title: 2TFP-Myc/2TFP-Myc mouse, 4C-Seq, rep4

description: R1:60 and R2:42

data_processing:
4CSeq has been processed using the 4Cpipe pipeline (https://doi.org/10.1016/j.ymeth.2019.07.014) over mm10 reference genome with Csp6I and NlaIII as first and second cutter, a view point at position chr15: 61985921 (TGGGGCACAAGCTGGAGTAC), a max mapping mismatch of 2, a normalization factor of 10000 with the top 10 fragments removed, a read quality trimming cutoff of 10 and a running mean window of 21 fragments. The rest of the parameters are as default. Data displayed has been summarised using the median over 4 replicates per condition.
Assembly: mm10
Supplementary files format and content: 4C-Seq: BigWig files with the smoothened coverage across genome for windows of 21 fragments
Library strategy: 4C-Seq

source_name: Mouse Embryonic Stem cells

extract_protocol:
For 4C-Seq expreiment, 5 million cells were used for each sample and replicate. When the culture reached the 70-80% confluency, cells were detached with trypsin 0.25% and then fixed with fresh 2% PFA. Then, the cell pellet was lysed with 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% v/v NP-40, 1.15% v/v Triton X-100 and 1x PIC. After this, we proceeded to chromatin digestion with Csp6I (CviQI) (ThermoFisher, #ER0211 or NEB, #R0639L). Digestion efficiency was checked by gel electrophoresis. Digestion products were directly used for the first ligation with T4 DNA ligase. After ligation, DNA was purified using phenol:chloroform and precipitated with 3M NaAC, pH 5.2 (1/10x vol.), glycogen (0.05- 1μg/μl final concentration) and 100% EtOH (~2.5x vol.). Then, we proceeded to the second digestion and ligation for library preparation. We used NlaIII (NEB, #R0125L) for the second digestion and digestion products were directly used for the ligation step. This second ligation was done in a large volume, to favor intra-molecular ligation events. After this, the final products were purified with AMpure XP beads on a magnet (Bechman Coulter,#A63881).
For 4C-Seq, The DNA obtained was used for library generation using 2 PCR rounds (Primers are listed in Supplementary Table 2). In PCR 1, we designed primers aligned to specific sequences of the view point and adaptors for the second PCR. This PCR was amplified with Expand long template system (Roche/merk, #11681834001). Then the product was purified with AMpure beads, and used as template for PCR 2. For the second PCR, we designed primers with P5 sequence for the forward (common for all the samples), and the reverse primers has P7 sequence and index sequences, different for each sample. This PCR was amplified with NEBNext Highfidelity 2X PCR master mix (NEB, #M0541S). Finally, products were purified with Ampure beads and sequenced by Illumina sequencing technology

value: Mouse Embryonic Stem cells

value: 4C-Seq Digestion with Csp6I and NlaIII

tag: view point

value: TGGGGCACAAGCTGGAGTAC


title: 1928,SI-GA-C1

status: Public on Mar 06 2024

type: SRA

city: Boston

first: Samia

last: Ali

state: Massachusetts

address: 800 Washington Street

department: Molecular Cardiology Research Institute

country: USA

institute: Tufts Medical Center

description: 10x Genomics, S4 Flow Cell

library_source: transcriptomic

data_processing:
Demultiplexing, barcode processing, gene counting were done using Cell Ranger software v6.0.1
Assembly: Fca126, GRCh38, mm10
Supplementary files format and content: Tab-separated values files, and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Whole Heart

extract_protocol:
Cryopreserved tissue was thawed in a 37°C water bath for 75 seconds. Nuclei were released from the tissue via dounce homogenization using a buffer containing Triton X-100 (0.1 v/v). The homogenate was filtered through a 10µM cell strainer and nuclei were pelleted (500 x g for 5 minutes at 4°C) and washed before being resuspended in 1% w/v BSA, 1X PBS, and  0.2 U/µL RNase inhibitor
Library was constructed according to manufacturers instructions (single cell 3' v3.1, 10x Genomics).

tag: tissue

value: Whole Heart

tag: cell type

value: Heart Tissue

tag: genotype

value: HOM


title: J774A.1 cells, B. pseudomallei + Mip inhibitor SF235, 4 hr, replicate1

city: Crawley

first: Jua

last: Iwasaki

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Pass filter data of fastq format were processed by Trimmomatic (v0.30)
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL.
Hisat2 (v2.0.1) was used to index reference genome sequence.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1)
Assembly: mm10
Supplementary files format and content: 1 excel sheet containing FPKM values for each sample

molecule: total RNA

source_name: Ascites

growth_protocol: J774A.1 murine macrophage cells were maintained in DMEM (Gibco, Life Technologies) supplemented with a final concentration of 1% GlutaMAX (Gibco, Life Technologies) and 10% heat-inactivated fetal calf serum (Gibco, Life Technologies) at 37°C with 5% CO2

extract_protocol:
RNA was extracted using the RNeasy Micro Plus kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq was prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit following manufacturers protocols

value: Ascites

tag: cell line

value: Macrophage

value: WT

tag: treatment

value: B. pseudomallei + SF235


title: 951,SI-GA-B1

description: 10x Genomics, S4 Flow Cell


title: 2TFP-Myc/2TFP-Myc mouse, 4C-Seq, rep3

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: R1:60 and R2:42

library_source: genomic

molecule: genomic DNA


title: 2TFP-Myc/2TFP-Myc mouse, 4C-Seq, rep2

description: R1:60 and R2:42


title: EPNST-RELA-1386

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
High quality base calls at Q30>80% were obtained for 50 million 150bp paired-end reads and mapped to the human genome (CRCh38) by STAR 2.4.0.1.
Assembly: Hg38
Supplementary files format and content: Quantification of RNA expression, as fragments per kilobase per million (FPKM), was derived by Cufflinks, which is provided here

molecule: polyA RNA

organism: Homo sapiens

source_name: TUMOR-RELA

extract_protocol:
RNA was isolated snap frozen PFA samples using an Allprep DNA/RNA mini kit (Qiagen) per manufacturers instructions
Libraries were prepared using the Tecan Universal Plus mRNA-Seq library preparation kit per manufacturers instructions

value: TUMOR-RELA

tag: tumor full_name

value: ependymoma, supratentorial ZFTA-RELA fusion

tag: Sex

value: M

tag: tumor stage

value: Presentation


title: 952,SI-GA-A2

description: 10x Genomics, S4 Flow Cell


title: 2TFP-Myc/2TFP-Myc mouse, 4C-Seq, rep1

description: R1:60 and R2:42


title: GFP-Myc/GFP-Myc mouse, 4C-Seq, rep4

description: R1:60 and R2:42

value: GFP-Myc/GFP-Myc


title: GFP-Myc/GFP-Myc mouse, 4C-Seq, rep3

description: R1:60 and R2:42


title: 944,SI-GA-A1

description: 10x Genomics, S4 Flow Cell


title: MEDGP34-1367

value: medulloblastoma group 3/4


title: MEDGP3-1355

value: medulloblastoma group 3


title: Input Vehicle 1

city: Cincinnati

first: Theresa

last: Alenghat

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw reads were aligned to UCSC mouse genome mm10 using STAR aligner.
Only uniquely aligned reads were used for downstream analysis, and redundant reads were deduplicated using Picard tool (Broad Institute).
Initial peak calling was performed against input control using Homer with options “-style histone -fdr 0.001”.
Differential domain calling was performed on transcription start sites (TSS) of RefSeq genes. TSS-associated H3K9Ac peaks were pooled and merged from n=3 of vehicle and butyrate conditions. Read counts were measured from each replicate within the merged peaks, which were then subjected to differential analysis using EdgeR
Peaks were annotated and associated with a nearby gene by Homer.
Assembly: mm10
Supplementary files format and content: Tab deliminted text file includes peaks for all samples and differentiatial analyses between Veh and Butyrate groups.

source_name: Ileum

extract_protocol:
Nuclear lysates were sonicated and histone chromatin complexes were immunoprecipitated with an H3K9Ac antibody (Millipore, 06-942). Libraries were prepared with the ThruPlex DNA-seq kit (Rubicon) and sequences on an Illumina NovaSeq 6000 platform. Sequencing depth: 20 million reads, sequencing condition: paired-end, 100 bp.
Libraries were prepared with the ThruPlex DNA-seq kit (Rubicon)

treatment_protocol: C57Bl/6 mice were treated with 150 mM of Butyrate for 7 days. Intestinal epithelial cells were isolated from the terminal ileum.

value: Ileum

value: Intestinal epithelial cells

value: Wild type

value: Vehicle


title: RNAseq zebrafish 1

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs, tsRNA (tRNA-derived small non-coding RNA), rsRNA (rRNA-derived small non-coding RNA), small snoRNAs, lncRNA, and mRNA, successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo-siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others.
We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM (transcripts per kilobase of exon model per million mapped reads) by StringTie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM values or raw counts for each Sample

organism: Danio rerio

source_name: oocyte

extract_protocol:
Total RNA from oocytes of different species were extracted with TRIzol Reagent (Ambion, USA), respectively.
Small RNA library construction. Briefly, the single oocytes were incubated at 72 °C for 3 min then cooled in ice. After 3′ adapter ligation, the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de-adenylates. Small RNAs were reverse-transcribed after 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel.
mRNA library construction. In brief, single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte, 1 μl of a 1/500,000-1/50,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added. After reverse transcription and PCR pre-amplification, cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.

value: oocyte

value: female

tag: Stage

value: MII

value: wild type


title: Butyrate 3

value: 150 mM Butyrate


title: zebrafish oxidation

value: NaIO4 oxidation


title: EPNPFA1-1347

value: ependymoma, posterior fossa group A1


title: MEDSHH-1397

source_name: TUMOR-MEDSHH

value: TUMOR-MEDSHH

value: medulloblastoma, SHH group


title: zebrafish control

value: control


title: PA-1340-1

source_name: TUMOR-PA

value: TUMOR-PA

value: pilocytic astrocytoma

value: M

value: Presentation


title: small RNA zebrafish 2

tag: molecule subtype

value: small RNA


title: Butyrate 1

value: Ileum

value: Intestinal epithelial cells

value: Wild type


title: RNA-con-in vitro 2

city: 33-浙江省

first: Ming

last: Zong

address: University Town, Chashan, Wenzhou

institute: Wenzhou Medical University

description: count.txt

data_processing:
CUT&Tag paired-end reads were aligned to the mouse genome (mm10) using Bowtie 2 (version 2.2.5) with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). Reads from PCR duplicates were removed using Picard ‘MarkDuplicates’. After confirming reproducibility between replicates, they were merged using Samtools‘merge’. Final bam files were converted to bigWig files of read coverages normalized to RPKM using deepTools (version 3.5.1) bamCoverage.
For RNA-seq analysis of all data, we downloaded the mouse reference genome (genome assembly: mm10) from the Ensembl database and used the HISAT2 software for read alignment with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. The expression level of each gene was quantified in terms of the normalized fragments per kilobase of transcript per million mapped reads (FPKM). Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm10

extract_protocol:
Oocytes were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Single Cell Full Length mRNA-Amplification Kit(N712, Vazyme) according to the manufacturer’s instructions.
Library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) according to the manufacturer’s instructions.

