barcodes.tsv.gz
S4.2t.features.tsv.gz
S4.2t.matrix.mtx.gz


title: Combo, replicate 2, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.3t.barcodes.tsv.gz
S4.3t.features.tsv.gz
S4.3t.matrix.mtx.gz


title: Primary breast tumor, scATAC-seq, Patient_15_45CB0L_ATAC


title: R6/2 Stuffler, 42


title: Combo, replicate 1, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.2t.barcodes.tsv.gz
S4.2t.features.tsv.gz
S4.2t.matrix.mtx.gz


title: R6/2 Stuffler, 16


title: Primary breast tumor, scRNA-seq, Patient_12_44F0AL_RNA


title: WholeBlood-Control-F-134


title: WholeBlood-Control-F-132


title: Anti-TIGIT, replicate 6, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.7t.barcodes.tsv.gz
S3.7t.features.tsv.gz
S3.7t.matrix.mtx.gz

value: anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: Primary breast tumor, scATAC-seq, Patient_12_44F0AL_ATAC


title: Anti-TIGIT, replicate 6, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.7t.barcodes.tsv.gz
S3.7t.features.tsv.gz
S3.7t.matrix.mtx.gz


title: R6/2 Stuffler, 31


title: WholeBlood-Control-F-131


title: Primary breast tumor, scRNA-seq, Patient_14_43E7CL_RNA


title: WT Stuffler, 40

value: WT


title: WholeBlood-Control-F-130


title: Primary breast tumor, scATAC-seq, Patient_14_43E7CL_ATAC


title: Anti-TIGIT, replicate 5, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.6t.barcodes.tsv.gz
S3.6t.features.tsv.gz
S3.6t.matrix.mtx.gz


title: Anti-TIGIT, replicate 5, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.6t.barcodes.tsv.gz
S3.6t.features.tsv.gz
S3.6t.matrix.mtx.gz


title: R6/2 NI, 36

value: No treatment


title: Primary breast tumor, scATAC-seq, Patient_14_43E7BL_ATAC


title: R6/2 NI, 34


title: WholeBlood-Control-F-129


title: WholeBlood-Control-F-127


title: Primary breast tumor, scRNA-seq, Patient_14_43E7BL_RNA


title: Anti-TIGIT, replicate 4, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.4t.barcodes.tsv.gz
S3.4t.features.tsv.gz
S3.4t.matrix.mtx.gz


title: R6/2 NI, 41


title: Primary breast tumor, scRNA-seq, Patient_11_3FCDEL_RNA


title: WholeBlood-Control-F-126


title: Anti-TIGIT, replicate 4, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.4t.barcodes.tsv.gz
S3.4t.features.tsv.gz
S3.4t.matrix.mtx.gz


title: Anti-TIGIT, replicate 1, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.1t.barcodes.tsv.gz
S3.1t.features.tsv.gz
S3.1t.matrix.mtx.gz


title: WholeBlood-Control-F-125


title: CON4

city: kai feng

first: zejin

last: liu

address: ximen street

country: China

institute: henan university

data_processing:
Sequencing data was trimmed for high quality sequence（Clean Data）using Cutadapt
The reference genome and gene annotation files were downloaded from genome website.
The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol Reagent (Invitrogen Life Technologies). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and  Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for  hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) by Suzhou PANOMIX Biomedical Tech Co., LTD

value: liver

value: ConA


title: CON3


title: Anti-TIGIT, replicate 1, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.1t.barcodes.tsv.gz
S3.1t.features.tsv.gz
S3.1t.matrix.mtx.gz

value: Female


title: Primary breast tumor, scRNA-seq, Patient_13_3D388L_RNA


title: WholeBlood-Control-F-123

value: Whole blood

value: Control


title: R6/2 NI, 1


title: CON2


title: Primary breast tumor, scATAC-seq, Patient_13_3D388L_ATAC


title: CON1


title: Anti-TIGIT, replicate 3, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.3t.barcodes.tsv.gz
S3.3t.features.tsv.gz
S3.3t.matrix.mtx.gz

value: Tumor


title: Primary breast tumor, scRNA-seq, Patient_10_3C7D1L_RNA


title: WholeBlood-Control-F-121


title: P2R44

value: P2X4R knockdown


title: Anti-TIGIT, replicate 2, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.2t.barcodes.tsv.gz
S3.2t.features.tsv.gz
S3.2t.matrix.mtx.gz

value: BALB/c

value: CD90+ T cells


title: P2R43


title: Primary breast tumor, scRNA-seq, Patient_9_3B3E9L_RNA

value: primary breast tumor


title: Anti-TIGIT, replicate 2, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.2t.barcodes.tsv.gz
S3.2t.features.tsv.gz
S3.2t.matrix.mtx.gz

value: 6-8 weeks


title: Primary breast tumor, scATAC-seq, Patient_10_3C7D1L_ATAC

value: ER-positive

value: PR-positive


title: P2R42


title: Primary breast tumor, scATAC-seq, Patient_9_3B3E9L_ATAC


title: P2R41


title: WholeBlood-Control-F-117


title: Primary breast tumor, scRNA-seq, Patient_8_3821AL_RNA


title: Anti-PDL1, replicate 5, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.6t.barcodes.tsv.gz
S2.6t.features.tsv.gz
S2.6t.matrix.mtx.gz

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, over 1 week


title: WholeBlood-Control-F-114


title: WholeBlood-Control-F-124


title: Primary breast tumor, scATAC-seq, Patient_11_3FCDEL_ATAC


title: Anti-TIGIT, replicate 3, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.3t.barcodes.tsv.gz
S3.3t.features.tsv.gz
S3.3t.matrix.mtx.gz

value: anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: Anti-PDL1, replicate 4, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.5t.barcodes.tsv.gz
S2.5t.features.tsv.gz
S2.5t.matrix.mtx.gz


title: iwat, 60% n6 HFD, ko, rep 3

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E Young Dr.

