title: S1

city: Wuhan

first: Junlin

last: Chen

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Brassica_napus.ZS11.v0.genome.fa
Raw reads were processed using fastp.
Reads were aligned to brassica napus reference genome （Brassica_napus.ZS11.v0.genome.fa）using hisat2.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Brassica napus

source_name: cotyledon

growth_protocol: growth in 1/2MS medium addition 1% suc

extract_protocol:
Toal RNA was extracted by using Eastep® Super Total RNA Extraction Kit (Promega) from cotyledon with three replications
mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads, and mRNAs were obtained by removing ribosomal RNAs from the total RNAs.

treatment_protocol: under dark for 4D, and then transferred to normal condition for 6h.

value: cotyledon

value: mutant

value: growth in 1/2MS medium addition 1% suc in dark for 4D, and then transferred to normal condition for 6h.


title: S2

status: Public on Dec 30 2023

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: genotype

tag: treatment


title: WT_GMP_rep2

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

country: USA

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA from cells was isolated using the TRIzol reagent
Libraries were prepared using the SMART-Seq v4 UltraTM Low Input kit (Takara Bio, #634891) followed by Illumina’s Nextera XT DNA Library Preparation kit (FC-131-1096, Illumina)

treatment_protocol: Cells were FACS-sorted from bone marrow and assayed subsequently by RNA-Seq

tag: strain background

tag: genotype/variation

value: wild type

value: bone marrow (BM)

tag: cell type


title: W1

value: WT


title: SP53, PRMT5 Sensitive Untreated 3

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

description:
SP53 DMSO 3
SSU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

data_processing:
STAR two-pass alignment and featureCounts
Pairwise comparisons within each cell type for treatment vs control with DESeq2
Assembly: hg38 and Gencode v33
Supplementary files format and content: tab-delimited text files

organism: Homo sapiens

source_name: lymphoma

growth_protocol: PDX in vivo

extract_protocol:
Total RNA was extracted using the Total RNA Purification Kit (Norgen Cat#17200) and QIAshredder Columns (Qiagen Cat#79654). RNA integrity was interrogated using the Agilent 2100 Bioanalyzer.
TrueSeq stranded mRNA libraries were prepared with Poly-A selection Ribodepletion library prep

value: lymphoma

tag: cell line

value: Mantle Cell Lymphoma

value: MCL

value: DMSO


title: WT_LSK_rep3

value: Lin-Sca1+cKit+ (LSK)


title: S3


title: SP53, PRMT5 Sensitive Treated 3

description:
SP53 PRT 3
SSPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: YTHDF1_KD_H1_YTHDF1_rep2

city: Guangzhou

first: Jingyuan

last: Zhang

address: 190 Kaiyuan Avenue,Science Park

institute: Guangzhou National Labratory

library_source: genomic

data_processing:
ChIP-seq Replicates were merged into one BED file.
ChIP-seq reads were were filtered by Trimmomatic (v0.35) parameters.
ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.2.5).
PCR duplicate reads were removed using SAMtools (v1.3.1) (with the parameters "-F 1804 -f 2 -q 30") and Picard tools MarkDuplicates (v1.90).
Peak calling was performed using the MACS2 (v2.1.0) callpeak module (with parameters "-p 0.01 --nomodel --extsize 150 -B --SPMR --keep-dup all") for transcription factor binding, and then peaks with q-value less than 1e-4 (RNF2) or 1e-1.5 (YTHDF1) were chosen for further analysis.. Enriched regions for histone modification were called at the FDR level of 1% using SICER (v1.1) with window sizes set to 200 bp, and gap sizes set to 600 bp.
Tracks of signal were computed using MACS2 bdgcmp module with parameter "-m FE".
Assembly: hg38
Supplementary files format and content: wig files present normalized signal density.
Supplementary files format and content: text files contain peak information.

molecule: genomic DNA

source_name: YTHDF1 KD human embryonic stem cells

growth_protocol: hESCs were cultured in mTESR1(STEMCELL Technologies)

extract_protocol:
Lysates were clarified from sonicated  histone-DNA complexes were isolated with antibody.
Libraries were prepared using a VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme).