value: oocyte


title: small RNA zebrafish 1

value: female

value: MII


title: Butyrate 2

value: 150 mM Butyrate


title: small RNA zebrafish 3

value: wild type


title: ahk3 ahk4, medial 16hour post wounding, biol rep 3

city: Durham

first: Suresh

last: Damodaran

state: North Carolina

address: 124 Science Drive, 3332 French Family Science center

department: Biology

institute: Duke University

data_processing:
Sequences were analyzed using QuantSeq 3'-mRNA-seq integrated data analysis pipeline on Bluebee platform.
The count data from HT-seq count analysis in Bluebee platform was used to perform differential gene expression analysis in DESeq2 pipeline in R software.
Assembly: Araport11
Supplementary files format and content: tab limited text files include gene read count data for each sample

organism: Arabidopsis thaliana

source_name: Hypocotyl

growth_protocol: Wt(Col-0) and ahk3ahk4 were germinated in continous light for over night after 3 days of stratification and grown in low light condition for 5days

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen).
Libraries were constructed following  QuantSeq 3'mRNA-Seq library prep kit FWD protocol.

treatment_protocol: Seedlings were excised above root shoot junction after 5 days of growth under low light condition and 2-3mm hypocotyl segments at basal and medial regions were dissected and collected.

value: ahk3 ahk4

tag: biol rep

value: biol rep 3

value: Hypocotyl

tag: region

value: medial

tag: time

value: 16 hour post wounding


title: PA-1335

value: TUMOR-PA

value: pilocytic astrocytoma


title: Vehicle 2

value: Vehicle


title: Vehicle 3


title: ahk3 ahk4, medial 16hour post wounding, biol rep 2

value: biol rep 2


title: Wt, medial, 16hour post wounding, biol rep 3

value: Wild type (Col-0)


title: ahk3 ahk4, medial 16hour post wounding, biol rep 1

value: biol rep 1


title: GFP-Myc/GFP-Myc mouse, 4C-Seq, rep2

description: R1:60 and R2:42

value: Mouse Embryonic Stem cells

value: GFP-Myc/GFP-Myc

value: 4C-Seq Digestion with Csp6I and NlaIII

value: TGGGGCACAAGCTGGAGTAC


title: MEDGP4-1336

value: medulloblastoma group 4

value: F

value: Presentation


title: RNAseq zebrafish 3

value: oocyte

value: female

value: MII

value: wild type


title: EPNST-RELA-135_1

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion


title: Input Buytrate 1

value: Ileum

value: Intestinal epithelial cells

value: Wild type

value: 150 mM Butyrate


title: PA-1330

value: TUMOR-PA

value: pilocytic astrocytoma


title: GFP-Myc/GFP-Myc mouse, 4C-Seq, rep1

description: R1:60 and R2:42

value: Mouse Embryonic Stem cells

value: GFP-Myc/GFP-Myc

value: 4C-Seq Digestion with Csp6I and NlaIII


title: Vehicle 1

value: Vehicle


title: RNAseq zebrafish 2


title: Wt, medial, 16hour post wounding, biol rep 2

value: Wild type (Col-0)

value: biol rep 2

value: Hypocotyl

value: medial

value: 16 hour post wounding


title: EPNST-RELA-1329

value: TUMOR-RELA

value: F

value: Presentation


title: ahk3 ahk4, medial 8hour post wounding, biol rep 3

value: ahk3 ahk4

value: biol rep 3

value: 8 hour post wounding


title: ahk3 ahk4, medial 8hour post wounding, biol rep 2


title: ACP-1305-1

source_name: TUMOR-ACP

value: TUMOR-ACP

value: adamantinomatous craniopharyngioma

value: M


title: ahk3 ahk4, medial 8hour post wounding, biol rep 1

value: biol rep 1


title: spinal cord, FIPI-3

city: Beijing

first: Zihan

last: Li

address: No. 10, Jiaomen North Road, Fengtai District, Beijing

institute: China Rehabilitation Science Institute

data_processing:
The information analysis process uses the raw reads obtained from sequencing on the Illumina platform, and then through the process of removing low-quality sequences, removing splice contamination, and other processes to complete the data processing to obtain high-quality sequences (Clean Reads), according to which the expression amount is calculated and comparative analysis of the data is carried out.
Though the R language (version 4.2.3),differential gene screening was mainly based on the criteria of fold change and q value (Padj value, corrected Pvalue value), and the genes that reached the criteria of log2 (Fold change)≥0.5 and q<0.05 were regarded as significant differential genes. The functional analysis was performed by the ClusterProfiler (4.7.1),such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG).
Assembly: GRCm38.90.chr
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spinal cord

extract_protocol:
The spinal cord tissues were collected from each group. The sequencing method was performed according to the manufacturer's standard protocol. The total RNA of the samples was first extracted and examined for the concentration and quality of the RNA. Then, the mRNA was enriched and purified with magnetic beads attached to oligo (dT), followed by the addition of Fragmentation Buer to split the mRNA into short fragments, and then this was used as a template, reverse transcription using random primers to synthesize the first strand of cDNA, then synthesize the second strand of cDNA. The product was subjected to end repair, addition of base A, and addition of sequencing junction. The library preparation was completed by screening out the tar-get fragments using magnetic beads and performing PCR amplification. After the library construction was completed, it was quantified and diluted to 1ng/ul. Q-PCR was performed using a fluorescent quantitative PCR instrument (Bio-RAD CFX) to determine the quality of the library, and the quality-qualified library was sequenced using the Illumina platform.
RNA libraries were prepared for sequencing using standard lllumina protocols, After qualifying the total RNA samples, purification is conducted based on the characteristics of mRNA from different sources. Eukaryotic mRNA, with a polyA tail structure at the 3' end, is enriched and purified using magnetic beads containing Oligo(dT). In contrast, prokaryotic mRNA lacks this feature, and a reagent kit is used to eliminate rRNA for obtaining more meaningful information. Fragmentation Buffer is added to the purified mRNA to break it into short fragments. Using the fragmented RNA as a template, the reverse transcription process is carried out with random primers, leading to the synthesis of the first cDNA strand. The addition of 2nd Strand Marking Buffer and 2nd Strand/End Repair Enzyme Mix is employed to synthesize the second cDNA strand. Subsequent steps involve end repair, addition of A bases, ligation of sequencing adapters, magnetic bead-based selection to recover the target fragments, and PCR amplification, completing the entire library preparation process.

value: spinal cord

tag: group

value: SCI

value: FIPI

value: 7 days after injury


title: Wt, medial, 8hour post wounding, biol rep 3

value: Wild type (Col-0)

value: Hypocotyl


title: spinal cord, FIPI-2


title: Wt, medial, 8hour post wounding, biol rep 2

value: biol rep 2

value: medial


title: Wt, medial, 8hour post wounding, biol rep 1


title: spinal cord, FIPI-1


title: ahk3 ahk4, medial 0hour post wounding, biol rep 3

value: 0 hour post wounding


title: Wt, medial, 0hour post wounding, biol rep 3


title: Wt, medial, 0hour post wounding, biol rep 2


title: PA-1302

value: TUMOR-PA

value: pilocytic astrocytoma

value: Presentation


title: ahk3 ahk4, medial 0hour post wounding, biol rep 2

value: ahk3 ahk4


title: spinal cord, SCI-3

value: control


title: PA-1272


title: GBM-1293

source_name: TUMOR-GBM

value: TUMOR-GBM

value: glioblastoma

value: F


title: Wt, medial, 16hour post wounding, biol rep 1

value: biol rep 1

value: 16 hour post wounding


title: ahk3 ahk4, basal, 16hour post wounding, biol rep 3

value: biol rep 3

value: basal


title: spinal cord, SCI-2

value: spinal cord

value: SCI

value: 7 days after injury


title: ahk3 ahk4, basal, 16hour post wounding, biol rep 1

value: Hypocotyl


title: PA-1268-1

value: M


title: spinal cord, SCI-1


title: PA-1266-1

value: TUMOR-PA


title: Wt, medial, 0hour post wounding, biol rep 1

value: Wild type (Col-0)

value: medial

value: 0 hour post wounding


title: ahk3 ahk4, basal, 16hour post wounding, biol rep 2

value: ahk3 ahk4

value: biol rep 2


title: EPNPFA2-1295-1

value: ependymoma, posterior fossa group A2

value: Presentation


title: Wt, basal, 16hour post wounding, biol rep 3


title: ATRT-MYC-1261-1

value: TUMOR-GBM

value: glioblastoma


title: Wt, basal, 16hour post wounding, biol rep 2

value: 16 hour post wounding


title: MEDGP4-1238

value: medulloblastoma group 4

value: F


title: ahk3 ahk4, medial 0hour post wounding, biol rep 1

value: biol rep 1


title: ahk3 ahk4, basal, 8hour post wounding, biol rep 2

value: basal

value: 8 hour post wounding


title: ahk3 ahk4, basal, 8hour post wounding, biol rep 3

value: biol rep 3

value: Hypocotyl


title: spinal cord, Sham1

value: spinal cord

value: Sham

value: control

value: 7 days after injury


title: Wt, basal, 16hour post wounding, biol rep 1

value: Wild type (Col-0)


title: ahk3 ahk4, basal, 8hour post wounding, biol rep 1

value: ahk3 ahk4


title: DMG-1210

source_name: TUMOR-DMG

value: TUMOR-DMG

value: diffuse midline glioma

value: Presentation


title: Wt, basal, 8hour post wounding, biol rep 3


title: Ctl2

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 815 Mercer Street D342

department: Bioengineering & Pathology & Laboratory Medicine

institute: University of Washignton

library_source: transcriptomic single cell

data_processing:
Cleaned reads were aligned to the reference genome (GRCm38/mm10) using STAR.11 Doublets were identified using scrublet and subsequently filtered out.
Further analysis and quality filtering was performed using the Seurat package in R. Nuclei were filtered out if they contained fewer than 200 UMI, over the top 1% quantile of UMI, or over 10% mitochondrial reads. Overall, 178,301 singlets across all cell types were sequenced with a mean UMI of 1452. Clustering was then performed following the standard approach, and cardiomyocytes were identified by clusters marked by canonical cardiomyocyte genes like Ttn and Myh6. Cells were further filtered for Ttn expression >= 1 and Myh6 > 0. A total of 30,528 cardiomyocyte nuclei with a mean 1763 UMI were subsequently used for downstream analyses. Reads were then normalized using the SCTransform function with the “glmGamPoi” method. Mitochondrial mapping rate was regressed out using the vars.to.regress argument. Principal component analysis was performed on the scaled data, and then cells were clustered on the first 6 principal components using the FindNeighbors function and the FindClusters function with resolution 0.5. To visualize the data, non-linear dimensional reduction via Uniform Manifold Approximation and Projection (UMAP) was used to project cells in 2D space on the basis of the first 6 principal components. 10 cardiomyocyte clusters were identified and cluster markers were identified using FindAllMarkers with the only.pos argument set to TRUE. Pseudotime analysis was performed using Monocle3 with the SeuratWrappers package.
Assembly: GRCm38
Supplementary files format and content: txt files containing cell annotations
Supplementary files format and content: txt files containing gene annotations
Supplementary files format and content: mtx files containing umi counts

source_name: Heart - ventricle

extract_protocol:
Whole heart samples were prepared using the single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) protocol published previously (Martin et. al 2023, doi: 10.1038/s41596-022-00752-0) with the following modifications. Briefly, 2 hearts from control and 2 hearts from KO mice were snap frozen in liquid nitrogen 2 weeks following MI. Nuclei were isolated from frozen tissues by grinding the frozen tissue with a mortar and pestle, lysing the powdered tissue in hypotonic lysis buffer B, and dissociating the tissue in a genlteMACS M tube run on the “Protein 001” program followed by 50 strokes in a Dounce homogenizer with a type A/loose pestle. Lysates were subsequently filtered through a 40μm filter and centrifuged at 500xg for 5 minutes at 4°C. The nuclear pellet was then resuspended in 0.3M SPBSTM and filtered through a 20μm filter. The nuclei were subsequently fixed in methanol/DSP for 5 minutes at room temperature. The fixed nuclei were subsequently rehydrated with 0.3M SPBSTM, spun down at 500xg for 5 minutes at 4°C, and resuspended in 0.3M SPBSTM. The fixed nuclei were then aliquoted, snap frozen, and stored at -80°C until sequencing.
Libraries were prepared according to the single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) protocol published previously (Martin et. al 2023, doi: 10.1038/s41596-022-00752-0). Briefly, fixed nuclei were distributed to wells of a 96 well plate and underwent reverse transcription which introduced a first index. Nuclei were then pooled and re-allocated to wells of a 96 well plate for incorporation of a second index by ligation. Nuclei were then pooled and split a third time for introduction of a third index by second-strand synthesis. Finally, libraries were purified and sequenced.