department: Pathology & Laboratory Medicine

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: inguinal white adipose tissue

extract_protocol:
The nuclear isolation procedure was adapted from a from a previously published protocol. iWAT (200 mg/mouse) was placed in a petri-dish containing 500 μl of ice-cold nuclei preparation buffer (NPB: 10mM Tris-HCl pH 7.5, 1.5 mM MgCl2, 10 mM KCl, 250 mM sucrose, 0.05% IGEPAL CA-630 and 0.2 mM DTT (pH 8.0) in DPPC water) and minced with scissors for 4 min. The samples were then transferred to a 2ml glass Dounce homogenizer containing 500 μl NPB, followed by 10 strokes with a loose pestle (pestle A) and 10 strokes with a tight pestle (pestle B). The homogenates were filtered through a 70 μm cell strainer into 50 ml conical tube. The filters were rinsed with an additional 2 ml NPB, after which the homogenates were transferred to 5 ml Eppendorf tubes and centrifuged at 1,000 xg for 10 min at 4°C in swing-buckets. The supernatant and floating lipid layer were carefully aspirated, and the nuclear pellet was resuspended in 500 μL NPB containing 1 U/μl RNase inhibitor (New England Biolabs, M0314). Nuclear suspensions from 2 independent mice were combined at this point and centrifuged in 1.5 ml Eppendorf tubes at 1,000 xg for 10 min at 4°C. Finally, the nuclear pellet was collected in 150 μl resuspension buffer (2 mM MgCl2, 1% BSA, 1U/μl RNase inhibitor in DPBS. All solutions were filter-sterilized prior to use. Finally, the nuclei suspensions were filtered through a 40 μm cell strainer (Flowmi Cell Strainer, Belart, NJ). Following counting using a Bürker pattern counting chamber, 10,000 nuclei per genotype were submitted for sNuc-seq using the 10x Genomics system.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, nuclei 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.

value: iWAT nuclei

value: inguinal white adipose tissue

tag: diet

value: Research Diets #12492 60% HFD

value: 18-22 weeks


title: WholeBlood-Control-F-113

value: Female


title: Primary breast tumor, scATAC-seq, Patient_8_3821AL_ATAC


title: Anti-PDL1, replicate 4, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.5t.barcodes.tsv.gz
S2.5t.features.tsv.gz
S2.5t.matrix.mtx.gz


title: iwat, 60% n6 HFD, ko, rep 2

description: 10x Genomics


title: WholeBlood-Control-F-111

value: Whole blood


title: iwat, 60% n6 HFD, ko, rep 1

description: 10x Genomics


title: WholeBlood-Control-F-120

value: Control


title: Anti-PDL1, replicate 3, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.4t.barcodes.tsv.gz
S2.4t.features.tsv.gz
S2.4t.matrix.mtx.gz

value: Tumor


title: Primary breast tumor, scATAC-seq, Patient_7_35EE8L_ATAC

value: PR-negative


title: WholeBlood-Control-F-118


title: iwat, 60% n6 HFD, wt, rep 3

description: 10x Genomics

value: WT


title: WholeBlood-Control-F-110


title: Anti-PDL1, replicate 5, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.6t.barcodes.tsv.gz
S2.6t.features.tsv.gz
S2.6t.matrix.mtx.gz

value: BALB/c

value: CD90+ T cells


title: Primary breast tumor, scRNA-seq, Patient_5_35A4AL_RNA

value: primary breast tumor

value: ER-negative


title: WholeBlood-Control-F-109


title: iwat, 60% n6 HFD, wt, rep 2

description: 10x Genomics


title: Anti-PDL1, replicate 2, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.3t.barcodes.tsv.gz
S2.3t.features.tsv.gz
S2.3t.matrix.mtx.gz

value: 6-8 weeks


title: WholeBlood-Control-F-107


title: Primary breast tumor, scATAC-seq, Patient_5_35A4AL_ATAC

value: PR-positive


title: iwat, 60% n6 HFD, wt, rep 1

description: 10x Genomics


title: Anti-PDL1, replicate 2, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.3t.barcodes.tsv.gz
S2.3t.features.tsv.gz
S2.3t.matrix.mtx.gz

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, over 1 week


title: kmt2d+EZH2 rep3

city: Rehovot

first: Ofir

last: Griess

address: Hetzel

country: Israel

institute: Weizmann Institute of Science

data_processing:
*library strategy: MARS-seq
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Assesment of quality with Fastqc
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
DEG using DESEQ2
Assembly: Hg39
Supplementary files format and content: the data obtained after DESeq2 DEG analysis, compared with WT OCI-Ly7. File includes base-mean, Log2FC, and adjusted p-value

source_name: Pleaural effrision

growth_protocol: Samples were grown in IMDM supplemented in 20% FBS and 1% P/S and maintained at 1-2*10^6 million cells/ml

extract_protocol:
2m cells were extracted for RNA with Nucleospin RNA isolation kit (Macherey Nagel), quality was checked with tapestation and concentration was examined by qubit
20ng of total RNA were converted to cDNA with barcodes, RNA was cleaned with Ampsure XP beads, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

value: Pleaural effrision

value: OCI-Ly7 kmt2d+EZH2

value: B

value: kmt2d-/- + EZH2 Y646N

value: No


title: Anti-PDL1, replicate 1, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.1t.barcodes.tsv.gz
S2.1t.features.tsv.gz
S2.1t.matrix.mtx.gz

value: Female


title: WholeBlood-Control-F-105

value: Whole blood

value: Control


title: iwat, ko_n3, 4

data_processing:
Fastq files were checked for quality, filtered, trimmed, and corrected for base pair mismatches using fastp (Version 0.23.2)
Salmon was used with full selective alignment to map reads to the mouse transcriptome and quantify transcript counts [mm10 - Ensembl – Release 97]
Transcript counts were summarized to the gene level using tximport package for R.
Assembly: mm10
Supplementary files format and content: .csv files contain Salmon-derived transcript abundances and raw counts from tximport summarized to the gene level

source_name: iWAT

extract_protocol:
Total RNA was extracted using TRIzol and RNeasy Mini Kit with on-column DNase I digestion (Qiagen)
Library preparation and sequencing was performed at the UCLA Technology Center for Genomics & Bioinformatics. Illumina sequencing-compatible cDNA libraries were synthesized from mRNA  enriched by Poly-A capture. 200bp paired-end sequencing cDNA libraries were analyzed with an Agilent TapeStation and sequenced on an Illumina NovaSeq S1 at 200 cycles. Read depth per sample averaged around 130M reads. Raw sequencing reads were demultiplexed using bcl2fastq (Illumina).

