title: EAE_Peak_ATAC

data_processing:
Samples for RNA modality were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 28nt(Read1)-10nt(Index1)-10nt(Index2)-90nt(Read2) setup using 'NovaSeqStandard' workflow in 'SP' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Samples for ATAC modalidity were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 50nt(Read1)-8nt(Index1)-24nt(Index2)-49nt(Read2) setup using 'NovaSeqStandard' workflow in 'SP' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Single cell multiome mouse (10X Genomics) data was processed with default parameters with cellranger-arc (v2.0.0) count function. Reads were aligned to mm10 (ata-cellranger-arc-mm10-2020-A-2.0.0) reference genome. Normalized single feature-barcode matrix combining all the samples from both modalities was calculated with the parameter cellranger-arc aggr with default parameters, samples were normalized to depth for both ATAC and gene expression modalities. which resulted in a median fragments per cell of 12928, median UMI counts per cell of 4240, median genes per cell of 1849 and 5769 cells.
We used Cellranger-arc called peaks for preQC measurements. After QC we run macs2 whithin Seurat/Signac to call the peaks, to recover consistent peak set within the whole dataset. For downstrean analyses we combined Signac v1.4.0 and Seurat v4.0.0 joint RNA and ATAC analysis. We used as QC metrics nCount_ATAC < 100000 & nCount_RNA < 25000 & nCount_ATAC > 500 & nCount_RNA > 500 & nucleosome_signal < 2 & TSS.enrichment > 1, which resulted in 5264 cells.
Gene activity was calculated over the 500bp promoter regions of annotated protein_coding genes from mm10 EnsEmbl79. Pooled replicates cells were identified based on CHRX and CHRY module score calculated from BiomaRt. Data processing was performed in RNA and ATAC modalities separately with Seurat/Signac. RNA modality was integrated with Harmony based on sample variable, normalized and dimension reduction PCA, dims=1:50. For the ATAC modality we performed latent semantic indexing (LSI) on the Harmony integrated space for dims=2:50. Using the weighted nearest neighbor (WNN) from Seurat v4 we computed the joint neighbor graph of RNA and ATAC modalities. We run FindClusters in the ATAC graph, RNA graph and joint WNN graph. Cells were annotated using transfer_anchors on the RNA modality to Falcao et al. 2019 scRNA-seq data and manually curated based on known gene markers, which allowed us to identify Astrocyte cells. By annotating the data to the Falcao et al. 2019 reference we can compare the cell clusters indentified in the scATAC-seq data to the single cell multiome cells clusters. We then called again the peaks using MACS2 on the identified cell clusters.
Peak to gene interaction were predicted based on co-accessibility and expression from identified celltypes using R package ArchR.
Genome_build: mm10
Supplementary_files_format_and_content: Output files from cellranger-arc (v2.0.0), as aligned RNA-seq and ATAC-seq modality bam files, filtered feature matrix h5 file, filtered expression matrix h5 file,  called ATAC fragments for Ctrl sample (P21208_1004) and EAE_Peak samle (P21208_1005).  Wig signal files for each identified celltype in Ctrl and EAE_Peak samples. Due to different number of cells in each celltype cluster, the wig files were built with a maximun of randomly selected 100 cells from each type. Predicted peak to gene interactions for each celltype, based on co-accessibility and expression as bedpe format. Bed file of identified celltype peaks. Processed data R object (.rds R.4.1.0) Signac 1.4.0/Seurat 4.0.5 used in the study.
Supplementary_files_format_and_content: Aggregated output matrix and ATAC fragments from both Ctrl and EAE_Peak sample, atac_fragments.tsv.gz and filtered_feature_bc_matrix.h5.

extract_protocol:
Mice were sacrificed with a ketaminol/xylazine intraperitoneal injection followed by intracardiac perfusion with PBS where after spinal cords were collected and dissociated using the adult brain dissociation kit (130-107-677, Miltenyi) following manufacturer’s instructions. Instead of myelin debris removal (Miltenyi), Percoll (Cytiva 17-0891-01) mixed with HBSS was used to generate a percoll gradient of 38% to remove myelin debris.
Immediately after dissociation, cells were stained with DAPI and sorted on a FACS Aria III cell sorter (BD Biosciences). Sox10GFP+/DAPI- cells were collected in PBS + 0.5% BSA. The pool of cells was then lysed and washed according to the Demonstrated Protocol: Nuclei Isolation for Single cell ATAC Sequencing (10x Genomics) with modifications from the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (10x Genomics)  as follows: the cells were centrifuged for 10 minutes at 300xg and 4°C, resuspended in ATAC lysis buffer (containing 0.01% IGEPAL (CA-630), 0.01% Tween-20, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and incubated on ice for 3 minutes. After the incubation, wash buffer (containing 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) was added on top without mixing and the nuclei were centrifuged for 5 min at 500xg and 4°C. Nuclei were washed once in Diluted Nuclei buffer (10x Genomics) containing 1% BSA, 1 mM DTT and 1 U/ul RNase inhibitor, and incubated for 60 minutes at 37°C in tagmentation mix (10x Genomics). The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression v1 Chemistry was used to create single nuclei ATAC and RNA libraries from the same cell. Two EAE and two CFA-Ctr animals were used for independent replicates. Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-24-49 read set-up for ATAC (minimum 25 000 read pairs per cell) and a 28-10-10-90 read set-up for RNA (minimum 20 000 read pairs per cell).
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

treatment_protocol: For the induction of EAE, the mouse model of MS, animals were injected subcutaneously with an emulsion of MOG35-55 peptide in complete Freud’s adjuvant (CFA; EK-2110 kit from Hooke Laboratories) followed by intraperitoneal injection with pertussis toxin in PBS (200 ng per animal) on the day of immunization and with 24 hours delay (according to manufacturer’s instructions). Control animals underwent the same treatment, but CFA without MOG35-55 peptide (CK-2110 kit from Hooke Laboratories) was used instead. Spinal cord and brains were collected at the peak of the disease when clinical score 3 has been reached, which corresponds to limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analyzed in this study.

tag: condition

value: Chromatin accessibility


title: Ctr_RNA

status: Public on Jan 28 2022

type: SRA

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Ctrl

value: Expression


title: 4h_Ctrl_1_tub

type: RNA

city: Philadelphia

first: Benjamin

last: Prosser

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

country: USA

institute: University of Pennsylvania

description: total RNA from mouse heart tissue harvested after 4 hours of ascorbic acid injection

hyb_protocol: NanoString probes were hybridized as per the manufacturer's protocol.

data_processing: The geometric means of the positive control values were used to threshold followed by data normalization using the geometric means of the three housekeeping genes (GAPDH, Rpl4, Tbp).

label: Nanostring Label

source_name: heart tissue

label_protocol: NanoString probes were labelled as per the manufacturer's protocol.

extract_protocol: total RNA was extracted from ~10mg of heart tissue using RNAzol as per the manufacturer's protocol

tag: time

tag: treatment

value: Ascorbic acid


title: 4h_Ctrl_3_tub


title: Ctr_ATAC

library_source: genomic

molecule: genomic DNA


title: EAE_Peak_RNA


title: 4h_Ctrl_2_tub


title: P11056_1140

data_processing:
Libraries were sequenced in Hiseq 2500 with a 50-8-8-50 read set-up and a minimum of 25000 read pairs per cell.
Reads were trimmed and aligned to mm10 reference assembly using Bowtie2. Reads were called individually for each sample using MACS2. Called peaks were merged using bedtools mergedbed. Fragment files and counts were obtained using the individual bam files as input for ChromVar R package, Resulting on 1029 cells.
ATAC signal was binarized and convert to gene activity score over 500bp promoters regions, then integrated using Seurat2 to scRNA-seq (Falcao, van Bruggen wt al. 2018) to assign cell identities “Predicted_celltypes”.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data as R object from Seurat package, includes scATAC fragments counts as “gene activity” over promoter region in the RNA assay. Integrated assay includes integration with scRNA-seq Falcao, van Bruggen et al. 2018.

source_name: EAE

growth_protocol: For the induction of EAE, the mouse model of MS, animals were injected subcutaneously with an emulsion of MOG35-55 peptide in complete Freud’s adjuvant (CFA; EK-2110 kit from Hooke Laboratories) followed by intraperitoneal injection with pertussis toxin in PBS (200 ng per animal) on the day of immunization and with 24 hours delay (according to manufacturer’s instructions). Control animals underwent the same treatment, but CFA without MOG35-55 peptide (CK-2110 kit from Hooke Laboratories) was used instead. Spinal cord and brains were collected at the peak of the disease when clinical score 3 has been reached, which corresponds to limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analyzed in this study.

extract_protocol:
Immediately after dissociation, cells were fixed in 1% formaldehyde (28906, ThermoFisher Scientific) for 10 minutes and quenched with glycine (125 mM) for 5 minutes at room temperature and then washed and stored in 0.5% BSA in PBS with 0.1% sodium azide at 4°C until further processing. The cells were counted and aliquots of 500.000 cells were centrifuged for 10 minutes at 1000xg and room temperature. Cells were resuspended in lysis buffer (containing 0.05% IGEPAL (CA-630), 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and incubated for 5 minutes at room temperature. After a 20-minute centrifugation at 1000xg at room temperature, the cells were incubated with anti-GFP antibody (FITC, 1:100, Ab6662, Abcam) and DAPI (0.5 ug/ml) in PBS containing 5% BSA for 20 minutes at room temperature. The cells were centrifuged for 10 minutes at 1000xg and resuspended in tagmentation mix (dH2O, 2x TD buffer (Wang et al., 2013) and Tn5 enzyme (Picelli et al., 2014)) and incubated for 30 minutes at 37°C. For both lysis and tagmentation buffers the volume was scaled up to match the number of cells (50 ul per 50.000 cells). Tagmentation reaction was stopped by addition of 40 mM EDTA. Cells were then centrifuged for 10 minutes at 1000xg and room temperature and resuspended in PBS + 0.5% BSA. Sox10 GFP+/DAPI+ cells were sorted on an Influx (BD Biosciences) in reverse crosslinking buffer (Chen et al., 2018) with single cells in each well of 96 well plates. Also Sox10 GFP-/DAPI+ cells were sorted as a negative control for the OL lineage. The plates were incubated overnight at 65°C ending with 10 minutes at 80°C the next day. PCR master mixes (NEBNext High fidelity, M0541S, NEB) containing unique barcoding primers per well were dispensed on top of the reverse crosslinking buffer and DNA was amplified with the following cycling conditions: 72°C for 5 min, 98°C for 30s; 20 cycles at 98°C for 10s, 63°C for 30s and 72°C for 1 min. PCR products were purified with the MinElute purification kit (Qiagen) and then PAGE purified to remove adapter dimers. Three EAE and two CFA-control animals were used for independent replicates. Libraries were sequenced on an Illumina Hiseq 2500 with a 50-8-8-50 read set-up and a minimum of 25 000 read pairs per cell.
scATACseq (PI-ATAC Chen et al., 2018)

treatment_protocol: Mice were sacrificed with a ketaminol/xylazine intraperitoneal injection followed by intracardiac perfusion with PBS where after brain and spinal cords were collected and dissociated using the adult brain dissociation kit (130-107-677, Miltenyi) following manufacturer’s instructions including myelin debris removal, but excluding the red blood cell removal step.