value: Heart - ventricle

value: Ctl

tag: time after_infarction


title: spinal cord, Sham3


title: Wt, basal, 8hour post wounding, biol rep 2

value: biol rep 2


title: DMG-1201

value: F


title: ahk3 ahk4, basal, 0hour post wounding, biol rep 3

value: basal

value: 0 hour post wounding


title: Wt, basal, 8hour post wounding, biol rep 1

value: biol rep 1

value: 8 hour post wounding


title: ahk3 ahk4, basal, 0hour post wounding, biol rep 2

value: Hypocotyl


title: ahk3 ahk4, basal, 0hour post wounding, biol rep 1


title: KO1

value: MBNL1 loss-of-function (KO)


title: MEDGP4-1195

value: medulloblastoma group 4

value: M


title: Ctl1


title: spinal cord, Sham2

value: spinal cord

value: Sham

value: control

value: 7 days after injury


title: Wt, basal, 0hour post wounding, biol rep 3

value: Wild type (Col-0)

value: biol rep 3


title: MEDWNT-1192

source_name: TUMOR-MEDWNT

value: TUMOR-MEDWNT

value: medulloblastoma, WNT group

value: Presentation


title: APAP2

city: DaLian

first: qi

last: cui

state: LiaoNing

address: DaLian

institute: 大连医科大学

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

source_name: liver

extract_protocol:
Total RNA was extracted by using TRIzol reagent and reverse transcribed with the iScript RT Supermix containing Moloney murine leukemia virus reverse transcriptase (M-MLV) and oligo (dT) primer mix (Bio-Rad).
RAN libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: WT

value: APAP 300mg/kg 12h


title: Wt, basal, 0hour post wounding, biol rep 1

value: biol rep 1

value: basal

value: 0 hour post wounding


title: GBM-1187-1

value: TUMOR-GBM

value: glioblastoma

value: F


title: KO2

value: Heart - ventricle

value: MBNL1 loss-of-function (KO)


title: GBM-1214


title: APAP1


title: RNAseq rat 5

organism: Rattus norvegicus

value: oocyte

value: female

value: MII

value: wild type


title: PA-1181

value: TUMOR-PA

value: pilocytic astrocytoma


title: RNAseq rat 4


title: saline3

value: liver

value: saline


title: RNAseq rat 3


title: RNAseq rat 2


title: ATRT-SHH-1170-X

source_name: TUMOR-ATRT

value: TUMOR-ATRT

value: atypical teratoid rhabdoid tumor

value: Recurrence


title: rat control

value: control


title: saline2

value: WT


title: APAP3

value: APAP 300mg/kg 12h


title: saline1


title: rat lgG IP

value: lgG IP


title: rat PIWIL1 IP

value: PIWIL1 IP


title: MEDGP34-1167

value: medulloblastoma group 3/4

value: F

value: Presentation


title: rat input

value: oocyte

value: female

value: MII

value: input


title: small RNA rat 3

value: wild type

value: small RNA


title: rat oxidation

value: NaIO4 oxidation


title: RNAseq rat 1


title: Ezh2_Y641F iMEFs Suz12 rep2 [D1371C43]

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

description: Ezh2_Y641F iMEFs Suz12 rep2

data_processing:
Adapters and low‐quality bases (<Q20) were removed from Cut&Run-Seq reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were mapped to the mouse reference genome mm10 with Bowtie2 (v2.2.5) using default parameters. PCR duplicates were with with Picard Tools MarkDuplicates (v1.97).
BigWig files were created using DeepTools bamCoverage (v3.0.2) with the following parameters: --normalizeUsingRPKM –ignoreForNormalization chrX chrY –samFlagInclude 64 –extendReads. Reads overlapping problematic, blacklisted regions (mm10-blacklist.v2.bed) were excluded from the computation of coverage with the option --blackListFileName.
In addition to scaling by library size, in order to remove any composition biases, we calculated a normalizing factor using the BioconductoR csaw::normFactors function. The normalization factor was passed onto DeepTools bamCoverage with the parameter --scaleFactor.
Assembly: mm10 for Cut&Run-Seq libraries
Supplementary files format and content: BigWig files of genome-wide enrichment of the probed histone modification/chromatin modifier.

source_name: iMEFs

growth_protocol: iMEFs were grown in Dulbecco’s Modified Eagle Medium (DMEM) high-glucose (4.5 g/L) supplemented with 10% fetal calf serum, nonessential amino acids and 2 mM L-glutamine at 37°C with 5% CO2 and 98% humidity.

extract_protocol:
Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018).
Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. Cut&Run-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100).
Cut&Run-Seq

value: iMEFs

tag: antibody


title: Wt, basal, 0hour post wounding, biol rep 2

value: Wild type (Col-0)

value: biol rep 2

value: Hypocotyl

value: basal

value: 0 hour post wounding


title: small RNA rat 2


title: PRC2 WT iMEFs Suz12 rep2 [D1371C42]

description: PRC2 WT iMEFs Suz12 rep2

value: WT


title: GBM-1144-1

value: TUMOR-GBM

value: glioblastoma

value: M


title: small RNA rat 1

value: oocyte


title: Ezh2_Y641F iMEFs Suz12 rep1 [D1371C41]

description: Ezh2_Y641F iMEFs Suz12 rep1


title: MEDGP3-1130-1

source_name: TUMOR-MED

value: TUMOR-MED

value: medulloblastoma

value: Presentation


title: WA19 hESC, siOct4, 0h PASE, rep3

city: Vienna

first: Markus

last: Hengstschläger

address: Währinger Straße 10

department: Institute of Medical Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
In a first step of raw data processing after sequencing, base calls were converted into lane-specific, multiplexed, unaligned BAM files suitable for long-term archival (IlluminaBasecallsToMultiplexSam, 2.19.2-CeMM).
In a second step, archive BAM files were demultiplexed into sample-specific, unaligned BAM files (IlluminaSamDemux, 2.19.2- CeMM).
NGS reads were then mapped to the Genome Reference Consortium GRCh38 assembly (hg38) via “Spliced Transcripts Alignment to a Reference” (STAR).
Aligned NGS reads overlapping Ensembl transcript features were counted with the Bioconductor (3.9) GenomicAlignments (1.20.1) package and transcript-level counts were aggregated to gene-level counts.
Differentially expressed genes were identified using the Bioconductor 3.14 packages “DESeq2” and “edgeR”.
Assembly: Genome Reference Consortium GRCh38 assembly (hg38).
Supplementary files format and content: Excel file includes raw counts for each sample.

growth_protocol: Feeder-independent WA19 hESC (NIHhESC-11-0100) were grown in colonies and maintained on Matrigel-coated plates in mTeSR1 at 37 °C and 5% CO2 with daily medium change (WiCell SOP-SH-002, version D).

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (#74134, Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions.

treatment_protocol: 72 hours after siRNA transfection, WA19 hESC were subjected to the 3D amniogenesis assay to generate PASE following the method described in the original publication (Shao et al. 2017).

value: embryonic stem cells

value: Oct4 knockdown

value: post-implantation amniotic sac embryoid (PASE) formation


title: WA19 hESC, siControl, 24h PASE, rep3


title: WA19 hESC, siOct4, 24h PASE, rep3


title: MEDGP3-1130-X

value: medulloblastoma group 3

value: Recurrence


title: PRC2 WT iMEFs Suz12 rep1 [D1371C40]

description: PRC2 WT iMEFs Suz12 rep1

value: iMEFs


title: WA19 hESC, siControl, 0h PASE, rep3


title: WA19 hESC, siOct4, 24h PASE, rep2


title: EPNST-RELA-1158-1

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion


title: WA19 hESC, siOct4, 0h PASE, rep2


title: ATRT-MYC-1127-1

value: TUMOR-ATRT

value: atypical teratoid rhabdoid tumor

value: F


title: WA19 hESC, siControl, 0h PASE, rep2

value: WT


title: WA19 hESC, siControl, 24h PASE, rep2


title: STHdhQ111/Q111, IFNg/LPS, Rep 1

city: Boca Raton

first: Jianning

last: Wei

state: FL

address: 777 Glades Road

department: Biomedical Science

institute: Florida Atlantic University

data_processing:
Cutadapt and perl scripts in house (LC Sciences) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). HISAT2 was used to map reads to the mouse genome (GRCm38.r101, ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/).
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
StringTie  was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2  between two different groups (and by R package edgeR between two samples). The mRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed mRNAs.
Assembly: GRCm38.r101
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: STHdhQ7/Q7  and STHdhQ111/Q111 (Coriell Institute for Medical Research) cells were cultured in DMEM supplemented with 10% FBS, 1% glutamine and 1% antibiotic-antimycotic solution at 33°C in a humidified incubator with 5% CO2. All cell lines were used within 20 passages after initial purchases.

extract_protocol:
RNA was isolated using the Direct-ZolTM RNA miniprep Plus kit according to the manufacturer’s instruction (Cat. #R2071, ZYMO RESEATCH). To reduce DNA contaminations, a 15-min on-column DNase I treatment was included.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: STHdhQ7 and Q111 cells were incubated with 100 ng/ml murine interferon-gamma (IFNg, ) and 5 ug/ml  lipopolysaccharide (LPS)  for 24 hours. Non-treated cells were used as controls. Twenty-four hours later, cells were directly harvested for RNA extraction.

value: immortal mouse striatal neuronal cell line

value: HD

value: IFNg/LPS 24 hours


title: STHdhQ111/Q111, IFNg/LPS, Rep 2


title: PA-1118-3

value: TUMOR-PA

value: pilocytic astrocytoma


title: MEDGP4-1155

value: medulloblastoma group 4

value: M

value: Presentation


title: STHdhQ111/Q111, control, Rep 3

value: control


title: MEDWNT-1128-1

value: TUMOR-MED

value: medulloblastoma


title: WA19 hESC, siOct4, 24h PASE, rep1

value: embryonic stem cells

value: Oct4 knockdown

value: post-implantation amniotic sac embryoid (PASE) formation


title: WA19 hESC, siControl, 0h PASE, rep1


title: STHdhQ111/Q111, control, Rep 2


title: NTERT cells- UV 3

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: IN

address: 635 N. Barnhill Dr. MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: UV treatment for tRNA Charge-Seq in NTERT cells

library_source: other

data_processing:
Pooled Samples were demultiplexed using python script to identify the sample specific barcode contained within the ligated adapter (5’- PO4-NNNNNXXXXXAGATCGGAAGAGCACACGTCTGAA-ddC-3’) where XXXXX is the unique sample-specific barcode.
Due to the small library footprint and long sequencing reads, it was necessary to trim the 5' ends of the reads using trimgalore
The trimmed reads were then aligned using bowtie2 to a custom reference consisting of mature tRNA sequences constructed from the GRCm38/mm10 (for MEF cells) or GRCh38/hg38 (for NTERT cells)-- references for both are supplied in this submission, and each reference was constructed from the UCSC gtRNAdb.
tRNA charging was assessed by parsing the aligned reads using a custom python script to identify the presence or absence of a 3' adenine base. The NaIO4 treatment performed during library prep  results in cleavage of the 3'-A if not protected by an amino-acyl bond.
Counts of charged and uncharged tRNA were then used to create plots and calculate statistical significance using R.
Assembly: Custom genome containing mature tRNA sequences from GRCm38/mm10 and GRCh38/hg38-- each supplied as fasta sequences
Supplementary files format and content: tab delimited text files containing counts of charged and uncharged tRNA
Library strategy: tRNA Charge-Seq

molecule: other

source_name: Cell Line

growth_protocol: MEF cells grown in high-glucose DMEM supplemented with 10% Fetal Bovine Serum and 1x Penicilin/Streptomycin. NTERT cells were maintained and passaged in low calcium EpiLife Complete media (Themo Fisher Scientific) supplemented with human keratinocyte growth supplement (HKGS; Themo Fisher Scientific) and 1000 U Penicillin-Streptomycin (PS) (Gibco Laboratories).