value: iWAT

value: KO

value: Male

value: 18-22 weeks


title: Jurkat shSOX4_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

source_name: Jurkat

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jurkat

value: T-ALL cells


title: Jurkat shSOX4_rep1


title: iwat, ko_n3, 2


title: iwat, ko_n3, 3


title: Control, replicate 3, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.4t.barcodes.tsv.gz
S1.4t.features.tsv.gz
S1.4t.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Tumor

value: CD90+ T cells


title: kmt2d+EZH2 rep2

value: Pleaural effrision

value: OCI-Ly7 kmt2d+EZH2

value: B


title: iwat, ko_n3, 1


title: Anti-PDL1, replicate 3, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.4t.barcodes.tsv.gz
S2.4t.features.tsv.gz
S2.4t.matrix.mtx.gz

value: Female

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, over 1 week


title: kmt2d rep3

value: OCI-Ly7 kmt2d lof

value: No


title: kmt2d rep2


title: iwat, wt_n3, 4

value: iWAT

value: WT


title: Jurkat shScb_rep1


title: Control, replicate 5, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.6t.barcodes.tsv.gz
S1.6t.features.tsv.gz
S1.6t.matrix.mtx.gz


title: Control, replicate 5, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.6t.barcodes.tsv.gz
S1.6t.features.tsv.gz
S1.6t.matrix.mtx.gz


title: kmt2d rep1


title: Jurkat shScb_rep2


title: EZH2 rep3

value: OCI-Ly7 EZH2 GOF

value: EZH2 Y646N


title: iwat, wt_n3, 3

value: Male

value: 18-22 weeks


title: iwat, wt_n3, 2


title: Control, replicate 4, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.5t.barcodes.tsv.gz
S1.5t.features.tsv.gz
S1.5t.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: EZH2 rep2


title: RNA-seq_HeLa_URCLNA_Rep3

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

data_processing:
For RNA-seq, adapter sequences were trimmed using trimmomatic (v 0.38).
RNA-seq reads were mapped to human genome GRCH38 withhisat2 (version:2.3.4.1) as paired-end, usinggenecodev28 gene annotation models.
RNA-seq read counts were obtained usingRsubread(version: 2.2.6).
For Experiment 1, RNA-seq read counts were normalized according to the genomic coverage of mappedDrosophilareads usingbedtools(version:2.29.2) andsamtools(version:1.7).
Differential gene expression analysis of RNA-seq was performed using R (v. 4.0.2) package DESeq2 (v. 1.28.1).
Assembly: GRCH38 and Drosophila melanogastergenome build5.41 from NCBI
Supplementary files format and content: BigWig files include normalized count data obtained from methods shown above.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovin serum (FBS) and penicillin/streptomycin under 5% CO2 at 37 °C.

extract_protocol:
RNA was purified using Sepasol-RNA I Super G with phenol-chloroform extraction and ethanol precipitation method.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) following manufacturer's instructions. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, requantified and sequenced as paired-end reads on the Illumina NovaSeq 6000 instrument.
4sU RNA-seq

treatment_protocol:
Experiment 1: HeLa cells were treated with 1,6-hexanediol and nascent RNAs were labeled with 4sU.
Experiment 2: HeLa cells were transfected with locked nucleic acid (LNA)-modified ASOs against URC and nascent RNAs were labeled with 500 μM 4sU .

value: HeLa

value: Cervical cancer cells

value: URC LNA


title: iwat, wt_n3, 1


title: Control, replicate 4, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.5t.barcodes.tsv.gz
S1.5t.features.tsv.gz
S1.5t.matrix.mtx.gz

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Tumor

value: CD90+ T cells


title: kmt2d+EZH2 rep1

value: Pleaural effrision

value: OCI-Ly7 kmt2d+EZH2

value: B

value: kmt2d-/- + EZH2 Y646N


title: Anti-PDL1, replicate 1, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.1t.barcodes.tsv.gz
S2.1t.features.tsv.gz
S2.1t.matrix.mtx.gz

value: Female

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, over 1 week


title: RNA-seq_HeLa_URCLNA_Rep1

value: WT


title: Primary breast tumor, scRNA-seq, Patient_7_35EE8L_RNA

value: primary breast tumor

value: ER-positive

value: PR-negative


title: iwat, ko_n6, 4

value: iWAT

value: KO

value: Male

value: 18-22 weeks


title: Control, replicate 3, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.4t.barcodes.tsv.gz
S1.4t.features.tsv.gz
S1.4t.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: RNA-seq_HeLa_ctrlLNA_Rep3

value: HeLa

value: Cervical cancer cells

value: control LNA


title: Control, replicate 2, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.3t.barcodes.tsv.gz
S1.3t.features.tsv.gz
S1.3t.matrix.mtx.gz

value: Tumor

value: CD90+ T cells


title: RNA-seq_HeLa_ctrlLNA_Rep2


title: iwat, ko_n6, 3


title: Control, replicate 2, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.3t.barcodes.tsv.gz
S1.3t.features.tsv.gz
S1.3t.matrix.mtx.gz

value: Female


title: OCI-Ly7 rep2

value: Pleaural effrision

value: B

value: WT

value: No


title: iwat, ko_n6, 2

value: iWAT


title: RNA-seq_HeLa_ctrlLNA_Rep1


title: iwat, ko_n6, 1

value: KO


title: DPSC-derived neurons from PWS and neurotypical control individuals

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
split-pipe_v1_0_3
Assembly: Hg38
Supplementary files format and content: read counts for each cell

source_name: cell line

growth_protocol: DPSC used in this study were isolated and cultured according to our previously described protocol and stored in the DPSC Repository (Goorha and Reiter 2017). Briefly, the dental pulp was removed from inside the tooth cavity and minced. Following removal, the pulp was digested with 3 mg/mL Dispase II and 4 mg/mL Collagenase I for 1 hour. Cells were then seeded on poly-D-Lysine coated 12-well plates with DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS), and 100 U/mL penicillin and 100 ug/mL streptomycin (Pen/Strep) (Fisher Scientific, Waltham, MA). Once confluent (80%) cultures were passaged using TrypLETM Express. Only early passage cells (<passage 4) were used for subsequent neuronal differentiation and molecular studies.

extract_protocol:
Parse Biosiences Cell Fixation Kit
Parse Biosciences Evercode Whole Transcriptome Kit

treatment_protocol: DPSC lines were seeded at 20,000 cells/cm2 on poly-D-lysine coated flasks with DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS), with 100 U/mL penicillin and 100 ug/mL streptomycin (Pen/Strep). At 80% confluence, the neuronal differentiation protocol was followed as previously published in Kiraly et al., 2009 (Kiraly et al. 2009) with an extended maturation phase (4 weeks versus 7 days) (Goorha and Reiter 2017). Briefly, DPSC were placed in 10μM 5-azacytidine (Acros Scientific, Geel, Belgium) in DMEM/F12 containing 2.5% FBS and 10ng/mL bFGF (Fisher Scientific, Waltham, MA) for 48 hours. Following epigenetic reprogramming, neuronal differentiation was induced by exposing the cells to 250μM IBMX, 50μM forskolin, 200nM TPA, 1mM db-cAMP (Santa Cruz, Dallas, TX), 10ng/mL bFGF (Invitrogen, Carlsbad, CA), 10ng/mL NGF (Invitrogen, Carlsbad, CA), 30ng/mL NT-3 (Peprotech, Rocky Hill, NJ), and 1% insulin-transferrin-sodium selenite premix (ITS) (Fisher Scientific, Waltham, MA) in DMEM/F12 for 3days. At the end of the neural induction period, neuronal maturation was performed by maintaining the cells in Neurobasal A media (Fisher Scientific, Waltham, MA) with 1mM db-cAMP, 2% B27, 1% N2 supplement, 30 ng/mL NT-3, and 1X Glutamax (Fisher Scientific, Waltham, MA) for 28 days.