tag: tissue

tag: cell type


title: siStat1_IFNg_210506M6

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
The bulk RNA-seq samples were preprocessed for adapter/quality trimming and then aligned to the transcriptome using STAR (Dobin et al., 2013) version 2.7 –quantMode –sjdbOverhang 99 with EnsEMBLv75 gtf annotations. Only uniquely mapped reads were retained for downstream analysis using SAMtools. Aligned samples were converted to bedgraph files using Deeptools bamcoverage for each strand and normalized to total of reads. Filtered fastq files were used in Salmon 0.8.2 to recover the raw reads counts and transcript per million (TPM) values per transcript and gene. The differential gene expression analysis was performed with EdgeR (McCarthy et al., 2012; Robinson et al., 2010) for paired samples, CalcNornFactors = TMM and design ~day+condition. Results from differential expression were plot using Enhancedvolcano package with log2 fold change and FDR from EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq strand separated  wig files for each individual sample and merged siStat1 ( ctrl and IFNg trated replicates) and siBach1 ( ctrl and IFNg trated replicates). All the civrage files (wig files) as normalized with the DeepTOols option RPKM. Differential gene expression output from EdgeR in csv file format.

source_name: Sox10GFP+ OPCs

growth_protocol: Brains from P4-P6 mouse pups were collected and dissociated with the neural tissue dissociation kit (P; 130-092-628, Miltenyi). OPCs were obtained by either FACS with Sox10GFP+ selection or by MACS with CD140a microbeads (Cd140a microbead kit, 130-101-547, Miltenyi). For each experiment, multiple brains were pooled to obtain a sufficient number of cells. Cells were seeded on poly-L-lysine (P4707, Sigma) coated plates and grown with OPC proliferation media consisting of DMEM/F12, GlutaMAX (10565018, ThermoFisher Scientific), N2 supplement (17502001, ThermoFisher Scientific) NeuroBrew 21 (130-097-263, Miltenyi), penicillin-streptomycin (15140122, ThermoFisher Scientific), PDGFaa (10ng/ml, 315-17, PeproTech) and bFGF (20ng/ml, 100-18B, PeproTech).

extract_protocol:
Cells were collected with qiazol (Qiagen) and stored at -80°C until further processing. RNA was extracted with the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. Contaminating DNA was degraded by treatment of the samples with RNase-free DNase (Qiagen) in column.
0.1-1ug of RNA was used to make RNA-seq libraries with the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) according to manufacturer's instructions. Four replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 150-8-8-150 read set-up.

treatment_protocol: For the transcription factor knockdowns siGENOME SMARTpool siRNA targeting non-target Ctr (D-001206-13-05, Dharmacon), Stat1 (M-058881-02-0005, Dharmacon) or Bach1 (M-042956-01-0005, Dharmacon) was used which contains a pool of 4 siRNA’s. 1 ug of siRNA was diluted in OPTIMEM (31985062, Gibco), mixed with lipofectamine2000 (11668027, Invitrogen) and allowed to form complexes for 20 minutes at room temperature. OPC primary cells were then incubated with the siRNA complexes in DMEM/F12, GlutaMAX (10565018, ThermoFisher Scientific) media without any supplements for 4 hours after which the medium was replaced with normal OPC proliferation media. After 48 hours, IFN-gamma (100 ng/ml) was added for 6 hours.

tag: replicate

tag: experiment


title: 6h_tax_3_reg

description: total RNA from isolated mouse cardiomyocytes after 6 hours of 10uM taxol

source_name: cardiomyocyte

value: Taxol


title: P11056_1139


title: 6h_tax_2_reg


title: P11056_1138


title: P11056_1137


title: P11056_1136


title: P11056_1135


title: siStat1_Control_210526M5


title: siStat1_IFNg_210526M6


title: siStat1_Control_210506M5


title: P11056_1134


title: P11056_1133


title: siStat1_IFNg_210511M8


title: P11056_1131


title: 6h_dmso_2_reg

description: total RNA from isolated mouse cardiomyocytes after 6 hours of DMSO

value: DMSO


title: P11056_1130


title: 6h_tax_1_reg


title: P11056_1132


title: siStat1_Control_210511M7


title: siPool_IFNg_210506M2


title: P11056_1128


title: P11056_1129


title: 6h_dmso_1_reg


title: P11056_1127


title: 6h_colch_3_reg

description: total RNA from isolated mouse cardiomyocytes after 6 hours of 10uM colchicine

value: Colchicine


title: siPool_Control_210506M1


title: P11056_1125


title: 6h_colch_2_reg


title: P11056_1141


title: P11056_1124


title: 4h_PE_2_tub

description: total RNA from mouse heart tissue harvested after 4 hours of 10mg/kg phenylephrine injection

value: Phenylephrine


title: siPool_IFNg_210526M2


title: P11056_1123


title: P11056_1122


title: siPool_Control_210526M1


title: 6h_colch_1_reg


title: 4d_PE_8_reg

description: total RNA from day 4 mouse heart tissue harvested after 10mg/kg phenylephrine injections on day 0 and day 2


title: P11056_1121


title: P11056_1120


title: P11056_1119


title: siPool_Control_210511M1


title: siPool_IFNg_210511M2


title: P11056_1118


title: siStat1_IFNg_210329Mm8


title: P11056_1117


title: P11056_1116


title: P11056_1114


title: 6h_dmso_3_reg


title: siStat1_Ctr_210329Mm7


title: 4d_PE_4_reg


title: 4d_PE_5_reg


title: 4d_PE_3_reg


title: siCtr_IFNg_210329Mm2


title: 4d_PE_2_reg


title: P11056_1112


title: P11056_1113


title: P11056_1111


title: P11056_1126


title: siCtr_Ctr_210329Mm1


title: 4d_PE_1_reg


title: P11056_1109


title: siBach1_IFNg_191114Ct4


title: P11056_1107


title: P11056_1106


title: P11056_1108


title: siBach1_Control_191114Ct3


title: 4d_Iso_8_reg

description: total RNA from day 4 mouse heart tissue harvested after 5mg/kg isoproterenol injections on day 0 and day 2

value: Isoproterenol


title: 4d_Iso_7_reg


title: P11056_1105


title: siPool_IFNg_191114Ct2


title: P11056_1104


title: P11056_1102


title: P11056_1103


title: siPool_Control_191114Ct1


title: 4d_Iso_5_reg


title: P11056_1101


title: 4d_PE_6_reg


title: 4d_Iso_3_reg


title: P11056_1115


title: siBach1_IFNg_191010Mk8


title: P11056_1098


title: P11056_1099


title: 4d_Iso_2_reg


title: P11056_1096


title: P11056_1097


title: P11056_1094


title: 4d_Ctrl_7_reg

description: total RNA from day 4 mouse heart tissue harvested after ascorbic acid injections on day 0 and day 2


title: siBach1_Control _191010Ct7


title: siBach1_IFNg_191010Ct8


title: siPool_Control _191010Mk1


title: 4d_Ctrl_8_reg


title: P11056_1092


title: siPool_IFNg_191010Mk2


title: P11056_1093


title: P11056_1095


title: P11056_1089


title: P11056_1110


title: P11056_1086


title: 4d_Ctrl_4_reg


title: P11056_1090


title: P11056_1091


title: P11056_1088


title: siPool_IFNg_191010Ct2


title: 4d_Ctrl_6_reg


title: 4d_Ctrl_1_reg


title: 4d_Iso_6_reg


title: P11056_1100


title: P11056_1085


title: 4d_Ctrl_2_reg


title: P11056_1084


title: siBach1_IFNg_190913Mk8


title: siBach1_Control _191010Mk7


title: P11056_1083


title: 4h_PE_6_reg


title: P11056_1082


title: P11056_1081


title: P11056_1080


title: P11056_1078


title: siBach1_Control _190913Mk7


title: 4h_PE_4_reg


title: P11056_1077


title: 4d_Ctrl_5_reg


title: P11056_1079


title: P11056_1076


title: siPool_IFNg_190913Mk2


title: siPool_Control _190913Mk1


title: P11056_1075


title: UMOD-KI/KI-5d

city: Cambridge

first: Jamie

middle: L

last: Marshall

state: MA

address: 75 Ames Street, Office 5013C

department: Kidney Disease Initiative

institute: Broad Institute

description:
Slide-seqV2
Puck_200210_04

data_processing:
Library strategy: Slide-seqV2
Slide-seqV2 Bead Structure: 8C18X7C2X8M1X
Puck Caller: https://github.com/MacoskoLab/PuckCaller
Slide-seq Pipeline: https://github.com/MacoskoLab/slideseq-tools
Kidney Slide-seq Pipeline: https://github.com/marshalljamie/Kidney-Slide-seq
Genome_build: genome build: GRCm38.81.fasta
Supplementary_files_format_and_content: processed data files format and content: BeadLocationsForR.csv, BeadLocationsForR_qc.csv with QCed cell type assignments, MappedDGEForR.csv provides RNA expression info, and .digital_expression.txt.gz provides RNA expression info

molecule: polyA RNA

source_name: kidney

tag: genotype

value: UMOD-KI/KI

tag: disease state

value: autosomal dominant tubulointersital kidney disease (ADTKD)

value: kidney cross-section

tag: age

value: 6 month


title: UMOD-KI/KI-5c

description:
Slide-seqV2
Puck_200210_03


title: P11056_1073


title: P11056_1087


title: P11056_1074


title: 4h_PE_2_reg


title: UMOD-KI/KI-5b

description:
Slide-seqV2
Puck_200210_02


title: P11056_1071


title: siPool_Control _191010Ct1


title: 4h_PE_3_reg


title: 4h_PE_1_reg


title: 4h_Iso_6_reg

description: total RNA from mouse heart tissue harvested after 4 hours of 5mg/kg isoproterenol injection


title: P11056_1070


title: UMOD-KI/KI-5a

description:
Slide-seqV2
Puck_200210_01


title: P11056_1069


title: P11056_1068


title: UMOD-KI/KI-4e

description:
Slide-seqV2
Puck_200131_23


title: P11056_1067


title: P11056_1066


title: UMOD-KI/KI-4d

description:
Slide-seqV2
Puck_200131_22


title: P11056_1065


title: P11056_1064


title: UMOD-KI/KI-4c

description:
Slide-seqV2
Puck_200131_21


title: P11056_1063


title: 4h_Iso_4_reg


title: 4h_Iso_3_reg


title: 4h_Iso_2_reg


title: P11056_1062


title: P11056_1061


title: P11056_1060


title: 4h_PE_5_reg


title: 4h_Iso_1_reg


title: P11056_1059


title: P11056_1058


title: P11056_1057


title: UMOD-KI/KI-4a

description:
Slide-seqV2
Puck_200131_13


title: UMOD-KI/KI-3e

description:
Slide-seqV2
Puck_200127_10


title: 4h_Ctrl_6_reg


title: P11056_1056


title: 4h_Ctrl_5_reg


title: P11056_1072


title: UMOD-KI/KI-3d

description:
Slide-seqV2
Puck_200127_09


title: P11056_1055


title: P11056_1054


title: 4h_Ctrl_4_reg


title: UMOD-KI/KI-3c

description:
Slide-seqV2
Puck_200127_08


title: P11056_1053


title: UMOD-KI/KI-3b

description:
Slide-seqV2
Puck_200127_07


title: P11056_1051


title: P11056_1052


title: P11056_1049


title: UMOD-KI/KI-3a

description:
Slide-seqV2
Puck_200127_06


title: P11056_1050


title: P11056_1048


title: 4h_Iso_5_reg


title: P11056_1047


title: 4h_Ctrl_2_reg


title: 4h_Ctrl_1_reg


title: UMOD-WT/WT-3a

description:
Slide-seqV2
Puck_200127_01

value: UMOD-WT/WT

value: control


title: P11056_1046


title: P11056_1045


title: 4h_Ctrl_3_reg


title: P11056_1044


title: UMOD-KI/KI-2e

description:
Slide-seqV2
Puck_200104_14


title: P11056_1043


title: UMOD-KI/KI-4b

description:
Slide-seqV2
Puck_200131_20


title: T24 rep. 3

city: Villefranche-sur-mer

first: Stefano

last: Tiozzo

address: 181 chemin du Lazaret

country: France

institute: CNRS - IMEV

data_processing:
removing of contaminating ribosomal RNA using SortmeRNA v2.1
cleaning, clipping, and filtering reads using Trimmomatic v0.30
transcriptome assembly from the remaining reads, using Trinity v2.11.0
Recover the best ORF per contig using TransDecoder v5.5.0, using a minimum protein length of 90 amino-acids
Reduce spurious redundancy by collapsing similar transcripts using cd-hit-est v4.6 with  default parameters
Mapping the sequencing reads on the obtained transcriptome using Kallisto v0.43.1
Identifying Differentially Expressed Genes using DeSeq2
Genome_build: De novo transcriptome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every contig and every sample