extract_protocol:
For genome-wide tRNA-charging assay, total RNA were extracted with Trizol reagent according to manufacturer's protocol. RNA were then oxidized by NaIO4 followed by deacylation at high pH. Next RNA were purified using ethanol precipitation and used for library preparation.
For genome-wide tRNA-charging assay: The purified tRNA samples were then treated with PNK (M0201, New England BioLabs) to remove the 3’-PO4 group from the uncharged tRNA. Next, 5’-adenylated adaptors carrying unique barcode (5’- PO4-NNNNNXXXXXAGATCGGAAGAGCACACGTCTGAA-ddC-3’; N-random nucleotides, XXXXX- is sample specific pentamer barcode, ddc-dideoxy cytidine) were ligated to the tRNAs using T4 RNA ligase2 truncated KQ (M0351L, New England BioLabs). tRNAs were then ligated to a 5’-adaptor (5’-rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC-3’) followed by reverse transcription using SuperScript IV RT kit (18090050, Invitrogen) and RT primer (5’-AGACGTGTGCTCTTCCGATCT-3’). Next the tRNA library was PCR amplified for 10 cycles by using Illumina multiplex PCR primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’) and Illumina barcode PCR Primer (5’-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’). PCR products were separated by an 8% non-denaturing polyacrylamide TBE gel (EC6215BOX, Invitrogen) and ~210 nt bands were excised, purified and subjected to HiSeq paired-end Illumina sequencing.

treatment_protocol: Cells treated with 100nM halofuginone for 6Hrs in high-glucose DMEM supplemented with 10% dialyzed Fetal bovine Serum and 1x Penicilin/Streptomycin. Control samples were treated with same dialyzed FBS containing media without halofuginone for 6Hrs. NTERT cells were treated with 400 J/m2 UV-B or left untreated (NT), followed by recovery for 3 hours.

value: Cell Line

value: NTERT

value: Immortalized human keratinocyte

value: 400 J/m^2 UV-B irradiation followed by 3hr recovery


title: GBM-1107

value: TUMOR-GBM

value: glioblastoma

value: F


title: GBM-1115


title: WA19 hESC, siControl, 24h PASE, rep1

value: WT


title: NTERT cells- UV 2


title: STHdhQ111/Q111, control, Rep 1

value: immortal mouse striatal neuronal cell line

value: HD


title: NTERT cells- UV 1


title: STHdhQ111/Q111, IFNg/LPS, Rep 3

value: IFNg/LPS 24 hours


title: EPNPFA2-1101-2

value: ependymoma, posterior fossa group A2

value: M

value: Recurrence


title: PA-1100-1

value: TUMOR-PA

value: pilocytic astrocytoma

value: Presentation


title: NTERT cells- Control 3

description: Control for tRNA Charge-Seq in NTERT cells

value: Cell Line

value: untreated


title: STHdhQ7/Q7, IFNg/LPS, Rep 3

value: normal


title: NTERT cells- Control 2

value: NTERT

value: Immortalized human keratinocyte


title: STHdhQ7/Q7, IFNg/LPS, Rep 2


title: NTERT cells- Control 1


title: WA19 hESC, siOct4, 0h PASE, rep1

value: embryonic stem cells

value: Oct4 knockdown

value: post-implantation amniotic sac embryoid (PASE) formation


title: STHdhQ7/Q7, IFNg/LPS, Rep 1

value: immortal mouse striatal neuronal cell line


title: Treg, noppx [86-9-AAGAGGCA-CTAGTCGA9]

city: Stanford

first: Cameron

middle: Scott

last: Bader

state: California

address: 269 Campus Drive, CCSR Room 2250

department: BMT and Cell Therapy

institute: Stanford University

data_processing:
Raw reads were aligned using STAR v2.6.1
Aligned .bam files were parsed using RSEM to generate raw expected reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file for all samples with raw read counts.

source_name: Treg, noppx

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (Zymo).
RNA libraries for RNA-seq were prepared using KAPA HyperPlus Kit following manufacturer's protocols.

value: CD4+ Treg

value: No prophylaxis


title: Treg, ppx [86-7-CTCTCTAC-TAAGGCTC7]

source_name: Treg, ppx

value: Single-agent prophylaxis


title: CD4, noppx [86-4-TCCTGAGC-TCTTACGC4]

source_name: CD4, noppx

value: CD4+ Tcon


title: GBM-1089-1

value: TUMOR-GBM

value: glioblastoma

value: F


title: CD4, ppx [86-8-CGAGGCTG-TCGCATAA8]

source_name: CD4, ppx


title: Treg, noppx [86-3-AGGCAGAA-ACTCTAGG3]


title: EPNPFA2-110-1

value: ependymoma, posterior fossa group A2

value: M

value: Presentation


title: ACP-1086-1

value: TUMOR-ACP

value: adamantinomatous craniopharyngioma


title: STHdhQ7/Q7, control, Rep 2

value: normal

value: control


title: STHdhQ7/Q7, control, Rep 3


title: MEDGP4-1066

value: medulloblastoma group 4


title: CD4, SOC [86-18-TAGGCATG-AGCTAGAA4]

source_name: CD4, SOC

value: SOC


title: Treg, noppx [86-1-TAAGGCGA-CTAGTCGA1]


title: STHdhQ7/Q7, control, Rep 1

value: immortal mouse striatal neuronal cell line


title: PA-1057-1

source_name: TUMOR-PA

value: TUMOR-PA

value: pilocytic astrocytoma


title: Treg, SOC [86-17-GGACTCCT-CTAGTCGA3]

source_name: Treg, SOC

value: CD4+ Treg


title: WT_L9

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

data_processing:
raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and eventually filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter if necessary.
Mapping of the reads were obtained using the STAR program against human genome (GRCm38) and the quantification of genes and transcripts were done with the RSEM program using  GENCODE.vM15 database .
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: RSEM quantification results including Expected counts, TPM and FPKM.

source_name: Sciatic nerve

extract_protocol:
Trizol Reagent + Genejet RNA cleanup and Concentration kit (Thermo Scientific)
TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E)
Total RNAseq after rRNA depletion

value: Sciatic nerve

value: WT


title: Treg, SOC [86-13-TAAGGCGA-AGGCTTAG1]


title: PA-1056-1


title: CD4, ppx [86-12-ATCTCAGG-TCTTACGC12]

value: CD4+ Tcon

value: Single-agent prophylaxis


title: KO_L8

value: Nae1 cKO


title: Treg, ppx [86-11-GCTCATGA-ACTCTAGG11]


title: EPNPFA1-1048

value: ependymoma, posterior fossa group A1

value: M


title: CD4, no ppx [86-10-GTAGAGGA-AGCTAGAA10]

source_name: CD4, no ppx

value: No prophylaxis


title: KO_L5


title: CD4, SOC [82-9-GTAGAGGA-TCTACTCT9]


title: CD4, noppx [86-2-CGTACTAG-AGCTAGAA2]


title: GBM-1035-1

source_name: TUMOR-GBM

value: TUMOR-GBM

value: glioblastoma

value: F

value: Presentation


title: Treg, SOC [82-8-CGAGGCTG-AGAGGATA8]

value: SOC


title: WT_L4


title: Treg, no ppx [82-4-GGACTCCT-CTCCTTAC4]

source_name: Treg, no ppx


title: CD4, no ppx [82-3-TCCTGAGC-TCTACTCT3]


title: WT_L3


title: CD4, no ppx [82-5-TAGGCATG-TACTCCTT5]


title: PA-1033-1


title: Treg, no ppx [82-2-CGTACTAG-AGAGGATA2]


title: CD4, SOC [86-14-CGTACTAG-ATAGCCTT2]


title: KO_L1


title: KO_K2


title: EPNPFA1-1013-3C

value: Recurrence


title: Treg, SOC [82-10-AAGAGGCA-CTCCTTAC10]


title: CD4, SOC [82-11-TAAGGCGA-CTCCTTAC11]


title: WT_K1


title: Treg, ppx [82-1-TAAGGCGA-ATAGAGAG1]


title: EPNPFA1-1013-2


title: GBM-1011-1


title: HOXD13_EGR1_Tag_Linker

city: Boston

first: Shubham

last: Khetan

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
Barcodes from sequencing libraries were mapped to the associated TFBS based on previously obtained TFBS-BC pairings. Barcode counts per TFBS were obtained for each library and merged into a single data frame. For differential activity analysis, read counts for the DBD-of-interest and a ‘No-DBD’ control, across 3 replicates each, were analyzed using DESeq2. TFBS significantly bound by the DBD-of-interest were identified by applying a false discovery rate (FDR) threshold of 5%.
Assembly: Custom: TFBS_BC_Combinations_all_10-mers_library.csv and TFBS_BC_Combinations_Output_UNIQUE.txt
Supplementary files format and content: TFBS_BC_Combinations_all_10-mers_library.csv: Comma separated strings of 10-bps TFBS, 25-bps Barcode, and count.
Supplementary files format and content: ReadCounts_perTFBS_all10mers_DF.txt: Tab separated read count matrix
Supplementary files format and content: dds_results_HOXD13_df.txt: DESeq2 output comparing read counts from ALFA-HOXD13 to the No-DBD control.
Supplementary files format and content: dds_results_EGR1_df.txt: DESeq2 output comparing read counts from ALFA-EGR1 to the No-DBD control
Supplementary files format and content: TFBS_BC_Combinations_Output_UNIQUE.txt: Tab separated strings of 9-bps TFBS, and 20-bps Barcodes.
Supplementary files format and content: ReadCounts_perTFBS_DF_DuplicatesNotRemoved_Tag_Linker.txt: Tab separated read count matrix
Library strategy: PADIT-seq