value: Embryonic stem cells

value: treated with YTHDF1 shRNA

value: YTHDF1 KD H1


title: YTHDF1_KD_H1_YTHDF1_rep1


title: W3


title: ChIP-seq_YTHDF1_KD_H1_input

data_processing:
ChIP-seq reads were were filtered by Trimmomatic (v0.35) parameters.
ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.2.5).
PCR duplicate reads were removed using SAMtools (v1.3.1) (with the parameters "-F 1804 -f 2 -q 30") and Picard tools MarkDuplicates (v1.90).
Peak calling was performed using the MACS2 (v2.1.0) callpeak module (with parameters "-p 0.01 --nomodel --extsize 150 -B --SPMR --keep-dup all") for transcription factor binding, and then peaks with q-value less than 1e-4 (RNF2) or 1e-1.5 (YTHDF1) were chosen for further analysis.. Enriched regions for histone modification were called at the FDR level of 1% using SICER (v1.1) with window sizes set to 200 bp, and gap sizes set to 600 bp.
Tracks of signal were computed using MACS2 bdgcmp module with parameter "-m FE".
Assembly: hg38
Supplementary files format and content: wig files present normalized signal density.
Supplementary files format and content: text files contain peak information.

tag: chip antibody

value: none (input)


title: SP53, PRMT5 Sensitive Untreated 1

description:
SP53 DMSO 1
SSU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: SP53, PRMT5 Sensitive Treated 1

description:
SP53 PRT 1
SSPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: W2


title: SP53, PRMT5 Resistant Treated 3

description:
SP53 PR PRT 3
SRPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: SP53, PRMT5 Sensitive Untreated 2

description:
SP53 DMSO 2
SSU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: SP53, PRMT5 Resistant Treated 2

description:
SP53 PR PRT 2
SRPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: KB_Naive_Spleen_Neutrophils, scRNA seq

city: Riverside

first: Emma

middle: Harriet

last: Wilson

state: CA

address: 900 University Avenue

institute: UC Riverside

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mus musculus Reference Genome
Supplementary files format and content: cloupe files, used to visualize and analyze data using Cloupe Browser

source_name: Purified from murine brain

extract_protocol:
Neutrophils were sorted from brain and spleen based on CD11b/Ly6G positivity. BMNCs and splenocytes were harvested as above at 4wpi. To obtain a large enough number of neutrophils for sequencing, 3 naïve and 3 infected mice were pooled for naïve and infected neutrophil splenocyte samples, and 7 infected mice were pooled for neutrophil BMNC sample. 3 separate infected mice were pooled for an unsorted BMNC control sample. Cells were incubated in fluorescent-conjugated antibodies for CD11b APCCy7 (Invitrogen) and Ly6G PE or PerCPCy5.5 (Clone 1A8; Invitrogen), rinsed, and resuspended at 1.0 x 107 concentration in FACS buffer with 10% FBS to minimize cell death during sorting. Neutrophils were sorted from pooled samples based on gating strategy of Ly6G+CD11b+ cells using a MoFlo Astrios EQ Cell Sorter at 3-4% pressure to maximize cell survival. Sorted cells were re-counted to determine viability, and a minimum of 1.0 x 104 sorted cells were used for single cell sequencing.   10x Sequencing and Analysis. Sorted Ly6G+CD11b+ cells and unsorted BMNC control sample were processed for single cell RNA sequencing according to 10x sample prep protocols for Steps 1-3 (Manual: CG000204 RevD); instructions were followed exactly. Time spent before loading sorted cells onto 10x Chromium controller for Step 1 was <1hr. Processed samples were analyzed after Steps 2 and 3 via Bioanalyzer by the UCR Genomics Core facility for viability and concentration before proceeding to next steps. Upon completion of the 10x protocol, samples were sent to the UC San Diego IGM Genomics Center for sequencing (500 million reads/sample).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Purified from murine brain