organism: Botryllus schlosseri

source_name: colony

growth_protocol: Twelve subclones of comparable size from this strain were separated with a razor blade and allowed to grow separately on individual glass slides

extract_protocol:
Extraction of total RNA was performed the same day in a single round, for the twelve samples, using the NucleoSpin® RNA XS Mascherey-Nagel kit (#740902.50)
Library preparation and sequencing were performed at the USC Epigenomic Center (Los Angeles, USA) according to the Illumina HiSeq 2500 protocol

treatment_protocol: Injured colonies : all zooids removed

value: Injured colony, all zooids removed

tag: time after injury

value: 24 hours


title: T24 rep. 2


title: P11056_1042


title: UMOD-KI/KI-2d

description:
Slide-seqV2
Puck_200104_10


title: T24 rep. 1


title: P11056_1041


title: T18 rep. 3

value: 18 hours


title: P11056_1040


title: UMOD-KI/KI-2c

description:
Slide-seqV2
Puck_200104_09


title: P11056_1039


title: T18 rep. 2


title: P11056_1038


title: T18 rep. 1


title: UMOD-KI/KI-2b

description:
Slide-seqV2
Puck_200104_07


title: UMOD-KI/KI-2a

description:
Slide-seqV2
Puck_200104_06


title: P11056_1035


title: T6 rep. 3

value: 6 hours


title: P11056_1034


title: T6 rep. 2


title: P11056_1033


title: P11056_1032


title: UMOD-WT/WT-2d

description:
Slide-seqV2
Puck_200104_04


title: T6 rep. 1


title: UMOD-WT/WT-3b

description:
Slide-seqV2
Puck_200127_05


title: UMOD-WT/WT-2c

description:
Slide-seqV2
Puck_200104_03


title: T0 rep. 3

value: 0 hours


title: P11056_1030


title: UMOD-WT/WT-2b

description:
Slide-seqV2
Puck_200104_02


title: P11056_1028


title: P11056_1029


title: P11056_1027


title: T0 rep. 2


title: P11056_1026


title: T0 rep. 1


title: UMOD-KI/KI-1e

description:
Slide-seqV2
Puck_200102_09


title: P11056_1022


title: P11056_1025


title: P11056_1021


title: UMOD-KI/KI-1d

description:
Slide-seqV2
Puck_191223_24


title: U2OS with EWS-FLI1 treated 6h rep3

city: Beijing

first: Chunyu

last: Yu

address: Xueyuan Road 38#

country: China

institute: Peking University

data_processing:
Illumina Casava 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 kallisto 0.46
Genome_build: hg38
Supplementary_files_format_and_content: Abundance table with raw gene counts and TPM values for every transcript and every sample

organism: Homo sapiens

source_name: U2OS cell line

growth_protocol: Wild type U2OS, U2OS integrated with mCherry-EWS-FLI1, and A673 cell lines were cultured in DMEM (HyClone) supplemented with 10% FBS (Gibco) and 100 units/mL penicillin and 100 μg/mL streptomycin (HyClone) at 37℃ with 5% CO2 in a humidified incubator (Above 10^7 cells in 10cm dish).

extract_protocol:
RNA was harvested using Trizol reagent. Sequenceing library were generated using Illumina VAHTS Universial V6 RNA-seq library Kit (Cat#NR604-01/02) following the manafacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each replicate was treated with 7.5μM LY2835219 for 0(untreated), 3 and 6 hours.

tag: cell line

value: U2OS cell line

tag: source

value: Osteosarcoma

tag: lineage

value: Bone

value: Overexpressing EWS-FLI1


title: U2OS with EWS-FLI1 treated 6h rep2


title: U2OS with EWS-FLI1 treated 6h rep1


title: UMOD-KI/KI-1c

description:
Slide-seqV2
Puck_191223_23


title: P11056_1037


title: P11056_1018


title: P11056_1036


title: UMOD-KI/KI-1b

description:
Slide-seqV2
Puck_191223_22


title: P11056_1017


title: P11056_1016


title: U2OS with EWS-FLI1 treated 3h rep3


title: P11056_1014


title: UMOD-WT/WT-2e

description:
Slide-seqV2
Puck_200104_05


title: P11056_1020


title: P11056_1015


title: U2OS with EWS-FLI1 treated 3h rep2


title: UMOD-WT/WT-1e

description:
Slide-seqV2
Puck_191223_20


title: P11056_1024


title: U2OS with EWS-FLI1 treated 3h rep1


title: P11056_1012


title: UMOD-WT/WT-2a

description:
Slide-seqV2
Puck_200104_01


title: UMOD-KI/KI-1a

description:
Slide-seqV2
Puck_191223_21


title: UMOD-WT/WT-1d

description:
Slide-seqV2
Puck_191223_19


title: U2OS with EWS-FLI1 untreated rep3

value: Untreated


title: P11056_1010


title: P11056_1009


title: UMOD-WT/WT-1c

description:
Slide-seqV2
Puck_191223_18


title: U2OS with EWS-FLI1 untreated rep2


title: P11056_1008


title: P11056_1007


title: UMOD-WT/WT-1b

description:
Slide-seqV2
Puck_191223_17


title: P11056_1023


title: U2OS with EWS-FLI1 untreated rep1


title: U2OS WT rep3

value: Wild type


title: P11056_1006


title: UMOD-WT/WT-1a

description:
Slide-seqV2
Puck_191223_15


title: P11056_1005


title: BTBR-ob/ob-4g

description:
Slide-seqV2
Puck_191223_14

value: BTBR-ob/ob

value: early diabetic kidney disease

value: 13 week


title: P11056_1004


title: P11056_1003


title: U2OS WT rep2


title: P11056_1002


title: P11056_1019


title: P11056_1001


title: P11056_1013


title: BTBR-ob/ob-4e

description:
Slide-seqV2
Puck_191223_12

value: kidney cross-section


title: A673 treated 6h rep3

source_name: A673 cell line

value: A673 cell line

value: Ewing tumor


title: PRMT1-KD_Rep1

first: Peter

last: Choi

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

data_processing:
Paired-end sequencing reads were aligned to the human genome reference build hg38 using STAR v2.7.2
Gene expression levels were estimated using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output of gene expression levels

source_name: LNCaP cells

growth_protocol: LNCaP cells were grown in RPMI supplemented with 10% Tet System Approved FBS (Takara, #631101), 100 U/mL penicillin, 100 ug/mL streptomycin, 2 mM L-glutamine, and 100 ug/mL Normocin (Invivogen).

extract_protocol:
Total RNA was collected from cells using the RNeasy Plus Mini Kit (QIAGEN, #74136).
RNA-sequencing libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche).

treatment_protocol: LNCaP cells transduced with a doxycycline-inducible shRNA targeting PRMT1 were cultured with or without 100 ng/mL doxycycline for 7 days.

value: dox-treated

value: PRMT1 knockdown


title: A673 treated 6h rep2


title: BTBR-ob/ob-4d

description:
Slide-seqV2
Puck_191223_11


title: BTBR-ob/ob-4c

description:
Slide-seqV2
Puck_191223_10


title: Control_Rep3

value: untreated

value: control


title: Control_Rep2


title: A673 treated 6h rep1


title: DIPG13 input

city: Memphis

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

data_processing:
Reads were trimmed using trimGalore and quality was assessed using FastQC
The resulting reads were aligned to hg19 using Bowtie2 (v2.3.5.1)
Spike-in normalization was performed by aligning the reads to the dm6 genome.
Epic2 was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigwig files

source_name: DIPG

growth_protocol: Diffuse intrinsic pontine glioma cells (SU-DIPG-IV) were lenti-virally infected with doxycyline inducible shRNA constructs targeting MAT2A followed by antibiotic selection

extract_protocol:
Chromatin immunoprecipitations (ChIP), using H3K36me3 antibodies, were carried out using the Diagenode SX-8G IP-Star Compact (Diagenode automated Ideal ChIP-seq Kit).
KAPA Hyper prep kit (Cat# KK8504, KAPA Biosystems) and KAPA Dual-indexed adapter kit (Cat# KK8722 KAPA Biosystems) were used to construct the ChIP-RX DNA library for sequencing on an Illumina platform following the manufacturer’s instructions. A

treatment_protocol: Cells were treated with doxycycline to induce shRNA expression

tag: antibody


title: BTBR-ob/ob-4b

description:
Slide-seqV2
Puck_191223_09


title: P11056_1011


title: DIPG13_noDOX


title: DIPG13_DOX

value: DOX


title: A673 treated 3h rep3


title: DIPG4_DOX input

value: SU-DIPG-IV


title: DIPG4_noDOX input


title: A673 treated 3h rep2


title: DIPG4_noDOX


title: BTBR-wt/wt-4f

description:
Slide-seqV2
Puck_191223_07

value: BTBR-wt/wt


title: A673 treated 3h rep1

value: Bone


title: A673 untreated rep3


title: BTBR-ob/ob-4f

description:
Slide-seqV2
Puck_191223_13


title: Control_Rep1


title: BTBR-wt/wt-4e

description:
Slide-seqV2
Puck_191223_05


title: U2OS WT rep1

value: U2OS cell line

value: Osteosarcoma


title: PRMT1-KD_Rep2


title: PRMT1-KD_Rep3


title: BTBR-wt/wt-4d

description:
Slide-seqV2
Puck_191223_04


title: A673 untreated rep2

value: Untreated

value: Wild type


title: RNA-Seq of HEK293 cells after mock knockdown, replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
For differential mRNA expression analysis, gene-level read counts were quantified using Salmon (version 0.8.2) and normalized by variance-stabilizing transformation using DESeq2.
To estimate the differential poly(A) site usage, we used QAPA with default settings, essentially as previously described (Ha KCH et. al. 2018. Genome Biology).To quantify the relative usage of proximal poly(A) sites, QAPA calculates the percentage of expression of a single 3′ UTR over the total expression level of all 3′ UTRs for a given gene. Lengthening events were defined as those with percentage of proximal Poly(A) Usage Index (PAU) group difference between siSp1 and siMock (PAU_Group_diff) < −20% and shortening events with PAU_Group_diff > 20%.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for Poly(A) usage (PAU) from QAPA analysis, PAU difference between siSP1 and siMock from APA analysis, and differential gene expression from DESeq2 analysis

source_name: Human embryonic kidney cells

growth_protocol: HEK293 cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

extract_protocol:
RNA was isolated from lysates using Trizol (Thermo Fisher Scientific) as described by the manufacturer and was treated with DNAse (Thermo Fisher).
1000 ng per sample was used in the library preparation. Sequencing libraries were constructed using Illumina’s TruSeq Stranded mRNA sample preparation protocol, as described in Illumina’s TruSeq mRNA sample preparation guide.