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
PADIT-seq experiment: To remove any supercoiling, PADIT-seq reporter libraries were first linearized with DrdI (NEB), which cuts a 12-bp DNA sequence (GACNNNN/NNGTC) only once in the pGL4.23 vector. For every DBD being tested, the following 30ul PURExpress IVTT reactions (NEB) were assembled: 10ul Solution A, 7.5ul Solution B, 1ul Murine RNase Inhibitor, 3ul 100mM rNTPs, 0.45ul 1000mM Magnesium Acetate, 3ul previously purified nbALFA-T7-RNA-Polymerase, ~300 ng linearized PADIT-seq reporter plasmid library, ‘pT7-ALFA-DBD-T7Term’. The linearized PADIT-seq reporter plasmid library was mixed with ‘pT7-ALFA-DBD-T7Term’ amplicons in an approximately 2:1 molar ratio. The 30ul PURExpress IVTT reactions were split into three wells, and all subsequent steps were performed separately (3 biological replicates).   cDNA synthesis of PADIT-seq reporter RNAs: After 4 hours at 37°C, the 10ul reactions were purified with RNAClean XP as per manufacturer’s instructions, eluting in 35ul Nuclease-free water. 2ul barcoded cDNA synthesis primers (0.1uM final each) were added to 18ul purified RNA, incubated at 75°C for 3 mins, then placed on ice. cDNA was synthesized by adding 10ul 2X Multiscribe reaction mix (Thermo Fisher), and incubating at 25°C for 20 minutes, followed by 37°C for 120 minutes. Minus reverse transcriptase controls were performed in parallel. Excess primers were removed from the cDNA:RNA duplexes by adding Exonuclease I and incubating at 37°C for 60 mins, followed by heat inactivation at 80°C for 20 mins. Quantitative PCR was performed to verify degradation of all excess primers, and to determine the threshold cycle of sample cDNAs.    PADIT-seq library preparation for Illumina Sequencing: For the small-scale PADIT-seq library, barcoded cDNAs synthesized from the reporter RNAs were pooled prior to PCR amplification. The pooled cDNA was amplified in a single PCR reaction using KAPA HiFi polymerase with primers 'MPRA_AmpliconEZ_FWD' and 'MPRA_AmpEZ_REV2.0'. This generated a PCR-1 product that was then used as template for a second PCR with primers '#34_MPRA' and ‘169_TruSeq_Multiplex_220_2’ to attach Illumina adapters and sample barcodes. In contrast, for the all-10mers PADIT-seq library, barcoded cDNAs were kept separate and amplified in individual PCR reactions rather than pooled. For each DBD, cDNA was amplified using KAPA HiFi HotStart Polymerase with primers 'MPRA_AmpliconEZ_FWD' and 'MPRA_AmpEZ_REV2.0'. This generated PCR-1 products that were cleaned and quantified. In the second PCR, '#34_MPRA' and indexed TruSeq primers were used to attach Illumina adapters and sample barcodes.
Construction of the all-10mers PADIT-seq reporter library: We designed and ordered two IDT Ultramers - one containing all possible 10-bp DNA sequences as candidate TFBS (‘All10mersTFBS_Top’), and another containing all possible 25-bp DNA sequences to serve as barcodes (‘25bpsBC_Bottom’). The two Ultramers were mixed in an equimolar ratio and double stranded in a single PCR cycle using KAPA HiFi polymerase. The pGL4.23 plasmid vector backbone was again PCR amplified in 2 steps with Q5 High-Fidelity 2X Master Mix. First, the backbone was amplified with primers ‘pGL4.23_FWD’ and ‘pGL4.23_REV’ to exclude the luciferase open reading frame. The resulting amplicon (2359-bps) was then further amplified with primers 'T7Term_pGL4.23_F_2.0' and 'pGL4.23_REV' to add a 56-bps DNA sequence as an overlapping region for Gibson Assembly, which was performed with the resulting amplicon (2415-bps) and the double-stranded oligo-pool mixed in equimolar ratios. Following desalting with a mixed cellulose esters (MCE) hydrophilic membrane (0.025 um), the assembled reporter library plasmid was electroporated into E. cloni 10G Supreme cells (n = 13 transformations). Based on plating experiments, the total number of transformants obtained was estimated to be 110 million, providing an average of ~100 barcodes per TFBS. The transformed cells were recovered, grown for 6.5 hrs, and maxi-prepped to obtain the complete all-10mers PADIT-seq reporter plasmid library containing over 100 million clones. Correct library assembly was validated by diagnostic PCR and Sanger sequencing of 10 colonies.   Obtaining TFBS-BC pairing in the all-10mers PADIT-seq reporter library: To obtain TFBS-BC pairings, the all-10mers PADIT-seq reporter library was PCR amplified using KAPA HiFi polymerase. Four forward primers were designed with partial Illumina adapters, 6N randomized bases, and 2-bps staggers (‘All_10mers_LibSeq_F1-4’). These were used individually with a single reverse primer (‘All_10mers_LibSeq_R’) to generate 4 PCR-1 products of expected sizes 213-219-bps (9 cycles). The 4 PCR-1 products were then used as template in PCR-2 (5 cycles) with TruSeq indexed primers to attach Illumina sample indexes. This generated 4 PCR-2 products of expected size 272-278-bps. After PCR amplification, the 4 products were SPRI cleaned and analyzed on Tapestation to confirm expected sizes. The 4 indexed libraries were sequenced separately on a NovaSeq6000 (2x150 bp reads). The sequencing data from each of the 4 indexed libraries (F1-F4) was combined and processed using custom scripts to extract unique TFBS-BC combinations along with their counts by matching the constant flanking regions. Barcodes unambiguously associated with only 1 TFBS across all 4 libraries were classified as ‘single TFBS barcodes’ and retained. The all-10mers PADIT-seq reporter plasmid library was amplified in 4 separate PCR reactions (F1-F4) with different TruSeq indexes to identify potential PCR-mediated recombination artifacts in the following way: for barcodes associated with multiple TFBS, an initial filter retained only TFBS observed independently in at least 2 of the 4 libraries. The rationale being that TFBS-BC occurrence in multiple independent libraries indicates likely true pairings versus artifacts of PCR-mediated recombination. After this first multi-library filtering step, any barcodes still associated with multiple TFBS were removed entirely to eliminate ambiguities. As an additional filter, barcodes where the top TFBS had fewer reads than the sum of discarded TFBS were removed. The ‘single TFBS barcodes’ and  vetted multiple TFBS barcodes were combined to obtain high-confidence 1:1 TFBS-BC pairs for downstream analysis. This multi-step filtering process leveraged the independently prepared sequencing libraries to remove incorrect and ambiguous TFBS-BC pairings arising from PCR-mediated recombination. It enabled retaining high-confidence barcode-TFBS pairs reproducibly identified across multiple libraries while discarding likely PCR artifacts and errors.

value: synthetic construct


title: Yy1_DEL_3351

city: Madison

first: Xuan

last: Pan

state: WI

address: 4470 Veterinary Medicine Building

institute: University of Wisconsin

data_processing:
RNA-seq reads were aligned by STAR (version 2.5.2b) to the mouse genome (version mm10) with GENCODE basic gene annotations (version M22).
Gene expression levels were quantified by RSEM (version 1.3.0)
Assembly: mm10
Supplementary files format and content: TSV: RSEM quantification results at the gene level

source_name: bone marrow

extract_protocol:
Total RNA was purified from sorted bone marrow LSK (Lin-Sca1+c-Kit+ )cells using RNeasy Micro kit (Qiagen)
Sequencing libraries were prepared by using Takara SMART-Seq V4 Ultra-Low Input according to the manufacturer’s specifications

value: bone marrow

value: LSK (Lin-Sca1+c-Kit+)


title: ATAC REH-Parental

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

data_processing:
reads were trimmed of adapters with trim_galore
reads were aligned to the reference with bowtie2
duplicates were marked with picard-tools
coverage tracks were made with igvtools
Assembly: hg38
Supplementary files format and content: The ".tdf" file format is an indexed, compressed binary file format to support the display of numeric data.

source_name: REH

growth_protocol: RPMI, 10% FBS, 1% penicillin/steptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
50,000 cells from culture were counted, pelleted and resuspended in 200ul of PBS.
Nextera dual indexed kit (Illumina) for NextSeq was used to prepare libraries for sequencing.

value: REH

value: REH-Parental


title: ATAC REH-Resistant

value: REH-Resistant

value: Anti-CD19 Immunotoxin


title: 97A

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
RNA-seq reads were aligned to hg19 using STAR aligner
Reads were annotated to transcripts using Gencode v18 annotation
Assembly: Gencode v18
Supplementary files format and content: CSV file includes raw counts for each samples

source_name: ventral white matter (BA 47)

extract_protocol:
Total RNA was isolated from ~30-50 mg white matter tissue using RNeasy Lipid Tissue Mini Kit (Qiagen, #74804) according to the manufacturer’s instructions
Globin mRNA was removed from total RNA using GLOBINclear (Invitrogen/Ambion). Next, RNA samples were subject to Ribo-zero depletion, and libraries prepared using the Illumina Truseq library preparation kit and sequenced on the Illumina HiSeq 2500 (2 x 50), generating a mean of 48 million reads per sample.

value: ventral white matter (BA 47)

tag: diagnosis

value: MDD

tag: suicide

value: Y

tag: age


title: EPNPFA1-1010

city: Aurora

first: Andrew

last: Donson

institute: CU Anschutz Medical Campus

data_processing:
High quality base calls at Q30>80% were obtained for 50 million 150bp paired-end reads and mapped to the human genome (CRCh38) by STAR 2.4.0.1.
Assembly: Hg38
Supplementary files format and content: Quantification of RNA expression, as fragments per kilobase per million (FPKM), was derived by Cufflinks, which is provided here

extract_protocol:
RNA was isolated snap frozen PFA samples using an Allprep DNA/RNA mini kit (Qiagen) per manufacturers instructions
Libraries were prepared using the Tecan Universal Plus mRNA-Seq library preparation kit per manufacturers instructions

tag: tissue

value: ependymoma, posterior fossa group A1

value: M


title: RNA REH-Resistant

data_processing:
reads were trimmed of adapters with trim_galore
reads were aligned to the reference genome with tophat2
genes were counted with htseq using the gencode.v24 primary assembly
Assembly: hg38
Supplementary files format and content: tab delimited txt file with Ensembl identifier and count columns

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA was eluted in RNAse free water. At least 1ug of total RNA was used to prepare libraries.
RNA libraries were prepared using TruSeq RNA library prep kit (Illumina) as per protocol.

tag: cell line

tag: genotype

value: anti-cd19 immunotoxin


title: 94A


title: PA-1034-1

value: TUMOR-PA

tag: tumor full_name

value: pilocytic astrocytoma

tag: treatment


title: DIPG-1009

source_name: TUMOR-DMG

value: TUMOR-DMG

value: diffuse midline glioma

tag: Sex

tag: tumor stage

value: Presentation


title: Yy1_DEL_3341

value: bone marrow

tag: cell type


title: 93A

value: F


title: Yy1_DEL_3329

value: LSK (Lin-Sca1+c-Kit+)


title: 8A


title: Yy1_DEL_3325


title: 84A


title: 89A

value: Normal

value: N


title: Ly19_EZH2Y646F_EPZ6438_rep2 [D1480T61 RNA-Seq]

data_processing:
Adapters and low‐quality bases (<Q20) were removed from paired-end reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were then mapped to the human reference genome hg19 using the STAR (v2.7.0a) aligner and the corresponding gene annotation from GENCODE: release 19/GRCh37.p13. The following parameters were used for mapping of RNA-Seq reads against the reference genome: --seedSearchStartLmax 20 --outSAMattributes NH HI NM MD --alignEndsType EndToEnd.
Gene counts were generated using FeatureCounts (Subread v1.5.1).
Assembly: hg19 for OCI-Ly19 and FL libraries.
Supplementary files format and content: Processed data files include raw gene counts.

growth_protocol: OCI-Ly19 cells were grown in RPMI medium supplemented with 10% FBS.

extract_protocol:
RNA was extracted using the RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. cDNA was further obtained using the High Capacity cDNA RT kit.
RNA from FL samples was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed on an automated Tapestation 4200 platform. RNA Integrity Numbers (RINs) were used to evaluate the integrity of RNA samples with > 7.0 considered intact and < 7.0 considered degraded.
OCI-Ly19 RNA-Seq libraries were prepared using the Swift Biosciences RNA library kit. FL RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: For EZH2 inhibitor treatments, control and EZH2 Y646F-expressing cells were grown in the presence of DMSO, 2mM UNC1999 or 3mM EPZ6438 for 10 days.