value: cell line

value: Human Dental Pulp Stem Cells

value: Neurons

value: Neurotypical control and Prader-Willi syndrome

value: Neuronal differentiation


title: Control, replicate 1, tumor, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.2t.barcodes.tsv.gz
S1.2t.features.tsv.gz
S1.2t.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: Control, replicate 1, tumor, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S1.2t.barcodes.tsv.gz
S1.2t.features.tsv.gz
S1.2t.matrix.mtx.gz

value: Tumor


title: iwat, wt_n6, 4

value: Male

value: 18-22 weeks


title: RNA-seq_HeLa_URCLNA_Rep2

value: HeLa

value: Cervical cancer cells

value: URC LNA


title: normal,rep3

city: Jinan

first: Xiaoqing

last: Wang

state: Shandong

address: 324 Jingwu Street, Jinan, Shandong 250021, P.R. China

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

data_processing:
Raw Data was processed with in-house scripts. The filtering criteria was as follows: 1) Remove the reads without 3’adapter 2) Remove the reads without insert fragment 3) Remove the reads contain too much A/T 4) Remove the reads which length is out of range 5) Remove the low-quality reads
Using Bowtie1 to build the reference genome index, and then mapping the clean reads to the genome.
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability.The software for identification and prediction is miRDeep2.
Assembly: hg38
Supplementary files format and content: TPM(.txt)

source_name: adjacent tissue

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol. RNA purity was checked using the kaiaoK5500Spectrophotometer (Kaiao,Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was separated by 15% agarose gels to extract the small RNA (18-30 nt). After precipitated by ethanol and centrifugal enrichment of small RNA sample, the library was prepared according to the method and process of Small RNA Sample Preparation Kit (Illumina, RS-200-0048). The main contents are as follows: 1) Connecting the 3' adaptor to the separated small RNA. 2) Connecting the 5' adaptor to the separated small RNA. 3) RT－PCR. 4) Recycling strips of 145-160bp (22-30nt RNA).

value: adjacent tissue


title: tumor,rep3

source_name: wilms tumor

value: wilms tumor


title: iwat, wt_n6, 3

value: iWAT

value: WT


title: RNA-seq_HeLa_HD_Rep3


title: chondrocytes, mitochondrial_3

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: chondrocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: chondrocytes

value: wt

value: mitochondria


title: iwat, wt_n6, 2


title: RNA-seq_HeLa_HD_Rep1


title: RNA-seq_HeLa_HD_Rep2


title: normal,rep2


title: chondrocytes, mitochondrial_2


title: EZH2 rep1

value: Pleaural effrision

value: OCI-Ly7 EZH2 GOF

value: B

value: EZH2 Y646N

value: No


title: RNA-seq_HeLa_NT_Rep3

value: NT


title: tumor,rep2


title: OCI-Ly7 rep3


title: iwat, wt_n6, 1

value: Male

value: 18-22 weeks


title: normal,rep1


title: OCI-Ly7 rep1


title: chondrocytes, vehicle_2

value: vehicle


title: RNA-seq_HeLa_NT_Rep2

value: HeLa

value: Cervical cancer cells


title: iwat, ko_sfa, 4

value: KO

value: SFA


title: RNA-seq_HeLa_NT_Rep1

value: WT


title: tumor,rep1

value: wilms tumor


title: iwat, ko_sfa, 3

value: iWAT


title: iwat, ko_sfa, 2


title: D1 Sample

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
10X Genomics Spaceranger
The raw counts generated byspaceranger countwere further processed using the R packageSeurat[102,103]. The “molecule_info.h5” files for each sample were imported into Seurat using the Load10X_Spatial() function. This function reads in the spot-level expression data along with the associated image of the tissue slice.  In order to correct for differences in number of spots under tissue and sequencing depths, the data was normalized using Seurat SCTransform() function, which builds regularized negative binomial models of gene expression to account for technical artifacts while preserving biological variance. The normalized gene expression data for both tissues was merged into the same object and then run through dimensionality reduction using RunPCA(), and clustering using the Seurat functions FindNeighbors(), FindClusters(), and RunUMAP() [104, 105]. The clustering was visualized using SpatialDimPlot(). SeuratFindAllMarkersfunction finds markers that define clusters by differential expression. It identifies positive markers of a single cluster compared to all other cells and outputs the differential expression results. These markers are compared to known markers of expected cell types and results from previous single-cell transcriptome studies in order to assign appropriate cell type labels. Cell type determinations were made by manually inspecting these results. Differential expression analysis is performed using MAST, a GLM-framework that treats cellular detection rate as a covariate [106].
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg Aligned fiducials of the tissue image
Supplementary files format and content: scalefactors_json.json scale factors in json format
Library strategy: Spatial transcriptomics

source_name: placenta

growth_protocol: Placental tissues were collected from pregnant patients with severe PE or gestational hypertension (GHTN).  Samples were matched for mode of delivery and infant gender.

extract_protocol: Samples were prepared using 10x Genomics Visium V4 Slide FFPE v2 chemistry, the Visium Human Transcriptome Probe Set v2.0,

value: placenta

value: Preeclampsia with severe features

value: No treatment


title: chondrocytes, vehicle_1

value: chondrocytes

value: wt


title: DU145 cells, ST6GAL1 OE, biol rep 3

city: Newcastle upon Tyne

first: Jennifer

last: Munkley

state: Tyne & Wear

address: International Centre for Life

country: United Kingdom

institute: Newcastle University

data_processing:
Analysis was conducted in Galaxy version 22.01
Quality control was performed with FastQC
Reads were quantified using featureCounts
Differential gene expression analysis was performed with limma-voom
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw read counts for each sample

source_name: Prostate cancer

extract_protocol:
RNEasy Kit following manufacturer's protocol (Qiagen)
TruSeq Stranded mRNA Sequencing Library Prep Kit following manufacturer's protocols.

value: Prostate cancer

value: ST6GAL1 overexpression


title: iwat, wt_sfa, 4

value: Male


title: FUS1

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Assembly: mm10
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Nuclei were extracted from hippocampal brain of mice.