treatment_protocol: Cells were transfected with siSP1 Silencer Select siRNA(Thermo Fisher) using Lipofectamine RNAiMAX (Thermo Fisher), as recommended by the manufacturer. Silencer Select control siRNA (Thermo Fisher) was used as a control (siMock). Cells were harvested 72 hours post transfection.

tag: knockdown

value: siMock


title: BTBR-wt/wt-4c

description:
Slide-seqV2
Puck_191223_03

value: 13 week


title: A673 untreated rep1


title: RNA-Seq of HEK293 cells after mock knockdown, replicate 1


title: RNA-Seq of HEK293 cells after knockdown of SP1, replicate 1


title: BTBR-wt/wt-4b

description:
Slide-seqV2
Puck_191223_02

value: kidney cross-section


title: BTBR-wt/wt-4a

description:
Slide-seqV2
Puck_191223_01


title: NHBE_GFP_rep3

city: Lausanne

first: Delphine

last: Grun

address: route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped to the human genome (hg19) using Hisat v2.1.0 with options -k 5 --rna-strandness RF --seed 42 -p 4 -x
Counts of reads on genes and TEs were computed using FeatureCounts with options -p -s 2 -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain read counts on genes or TEs

source_name: human bronchoepithelial cells

growth_protocol: Cultured in PneumaCult EX Plus (StemCell, 05040) during the expansion phase, according to manufacturer’s instructions. Then passaged into 6.5 mm Transwell inserts with a 0.4 um pore size (Corning, CLS3470-48EA) at a density of 100’000 cells/cm2 with 100 ul and 500 ul PneumaCult EX Plus in the apical and basal chambers respectively for further expansion. Upon confluence, medium in the apical chamber was removed and medium in the basal chamber was replaced by PneumaCult ALI (StemCell, 05001). Cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using a NucleoSpin RNA XS (Macherey-Nagel, 74090250) as per the manufacturer’s protocol.
TruSeq Stranded mRNA Library Prep kit

treatment_protocol: Lentiviral vectors for the inducible overexpression of ZNF676-3HA or LacZ-3HA were added to the medium in the apical chamber upon transition into transwells. Expression was induced with doxycycline.

value: Primary normal human bronchoepithelial cells (Lonza, CC-2540S) transduced with LacZ-3HA, replicate 3

tag: culture

value: PneumaCult EX Plus, then passaged into transwells, then PneumaCult ALI


title: NHBE_GFP_rep2

value: Primary normal human bronchoepithelial cells (Lonza, CC-2540S) transduced with LacZ-3HA, replicate 2


title: OP.41

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

data_processing:
QC with Fastqc and trimming with fastp
alignment of the reads with hisat 2
Counting reads to genomic features with featureCounts using Homo_sapiens.GRCh38.103.gtf as reference. Command: featureCounts -T 7 -p -s 2 -t transcript -g gene_name -a Homo_sapiens.GRCh38.103.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: central Amygdala

extract_protocol:
Amygdala samples from humans with OUD and unaffected controls were processed for total RNA isolation using the mirVana miRNA Isolation Kit (ThermoFisher Scientific, San Diego, CA, USA) and Zymo purification kit (Zymo Research, Irvine, CA, USA).
Libraries were prepared with the KAPA RNA HyperPrep Kit with RiboErase (Roche, Basel, Switzerland), which removes both cytoplasmic and mitochondrial ribosomal RNA (rRNA) species and uses random priming in cDNA synthesis, according to the manufacturer’s protocol. The rRNA-depleted libraries were subsequently sequenced on an Illumina Novaseq sequencer at 100-million-read target coverage (100 bp paired-end reads) at the Yale Center for Genome Analysis facility.

value: opioid use disorder (OUD)

value: Brain

tag: brain region

value: central Amygdala


title: BTBR-ob/ob-3g

description:
Slide-seqV2
Puck_191206_04

value: BTBR-ob/ob

value: early diabetic kidney disease


title: OP.40


title: NHBE_GFP_rep1

value: Primary normal human bronchoepithelial cells (Lonza, CC-2540S) transduced with LacZ-3HA, replicate 1


title: NHBE_ZNF676_rep3

value: Primary normal human bronchoepithelial cells (Lonza, CC-2540S) transduced with ZNF676-3HA, replicate 3


title: NHBE_ZNF676_rep2

value: Primary normal human bronchoepithelial cells (Lonza, CC-2540S) transduced with ZNF676-3HA, replicate 2


title: OP.42


title: BTBR-ob/ob-3f

description:
Slide-seqV2
Puck_191206_03


title: NHBE_ZNF676_rep1

value: Primary normal human bronchoepithelial cells (Lonza, CC-2540S) transduced with ZNF676-3HA, replicate 1


title: OP.39


title: DIPG4_DOX

value: SU-DIPG-IV

value: DOX


title: BTBR-ob/ob-3e

description:
Slide-seqV2
Puck_191206_02


title: 293T_ZNF728_IP

data_processing:
Alignement of reads was performed with bowtie2.
Filtering of bam files was performed using a blacklist fom UCSC and a greylist derived from TI using GreyListChIP Bioconductor package.
Peak calling for ChIP-seq was performed using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: A bed file containing the output of MACS2 peak calling is provided.

source_name: Transduced HEK293T human cell line

growth_protocol: HEK293T cells were cultured in DMEM (Gibco, 41966029) supplemented with 10% FCS and 1% penicillin/streptomycin/glutamine and passaged with Trypsin-EDTA (Gibco, 25200056) after a PBS wash. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
30 million cells per IP were collected and the chromatin was prepared and sonicated as described (Imbeault et al., 2017).  Total input samples (one per cell line) were collected. The IP was then performed with the anti‐HA.11 antibody (clone 16B12, Covance, MMS-101P) incubated overnight at 4°C on a rotating wheel, and captured using protein G Dynabeads (Thermo Fisher, 10004D). Samples then underwent 5-minute washes on a rotating wheel: twice in low salt buffer (10 mM Tris-HCl pH 8, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.15% SDS, 1x PMSF), once in high salt buffer (10 mM Tris-HCl pH 8, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1x PMSF), once in LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% NaDOC, 1x PMSF). TE buffer was then added to the beads and the supernatant was removed.  Beads were resuspended in elution buffer (TE buffer, 1% SDS, 150 mM NaCl), treated with Proteinase K (Thermo Fisher, AM2548) and decrosslinked overnight at 65°C and 1100 rpm. The DNA was then purified using a MinElute PCR Purification kit (Qiagen, 28004).
NextSeq v2.5 (with Illumina protocol #15048776)

treatment_protocol: HEK293T were transduced with lentiviral constructs coding for 3HA-tagged ZNF728 in the pTRE backbone and selected with puromycin. Cells were then cultured in doxycycline in order to induce expression of the construct.

value: HEK293T transduced with ZNF728-3HA, HA IP, replicate 1

value: DMEM + 10% FCS + penicillin/streptomycin/glutamine


title: OP.38


title: BTBR-ob/ob-3d

description:
Slide-seqV2
Puck_191206_01

value: kidney cross-section

value: 13 week


title: H1_input_S11

data_processing:
Alignement of reads was performed with bowtie2.
PCR duplicates in H1 cells were removed using the MarkDuplicates picard tool.
Filtering of bam files was performed using a blacklist fom UCSC and a greylist derived from TI using GreyListChIP Bioconductor package.
Peak calling for ChIP-seq was performed using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: A bed file containing the output of MACS2 peak calling is provided.

source_name: H1 human embryonic stem cells input

growth_protocol: HEK293T cells were cultured in DMEM (Gibco, 41966029) supplemented with 10% FCS and 1% penicillin/streptomycin/glutamine and passaged with Trypsin-EDTA (Gibco, 25200056) after a PBS wash. H1 hESCs (WA01) were purchased from WiCell and cultured on matrigel (BD, 354277) in mTeSR1 medium (StemCell, 85850). They were passaged using TrypLE (Gibco, 12604021) and the medium was supplemented with 10 uM Y-27632 (abcam, ab120129) during the first 24 hours after splitting. Both cell lines were maintained at 37°C with 5% CO2.

treatment_protocol: Both cell lines were transduced with lentiviral vectors stably overexpressing 3HA-tagged ZNF676 and selected respectively with puromycin or blasticidin. HEK293T were transduced with the construct in the pTRE backbone and subsequently treated with doxycycline to induce expression. H1 were transduced with the construct in the pRRL-IRES-Blast backbone.

value: H1 input

value: mTeSR1 medium (StemCell, 85850) on matrigel (BD, 354277). +10 uM Y-27632 (abcam, ab120129) during first 24 hours after passaging.


title: 293T_Input_S7

source_name: HEK293T human cell line input

value: HEK293T input


title: OP.37

value: opioid use disorder (OUD)

value: Brain


title: H1_ZNF676_rep3

source_name: Transduced H1 human embryonic stem cells

value: H1 transduced with ZNF676-3HA, HA IP, replicate 3


title: H1_ZNF676_rep2

value: H1 transduced with ZNF676-3HA, HA IP, replicate 2


title: BTBR-ob/ob-3c

description:
Slide-seqV2
Puck_191204_24

value: BTBR-ob/ob

value: early diabetic kidney disease


title: H1_ZNF676_rep1

value: H1 transduced with ZNF676-3HA, HA IP, replicate 1


title: OP.36

value: central Amygdala


title: 293T_ZNF676_rep2

value: HEK293T transduced with ZNF676-3HA, HA IP, replicate 2


title: RNA-Seq of HEK293 cells after knockdown of SP1, replicate 2


title: BTBR-ob/ob-3b

description:
Slide-seqV2
Puck_191204_23


title: OP.35


title: 293T_ZNF676_rep3

value: HEK293T transduced with ZNF676-3HA, HA IP, replicate 3


title: 293T_ZNF676_rep1

value: HEK293T transduced with ZNF676-3HA, HA IP, replicate 1


title: BTBR-ob/ob-3a

description:
Slide-seqV2
Puck_191204_22


title: OP.33


title: OP.34


title: BTBR-wt/wt-3g

description:
Slide-seqV2
Puck_191204_20

value: BTBR-wt/wt

value: control


title: A549_shMUT#2-1

city: NEW YORK

first: John

last: Blenis

state: NY

address: 413 E 69TH ST FL 13

institute: Weill Cornell Medicine

data_processing:
The “TopHat” algorithm was used to align the reads to the hg38 genome
The alignments (31.3-46.2 M aligned pairs) in the BAM files were further analyzed using the Cufflinks suite of programs (running consecutively: Cufflinks à Cuffcompare à Cuffdiff)
Cufflinks was run using the hg38-genes as a reference data base. By doing so, the output shows the known genes with their RNA-Seq metrics (as FPKM = Fragments Per Kilobase of exon model per Million mapped fragments), but novel transcripts are not identified. The 9 (3 x 3 replicates) cufflinks outputs were compared using cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: lung epithelial cells