value: B cell lymphoma


title: 82A

value: ventral white matter (BA 47)


title: WT_719015


title: Ly19_EZH2Y646F_EPZ6438_rep1 [D1480T60 RNA-Seq]


title: 73A


title: 55A

value: MDD


title: WT_717751


title: 48A


title: 34A

value: Y


title: WT_714157


title: 24A


title: WT_714154


title: Ly19_EZH2Y646F_UNC1999_rep1 [D1480T58 RNA-Seq]


title: 15A


title: Ly19_EZH2Y646F_mock_rep1 [D1480T56 RNA-Seq]

value: mock


title: Smc3_Yy1_DEL_6039


title: Ly19_EZH2Y646F_UNC1999_rep2 [D1480T59 RNA-Seq]


title: 21A

value: M


title: 154A


title: 152A


title: 153A


title: 146A


title: Ly19_EV_EPZ6438_rep2 [D1480T55 RNA-Seq]

value: Empty vector


title: Smc3_Yy1_DEL_5094


title: Smc3_Yy1_DEL_6015


title: 142A


title: 141A


title: Ly19_EV_EPZ6438_rep1 [D1480T54 RNA-Seq]


title: 131A


title: Smc3_Yy1_DEL_5088


title: Ly19_EV_UNC1999_rep2 [D1480T53 RNA-Seq]


title: 44A


title: 104A


title: Ezh2 +/+ m649, D21 GSK-J4

city: Baltimore

first: Christine

middle: W

last: Gao

state: MD

address: 733 N. Broadway, Rm 406

institute: Johns Hopkins University School of Medicine

data_processing:
Reads were pseudoaligned to the GRCm38 transcriptome (Ensembl release 102) using Salmon 1.9.0 for paired-end reads, with selective alignment and GC bias correction enabled.
Raw transcript-level counts were imported and summarized to genes with tximeta 1.12.4.
Surrogate variables were accounted for with sva 3.42.0.
DESeq2 1.34.0 was used to perform differential expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited file with raw read counts and TPM for each sample.

source_name: osteoblast

growth_protocol: Bone marrow mesenchymal stem cells (BM-MSCs) were isolated from 10 wk-old mice and cultured at 37°C, 5% CO2, in MEM Alpha with 15% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/mL streptomycin. BM-MSCs were differentiated to osteoblasts by further supplementation of growth media with 0.05 mg/mL L-ascorbic acid, 10 mM β-glycerophosphoric acid, and 102 nM dexamethasone.

extract_protocol:
Cells were homogenized with TRIzol reagent, followed by phenol-chloroform separation. Total RNA was purified from the aqueous phase using the Zymo RNA Clean and Concentrator-5 kit with DNase I treatment.
Library preparation was performed with the NEBNext Ultra II RNA Library Prep kit in conjunction with NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: To test GSK-J4 as a therapeutic agent, cells were treated with either 2 µM GSK-J4 or an equivalent volume of vehicle (DMSO) for the first 7 days of osteoblast differentiation. Differentiation continued until sample collection on D21.

value: osteoblast

value: 2 uM GSK-J4

tag: strain

value: female


title: Ly19_EV_UNC1999_rep1 [D1480T52 RNA-Seq]


title: U21983

data_processing:
Reads were aligned to hg19 using STAR aligner
Reads were annotated to transcripts using Gencode v18 annotation
Assembly: Gencode v18 annotation
Supplementary files format and content: CSV file includes raw counts for each samples

source_name: Periperal blood

extract_protocol:
Blood was collected from all study participants using RNA Paxgene vacutainer tubes. PAXgene blood tubes were thawed quickly and brought to room temperature prior to total RNA isolation according to the manufacturer’s instructions, and Globin mRNA was removed using GLOBINclear (Invitrogen/Ambion).
RNA samples were subject to Ribo-zero depletion, and libraries prepared using the Illumina Truseq library preparation kit and sequenced on the Illumina HiSeq 2500 (2 x 50), generating a mean of 48 million reads per sample.

value: Periperal blood

tag: suicide attempt

tag: si group

value: No SI


title: Ly19_EZH2Y646F_mock_rep2 [D1480T57 RNA-Seq]


title: Ezh2 R684C/+ m648, D21 GSK-J4

tag: time


title: U21940

value: High SI


title: Ezh2 R684C/+ m638, D21 GSK-J4


title: ACP-1000-1

source_name: TUMOR-ACP

value: TUMOR-ACP

value: adamantinomatous craniopharyngioma

value: Presentation


title: U21888

value: N


title: Ly19_EV_mock_rep1 [D1480T50 RNA-Seq]

value: B cell lymphoma


title: Ezh2 +/+ m637, D21 GSK-J4


title: U21848


title: P28T4-593746 [D1327T30 RNA-Seq]

source_name: Follicular lymphoma

value: Follicular lymphoma

value: EZH2 mut.


title: U21838

value: MDD


title: 2011-29,SI-GA-B5

first: Samia

last: Ali

state: Massachusetts

address: 800 Washington Street

institute: Tufts Medical Center

description: 10x Genomics, S4 Flow Cell

data_processing:
Demultiplexing, barcode processing, gene counting were done using Cell Ranger software v6.0.1
Assembly: Fca126, GRCh38, mm10
Supplementary files format and content: Tab-separated values files, and matrix files

organism: Felis catus

source_name: Septal Tissue

extract_protocol:
Cryopreserved tissue was thawed in a 37°C water bath for 75 seconds. Nuclei were released from the tissue via dounce homogenization using a buffer containing Triton X-100 (0.1 v/v). The homogenate was filtered through a 10µM cell strainer and nuclei were pelleted (500 x g for 5 minutes at 4°C) and washed before being resuspended in 1% w/v BSA, 1X PBS, and  0.2 U/µL RNase inhibitor
Library was constructed according to manufacturers instructions (single cell 3' v3.1, 10x Genomics).

value: Septal Tissue

value: Heart Tissue

value: WT


title: U21844

value: F

value: Healthy control


title: U21824

value: M

value: Y


title: P16T3-609478 [D1327T28 RNA-Seq]


title: P162T3-593921 [D1327T29 RNA-Seq]


title: 109A

value: ventral white matter (BA 47)


title: Ezh2 R684C/+ m627, D21 GSK-J4

value: osteoblast

value: 2 uM GSK-J4

value: female


title: P42T2-522492 [D1327T27 RNA-Seq]

value: EZH2 wt


title: U21837

value: Periperal blood

value: No SI


title: U21796

value: High SI


title: 2011-26,SI-GA-A5

description: 10x Genomics, S4 Flow Cell


title: U21944

value: N


title: 2011-41,SI-GA-H4

description: 10x Genomics, S4 Flow Cell


title: Ezh2 R684C/+ m636, D21 GSK-J4


title: P124T2-628394 [D1327T26 RNA-Seq]

value: Follicular lymphoma

value: EZH2 mut.


title: Ezh2 +/+ m635, D21 GSK-J4


title: U21774

value: MDD


title: Ezh2 +/+ m626, D21 GSK-J4


title: Ly19_EV_mock_rep2 [D1480T51 RNA-Seq]

value: B cell lymphoma

value: Empty vector

value: mock


title: U21871

value: F

value: Healthy control


title: Ezh2 R684C/+ m622, D21 GSK-J4


title: 2011-34,SI-GA-G4

description: 10x Genomics, S4 Flow Cell

value: Septal Tissue

value: Heart Tissue

value: HOM


title: P93T3-442281 [D1327T25 RNA-Seq]


title: Ezh2 +/+ m621, D21 GSK-J4

value: osteoblast

value: 2 uM GSK-J4

value: female


title: 2011-33,SI-GA-F4

description: 10x Genomics, S4 Flow Cell


title: U21773

value: Periperal blood


title: P89T2-409205 [D1327T24 RNA-Seq]


title: Ezh2 R684C/+ m615, D21 GSK-J4


title: P14T2-531043 [D1327T23 RNA-Seq]


title: 2011-28,SI-GA-E4

description: 10x Genomics, S4 Flow Cell


title: U21734

value: No SI


title: Ezh2 +/+ m614, D21 GSK-J4


title: 2011-35,SI-GA-A4

description: 10x Genomics, S4 Flow Cell


title: U21732

value: M

value: Y

value: High SI


title: RNAseq_GBM4_shNOVA1KD2_2

first: Yuhki

last: Saito

address: 1230 York Ave

institute: Rockefeller University

data_processing:
CLIP: We followed standard/BruU-CLIP data analysis pipeline using CTK (https://zhanglab.c2b2.columbia.edu/index.php/Standard/BrdU-CLIP_data_analysis_using_CTK). The deposited fastq files are raw data before collapsing PCR duplicates.
CLIP: removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG), collapsing of exact sequences and stripping of random barcodes
CLIP: alignment with BWA (hg19). RNAseq: alignment with STAR (hg19)
CLIP: collapsing of PCR duplicates (unique CLIP tags)
CLIP: Peak calling by using unique CLIP tags
Assembly: hg19
Supplementary files format and content: Bedgraph files generated from NOVA1 or AGO unique CLIP tags and RNAseq reads for genome browser

source_name: GBM cells derived from a patient

growth_protocol: DMEM/N2/EGF/FGF medium. Detailed desription in accompanying paper.

extract_protocol:
GBM cells derived from a patinet were UV-irradiated and subjected to CLIP with  anti-NOVA1 antibody (ab183024 from Abcam) and anti-AGO antibody (2A8: from Dr. Zissimos Mourelatos) and RNAseq (shControl vs shNOVA1KD1 & 2).
CLIP: Partial RNase A digestion, linker ligation, reverse transcription, criculation and PCR amplificiation. RNAseq: Illumina High-throughput TruSeq RNA Sample preparation: ribozero or poly(A) selection.

value: GBM cells derived from a patient

value: GBM


title: Ezh2 +/+ m649, D21 DMSO

value: 0 uM GSK-J4


title: RNAseq_GBM4_shNOVA1KD2_1


title: Ezh2 R684C/+ m648, D21 DMSO


title: RNAseq_GBM4_shNOVA1KD1_2


title: 2011-38,SI-GA-B4

description: 10x Genomics, S4 Flow Cell


title: Ezh2 +/+ m637, D21 DMSO


title: Ezh2 R684C/+ m638, D21 DMSO


title: RNAseq_GBM4_shNOVA1KD1_1


title: 15-098,SI-GA-D4

description: 10x Genomics, S4 Flow Cell


title: 15-071,SI-GA-C4

description: 10x Genomics, S4 Flow Cell


title: U21675

value: MDD

value: N


title: U21663

value: F


title: U21755

value: Healthy control


title: U21639


title: input3

data_processing:
Raw reads were filtered by BGI to remove adapter sequences and low quality reads.
Cleaned reads were aligned to reference genomes (Rnor6.0) using STAR with de novo junction discovery and summarized at the gene level using featureCounts.
Differential expression analysis was completed using DESeq2 using the standard workflow.
Assembly: Rnor6.0
Supplementary files format and content: csv file containing raw counts for each gene for each sample.

source_name: neonatal rat ventricular cardiomyocyte

growth_protocol: Neonatal murine ventricular cardiomyocytes were freshly isolated from rat ventricular tissue at P1-2. Ventricles were enzymatically dissociated in ADS buffer (116.3mM NaCl, 19.9mM HEPES, 10.8mM NaH2PO4, 5.5mM glucose, 5.4mM KCl, and 0.83mM MgSO4) containing 5mg/mL Type II Collagenase, 1mg/mL Pancreatine, and 5U/mL DNAseI. Dissociated cells were passed through a 70μm filter and pre-plated on uncoated tissue culture plastic for at least 1.5 hours at 37°C to deplete non-myocytes. Ventricular myocytes were then collected, pelleted, resuspended, and plated on gelatin-coated tissue culture dishes at a density of 1.25*105 cells/cm2. Cells were transduced with adenoviruses at the time of plating at an MOI of 100. Plating media (67.2% DMEM, 16.8% M199, 10% horse serum, 5% fetal bovine serum, 1% penicillin/streptomycin) was used for the first 24 hours of culture after which cells were maintained in maintenance media (46.9% DMEM, 46.9% M199, 5% fetal bovine serum, 1% penicillin/streptomycin, 0.2% insulin-transferrin-selenium, 0.1% chemically defined lipid).