value: neutrophils


title: KB_Infected_Spleen_Neutrophils, scRNA seq

description: 10x Genomics


title: H1_input_rep1

data_processing:
ChIP-seq Replicates were merged into one BED file.
ChIP-seq reads were were filtered by Trimmomatic (v0.35) parameters.
ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.2.5).
PCR duplicate reads were removed using SAMtools (v1.3.1) (with the parameters "-F 1804 -f 2 -q 30") and Picard tools MarkDuplicates (v1.90).
Peak calling was performed using the MACS2 (v2.1.0) callpeak module (with parameters "-p 0.01 --nomodel --extsize 150 -B --SPMR --keep-dup all") for transcription factor binding, and then peaks with q-value less than 1e-4 (RNF2) or 1e-1.5 (YTHDF1) were chosen for further analysis.. Enriched regions for histone modification were called at the FDR level of 1% using SICER (v1.1) with window sizes set to 200 bp, and gap sizes set to 600 bp.
Tracks of signal were computed using MACS2 bdgcmp module with parameter "-m FE".
Genome_build: hg38
Supplementary_files_format_and_content: wig files present normalized signal density.
Supplementary_files_format_and_content: text files contain peak information.

source_name: Human embryonic stem cells

value: untreated


title: YTHDF1_KD_H1_input_rep1


title: H1_YTHDF1_rep1


title: mouse RPE-choroid complex AAV-PDGF-D rep1-2

first: Zhen

last: Xiong

address: No.7 Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
Single-cell RNA-sequencing data was pre-processed using Cell Ranger 6.1.0 using default settings from 10X Genomics
Cells with less than 500 genes detected, or greater than 10% mitochondrial genes were excluded from the analysis, as well as genes detected in less than 10 cells
Single-cell transcriptome analysis was performed using the Seurat 4.0 R packages with default functions
Genome_build: GRCm38
Supplementary_files_format_and_content: gzipped file format containing annotated Seurat object

source_name: RPE-choroid complex

extract_protocol:
To isolate viable single cells from RPE/choroid tissue, the mice were euthanized and then enucleated one eye for further processing. Each eye was cleaned from extraocular tissue and a circumpherencial incision was performed around the limbus cornea to remove the anterior segment, including cornea, lens, iris and ciliary body. The retina was carefully separated from the choroid, then each RPE-choroid tissue was cut into eight petals.  RPE/choroid tissue was digested with 200μL of solution containing 52U/ml Papain, Suspension (Worthington,LS003126),3mg/ml DNase I (BioFroxx,1121MG010) at 37°C for 15 min. Single cell suspension was created by pipetting up and down for several times with 10μL pipette , then filtered through a 45-µm cell strainer before being loaded onto the 10x Genomics Chromium instrument.
The scRNA-seq libraries were generated using the 10x Genomics Chromium Single Cell v3 reagent kit according to the manufacturer’s instructions

treatment_protocol: Female mice pupils (8 weeks old) with subretinal injection of AAV-PDGF-D or AAV-GFP after 4 weeks were used in the study.

tag: strain

value: RPE-choroid complex

value: RPE-specific AAV-PDGF-D


title: H1_RNF2_rep2


title: ChIP-seq_YTHDF1_KD_H1_H2AK119ub


title: ITD_LSK_rep3

value: Flt3-ITD (ITD)


title: ChIP-seq_H1_input


title: mouse RPE-choroid complex AAV-GFP rep1

value: RPE-specific AAV-GFP


title: ChIP-seq_H1_H2AK119ub


title: H1_YTHDF1_rep2


title: mESC_HPRT1R_clone2_PolII_ChIP_rep2

first: Brendan

middle: R.

last: Camellato

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Langone Health

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the GRCm38/mm10  genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 2652783500
Assembly: GRCm38/mm10  + HPRT1/HPRT1R, GRCm38/mm10 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