growth_protocol: A549 cells were maintained in RPMI media supplemented with 10% FBS and penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using the PureLink RNA isolation kit (Life Technologies) and contaminant DNA was digested with DNAse I (Amplification grade, Sigma-Aldrich)
"Active Motif" processed 1 µg of total RNA (RIN values all 10.0) to obtain polyA RNA. The TruSeq RNA Sample Preparation v2 Guide protocol was followed (Illumina, Part # 15026495 Rev. F) as per the manufacturer indications.
Libraries were sequenced on Illumina NextSeq 500 as paired-end 42-nt reads, to a depth of 34.0 – 49.0 M read pairs

treatment_protocol: Cellswere transduced with lentivus with shGFP, shMUT#1 and shMUT#2

tag: cell line origin

value: non-small cell lung cancer

value: shMUT#2 for 10 days


title: BTBR-wt/wt-3f

description:
Slide-seqV2
Puck_191204_18

value: kidney cross-section

value: 13 week


title: A549_shMUT#2-2

tag: treatment


title: OP.32

value: opioid use disorder (OUD)

tag: tissue


title: A549_shMUT#1-3

value: shMUT#1 for 10 days


title: A549_shMUT#1-2


title: OP.31

value: Brain


title: A549_shGFP-3

value: shGFP for 10 days


title: A549_shMUT#1-1


title: A549_shGFP-2


title: BTBR-wt/wt-3d

description:
Slide-seqV2
Puck_191204_16


title: 293T_ZNF728_TI

source_name: 293T human cell line input

value: HEK293T input

value: DMEM + 10% FCS + penicillin/streptomycin/glutamine


title: O30


title: BTBR-wt/wt-3c

description:
Slide-seqV2
Puck_191204_15


title: shPRMT1_H3K27ac-IP_Rep1

data_processing:
ChIP-seq data were processed with the ChiLin pipeline (code version 2.0, db version 1.0) in simple mode using bwa to align to the hg38 human reference genome and MACS2 to call peaks, using the ‘narrow’ setting. For each condition, two replicate IP samples were processed along with their corresponding input DNA controls.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files generated for each replicate using ChiLin pipeline.

growth_protocol: LNCaP cells were grown in RPMI supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, 2 mM L-glutamine, and 100 ug/mL Normocin (Invivogen).

extract_protocol:
10 million cells were fixed using 1% formaldehyde (Thermo Fisher Scientific, BP531-25) for 10 minutes at room temperature followed by quenching with 125 mM glycine (Sigma-Aldrich, #50046). Cells were rinsed twice with PBS and resuspended in 1 mL lysis buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitor cocktail (Roche, #11836170001). Chromatin was sheared to 200-500 base pairs using a Covaris E220 sonicator and cleared by centrifugation for 15 minutes at 19,000 x g. Antibodies (AR, 9 μg, Abcam, ab74272; H3K27ac, 1 μg, Diagenode, C15410196) were incubated with 40 μL of protein A/G Dynabeads (Thermo Fisher Scientific, #10002D, #10003D) for at least 6 hours at 4°C before overnight incubation at 4°C with sonicated chromatin. Chromatin-bead complexes were washed 5 times with 1 mL LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and rinsed twice with 1 mL TE buffer (10 mM Tris pH 7.5, 0.1 mM EDTA). Immunoprecipitated chromatin was resuspended in 100 μL elution buffer (100 mM NaHCO3, 1% SDS) and treated with RNase A (Thermo Fisher Scientific, #12091021) for 30 minutes at 37°C. Crosslinks were reversed in the presence of proteinase K (Thermo Fisher Scientific, #25530049) for 16 hours at 65°C, and the eluted DNA was purified using a MinElute PCR Purification Kit (QIAGEN, #28006).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (NEB, #E7645).

treatment_protocol: For samples with PRMT1 knockdown, LNCaP cells were lentivirally transduced with pLKO.5 encoding an shRNA targeting either LacZ or PRMT1 and selected on puromycin. For samples with small-molecule PRMT1 inhibition, LNCaP cells were treated with DMSO or furamidine (8 μM).

value: H3K27ac, Diagenode, C15410196

value: LNCaP


title: O28

value: central Amygdala


title: O29


title: A549_shGFP-1


title: shPRMT1_H3K27ac-INPUT_Rep2


title: BTBR-wt/wt-3e

description:
Slide-seqV2
Puck_191204_17


title: shPRMT1_H3K27ac-INPUT_Rep1


title: BTBR-ob/ob-4a

description:
Slide-seqV2
Puck_191223_08

value: BTBR-ob/ob

value: early diabetic kidney disease


title: BTBR-wt/wt-3a

description:
Slide-seqV2
Puck_191204_13

value: BTBR-wt/wt


title: A549_shMUT#2-3


title: WT 3

city: Bethesda

first: Natalie

last: Porat-Shliom

state: MD

address: Building 10, Room 12C207 MSC 1

department: Thoracic and GI Malignancies Branch

institute: National Cancer Institute

data_processing:
Basecalling was performed using RTA version 2.11.3
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Mapping to the mouse genome mm9 was performed using STAR 2.7.0f
Counting was done using RSEM package 1.3.1
Genome_build: mm9
Supplementary_files_format_and_content: Comma-separated text file containing counts for all samples

source_name: Liver

extract_protocol:
Mice were anesthetized using 2% isoflurane and subsequently sacrificed using cervical dislocation. The left lobe of the liver was collected from three mice per group and snap-frozen in liquid nitrogen. ~20 mg per sample was homogenized using a TissueLyser II (Qiagen) and total RNA using the Qiagen RNeasy Mini Kit (#74104). The RNA yield was determined using a High-sensitivity RNA ScreenTape Analysis (Agilent) on an Agilent TapeStation Instrument. This analysis was done by the Center for Cancer Research (CCR) Genomics Core. Samples with a RIN > 8.0 were sent for bulk mRNA sequencing.
Sequencing was done by the CCR Sequencing Facility at the Frederick National Laboratory for Cancer Research. Briefly, the TruSeq mRNA library kit (Illumina) was used to prepare the mRNA library following the manufacturer’s instructions. 200ng of total RNA was used as the input to an mRNA capture with oligo-dT coated magnetic beads. The mRNA was fragmented, and then a random-primed cDNA synthesis was performed. To prepare the library, the resulting double-strand cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed. The final purified product was then quantitated by qPCR before cluster generation and sequencing. Six mRNA-Seq samples were pooled and sequenced on NextSeq using paired-end sequencing and a read length of 76 (2 x 76 cycles).

treatment_protocol: Three 6 weeks old wild type (WT) and 3 LKB1 fl/fl mice were injected with AAV8 Cre

value: Liver

tag: strain

value: normal


title: shPRMT1_AR-IP_Rep1

value: AR, Abcam, ab74272


title: O26


title: WT 2


title: P11056_1031

source_name: EAE

tag: cell type


title: shPRMT1_H3K27ac-IP_Rep2


title: O25


title: shPRMT1_AR-INPUT_Rep2


title: shPRMT1_AR-IP_Rep2


title: WT 1


title: KO 3

value: LKB1 knock out


title: O24


title: BTBR-ob/ob-2i

description:
Slide-seqV2
Puck_191204_12

source_name: kidney

value: kidney cross-section

value: 13 week


title: O27

value: opioid use disorder (OUD)


title: shLacZ_H3K27ac-IP_Rep2

value: shLacZ


title: O23

value: Brain


title: BTBR-ob/ob-2e

description:
Slide-seqV2
Puck_191204_05


title: O22


title: KO 2


title: BTBR-ob/ob-2f

description:
Slide-seqV2
Puck_191204_07


title: BTBR-wt/wt-3b

description:
Slide-seqV2
Puck_191204_14

value: control


title: BTBR-ob/ob-2d

description:
Slide-seqV2
Puck_191204_04


title: KO 1


title: C.21

value: Unaffected


title: shLacZ_H3K27ac-INPUT_Rep2


title: shLacZ_H3K27ac-INPUT_Rep1


title: BTBR-ob/ob-2b

description:
Slide-seqV2
Puck_191204_03


title: BTBR-ob/ob-2a

description:
Slide-seqV2
Puck_191112_08


title: shLacZ_AR-IP_Rep2


title: BTBR-ob/ob-2g

description:
Slide-seqV2
Puck_191204_08


title: BTBR-ob/ob-2h

description:
Slide-seqV2
Puck_191204_09


title: C19


title: BTBR-wt/wt-2b

description:
Slide-seqV2
Puck_191112_02


title: C16


title: BTBR-wt/wt-2e

description:
Slide-seqV2
Puck_191112_13


title: shLacZ_H3K27ac-IP_Rep1

value: H3K27ac, Diagenode, C15410196


title: C.18


title: BTBR-wt/wt-2a

description:
Slide-seqV2
Puck_191112_04


title: C13


title: BTBR-ob/ob-1d

description:
Slide-seqV2
Puck_191109_20


title: C17


title: shLacZ_AR-IP_Rep1

value: LNCaP


title: Furamidine_H3K27ac-IP_Rep2

value: Furamidine


title: BTBR-wt/wt-2d

description:
Slide-seqV2
Puck_191112_07


title: C20

value: central Amygdala


title: shLacZ_AR-INPUT_Rep1


title: C15


title: BTBR-ob/ob-1c

description:
Slide-seqV2
Puck_191109_19

value: BTBR-ob/ob

value: early diabetic kidney disease


title: shPRMT1_AR-INPUT_Rep1


title: Furamidine_H3K27ac-IP_Rep1


title: Furamidine_H3K27ac-INPUT_Rep1


title: BTBR-wt/wt-2c

description:
Slide-seqV2
Puck_191112_05

value: BTBR-wt/wt


title: C.12


title: BTBR-ob/ob-1b

description:
Slide-seqV2
Puck_191109_18


title: Furamidine_AR-IP_Rep2


title: BTBR-ob/ob-1a

description:
Slide-seqV2
Puck_191109_14


title: C11


title: Furamidine_AR-IP_Rep1


title: C.10


title: Furamidine_AR-INPUT_Rep2


title: BTBR-wt/wt-1e

description:
Slide-seqV2
Puck_191109_10


title: C14


title: C.9


title: Furamidine_AR-INPUT_Rep1


title: BTBR-wt/wt-1c

description:
Slide-seqV2
Puck_191109_08


title: DMSO_H3K27ac-IP_Rep2

value: DMSO


title: BTBR-wt/wt-1d

description:
Slide-seqV2
Puck_191109_09


title: C8


title: BTBR-wt/wt-1a

description:
Slide-seqV2
Puck_191109_06


title: BTBR-wt/wt-1b

description:
Slide-seqV2
Puck_191109_07


title: C.7


title: DMSO_H3K27ac-INPUT_Rep2


title: Furamidine_H3K27ac-INPUT_Rep2


title: C.5


title: C.4


title: DMSO_H3K27ac-INPUT_Rep1


title: DMSO_H3K27ac-IP_Rep1


title: DMSO_AR-IP_Rep2

value: AR, Abcam, ab74272


title: COM3

city: San Francisco

first: Xin

last: Chen

state: CA

address: 513 Parnassus St.