extract_protocol:
Total RNA was extracted using TRIzol and the Qiagen RNeasy kit.
Libraries were prepared at BGI using their standard approach based on the DNBseq platform.

treatment_protocol: Cells were adenovirally transduced with a FLAG-tagged MBNL1 construct (AdMBNL1-FL, MOI 100) for 48hours. Myocytes were scraped in cold 1X PBS and pelleted by centrifugation for 3 minutes at 1000rpm. Cells were then lysed in RIP buffer [150mM KCl, 25mM Tris-HCl pH 7.4, 5mM EDTA, 0.5% NP-40, 0.5mM DTT, 100U/mL RNAse OUT Recombinant Ribonuclear Inhibitor (ThermoFisher 10777019), and 1X complete EDTA-free Protease Inhibitor Cocktail (Sigma 11836170001)]. Lysates were mechanically sheared by Dounce homogenization with a type B (tight) pestle using 18 strokes. Nuclear membrane and debris were pelleted by centrifugation at 13000 rpm for 10 minutes at 4°C. For each IP, 10% of the input lysate was placed directly into TRIzol; remaining lysates were then incubated overnight with 5μg of either Rabbit-anti-FLAG (Sigma F7425) or Rabbit IgG Isotype control (Cell Signaling 3900S) antibody at 4°C with gentle rotation. Following overnight incubation, 40μL of Dynabeads Protein A (ThermoFisher 10001D) were washed 6x in RIP buffer and then added to RIP lysates for 1 hour at 4°C with gentle rotation. Beads and bound material were collected using a DynaMag magnet, and the beads were washed 6x in RIP buffer and 1x in PBS containing 0.5mM DTT, 100U/mL RNAse OUT, and 1x complete EDTA-free Protease Inhibitor Cocktail. Following washing, TRIzol was added to isolate bound RNA.

value: neonatal rat ventricular cardiomyocyte

tag: condition

value: Input


title: input2


title: RNAseq_GBM4_shControl_2


title: Ezh2 R684C/+ m636, D21 DMSO

value: osteoblast


title: RNAseq_GBM4_shControl_1


title: Ezh2 +/+ m635, D21 DMSO


title: U21633


title: RNAseq_GBM3_shNOVA1KD2_2


title: U21702


title: flag3

value: RIP


title: Ezh2 R684C/+ m627, D21 DMSO

value: female


title: U21593

value: Periperal blood

value: Low SI


title: flag2


title: U21586


title: flag1


title: RNAseq_GBM3_shNOVA1KD1_1


title: RNAseq_GBM3_shControl_2


title: U21570


title: Ezh2 +/+ m621, D21 DMSO


title: U21517


title: CnR8_YAP

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

description:
CUT&RUN-seq
n/a

data_processing:
Base calling was performed using Illumina's CASAVA software or FASTQ generation software v1.0.0 and the quality of the generated FASTQ files was analyzed with FastQC.
For Cut&Run sequencing, fastq-files were imported to the Galaxy web-based analysis portal and reads were aligned to the human genome (hg19) using Bowtie2. All paired CUT&RUN reads were filtered by using a Phred score cutoff of 30 and mitochondrial reads were removed. Peaks were called with MACS2.
DeepTools 2 was used to create CUT&RUN profiles. First, normalized bigWig files were created using bamcoverage with a bin size of 10 and normalizing to counts per million reads mapped (CPM). BigWig files were used to compute reads centered on YAP-seq peak summits (called with MACS2) using computeMatrix. Profiles were created with plotProfile tools. CUT&RUN data were visualized with the Integrated Genome Viewer.
Assembly: hg19
Supplementary files format and content: For CUT&RUN-seq, the provided processed files are bigwig files for data display in a genome browser.
Library strategy: CUT&RUN

growth_protocol: Uveal melanoma cells (92.1) were maintained in RPMI-1640 medium supplemented with with 10% FCS and 1% penicillin/ streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
For Cut&Run sequencing, cells were washed twice and then coupled to ConA-coated magentic beads (Polysciences Europe). Cells were resuspended with antibody buffer (0.005% digitonin and 2 mM EDTA). Then cells were incubated with the antibody (see for details above) for 2 hours at RT. Cells were then washed in the presence of digitonin and 700 ng/ml MNase was added per sample for 1 hour at 4°C, followed by two more washes.
Following the initial washes, the MNase treated cells were washed once in low salt rinse buffer and then incubated in buffer containing CaCl2 and digitonin to activate the protein A-MNase. The DNA was digested for 30 min on ice and the Mnase activity was then stoped in the presence of 50 µg/ml Rnase A. DNA fragments were released at 37°C for 30 min and the decrosslinking was done for 1 hour at 50°C in the presence of Proteinase K. DNA was extracted wit phenol-chloroform and DNA was precipitated with ethanol and resuspended in TE buffer.
In some cases (Cut&Run samples where antibodies were used for H3K4me1, H3K4me3, H3K27ac and H4ac), a 1 min crosslinking with 1% formaldehyde was performed. In these cases, all buffers were used without digitonin and instead 0.05% SDS and 0.1% Triton X-100 were added to the wash buffer.
The DNA libraries were prepared with 6 ng of CUT&RUN DNA fragments, using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. The libraries were PCR-amplified with 15 PCR cycles using the NEBNext Multiplex Oligos for Illumina Kit. The libraries were purified using Agencourt AMPure XP beads (Beckman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
followed by sequencing.

treatment_protocol: The 92-1 cells were not specifically treated for the Cut&Run experiment.

value: Uveal Melanoma

tag: cell cycle synchronization

value: unsynchronized

tag: specifics for sample preparation

value: not applicable

tag: spike-in

tag: chip/cut&run antibody

value: YAP1 (NB110-58358; Novus Biologicals)


title: U21514

tag: tissue

tag: age

value: M

tag: diagnosis

value: No SI


title: RNAseq_GBM3_shNOVA1KD2_1

value: GBM cells derived from a patient

tag: genotype

value: GBM


title: Ezh2 +/+ m614, D21 DMSO

tag: treatment

value: 0 uM GSK-J4


title: U21511

tag: Sex

value: F

value: MDD

value: Y

value: High SI


title: CnR8_H4ac

description:
CUT&RUN-seq
n/a

tag: cell line

value: Acetyl Histone H4 (#06-598; Merck)


title: CnR8_IgG_merged

description:
CUT&RUN-seq
n/a

tag: cell type

value: merge of two IgG samples

value: IgG (control)


title: Ezh2 R684C/+ m748, D14 untreated, rep2

value: osteoblast

value: untreated

tag: strain

value: female


title: U21621

value: Periperal blood

tag: suicide attempt

value: N


title: CnR3_H3K27ac

description:
CUT&RUN-seq
n/a

value: Uveal Melanoma

value: unsynchronized

value: not applicable


title: Ezh2 +/+ m626, D21 DMSO


title: Ezh2 R684C/+ m748, D14 untreated, rep1


title: RNAseq_GBM2_shNOVA1KD2_1

value: GBM cells derived from a patient

value: GBM


title: RNAseq_GBM2_shNOVA1KD2_2


title: U21499

value: F

tag: si group


title: U-WT-3

city: Guangzhou

first: Chengjie

last: Geng

state: 广东

address: 广东省广州市天河区黄埔道西601

department: Life and Science Department

institute: Jinan University

data_processing:
Gene expression quantification was performed using StringTie software
DEseq2 (1.26.0) software was used for differential expression analysis between sample groups
Assembly: GRCh38.103
Supplementary files format and content: tab-delimited list file includes raw counts for each Sample
Supplementary files format and content: tab-delimited list file includes FPKM vakues for each Sample

source_name: adult lymphoma

growth_protocol: U2932 cells  cells were maintained in Dulbecco's modified Eagle medium containing 10% fetal bovine serum in a humidified 5% CO2 incubator at 37 °C.

extract_protocol:
RNA extraction was done using TRIzol Reagent.1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols

treatment_protocol: 1 × 105  U2932 cells were treated with 100 μM artesunate or DMSO  for 24 h.

value: adult lymphoma

value: diffuse large B-cell lymphoma cells

value: WT


title: input1

first: Jennifer

last: Davis

institute: University of Washignton

value: neonatal rat ventricular cardiomyocyte

value: Input


title: RNAseq_GBM3_shNOVA1KD1_2


title: RNAseq_GBM2_shNOVA1KD1_2


title: Ezh2 R684C/+ m622, D21 DMSO

value: 0 uM GSK-J4

tag: time


title: U21473

value: MDD

value: High SI


title: RNAseq_GBM3_shControl_1


title: Ezh2 +/+ m740, D14 untreated, rep2

value: osteoblast

value: untreated

value: female


title: RNAseq_GBM2_shNOVA1KD1_1


title: U-WT-2

address: 广东省广州市天河区黄埔道西601


title: U-WT-1

address: 广东省广州市天河区黄埔道西601


title: Ezh2 R684C/+ m615, D21 DMSO


title: Ezh2 +/+ m740, D14 untreated, rep1


title: Ezh2 R684C/+ m739, D14 untreated, rep2


title: Ezh2 R684C/+ m739, D14 untreated, rep1


title: U21434

value: Periperal blood

value: Y


title: U21448

value: Healthy control

value: N

value: No SI


title: RNAseq_GBM2_shControl_2

value: GBM cells derived from a patient

value: GBM


title: U-A-2

address: 广东省广州市天河区黄埔道西601

value: adult lymphoma

value: diffuse large B-cell lymphoma cells

value: 100 microM artesunate


title: RNAseq_GBM2_shControl_1


title: U-A-3

address: 广东省广州市天河区黄埔道西601

value: WT


title: Ezh2 R684C/+ m729, D14 untreated, rep2


title: U21425

value: M


title: RNAseq_GBM1_shNOVA1KD2_1


title: Ezh2 R684C/+ m729, D14 untreated, rep1


title: RNA REH-Parental

value: REH

value: REH-Parental


title: U-A-1

address: 广东省广州市天河区黄埔道西601


title: U21422

value: MDD


title: RNAseq_GBM1_shNOVA1KD1_2


title: U21414

value: F


title: Ezh2 +/+ m728, D14 untreated, rep2

value: osteoblast

value: untreated

value: female


title: RNAseq_GBM1_shNOVA1KD1_1


title: U21440

value: Periperal blood

value: Y

value: High SI


title: D6-ZFP-VP64-screen

city: Melbourne

first: Charles

last: Bell

state: VICTORIA

address: VCCC, Gate 1, 14 Flemington Road

department: Cancer Research

institute: Peter MacCallum Cancer Centre

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
Assembly: Hg19
Supplementary files format and content: Guide Counts file

source_name: Haematopoetic

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37C).

extract_protocol:
Genomic DNA was extracted using Monarch Genomic DNA purification kit
PCR was conducted to maintain guide representation, using Q5 High Fidelity DNA Polymerase

treatment_protocol: K562 cells containing Cas9 were infected with a sgRNA library. For the transcription screens, GFP negative, guide positive cells were sorted on D5, D6 and D7 after guide infection. For dropout screen, cells were grown until D14, before being isolated for sequencing.

value: Haematopoetic


title: D7-ZFP-VP64-screen


title: Ezh2 +/+ m728, D14 untreated, rep1


title: RNAseq_GBM1_shControl_2

value: GBM cells derived from a patient

value: GBM


title: Ezh2 +/+ m722, D14 untreated, rep2


title: D5-ZFP-VP64-screen


title: U21383

value: N


title: U21360


title: RNAseq_GBM1_shNOVA1KD2_2


title: U21335

value: No SI


title: Ezh2 +/+ m722, D14 untreated, rep1


title: RNAseq_GBM1_shControl_1


title: GIST-T1, InsH, RCMC rep2

first: Kyung Lock

last: Kim

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC hg38 genome using Juicer (default setting, version 1.6).
Deduplicated paired reads were filtered by mapping quality score (MAPQ ≥ 30) and filtered to retain those reads where both read mates lay within the capture region of interest (chr11:69.4-70.4Mb).
These filtered reads were converted to contact matrices (.hic format file) using Juicerbox_Tools with Pre at base pair delimited resolutions of 1 Mb, 500 kb, 100 kb, 25 kb, 10 kb, 5 kb, 1 kb and 500 bp. All contact matrices used for further analysis were KR-normalized with Juicer.
Assembly: hg38
Supplementary files format and content: hic files contains all valid Micro-C pairs with multiple resolutions

growth_protocol: GIST-T1 cell line was obtained from Cosmo Biosciences. Cells were passaged in DMEM with 10% serum, 1X antibiotics and 1X Glutamax (Life Technologies).