source_name: mESC, synHPRT1R integrated on chrX, clone 2, PolII ChIP, rep 2

growth_protocol: Cells were cultured in 80/20 medium, which consists of 80% 2i medium (1:1 mixture of Advanced DMEM/F12 (ThermoFisher 12634010) and Neurobasal-A (ThermoFisher 10888022) supplemented with 1% N2 Supplement (ThermoFisher 17502048), 2% B27 Supplement (ThermoFisher 17504044), 1% GlutaMAX™ (ThermoFisher 35050061), 1% Pen-Strep (ThermoFisher 15140122), 0.1 mM 2-mercaptoethanol (Sigma M3148), 1,250 U/mL LIF (ESGRO ESG1107l), 3 μM CHIR99021 (R&D Systems 4423), and 1 μM PD0325901 (Sigma PZ0162)), and 20% mESC medium (KnockOut™ DMEM (ThermoFisher 10829018) supplemented with 15% FBS (BenchMark 100106), 0.1 mM 2-mercaptoethanol, 1% GlutaMAX™, 1% MEM non-essential amino acids (ThermoFisher 11140050), 1% nucleosides (EMD Millipore ES-008-D), 1% Pen-Strep, and 1,250 U/mL LIF). mESCs were maintained on plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37oC in a humidified incubator with 5% CO2.

extract_protocol:
Cells were grown to medium confluency in 6-well plates. Cells were harvested by washing once with PBS, disso-ciating into single-cell suspending with TrypLE Express (ThermoFisher 12604013) and then neutralizing with mESC media. Crosslinking was performed by adding formaldehyde to a final concentration of 0.1% (v/v), and cells were incubated at room temperature for 5 minutes with occasional mixing by in-version. Crosslinking was stopped by quenching with 125 mM glycine, incubating at room temperature for 5 minutes with occasional mixing by inversion. DMSO was added to a final concentration of 10% (v/v) and cells were frozen in aliquots of ~106 cells.
~10^6 crosslinked and frozen mESCs were thawed and processed for CUT&RUN using the CUTANA™ ChIC/CUT&RUN kit (EpiCy-pher 14-1048) according to the manufacturer’s protocol. Antibodies were all used at 0.5 μg: rabbit IgG negative control (EpiCypher 13-0042), H3K4me3 (EpiCypher 13-0041), H3K27ac (EpiCypher 13-0045), H3K27me3 (Active Motif 39055, RRID: AB_2561020), Pol II (Santa Cruz Biotechnology sc-56767). Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs E7645L) according to the manufacturer's protocol.

value: BL6xCAST with synHPRT1R integrated on chrX


title: SP53, PRMT5 Resistant Untreated 1

description:
SP53 PR DMSO 1
SRU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: lymphoma


title: mouse RPE-choroid complex AAV-PDGF-D rep1-1


title: MUT1

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

description:
Sample_125893
miRNA

data_processing:
All RNA-seq data were mapped to the mm10 genome of human using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Aligned reads were assembled using Cufflinks (v2.2.1) and assembled transcriptome catalog were used as input for Cuffdiff2 to determine expression levels (FPKM, Fragments Per Kilobase per Million mapped reads) and differential expression between conditions using default options. Genes with p<0.01 were considered to be differentially expressing genes.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts and FPKM values data

source_name: Mouse Embryonic Fibroblast

growth_protocol: MEFs were cultured in DMEM supplemented with 15%  FBS ,1% NEAA

extract_protocol:
The miRNA was extracted using Trizol reagent (Ambion) and further purified according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for miRNA-seq libraries.

value: Mouse Embryonic Fibroblast

value: Fbxw7 KO


title: H1_input_rep2


title: YTHDF1_KD_H1_input_rep2


title: SP53, PRMT5 Resistant Untreated 2

description:
SP53 PR DMSO 2
SRU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: Mantle Cell Lymphoma

value: MCL

value: DMSO


title: MUT3

description:
Sample_125895
miRNA


title: SP53, PRMT5 Resistant Untreated 3

description:
SP53 PR DMSO 3
SRU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: H1_RNF2_rep1

value: Embryonic stem cells


title: CCMCL, PRMT5 Sensitive Treated 1

description:
CCMCL PRT 1
CSPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: CCMCL


title: MUT2

description:
Sample_125894
miRNA


title: H1_H2AK119ub_rep2


title: CCMCL, PRMT5 Sensitive Treated 2

description:
CCMCL PRT 2
CSPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: mESC_HPRT1R_clone2_PolII_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, PolII ChIP, rep 1


title: mESC_HPRT1R_clone2_IgG_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, IgG ChIP, rep 1