extract_protocol:
The nuclei obtained from total tissue were resuspended in 700μL Nuclei lysis buffer containing only 0.2% SDS. Fixed nuclei were sonicated with 15 cycles of 30sec ON / 30sec OFF. We used a primary rabbit antibody anti-FUS 15μg/ChIP (Bethyl, Ref: A300-293A). On the next day samples were incubated with 50ul/ChIP magnetic beads (Diagenode, Dynabeads protein A, Ref: 10002D) at 4°C during 2h. Beads were previously washed three times in ChIP dilution buffer with 0,1% SDS and blocked O/N at 4°C with BSA. ChIP-DNA were then washed 5 min in several buffers, using a magnetic rack: Low salt, High Salt, LiCL and TE buffer. ChIP-DNA was then incubated in 300 ul elution buffer (1% SDS, 0.1 M NaHCO3 in ddH2O) at RT for 5 min and at 65°C for 10 min. Crosslinkings were reversed by addition of 0,2M NaCL, O/N at 65°C. Then DNAs were purified with RNAse (Abcam, Ref: ab52579) at 37°C for 30 min, and in Proteinase K buffer (Invitrogen, Ref: 100005393) at 45°C for 1h. Finally, DNAs were extracted with the MicroChIP Diapure columns (Diagenode, Ref: C03040001) and quantification of DNA concentrations were calculated using the Qubit. All samples reached the minimum of 2ug required for sequencing.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 2.5 to 10ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 4 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: hippocampus

value: Neu+ cells

value: FUSdeltaNLS/+

tag: chip antibody

value: anti-FUS


title: FUS2


title: WT2


title: chondrocytes, mitochondrial_1

value: mitochondria


title: iwat, wt_sfa, 3

value: SFA

value: 18-22 weeks


title: iwat, ko_sfa, 1

value: KO


title: DU145 cells, OEControl for ST6GAL1 OE, biol rep 2

value: Lenti-ORF control


title: DU145 cells, OEControl for ST6GAL1 OE, biol rep 3


title: UC-MSCs,PS

city: jinan

first: Feifei

last: Shen

address: wenhua West Road

institute: Shandong university

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: csv(fpkm)

source_name: primary cell

growth_protocol: UC-MSCs were cultured in α-MEM medium containing 10% FBS + 1% P/S in an incubator at 37°C, with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: primary cell

value: UC-MSCs


title: A1 Sample

value: placenta

value: Gestational hypertension

value: No treatment


title: WT1

value: WT


title: chondrocytes, vehicle_3

value: chondrocytes

value: wt

value: vehicle


title: DU145 cells, OEControl for ST6GAL1 OE, biol rep 1

value: Prostate cancer


title: DaroR_RNA_SIGA2

city: Houston

first: Tianyi

last: Zhou

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: siGATA2, cultured in 10uM Darolutamide

data_processing:
fastqc
trim_galore trimed adaptors
bwa mapping
featurecounts
deseq2
Assembly: hg38
Supplementary files format and content: table deliminated txt including raw counts

growth_protocol: All cells were grown in RPMI1640 with 10% FBS and antibiotics at 37°C in a humidified atmosphere at 5% CO2

extract_protocol:
RNA were extracted using Qiagen Rneasy plus kit
mRNAlibrarypreparation were done by Novogene
Poly A enrichment

treatment_protocol: DMSO group were treated with only the solvant DMSO for 24 hours, R1881 group were treated with 1nM R1881 dissolved in DMSO for 24 hours, Daro group were treated with 10uM darolutamide for 24 hours, DaroR group were treated with 10uM darolutamide for 12 months, DaroR-siCtl group were treated with siRNA control, DaroR-siGATA2 group were treated with siGATA to knockdown GATA2 expression, DaroR-siAR group were treated with siAR to knockdown AR expression

value: LNCaP

value: hormone non-sensitive prostate cancer

value: siRNA treated

value: siGATA2, cultured in 10uM Darolutamide


title: Input FUS2

value: hippocampus

value: Neu+ cells

value: FUSdeltaNLS/+

value: none (input)


title: DaroR_RNA_SIGA1

description: siGATA2, cultured in 10uM Darolutamide


title: iwat, wt_sfa, 1

value: iWAT

value: SFA

value: Male

value: 18-22 weeks


title: DaroR_RNA_SIAR2

description: siAR, cultured in 10uM Darolutamide

value: siAR, cultured in 10uM Darolutamide


title: Input FUS1


title: 253 RNA

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapping against human reference genome hs37d5 using STAR-2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region (Gencode29) associated with each gene.
To account for differences in library size between samples, Trimmed Mean of M values (TMM) normalization using calcNormFactors(), also from edgeR, was applied.
All data were then transformed using voom.
Assembly: hs37d5
Supplementary files format and content: tab-delimited text files include raw gene count for each sample

source_name: ovarian tumors

extract_protocol:
RNA was harvested using the Qiagen All-Prep RNA isolation kit
RNA libraries were prepared by using Illumina TruSeqTM RNA Exome Library Preparation Kit (Illumina Inc., San Diego, CA) , following the manufacturer’s protocol

tag: yob decade

tag: pre/post menopause

value: post


title: DU145 cells, ST6GAL1 OE, biol rep 2

tag: tissue

value: ST6GAL1 overexpression


title: UC-MSCs,SIS-PS

value: primary cell

value: UC-MSCs


title: DaroR_RNA_SIAR1

description: siAR, cultured in 10uM Darolutamide

value: Prostate cancer

value: LNCaP

tag: treatment


title: Input WT2

value: WT


title: 250 RNA

value: pre


title: 254 RNA


title: C3-input

city: Taiyuan

first: Tingjuan

last: Huang

address: NO.56 Road Jiefang

institute: Shanxi Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads would be processed to get high quality clean reads according to four stringent filtering standards use fastp(version：0.20.0 )
Short reads alignment tool Bowtie2 (2.2.8) [2] was used for mapping reads to ribosomeRNA (rRNA) database. The rRNA mapped reads were then removed.
he rRNAremoved reads of each sample were then mapped to mus_musculus Ensembl release-100  genome use HISAT2（version: 2.1.0）
exomePeak2 (version: 1.0.0) software was used to identify read-enriched regions from MeRIP-seq data. Dynamic Poisson Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value<0.05.
Assembly: mus_musculus Ensembl release-100
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: m6A sequencing in liver of normal mice, Input control group

extract_protocol:
Total RNA is extracted from tissues using Trizol reagent, cells are lysed and RNA is released, which is reduced by isopropanol precipitation.
After total RNA was extracted, the enriched RNA was fragmented into short fragments (about 100nt) by using fragmentation buffer. RNA was divided into two parts,one of which was used as the input (no IP experiment was performed). The other RNA was enriched with m6A specific antibody. The enriched RNA was reverse transcripted into cDNA with random primers. Next, the cDNA fragments was end repaired, andligated to Illumina sequencing adapters.