department: Bioengineering and Therapeutic Sciences

institute: UCSF

data_processing:
Original image data file from high-throughput sequencing platforms (Illumina Novoseq 6000) is transformed to Raw Reads by CASAVA base recognition.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the  reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses  sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. So it's necessary to filter the raw reads and get the clean reads. The filtering process is as follows:(1) Remove reads containing adapters.(2) Remove reads containing N > 10% (N represents the base cannot be determined).(3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Gene read counts were in Ensemble ID and converted to Entrez ID using the Bioconductor Package Maintainer org.Mm.eg.db, version 3.8.2. Duplicated and not annotated genes were removed. Data were filtered out with genes with row means less than 5.
The edgeR package was used for the fpkm calculation, data normalization, and differentially expressed genes identification. Differentially expressed genes were limited  by a p-value of 0.05 and FDR (False Discovery Rate) of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM data for every gene and every sample

extract_protocol:
Liver tissues were flash frozen on dry ice. RNA was extracted using the Zymo Quick-RNA Miniprep Kit (Cat# D7001, Zymo Research, Irvine, CA), followed by quantification with Nanodrop. The RNA quality control was determined using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA) and the Bioanalyzer (Agilent Technologies, Santa Clara, CA UAS).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: TVB3664 (10mg/kg/day), cabozantinib (60mg/kg/day), cabozantinib (60mg/kg/day) + TVB3664 (10mg/kg/day), or vehicle was orally administered via gavage. One cycle of treatment includes 6 consecutive dosing days and 1 day of washout. Mice were sacrificed after 3 cycles of treatment.

value: FVB/N

value: HCC induced by loss of PTEN and c-MET overexpression

value: Cabozantinb and TVB3664


title: COM4


title: COM2


title: C.2


title: DMSO_AR-IP_Rep1


title: HEK293T ZNF728

data_processing:
Alignement of reads was performed with bowtie2.
Peak calling for ChIP-seq was performed using MACS. A previously published composite total input file derived from multiple ChIP-exo experiments (Imbeault et al., 2017) was used as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED files from MACS output

growth_protocol: Human embryonic kidney-derived HEK293T cells were maintained in Dulbecco's modified Eagle's complete medium supplemented with 10% fetal bovine serum, 0.29 mg/ml L-glutamine, and 100 U/ml penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
ChIP-exo was performed as described (Imbeault et al., 2017).
NextSeq v2.5 (with Illumina protocol #15048776)

treatment_protocol: Transduced cell lines were selected using puromycin (1 ug/ml) for 7 days and induced using doxycyclin (1 ug/ml) for a few days before fixation with formaldehyde (1% for 10 min).

value: HEK293T transduced with ZNF728-3HA, HA IP, exonuclease treated

value: DMEM + 10% FCS + penicillin/streptomycin/glutamine


title: COM1


title: DMSO_AR-INPUT_Rep2


title: C.1

value: Brain


title: HEK293T ZNF676

value: HEK293T transduced with ZNF676-3HA, HA IP, exonuclease treated


title: TVB4


title: DMSO_AR-INPUT_Rep1


title: TVB3


title: NC_ADIPOSE1228

city: Guangzhou

first: Pengsen

last: Wu

address: NO. 54, Xianlie Road (South), Yuexiu District

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
The Illumina output was processed using Cell Ranger 3.0.2 (10×Genomics, CA, USA).
Cells of sufficient complexity were clustered and t-distributed stochastic neighbor embedding (t-SNE) plots were generated for visualization using the Seurat R package (31).
Genome_build: hg19
Supplementary_files_format_and_content: nCount_RNA, nFeature_RNA, barcode information of TAO and control sample.

source_name: orbital adipose tissue

extract_protocol:
Following Gel Beads-in-emulsion (GEMs) generation, the Gel Bead is dissolved, primers are released, and any copartitioned cell is lysed. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA.
RNA was then reverse-transcribed into cDNA libraries using a 10x Genomics Chromium machine following the manufacturer’s instructions.
DNA sequencing was performed on a NovaSeq 6000 Sequencing System (Illumina, CA, USA) using a paired-end 150 sequencing mode.

treatment_protocol: Single cells were isolated and lysed with collagenase buffer composed of 5 mg/mL collagenase IV and 10 U/mL DNase Ⅰ at 37°C for 50 minutes (all from Sigma-Aldrich, St. Louis, USA). Subsequently, filtration and red blood cell removal were performed using the MACS Dead Cell Removal Kit (Miltenyi Biotec, Bergisch Gladbach, Germany).

value: derived from healthy control patient

value: orbital adipose tissue


title: 5-8F-shHDAC4-2

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

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 Homo_sapiens.GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DESeq software was used to calculate the RPKM
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).  Data in processed data files were from alignment to UCSC hg19.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: nasopharyngeal carcinoma cell lines

growth_protocol: 10% FBS in DMEM

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions

value: nasopharyngeal carcinoma cell lines

tag: passages


title: 5-8F-shHDAC4-1


title: TVB2


title: 5-8F-Scr

description: shRNA-NC

value: scramble


title: TGFb_T3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Genome_build: hg19
Supplementary_files_format_and_content: Text files include raw gene counts for every gene and every sample，FPKM values for each Sample，differential expressed genes between TGFb group and control group.

source_name: orbital connective tissue

growth_protocol: Orbital adipose/connective tissue was minced into 1–2 mm3 pieces, and placed in 10–cm culture dishes containing high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum and 1% penicillin/streptomycin (all from Gibco Laboratories, New York, USA), and incubated at 37°C with 5% CO2. Culture medium was renewed every 3–4 days. After the cells migrated out of the tissue pieces, OFs were passaged with standard trypsinization techniques when reaching 90% confluence. After passaging, the cells were grown in proliferation medium (DMEM supplemented with 10% FBS and 1% penicillin/streptomycin) using standard cell culture protocols.

extract_protocol:
Following the manufacturer’s instructions, the total RNA was extracted from cultured cells using the RNA Purification Kit (Accurate Biology, Hunan, China).
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The TGFb group were treated with TGFβ1 for 24 hours

value: orbital connective tissue derived orbital fibroblasts

value: treated with TGFβ1 for 24 hours

value: derived from thyroid associated ophthalmopathy patient


title: TVB1


title: C.6

value: Unaffected

value: central Amygdala


title: TGFb_T2


title: CAB4

value: Cabozantinb


title: Sample 16 tp_skin_1

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

data_processing:
Read alignment and gene counting with single-cell resolution were performed with CellRanger v3.0.0 (10x Genomics, Inc), using the default parameters and the pre-built human reference v3.0.0 (10x Genomics, Inc) based on Ensembl GRCh38 release 93.
Genome_build: GRCh38 (Ensembl release 93)
Supplementary_files_format_and_content: Cellranger compressed files contains the filtered UMI counts matrix (Market Exchange Format for sparse matrices) and TSV files with genes and barcode sequences (corresponding to row and column indices respectively) as output by Cell Ranger. Snpclust compressed files contain all output from snpclust (https://github.com/10XGenomics/single-cell-3prime-snp-clustering).

source_name: skin derived

extract_protocol:
Skin cells were isolated from 4 mm punch biopsies from the breast and / or abdomen following a standardized digestion protocol with the gentleMACS™ Dissociator and a whole skin dissociation kit containing enzyme A and D (both Miltenyi Biotec). They were then FACS-sorted for live (Hoechst 33258 negative or propidium iodide negative) CD45+ lymphocytes.
Libraries were constructed with the Chromium Single Cell 3' Reagents v2 (10x Genomics, Inc). The libraries were sequenced with the Illumina HiSeq 4000 (Illumina, Inc.) according to the manufacturer’s instructions, with 150-bp and 100-bp length for healthy donor samples and allo-HSCT patient samples, respectively.

tag: donor

tag: health state

value: allo-hsct

tag: cd45 status

tag: gating

value: lmphocytes


title: TGFb_T1

tag: disease state


title: Sample 15 tp_blood_1

source_name: blood derived

extract_protocol:
Fresh peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation of blood using Biocoll (Merck). Live CD45+ lymphocytes (clone 2D1, Biolegend) were sorted (BD FACSAria Fusion, BD Biosciences) to a purity of over 98% after preincubation with Human TruStain FcX (Biolegend).
Libraries were constructed with the Chromium Single Cell 3' Reagents v2 (10x Genomics, Inc). The libraries were sequenced with the Illumina HiSeq 4000 (Illumina, Inc.) according to the manufacturer’s instructions, with 150-bp and 100-bp length for healthy donor samples and allo-HSCT patient samples, respectively.


title: CAB3

value: FVB/N

value: HCC induced by loss of PTEN and c-MET overexpression


title: Input for ChIP, replicate 2

data_processing:
ChIP-seq analysis was performed essentially as described previously (Schmitages F. et al. 2016. Genome Research).   Illumina adaptor sequences were removed from the 3′ ends of 51-nt reads, and the remaining reads were mapped to the human genome hg19 using Bowtie 2 with default settings.
After removal of duplicate reads, peaks were called jointly on immunoprecipitated and input samples with MACS2 (version 2.1.2).
We identified motifs using the sequence of the +250 bp region around the top 500 peak summits using MEME-ChIP with the following setting: -dna -meme-nmotifs 5 -meme-mod anr -meme-p 8 -dreme-e 0.05 -meme-minw 6 -meme-maxw 20 -meme-minsites 100.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing summit peaks generated with MACS2

source_name: Human embryonic kidney cells

growth_protocol: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

extract_protocol:
ChIP (Chromatin Immunoprecipitation) was performed as previously described (Najafabadi et al., Nat. Biotechnol. (2015)). Briefly, ~20 million HEK293 cells were crosslinked in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). SP1 was immunoprecipitated from the lysate with 10ug of Sp1 antibody (Santa Cruz) and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP-seq library kits (Illumina) according the manufacturer's instructions followed by PCR amplification and agarose gel size selection.

treatment_protocol: Wild-type HEK293 cells were cross-linked for 10 min in 1% formaldehyde.

tag: cell line

value: no antibody used for input samples


title: CTRL_T3

value: untreated


title: C.3

value: Brain


title: Sample 14 hd_skin_1

value: healthy


title: CAB2


title: CTRL_T2


title: eWAT_HFD_WT, mixed samp

city: Shanghai

first: Jiqiu

last: Wang

address: No. 197, Ruijin 2nd Road

department: Endocrinology and Metabolism

institute: Ruijin Hospital

description: Gene expression data from eWAT of mice under HFD diet

hyb_protocol: The procedure was performed according to the manufacturer's instructions.

data_processing: The data were analyzed with Partek GS 6.5.

label: biotin

source_name: male mice_eWAT, HFD diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: 50 mg eWAT samples were collected from 2-month-old mice under chow diet (n=3) and 6-month-old mice under HFD  (n=3), respectively.

extract_protocol: 3 samples form the same group were mixed together for RNA extraction. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HFD was initiated from 2 month old and lasting for 4 months.

value: eWAT

tag: genotype

value: WT

tag: age

value: 6 month

tag: Sex

value: male

value: high-fat diet


title: Sample 13 hd_blood_1


title: CAB1


title: Input for ChIP, replicate 1

tag: antibody


title: CTRL_T1

value: orbital connective tissue derived orbital fibroblasts

value: derived from thyroid associated ophthalmopathy patient


title: eWAT_chow_KO, mixed samp

description: Gene expression data from eWAT of mice under chow diet

scan_protocol: The procedure was performed according to the manufacturer's instructions.