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified by phenol chloroform extraction and DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-8 PCR cycles on the thermocycler and purified using AMPure XP beads (Beckman Coulter). Purified libraries were pooled in a 1:1 ratio to a total of 2-4 µg of DNA. Following the Twist Standard Hybridization Target Enrichment Protocol (Twist Biosciences), this library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 9 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). The target enriched library pool was submitted for sequencing.
Micro-C

value: cell line established from a metastatic GIST

value: InsH


title: D6-ZFP-VP64-library-control


title: GIST-T1, InsG, RCMC rep2

value: InsG


title: U21333


title: Ezh2 +/+ m721, D14 untreated, rep1


title: D5-ZFP-VP64-library-control


title: Ezh2 R684C/+ m720, D14 untreated, rep2


title: U21331


title: GIST-T1, InsE, RCMC rep2

value: InsE


title: U21328

value: M

value: MDD


title: U21384


title: Ezh2 R684C/+ m720, D14 untreated, rep1

value: osteoblast


title: GIST-T1, control, RCMC rep2

value: WT


title: D7-ZFP-VP64-library-control


title: Ezh2 R684C/+ m719, D14 untreated, rep2

value: untreated

value: female


title: R47H_B_1

city: Cambridge

first: Jay

last: Penney

address: 77 Massachusetts Avenue

department: Picower Institute

institute: Massachusetts Institute of Technology

data_processing:
Reads were aligned to the human genome reference GRCh38/hg38 using the R software package Rsubread
Mapped reads were converted to gene level counts using the featureCounts function of Rsubread with “strandSpecific” parameter set to 0
Differential analysis was performed using DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: Excel file contains raw counts for each sample

source_name: iPSC

growth_protocol: iPSCs were differentiated to iPSC-microglia per McQuade et al., 2018 and grown in iMBM media supplemented with 25 ng/mL mCSF and 100 ng/mL IL34.

extract_protocol:
RNA was extracted using the QIAGEN Rneasy Plus mini kit.
Libraries for RNA-seq were generated using NEB Ultra II kit following manufacturers protocols.

treatment_protocol: Initial RNA-seq was performed on untreated cells. Inflammatory treatments were performed with either 50 ng/mL IFNgamma or 100 ng/mL LPS for 2 hours before collection of RNA for sequencing.

value: iPSC

value: iPSC-microglia

value: TREM2 R47H/+


title: GIST-T1, InsH, RCMC rep1


title: U21272

value: Periperal blood

value: F


title: R47H_B_2


title: U21269

value: N


title: R47H_A_3


title: Ezh2 +/+ m721, D14 untreated, rep2


title: GIST-T1, InsG, RCMC rep1


title: GIST-T1, InsF, RCMC rep1

value: InsF


title: U21259

value: Y

value: High SI


title: Ezh2 +/+ m709, D14 untreated, rep2


title: R47H_A_2


title: GIST-T1, InsF, RCMC rep2

value: cell line established from a metastatic GIST


title: Ezh2 R684C/+ m719, D14 untreated, rep1


title: Ezh2 +/+ m709, D14 untreated, rep1


title: R47H_A_1


title: GIST-T1, InsE, RCMC rep1

value: InsE


title: CTRL_B_3


title: GIST-T1, control, RCMC rep1


title: R47H_B_3


title: Ezh2 R684C/+ m705, D14 untreated, rep2


title: U21249

value: Healthy control

value: No SI


title: Ezh2 R684C/+ m705, D14 untreated, rep1

value: osteoblast


title: CTRL_B_2

value: WT


title: U21313

value: MDD


title: R47H_B_2_LPS

value: 100 ng/mL LPS, 2 hrs


title: U21253

value: M


title: D30, Adult3

city: Ithaca

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
trim_galore (with cutadapt) was used to trim and filter reads.
hisat2 was used to map reads to the mouse mm10.
featureCounts was used to count  reads to exons (-s 0 -Q 50).
Assembly: mm10
Supplementary files format and content: raw counts: Matrix table with raw gene counts for every gene and every sample

source_name: CD8+ T cells

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a Qubit and integrity assessed on a Fragment Analyzer.
RNA-seq libraries were prepared from 10ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial [polyA+ isolation/rRNA depletion].

tag: developmental stage

value: Adult

value: CD8+ T cells

value: P14 TCR Transgenic

tag: infection

value: LCMV clone 13 infection (in vivo)

value: 30 days post infection


title: CTRL_B_1

value: iPSC

value: iPSC-microglia


title: U21232

value: Periperal blood

value: N


title: U21239

value: F

value: High SI


title: R47H_A_2_LPS

value: TREM2 R47H/+


title: CTRL_A_3


title: D30, Adult1


title: D30, Adult2


title: R47H_B_1_LPS


title: CTRL_A_2


title: U21223

value: No SI


title: U21220

value: Y


title: R47H_B_2_IFN

value: 50 ng/mL IFNg, 2 hrs


title: U21221

value: MDD


title: CTRL_A_1

value: WT


title: D30, Neonate2

value: neonatal


title: U21181

value: M


title: U21219

value: Healthy control


title: R47H_A_2_IFN


title: D30, Neonate1

value: CD8+ T cells

value: P14 TCR Transgenic

value: LCMV clone 13 infection (in vivo)


title: DPSC-OCT4_rep2

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

institute: Australian National University

data_processing:
Single-end RNA sequencing reads were aligned to the GRCh37 version of the human genome using STAR.
Gene expression was quantified using featureCounts, using GRCh37 gene annotation obtained from Ensembl (vep_95_GRCh37).
Differential gene expression analysis was performed using R/Bioconductor packages limma-voom and edgeR. Significance was set at a false discovery rate (FDR) <0.05 and differentially expressed genes (DEGs) were selected using a log2 fold change (logFC) > +2/-2
Functional enrichment analysis of DEGs was performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases and Molecular Signatures Database (MSigDB) v7.1.
Assembly: GRCh37.75
Supplementary files format and content: Tab-delimited text file

source_name: Dental pulp

extract_protocol:
RNA was extracted from cells using the PureLink™ RNA Mini Kit (Invitrogen). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Universal Plus™ mRNA-Seq Library Preparation Kit (NuGEN Technologies Inc.) following manufacturer’s protocols.
mRNA-seq single end

value: Dental pulp

value: Dental pulp stem cells

value: OCT4-lentiviral transduction and neural induction


title: R47H_A_1_IFN

value: iPSC

value: iPSC-microglia


title: DPSC-OCT4_rep3


title: Clone13, Neo 3

value: wildtype

value: 8 days post infection


title: U21177

value: Periperal blood

value: F

value: N

value: Low SI


title: Clone13, Neo 2

value: neonatal


title: R47H_B_2_UNTR

value: TREM2 R47H/+


title: U21174

value: M

value: MDD

value: Y

value: High SI


title: R47H_B_1_IFN

value: 50 ng/mL IFNg, 2 hrs


title: DPSC-OCT4_rep1

value: Dental pulp

value: Dental pulp stem cells


title: Clone13, Neo 1

value: CD8+ T cells

value: LCMV clone 13 infection (in vivo)


title: D30, Neonate3

value: P14 TCR Transgenic

value: 30 days post infection


title: R47H_A_1_LPS

value: iPSC

value: iPSC-microglia

value: 100 ng/mL LPS, 2 hrs


title: R47H_B_1_UNTR


title: Clone13, Adult 3

value: Adult

value: wildtype

value: 8 days post infection


title: DPSC-EV_rep4

value: control

value: empty lentiviral transduction and neural induction


title: U21154

value: Periperal blood

value: F

value: Healthy control

value: N

value: No SI


title: R47H_A_2_UNTR

value: TREM2 R47H/+


title: DPSC-OCT4_rep4

value: Dental pulp

value: Dental pulp stem cells

value: OCT4-lentiviral transduction and neural induction


title: DPSC-EV_rep3


title: DPSC-EV_rep2


title: U21148

value: M


title: R47H_A_1_UNTR

value: iPSC

value: iPSC-microglia


title: Clone13, Adult 2

value: Adult

value: CD8+ T cells

value: LCMV clone 13 infection (in vivo)


title: U21143

value: MDD

value: Low SI


title: Clone13, Adult 1

value: wildtype

value: 8 days post infection


title: CTRL_B_2_LPS

value: WT

value: 100 ng/mL LPS, 2 hrs


title: DPSC_rep4

value: standard growth conditions


title: DPSC_rep3


title: mPFC, SUS, 3

city: Seoul

first: Sihwan

last: Seol

address: 84, Heukseok-ro

country: South Korea

institute: Chung-Ang University

data_processing:
Preprocessing was performed to eliminate artifacts (low quality, adapter sequence, contaminated DNA, or PCR duplicates) from sequenced raw reads by using Trimmomatic (version 0.38).
The preprocessed reads were mapped to the reference genome (mm10) by using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.1.0) program, which can handle spliced reads through Bowtie2 aligner, to generate aligned reads.
StringTie (version 1.3.4d) was used for transcript assembly and quantification.
Assembly: mm10
Supplementary files format and content: a csv file include normalized values, FPKM values, read counts for each sample

source_name: brain

extract_protocol:
The RNA was isolated with the RNeasy Micro kit (74004, QIAGEN, Hilden, Germany)
Total RNA was transformed into cDNA libraries by using the TruSeq Stranded Total RNA LT Sample Prep Gold kit in accordance with the manufacturer’s instructions (Illumina, USA).

value: brain

value: male

tag: treatment (phenotype)

value: chronic unpredictable stress (susceptible)

tag: group

value: SUS


title: U21127

value: Periperal blood

value: M

value: N

value: High SI


title: CTRL_B_1_LPS

value: iPSC

value: iPSC-microglia


title: CTRL_A_2_LPS


title: U21091

value: F

value: MDD


title: DPSC_rep2

value: Dental pulp

value: Dental pulp stem cells


title: CTRL_B_2_IFN

value: WT

value: 50 ng/mL IFNg, 2 hrs


title: mPFC, SUS, 1


title: U21015

value: Y

value: No SI


title: mPFC, RES, 3

value: brain

value: male

value: chronic unpredictable stress (resilient)

value: RES


title: DPSC_rep1

value: standard growth conditions