value: Liver

tag: Sex

value: male

value: 12 weeks

value: Control

tag: rip antibody


title: DaroR_RNA_CTL2

description: siRNA control, cultured in 10uM Darolutamide

tag: cell type

value: hormone non-sensitive prostate cancer

tag: genotype

value: siRNA treated


title: Input WT1

value: hippocampus

value: Neu+ cells

value: none (input)


title: C2-IP

source_name: m6A sequencing in liver of normal mice, Immunoprecipitation group

tag: age

tag: strain


title: 249 RNA


title: 247 RNA

value: post


title: DaroR_RNA_2

description: treated with 10uM Darolutamide

tag: cell line

value: Drug treated


title: 248 RNA


title: 16LT_FUS 4 H3K27me3

source_name: ChIPed DNA obtained from purified nuclei of mouse total hippocampus

extract_protocol:
Sorted NeuN+ nuclei were  subjected to ChIP-sequencing using antibodies against the H3K27me3 histone mark. They were resuspended in Nuclei lysis buffer (10 mM EDTA, 50mM Tris-HCL pH8.1, 1mM NaBu and 0,4%SDS in ddH2O) with PIC in a 15 ml TPX tube. Nuclei were sonicated using the sonicator (Bioruptor Plus sonication device, Diagenode) with 17 cycle of 30sec ON / 30sec OFF on High Power with breaks to vortex tubes every 5 min. 4uL of supernatants were checked on 1,5% agarose gel to confirm DNA fragmentation of approximately bellow 500bp after sonication and between 500bp and 100bp after a rapid decrosslinking protocol. Sonicated chromatin was centrifuged at 4°C, 14000g for 10 min to get rid of debris. Supernatants were diluted in ChIP Dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-Cl, pH 8.1, 167 mM NaCl in ddH2O) to obtain a final concentration of 0,1%SDS. Approximately 40 000 nuclei were saved before IP for total input chromatin and the rest of the sample were split in a minimum of 400 000 nuclei per ChIP. Samples were incubated overnight (O/N) at 4°C with the following primary Ab: rabbit anti-H3K27me3, 5ug/ChIP (Diagenode, Ref: C15410195). On the next day samples were incubated with 50ul/ChIP magnetic beads (Diagenode, Dynabeads protein A, Ref: 10002D) at 4°C during 2h. Beads were previously washed three times in ChIP dilution buffer with 0,1% SDS and blocked O/N at 4°C with BSA. ChIP-DNA were then washed 5 min in several buffers, using a magnetic rack: Low salt, High Salt, LiCL and TE buffer. ChIP-DNA was then incubated in 300 μl elution buffer (1% SDS, 0.1 M NaHCO3 in ddH2O) at RT for 5 min and at 65°C for 10 min. Crosslinkings were reversed by addition of 0,2M NaCL, O/N at 65°C. Then DNAs were purified with RNAse (Abcam, Ref: ab52579) at 37°C for 30 min, and in Proteinase K buffer (Invitrogen, Ref: 100005393) at 45°C for 1h. Finally, DNAs were extracted with the MicroChIP Diapure columns (Diagenode, Ref: C03040001) and quantification of DNA concentrations were calculated using the Qubit. All samples reached the minimum of 2ug required for sequencing.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 2.2-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: NeuN+ cells

value: FUSdeltaNSL/+


title: C1-IP


title: 15LT_FUS 3 H3K27me3


title: DaroR_RNA_CTL1

value: Prostate cancer

value: siRNA control, cultured in 10uM Darolutamide


title: 246 RNA


title: C2-input


title: C1-input


title: 13LT_WT 1 H3K27me3

value: WT


title: 14LT_WT 2 H3K27me3


title: 245 RNA

value: pre


title: DaroR_RNA_1

description: treated with 10uM Darolutamide

value: LNCaP


title: iwat, wt_sfa, 2

value: iWAT

value: SFA

value: Male

value: 18-22 weeks


title: Daro_RNA_2

description: treated with 10uM Darolutamide

value: hormone sensitive prostate cancer


title: 4LT_FUS 4 Input

value: hippocampus


title: Daro_RNA_1

description: treated with 10uM Darolutamide


title: 244 RNA


title: B3-input

source_name: m6A sequencing in liver of mice induced by BDL, Input control group

value: Liver

value: male

value: 12 weeks

value: Hepatic fibrosis


title: R1881_RNA_2

description: treated with 1nM R1881

value: Drug treated


title: 243 RNA


title: C3-IP

value: Control


title: B2-IP

source_name: m6A sequencing in liver of mice induced by BDL, Immunoprecipitation group


title: B3-IP


title: 241 RNA


title: B2-input

value: none (input)


title: R1881_RNA_1

description: treated with 1nM R1881

value: Prostate cancer


title: 2LT_WT 2 Input

value: NeuN+ cells

value: WT


title: Veh_RNA_2

description: treated with the solvant DMSO

value: LNCaP

value: DMSO


title: 240 RNA

value: post


title: B1-IP


title: 1LT_WT 1 Input


title: 20_FUS4 H4K12Ac

description: NSLC 314 FUS4 H4K12ac

source_name: ChIPed DNA obtained from FACS sorted NeuN+ cells from brain of mouse total hippocampus