source_name: male mice_eWAT, chow diet

value: Lgr4 KO

value: 2 month

value: chow diet


title: ChIP of SP1, replicate 2

value: Sp1 monoclonal antibody (SANTA CRUZ  Biotechnology)


title: eWAT_HFD_KO, mixed samp


title: Win1_shScramble_rep3

data_processing:
Reads were mapped to the human genome (hg19) using Hisat v2.1.0 with options -k 5 --seed 42 -p 4 -x
Counts of reads on genes and TEs were computed using FeatureCounts with options -p -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain read counts on genes or TEs

source_name: Win1 naive embryonic stem cells

growth_protocol: Win1 naive hESCs were obtained from the Whitehead Institute (Theunissen et al. 2014) and cultured in 4i/L/A on gelatin (Millipore, ES-006-B) and DR4+ MEF feeders. MEF feeders were produced from irradiation-inactivated passage 1 DR4+ mouse embryonic fibroblasts cultured in DMEM with 15% FCS, 1% penicillin/streptomycin/glutamine (Thermo Fisher, 10378016), 1x non essential amino acids (Thermo Fisher, 11140035), 1 mM sodium pyruvate (Sigma, S8636) and 0.1 mM beta-mercaptoethanol (Thermo Fisher, 31350010).

extract_protocol:
RNA was extracted with a High Pure RNA Isolation kit (Roche, 11828665001) according to manufacturer’s instructions.
TruSeq Stranded mRNA Library Prep kit (Illumina, 20020594)

treatment_protocol: Lentiviral vectors coding for an shRNA against ZNF676 (TRCN0000107578) in the pLKO backbone were used to transduce Win1 cells in suspension. Selection with puromycin (0.25 ug/ml) was performed.

value: Embryo-derived Win1 naive human embryonic stem cells transduced with pLKO-shScramble, replicate 3


title: ChIP of SP1, replicate 1


title: VEH4

value: FVB/N

value: HCC induced by loss of PTEN and c-MET overexpression

value: Vehicle


title: Win1_shScramble_rep2

value: Embryo-derived Win1 naive human embryonic stem cells transduced with pLKO-shScramble, replicate 2


title: TAOADIPOSE1123

value: derived from active TAO patient

value: orbital adipose tissue


title: Win1_shScramble_rep1

value: Embryo-derived Win1 naive human embryonic stem cells transduced with pLKO-shScramble, replicate 1


title: VEH2


title: Sample 4_day9_batch2

city: Ann Arbor

first: Xufeng

last: Xue

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering

institute: University of Michigan

data_processing:
Illumina NovaSeq-6000 for basecalling
10x Genomics Cell Ranger pipeline (version 3.1.0) for barcoding, alignment, filtering
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix. RDS file is generated using Seurat, including integrated data of day4, day9 and day21 from batch 1.

source_name: hESC-derived neural tube-like structure

extract_protocol:
microfluidic neural tube-like structures were dissociated into single cells using accutase. Dissociated cells were then lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v2). The libraries were sequenced on Illumina NovaSeq-6000 with paired-end sequencing (One sample per flow cell).

tag: timepoint

tag: batch


title: Sample 2_day9_batch1


title: Win1_shZNF676_rep3

value: Embryo-derived Win1 naive human embryonic stem cells transduced with pLKO-shZNF676, replicate 3


title: VEH1

tag: treatment


title: rosa26cre_batch3_sample_41

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

hyb_protocol: 3.8 µg fragmented and labeled sense-strand single-stranded cDNA were hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays for 16 h at 45 °C and 60 rpm in an Affymetrix GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: The .CEL files were read into R (version 3.5.1) using the package oligo. Data normalization was performed per batch, with the RMA algorithm. Samples from the three batches were then combined and batch effect was corrected using the ComBat function from the sva package.

label: Biotin

label_protocol: The Affymetrix GeneChip Whole Transcript (WT) PLUS Reagent Kit Protocol was used for the preparation of biotinylated sense-strand single-stranded cDNA from 200ng of total RNA, followed by an enzymatic fragmentation and terminal labeling with biotin.

extract_protocol: Fresh tumor tissues were isolated and fresh frozen. Afterwards, total RNA was extracted using  RNeasy Mini Kit (Quiagen) following the manufacturer’s suggested protocol. Genomic DNA was removed using a gDNA eraser step.

tag: localization

value: intracranial

tag: localization details

value: lateral, trigeminal

tag: age (weeks)

tag: tumor classification

value: MYC


title: Sample 1_day4


title: Win1_shZNF676_rep2

value: Embryo-derived Win1 naive human embryonic stem cells transduced with pLKO-shZNF676, replicate 2


title: rosa26cre_batch3_sample_40

value: brain, subventricular zone

value: SHH


title: FVB3

tag: strain

tag: tissue

value: Normal liver tissue

value: Negative control, No treatment


title: FVB2


title: FVB1


title: Win1_shZNF676_rep1

value: Embryo-derived Win1 naive human embryonic stem cells transduced with pLKO-shZNF676, replicate 1


title: eWAT_chow_WT, mixed samp

value: eWAT

value: WT

value: 2 month

value: male

value: chow diet


title: PD004 Chromatin accessibility

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

institute: Karolinska Institutet

data_processing:
Nuclei were isolated from two 10mg fresh-frozen human grey matter brain samples (collected under the Imperial College Research Ethics Committee ICREC_14_2_11), using Nuclei Pure Prep Nuclei Isolation Kit (Sigma Aldrich) with the following modifications. The tissue was lysed in Nuclei Pure Lysis Solution with 0.1% Triton X, 1mM DTT and 0.4U/ul SUPERase-In™ RNase Inhibitor (ThermoFisher Scientific) freshly added before use, and homogenized with the help first of a 23G and then of a 29G syringe. Cold 1.8M Sucrose Cushion Solution, prepared immediately before use with the addition of1mM DTTand 0.4U/ul RNase Inhibitor, was added to the suspensions before they were filtered through a 30μm strainer. The lysates were then carefully and slowly layered on top of 1.8M Sucrose Cushion Solution previously added in new Eppendorf tubes. Samples were centrifuged for 45 minutes at 16000xg at 4°C. Pellets were re-suspended in Nuclei Storage Buffer with RNase Inhibitor, transferred in new Eppendorf tubes and centrifuged twice for 5 minutes at 500xg at 4°C. Finally purified nuclei were re-suspended in Nuclei Storage Buffer with RNase Inhibitor, stained with trypan blue and counted using Countess II (Life technology). After count, nuclei permeabilization was carried out following the demonstrated protocol for single cell multiome ATAC + Gene Expression sequencing from 10x Genomics. A total of 12,000 estimated nuclei from each sample was used for the transposition step and then loaded on the Chromium Next GEM Single Cell Chip J. ATAC library and gene expression library construction was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions. Libraries were sequenced using Illumina NovaSeq 6000 System and NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles), aiming at a minimum sequencing depth of 30K reads/nucleus.
Single cell multiome human (10X Genomics) data samples were processed with default parameters with cellranger-arc (v2.0.0) count function. Reads were aligned to GRCh38 (refdata-cellranger-arc-GRCh38-2020-A-2.0.0) reference genome. Which resulted for each sample PD003 and PD004 of a median fragments per cell of 21422/22379, median UMI counts per cell of 7407/8189, median genes per cell of 2972/3268 and 5272/4513 cells.
Normalized single feature-barcode matrix combining the two individuals from both modalities was calculated with the parameter cellranger-arc aggr with default parameters, samples were normalized to depth for both ATAC and gene expression modalities. We used Cellranger-arc called peaks for preQC measurements. After QC we run macs2 whithin Seurat/Signac to call the peaks, to recover consistent peak set within the whole dataset. For downstrean analyses we combined Signac v1.4.0 and Seurat v4.0.0 joint RNA and ATAC analysis. We used as QC metrics nCount_ATAC < 100000 & nCount_RNA < 100000 & nCount_ATAC > 1000 & nCount_RNA > 1000 & nucleosome_signal < 2 & TSS.enrichment > 1, which resulted in a total 4194 and 3670 cells from each individual sample.
Dimension reduction and Findclusters was performed same as for single cell multiome mouse data. Samples were integrated using Harmony on the patient variable. Cells were annotated using a panel of canonical markers for main brain cell types; 'PLP1','MAG','MOG','OPALIN' for Oligocendrocytes. 'PDGFRA','SOX6','BCAN' for OPCs. 'FGFR3','GFAP','SLC14A1','AQP4' for Astrocytes. 'P2RY12','SPP1','CSF1R','IRF8' for Microglia. 'SLC17A7','FEZF2','RORB' for Excitatory Neurons. 'GAD1','ADARB2','LHX6' for Inhibitory Neurons. 'CLDN5','FLT1','EPAS1', 'EPS8','LAMA2' for Endothelial and Stromal cells. In order to get clear celltypes on the ATAC called peaks we discarded combinations of canonical markers from different main celltypes from the RNA expression. We then called peaks using MACS2 grouped by defined celltype.
Peak to gene interaction were predicted based on co-accessibility and expression from identified celltypes using R package ArchR.
Genome_build: hg38
Supplementary_files_format_and_content: Output files from cellranger-arc (v2.0.0), filtered feature matrix h5 file, filtered expression matrix h5 file,  called ATAC fragments for both samples.  Wig signal files for each identified celltype in each sample and both combined. Due to different number of cells in each celltype cluster, the wig files were built with a maximun of randomly selected 200 cells from each type. Predicted peak to gene interactions for each celltype, based on co-accessibility and expression as bedpe format. Bed file of identified celltype peaks. Processed data R object (.rds R.4.1.0) Signac 1.4.0/Seurat 4.0.5 used in the study.
Supplementary_files_format_and_content: Interactions pek2gene in .bedpe format.

source_name: Brain gray matter

extract_protocol:
Mice were sacrificed with a ketaminol/xylazine intraperitoneal injection followed by intracardiac perfusion with PBS where after spinal cords were collected and dissociated using the adult brain dissociation kit (130-107-677, Miltenyi) following manufacturer’s instructions. Instead of myelin debris removal (Miltenyi), Percoll (Cytiva 17-0891-01) mixed with HBSS was used to generate a percoll gradient of 38% to remove myelin debris.
Immediately after dissociation, cells were stained with DAPI and sorted on a FACS Aria III cell sorter (BD Biosciences). Sox10GFP+/DAPI- cells were collected in PBS + 0.5% BSA. The pool of cells was then lysed and washed according to the Demonstrated Protocol: Nuclei Isolation for Single cell ATAC Sequencing (10x Genomics) with modifications from the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (10x Genomics)  as follows: the cells were centrifuged for 10 minutes at 300xg and 4°C, resuspended in ATAC lysis buffer (containing 0.01% IGEPAL (CA-630), 0.01% Tween-20, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and incubated on ice for 3 minutes. After the incubation, wash buffer (containing 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) was added on top without mixing and the nuclei were centrifuged for 5 min at 500xg and 4°C. Nuclei were washed once in Diluted Nuclei buffer (10x Genomics) containing 1% BSA, 1 mM DTT and 1 U/ul RNase inhibitor, and incubated for 60 minutes at 37°C in tagmentation mix (10x Genomics). The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression v1 Chemistry was used to create single nuclei ATAC and RNA libraries from the same cell. Two EAE and two CFA-Ctr animals were used for independent replicates. Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-24-49 read set-up for ATAC (minimum 25 000 read pairs per cell) and a 28-10-10-90 read set-up for RNA (minimum 20 000 read pairs per cell).
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

treatment_protocol: For the induction of EAE, the mouse model of MS, animals were injected subcutaneously with an emulsion of MOG35-55 peptide in complete Freud’s adjuvant (CFA; EK-2110 kit from Hooke Laboratories) followed by intraperitoneal injection with pertussis toxin in PBS (200 ng per animal) on the day of immunization and with 24 hours delay (according to manufacturer’s instructions). Control animals underwent the same treatment, but CFA without MOG35-55 peptide (CK-2110 kit from Hooke Laboratories) was used instead. Spinal cord and brains were collected at the peak of the disease when clinical score 3 has been reached, which corresponds to limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analyzed in this study.