extract_protocol:
Sorted NeuN+ nuclei were  subjected to ChIP-sequencing using antibodies against the 3 histone marks: H3K27ac, H3K4me3 and H4K12ac. They were resuspended in Nuclei lysis buffer (10 mM EDTA, 50mM Tris-HCL pH8.1, 1mM NaBu and 1% SDS in ddH2O) with PIC in a 15 ml TPX tube. Nuclei were sonicated using the sonicator (Bioruptor Plus sonication device, Diagenode) with 17 cycle of 30sec ON / 30sec OFF on High Power with breaks to vortex tubes every 5 min. 4uL of supernatants were checked on 1,5% agarose gel to confirm DNA fragmentation of approximately bellow 500bp after sonication and between 500bp and 100bp after a rapid decrosslinking protocol. Sonicated chromatin was centrifuged at 4°C, 14000g for 10 min to get rid of debris. Supernatants were diluted in ChIP Dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-Cl, pH 8.1, 167 mM NaCl in ddH2O) to obtain a final concentration of 0,1%SDS. Approximately 40 000 nuclei were saved before IP for total input chromatin and the rest of the sample were split in a minimum of 400 000 nuclei per ChIP. Samples were incubated overnight (O/N) at 4°C with the following primary Ab: rabbit anti-H4K12ac, 9ug/ChIP (Diagenode, Ref: C15410331), rabbit anti-H3K4me3, 4,25ug/ChIP (Diagenode, Ref: C15410003-10), rabbit anti-H3K27ac, 3,1ug/ChIP (Abcam, Ref: ab4729). On the next day samples were incubated with 50ul/ChIP magnetic beads (Diagenode, Dynabeads protein A, Ref: 10002D) at 4°C during 2h. Beads were previously washed three times in ChIP dilution buffer with 0,1% SDS and blocked O/N at 4°C with BSA. ChIP-DNA were then washed 5 min in several buffers, using a magnetic rack: Low salt, High Salt, LiCL and TE buffer. ChIP-DNA was then incubated in 300 μl elution buffer (1% SDS, 0.1 M NaHCO3 in ddH2O) at RT for 5 min and at 65°C for 10 min. Crosslinkings were reversed by addition of 0,2M NaCL, O/N at 65°C. Then DNAs were purified with RNAse (Abcam, Ref: ab52579) at 37°C for 30 min, and in Proteinase K buffer (Invitrogen, Ref: 100005393) at 45°C for 1h. Finally, DNAs were extracted with the MicroChIP Diapure columns (Diagenode, Ref: C03040001) and quantification of DNA concentrations were calculated using the Qubit. All samples reached the minimum of 2ug required for sequencing.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: FUSdeltaNSL/+


title: Veh_RNA_1

description: treated with the solvant DMSO


title: 19_WT3 H4K12Ac

description: NSLC 313 WT3 H4K12ac


title: 239 RNA

value: pre


title: B1-input


title: DaroR_ChIP_IN

description: treated with 10uM Darolutamide

data_processing:
fastqc
trim_galore trimed adaptors
Botie2 mapping
Macs2 peak calling
Deeptool and Bedtool
Assembly: hg19
Supplementary files format and content: bigwig file
Supplementary files format and content: narrowpeak file

extract_protocol:
ChIP were performed using Active motif HS ChIP kit
Genomic DNA were extracted by Active motif HS ChIP kit

treatment_protocol: DMSO group were treated with only the solvant DMSO for 4 hours, R1881 group were treated with 1nM R1881 dissolved in DMSO for 4 hours, Daro group were treated with 10uM darolutamide for 4 hours, DaroR group were treated with 10uM darolutamide for 12 months

value: hormone sensitive prostate cancer


title: 238 RNA


title: lung cancer, model, MF3

city: Nanyang

first: Zhenzhen

last: Guo

address: No. 163Wolong Road, Wolong District

department: College of Chemistry and Pharmaceutical Engineering

institute: Nanyang Normal University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: model

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) for the construction of sequencing libraries.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,CA, USA) according to the manufacturer’s instructions

value: lung cancer

value: model


title: DaroR_ChIP_AR

description: treated with 10uM Darolutamide

value: AR Active Motif


title: 18_FUS2 H4K12Ac

description: NSLC 312 FUS2 H4K12ac

value: hippocampus


title: 237 RNA


title: 3LT_FUS 3 Input


title: 17_WT1 H4K12Ac

description: NSLC 311 WT1 H4K12ac


title: lung cancer, model, MF2


title: Daro_ChIP_IN

description: treated with 10uM Darolutamide


title: lung cancer, model, MF1


title: Daro_ChIP_AR

description: treated with 10uM Darolutamide


title: 16_FUS4 H3K4me3

description: NSLC 310 FUS4 H3K4me3


title: 236 RNA


title: lung cancer, treatment, GF3

source_name: artemisinin treatment

value: artemisinin treatment


title: 235 RNA


title: 14_FUS4 H3K27Ac

description: NSLC 308 FUS4 H3K27ac


title: 234 RNA


title: lung cancer, treatment, GF2


title: R1881_ChIP_IN

description: treated with 1nM R1881

value: Drug treated


title: R1881_ChIP_AR

description: treated with 1nM R1881


title: lung cancer, treatment, GF1


title: DMSO_ChIP_IN

description: treated with the solvant DMSO


title: 231 RNA


title: ChIP_EZH2_WT_rep2

city: San Diego

first: Wendy

address: 9500 Gilman Drive #0651

institute: University of California San Diego

description: ChIP-seq

data_processing:
All the ChIP-seq libraries were sequenced with single-end 100 bp reads on NovaSeq 6000. Raw reads were firstly evaluated by FastQC and trimmed by Cutadapt to get high-quallity clean reads.
Single-end raw reads of ChIP-seq data were mapped to the mouse genome (GENCODE assembly GRCm38/mm10) by bowtie2 in the local mapping mode with parameter “--local”, followed by PCR deduplication by SAMTools with the utility markedup (Li et al., 2009). Peaks were called from the uniquely mapped reads using MACS2 (Version 2.2.6) (Zhang et al., 2008) in the narrow peak-calling mode with default parameters.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed data are in BigWig format

source_name: Th17 cells

extract_protocol:
Cells were washed once with ice-cold PBS and pelleted at 1000 g for 5 min at 4°C. Crosslinked cells were resuspended in ice-cold hypotonic buffer, and centrifuged at 1000 g for 5 min at 4°C to obtain a nuclear fraction. Nuclear pellets were resuspended in  either LB3 buffer for H3K27me3 (Active motif, 39155) or PIPA-NR buffer for SUZ12 (Abcam, ab12073) and EZH2 (Invitrogen, 49-1043). Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles. Samples were centrifuged at 15000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation. LB3 lysate was diluted 1.1-fold with 10% Triton X-100, and 1% of the lysate was kept as ChIP input.
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions. DNA was purified and eluted following by amplification for 16 cycles PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. The amplified libraries were purified, eluted and size selected using PAGE/TBE gel for 225-325 bp fragments by gel extraction, and single-end sequenced on NovaSeq 6000 (Illumina). The eluted input DNA was prepared for libraries as described for ChIP samples.

value: Th17 cells

value: untreated


title: 10_WT3 H3K27Ac

description: NSLC 304 WT3 H3K27ac


title: DMSO_ChIP_AR

description: treated with the solvant DMSO

value: Prostate cancer


title: ChIP_EZH2_WT_rep1

description: ChIP-seq


title: 230 RNA


title: 9_WT3 Input

description: NSLC 303 WT3 Input

value: NeuN+ cells

value: none (input)


title: 229 RNA


title: 8_FUS2 H3K4me3

description: NSLC 302 FUS2 H3K4me3


title: Input_SUZ12_WT_rep2

extract_protocol:
Cells were washed once with ice-cold PBS and pelleted at 1000 g for 5 min at 4°C. Crosslinked cells were resuspended in ice-cold hypotonic buffer, and centrifuged at 1000 g for 5 min at 4°C to obtain a nuclear fraction. Nuclear pellets were resuspended in  either LB3 buffer for H3K27me3 (Active motif, 39155) or PIPA-NR buffer for SUZ12 (Abcam, ab12073). Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles. Samples were centrifuged at 15000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation. LB3 lysate was diluted 1.1-fold with 10% Triton X-100, and 1% of the lysate was kept as ChIP input.
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions. DNA was purified and eluted following by amplification for 16 cycles PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. The amplified libraries were purified, eluted and size selected using PAGE/TBE gel for 225-325 bp fragments by gel extraction, and single-end sequenced on NovaSeq 6000 (Illumina). The eluted input DNA was prepared for libraries as described for ChIP samples.

tag: antibody

value: input

value: WT


title: 228 RNA

value: post


title: SKkbNB

city: Noida

first: Adhiraj

last: Roy

state: Uttar Pradesh

address: Sector 125

department: AIMMSCR

country: India

institute: Amity University

data_processing:
All 150 bp paired end raw reads from Illumina NovaSeq 6000 sequencer were quality checked for low quality bases and adapter sequences, i.e AGATCGGAAGA (Processing of raw reads). Quality check was done using in-house perl scripts.
All the processed reads were aligned to Human hg38 genome (https://asia.ensembl.org/Homo_sapiens/Info/Index) using Hisat2-2.2.1.
StringTie-2-2.1  a fast and highly efficient assembler was used for  alignments into potential transcripts.
The "R" package DESeq2 has been used for differential gene expression analysis based on the negative binomial distribution. DeSeq2 estimates variance-mean dependence in count data from high_x0002_throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Assembly: Human hg38 genome
Supplementary files format and content: gtf

source_name: Ovary

growth_protocol: Epithelial ovarian cancer (EOC) cell lines OVCAR8 & SKOV3 were grown in DMEM and McCoy's media supplemented with 10% fetal bovine serum (FBS), 1× penicillin/streptomycin and maintained in humidified incubator containing 5% CO2 at 37 ◦C

extract_protocol:
Total RNA was isolated using Trizol reagent (Life technologies, USA) and 250  ng of total RNA was used for the construction of sequencing libraries
Library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (Catalog: E7775S, New England Biolabs).
mRNAs were primed with NEBNext Random Primers and chemically fragmented in a magnesium-based buffer in order to get an inserts of ~200 nucleotides. The fragmented mRNAs were reverse transcribed to form cDNA and the first strand cDNA reactions were converted to ds DNA. The double stranded cDNA fragments obtained were cleaned up by using 1.8X of AMPure XP beads (Catalog: A63881, Beckman Coulter). The library concentration was determined in a Qubit.3 Fluorometer (Catalog: Q33216, Life technologies using The Qubit dsDNA HS (High Sensitivity) Assay Kit (Catalog: Q32854, ThermoFisher Scientific). The library quality assessment was done using Agilent D5000 ScreenTape System (Catalog: 5067-5588, Agilent) and Agilent D1000 ScreenTape System (Catalog: 5067- 5582, Agilent) in a 4150 TapeStation System (Catalog: G2992AA, Agilent).

treatment_protocol: EOC cell lines were treated with 1 μM of PKD inhibitors CRT0066101 and kb-NB142-70 for 16 Hrs.

value: Ovary

value: Ovarian cancer

value: PKD inactivated


title: SKkbNB 2


title: Input_SUZ12_WT_rep1


title: 6_FUS2 H3K27Ac

description: NSLC 300 FUS2 H3K27ac

value: FUSdeltaNSL/+


title: SKCRT 2


title: Input_H3K27me3_WT_rep2


title: 13_FUS4 Input

description: NSLC 307 FUS4 Input


title: SKCRT


title: 226 RNA

value: pre


title: 5_FUS2 Input

description: NSLC 299 FUS2 Input


title: 227 RNA


title: 4_WT1 H3K4me3

description: NSLC 298 WT1 H3K4me3


title: SKDMSO 2

value: Wild type

value: Untreated


title: 12_WT3 H3K4me3

description: NSLC 306 WT3 H3K4me3

value: hippocampus


title: 233 RNA


title: 225 RNA


title: Input_H3K27me3_WT_rep1


title: Input_H3K27me3_Malat1KO_rep2

value: Malat1 KO


title: SKDMSO


title: 2_WT1 H3k27Ac

description: NSLC 296 WT1 H3K27ac


title: 224 RNA


title: Input_H3K27me3_Malat1KO_rep1

value: Th17 cells


title: 1_WT1 Input

description: NSLC 295  WT1 Input


title: ChIP_SUZ12_WT_rep2


title: OVkbNB 2


title: 221 RNA


title: ChIP_SUZ12_WT_rep1


title: OVkbNB


title: Malat1KO_Th17 rep1

description:
RNA-seq
Ribosome depeted RNA

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM19 annotation
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
Those with confidence score less than 0.99 were filtered out
Known genomic variations were obtained from the Mouse Genomes Project (ftp://ftp-mouse.sanger.ac.uk/current_snps/mgp.v5.merged.snps_all.dbSNP142.vcf.gz). Variants were removed from the resulting candidate list if they overlapped with the known genomic variations
All remaining candidates were annotated based on GENCODE.vM19
Genome_build: mm10
Supplementary_files_format_and_content: differential analysis tab-delimited text files include raw counts, normalized counts values log2FoldChange and pvalue for each gene
Supplementary_files_format_and_content: sailor analysis tab-delimited text files include position and edit % of each edited sites

source_name: Th17 72h cells

growth_protocol: Naïve CD4+ T cells was cultured under Th17 polarization condition with 0.1 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience).

extract_protocol:
RNA were isoalted using Qiagen Rneasy mini kit (74106)
Ribosome-depleted RNAs were used to generate the cDNA libraries using the KAPA Hyper Prep Kit (KR0961) according to the instructions. Briefly, DNA was end-repaired and A-tailing to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-liagation clean was used to remove the extra adapters. Then the adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles, follwed with post-ampilcation clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: Naïve [untreated] or Th17 [treated with 0.25 μg/mL anti-CD3ε (eBioscience), 1 μg/mL anti-CD28 (eBioscience), 0.1ng/mL TGF-β (R&D Systems), and 20 ng/mL IL-6 (R&D Systems) for 48 and 72hrs].

value: culture Th17

value: Malat1 knockout


title: 220 RNA


title: ChIP_H3K27me3_WT_rep2


title: OVCRT 2


title: OVCRT


title: ChIP_H3K27me3_WT_rep1


title: 219 RNA