tag: condition

value: Ctrl

value: Chromatin accessibility


title: P60_Sup_3

first: Malcolm

last: Low

address: 1000 wall street

department: Molecular & Integrative Physiology

data_processing:
We checked the quality of the raw reads data for each sample using FastQC (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We aligned reads to the reference genome (UCSC mm10) , using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
We ran differential expression analysis using HTSeq/DESeq2, with UCSC mm10.fa as the reference genome sequence
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hypothalamus

extract_protocol:
Mice (Pomc-CreER; ROSA26eGFP-L10a) were euthanized and decapitated. Brain was removed from the skull and the arcuate nucleus was isolated from a 2-mm thick coronal slices using a brain matrix. Tissues were then homogenized and the subsequent tissue lysate was subjected to immunopurification steps
The ribo-depletion kit (RiboGone, Takara, CA) and SMARTer Stranded total RNA sample prep kit were used to remove excess ribosomal RNA and synthesize cDNA library.

value: hypothalamus

value: postnatal day 60

tag: molecule subtype

value: ribo-depleted mRNA


title: P60_PD_3


title: PD004 Expression

value: Expression


title: 190426Mk3_Ifng

description: ATACseq (Buenrostro et al., 2013)

data_processing:
Bulk ATAC-seq reads were trimmed and aligned with Bowtie2 with TN5 shifted tagAlign for ATAC pipeline. Aligned reads were filtered and duplicates removes (CutAdapt mark duplicates), more detail Kundaje Lab pipeline. Peaks were called with MACS2, with specific parameters for ATAC-seq peak calling (TN5 shifted tagAlign for ATAC pipeline). Peaks signal files, the wig files, were normalize to total number of reads per sample with DeepTools in order to visualize them.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ATAC-seq peaks signal in wig files normalized to total read count.

source_name: Sox10GFP+ OPCs

growth_protocol: Brains from P4-P6 mouse pups were collected and dissociated with the neural tissue dissociation kit (P; 130-092-628, Miltenyi). OPCs were obtained by either FACS with Sox10GFP+ selection or by MACS with CD140a microbeads (Cd140a microbead kit, 130-101-547, Miltenyi). For each experiment, multiple brains were pooled to obtain a sufficient number of cells. Cells were seeded on poly-L-lysine (P4707, Sigma) coated plates and grown with OPC proliferation media consisting of DMEM/F12, GlutaMAX (10565018, ThermoFisher Scientific), N2 supplement (17502001, ThermoFisher Scientific) NeuroBrew 21 (130-097-263, Miltenyi), penicillin-streptomycin (15140122, ThermoFisher Scientific), PDGFaa (10ng/ml, 315-17, PeproTech) and bFGF (20ng/ml, 100-18B, PeproTech).

extract_protocol:
Cells were harvested by TrypLE incubation at 37°C for 5 minutes, collection in cell culture medium and washing in PBS.
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor adaptations. Primary OPCs were incubated with TrypLE () at 37°C for 5 minutes and collected in cell culture media. 60,000 cells per condition were washed with PBS and lysed with lysis buffer (containing 0.1% IGEPAL (CA-630), 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and centrifuged for 20 minutes at 500xg and 4°C. Cells were then resuspended in tagmentation mix (dH2O, 2x TD buffer (Wang et al., 2013) and Tn5 enzyme (Picelli et al., 2014)) for 30 minutes at 37°C. The DNA was purified pre- and post-PCR with the MinElute purification kit (Qiagen) and then PAGE purified to remove adapter dimers. Three replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-8-50 read set-up.

treatment_protocol: Cells were treated with either dexamethasone (1uM, D4902, Sigma) or IFN-gamma (100ng/ml, 485-MI-100, R&D) for 48 hours.

tag: mouse model

value: EAE

tag: cell type

value: Sox10GFP+ OPCs

value: IFNg

tag: replicate


title: PD003 Chromatin accessibility


title: Sox2cre_batch3_sample_37

value: intracranial

value: brain, lateral

value: MYC


title: P60_Sup_2

tag: age


title: 190426Mk2_Dexa

description: ATACseq (Buenrostro et al., 2013)

value: Dexa


title: VEH3

value: FVB/N

value: HCC induced by loss of PTEN and c-MET overexpression

value: Vehicle


title: DIPG13p-MAT2A_shRNA 4 + DOX Replicate 3

city: Pittsburgh

first: Sameer

last: Agnihotri

state: PENNSYLVANIA

address: 530 45TH ST, 7TH FL BAY 20 RANGOS RESEARCH

department: Neurosurgery

institute: University of Pittsburgh

data_processing:
Qiagen
Short  read sequences (150 bp, mate paired) obtained from sequencing were trimmed and further mapped to the reference human genome (hg19), and gene sequences were aligned using the Bowtie algorithm employed in the CLC genomics Software suite ((Ensemble version 54), Qiagen, CLC workbench 2020)
Genes with Transcript per million (TPM) values < 1 were considered to be not expressed at a sufficient level to permit reliable quantification and were removed
Sample counts were then normalized to counts per million (CPM) and transformed (log2CPM+2) using the edgeR package in the R computing environment
DeSeq and DESeq2 statistical packages in R were used to identify significant changes in gene expression between experimental conditions
Genome_build: mm9, hg19
Supplementary_files_format_and_content: matrix file containing normalized data, output from Deseq 2, with Edge

source_name: DIPG13p-MAT2A_shRNA 4 + DOX

extract_protocol:
RNA was extracted from samples using the Qiagen RNeasy mini kit (Cat#74104) as per manufactures instructions
Strand-specific RNA-Seq library preparation and sequencing were performed at Novogene Biotech (Beijing, China) using standard Illumina protocols

tag: cell line

tag: genotype/variation

value: Dox Inducible Mat2A Knockdown

value: +DOX


title: Sox2cre_batch3_sample_39

value: brain, basal

value: SHH


title: Sox2cre_batch3_sample_36

value: extracranial

value: shoulder


title: P60_PD_2

value: hypothalamus

value: postnatal day 60

value: ribo-depleted mRNA


title: Sample 3_day21

tag: timepoint


title: shLacZ_AR-INPUT_Rep2

city: Philadelphia

first: Peter

last: Choi

address: 3501 Civic Center Blvd, CTRB 4400

data_processing:
ChIP-seq data were processed with the ChiLin pipeline (code version 2.0, db version 1.0) in simple mode using bwa to align to the hg38 human reference genome and MACS2 to call peaks, using the ‘narrow’ setting. For each condition, two replicate IP samples were processed along with their corresponding input DNA controls.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files generated for each replicate using ChiLin pipeline.

source_name: LNCaP cells

extract_protocol:
10 million cells were fixed using 1% formaldehyde (Thermo Fisher Scientific, BP531-25) for 10 minutes at room temperature followed by quenching with 125 mM glycine (Sigma-Aldrich, #50046). Cells were rinsed twice with PBS and resuspended in 1 mL lysis buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitor cocktail (Roche, #11836170001). Chromatin was sheared to 200-500 base pairs using a Covaris E220 sonicator and cleared by centrifugation for 15 minutes at 19,000 x g. Antibodies (AR, 9 μg, Abcam, ab74272; H3K27ac, 1 μg, Diagenode, C15410196) were incubated with 40 μL of protein A/G Dynabeads (Thermo Fisher Scientific, #10002D, #10003D) for at least 6 hours at 4°C before overnight incubation at 4°C with sonicated chromatin. Chromatin-bead complexes were washed 5 times with 1 mL LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and rinsed twice with 1 mL TE buffer (10 mM Tris pH 7.5, 0.1 mM EDTA). Immunoprecipitated chromatin was resuspended in 100 μL elution buffer (100 mM NaHCO3, 1% SDS) and treated with RNase A (Thermo Fisher Scientific, #12091021) for 30 minutes at 37°C. Crosslinks were reversed in the presence of proteinase K (Thermo Fisher Scientific, #25530049) for 16 hours at 65°C, and the eluted DNA was purified using a MinElute PCR Purification Kit (QIAGEN, #28006).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (NEB, #E7645).

value: shLacZ

tag: antibody

value: LNCaP


title: DIPG13p-MAT2A_shRNA 4 + DOX Replicate 2

tag: treatment


title: P60_Sup_1


title: rosa26cre_batch3_sample_34

tag: batch

tag: localization

value: Gland


title: DIPG13p-MAT2A_shRNA 4 + DOX Replicate 1


title: rosa26cre_batch3_sample_35

value: spinal

tag: localization details

value: spinal tumor

tag: age (weeks)

value: MYC


title: P60_PD_1

tag: strain


title: DIPG13p-MAT2A_shRNA 4 Replicate 3

source_name: DIPG13p-MAT2A_shRNA 4

value: -DOX


title: P12_Sup_3

tag: tissue

value: postnatal day 12


title: DIPG13p-MAT2A_shRNA 4 Replicate 2

value: Dox Inducible Mat2A Knockdown


title: 190419Mk1_Ctr

description: ATACseq (Buenrostro et al., 2013)

value: EAE

value: Sox10GFP+ OPCs

tag: condition

value: Ctr


title: rosa26cre_batch3_sample_33

value: intracranial

value: brain, lateral to the cerebellum

tag: tumor classification


title: 190419Mk2_Dexa

description: ATACseq (Buenrostro et al., 2013)

tag: mouse model

value: Dexa


title: P12_PD_3

value: hypothalamus

tag: molecule subtype


title: rosa26cre_batch3_sample_32

value: brain, basal

value: SHH


title: rosa26cre_batch3_sample_38

value: brain, subventricular zone


title: DIPG13p-MAT2A_shRNA 4 Replicate 1


title: 190218Mk6_Ifng

description: ATACseq (Buenrostro et al., 2013)

tag: cell type

value: IFNg

tag: replicate


title: rosa26cre_batch3_sample_31

value: extracranial

value: facial, maxillar


title: P12_Sup_2

tag: age

value: ribo-depleted mRNA


title: rosa26cre_batch3_sample_30

value: mouth

value: MYC


title: 190218Mk5_Dexa

description: ATACseq (Buenrostro et al., 2013)


title: P12_PD_2

value: postnatal day 12


title: 190218Mk4_Ctr

description: ATACseq (Buenrostro et al., 2013)

value: EAE


title: TWCM-13-102

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Genome_build: GRCh38 V3.0.0
Supplementary_files_format_and_content: Seurat V4 R Objects
Supplementary_files_format_and_content: I*Counts.csv: Comma-separated expression matrices.

source_name: Transmural LV Apex

extract_protocol:
Transmural tissue samples were removed from the left ventricle apex during LVAD implantation or after whole heart explantation. Samples for single cell were processed fresh by enzymatic digestion while samples for single nuclei were frozen in liquid nitrogen and stored at -80C until use and processed by mechanical homogenization. All single cell/nuclei suspensions were sorted by FACS to remove debris and dead cells.
10X Genomics Chromium Single Cell 5’ Reagent V1.1.

value: Transmural LV Apex

tag: storage condition

tag: technology

value: Single Nuclei

tag: disease state

value: Dilated cardiomyopathy


title: TWCM-13-285

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: P12_Sup_1