title: WT3

description:
Sample_125892
miRNA

value: WT


title: mESC_HPRT1R_clone2_IgG_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 2, IgG ChIP, rep 2


title: KB_Infected_BMNCs, scRNAseq

description: 10x Genomics

value: Purified from murine brain

value: brain mononuclear cells


title: mESC_HPRT1R_clone2_H3K4me3_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 2, H3K4me3 ChIP, rep 2


title: CCMCL, PRMT5 Sensitive Treated 3

description:
CCMCL PRT 3
CSPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: mESC_HPRT1R_clone2_H3K27ac_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, H3K27ac ChIP, rep 1


title: MUT-1

extract_protocol:
The RNA was extracted using Trizol reagent (Ambion) and further purified according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.


title: Bob2

first: fan

last: chen

state: Hubei

address: Nanhu Av. 4

institute: Hubei Academy of Agricultural Sciences

data_processing:
The quantification of all libraries was done using the High DNA Sensitivity Bioanalyzer 2100 (Agilent) and real time QPCR. All libraries were sequenced using 150bp paired-end on the Illumina Novaseq platform.
Raw RNA was filtered by Trimmomatic, and the sus scrofa reference genome (NCBI.Sscrofa10.2) was obtained.
Index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
Htseq-count was used to count the reads numbers mapped to each gene.
Differential expression analysis of Bobcat339 and Control groups were performed using the DESeq2 R package (1.16.1)
Assembly: NCBI.Sscrofa10.2
Supplementary files format and content: tab-delimited file includes COUNT and FPKM values for each Sample

organism: Sus scrofa

source_name: embryos

growth_protocol: The electro-activated oocytes were incubated in PZM-3 containing 7.5 µg/mL of cytochalasin B for 3 h. Next, they were washed and cultured in a 4-well dish containing 500 µL PZM-3 with 0.4% bovine serum albumin (BSA) at 38.5 °C under 5% CO2 for 48 h.

extract_protocol:
The total RNA of each sample（4-cell embryos） was extracted using Invitrogen TRIzol® .
RNA libraries for RNA-seq were prepared using the  smart-seq2 system.

treatment_protocol: Bob group was treated with 50 µM Bobcat339, con(control)group was treated with 50 µM  DMSO.

value: embryos

value: primary culture cell

value: parthenogenetic 4-cell stage embryos

value: 50 µM Bobcat339


title: mESC_HPRT1R_clone1_PolII_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, PolII ChIP, rep 2


title: mESC_HPRT1R_clone2_H3K27me3_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 2, H3K27me3 ChIP, rep 2


title: WT2

description:
Sample_125891
miRNA


title: H1_H2AK119ub_rep1

value: untreated


title: WT1

description:
Sample_125890
miRNA


title: WT-2


title: mESC_HPRT1R_clone2_H3K27ac_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 2, H3K27ac ChIP, rep 2

value: BL6xCAST with synHPRT1R integrated on chrX


title: Bob1


title: SP53, PRMT5 Resistant Treated 1

description:
SP53 PR PRT 1
SRPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: lymphoma


title: CCMCL, PRMT5 Sensitive Untreated 3

description:
CCMCL DMSO 3
CSU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: WT-1

value: Mouse Embryonic Fibroblast


title: Patient-derived AML sample #88_transduced with XBP1-encoding lentivirus_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg38 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

growth_protocol: Human AML cells were cultured ex vivo in complete IMDM (Hyclone SH30259.01; containing 20% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, MEM nonessential amino acids, 50 I.U/ml penicillin, 50 mg/ml streptomycin, 55 mM beta-mercaptoethanol) supplemented with 50 ng/ml SCF (sample #41) or with 50 ng/ml SCF, 20 ng/ml GM-CSF, 50 ng/ml FLT3 ligand, 20 ng/ml IL-3, 20 ng/ml IL-6 (sample #88).

extract_protocol:
Total RNA from cells was isolated using the TRIzol reagent
Transcriptome were determined from messenger RNA prepared using the Illumina TruSeq Stranded mRNA Sample Libraries.

treatment_protocol: AML cells were transduced with XBP1 or control (non-signaling hCD25 protein) lentivirus expressing IRES-ZsGreen for 72 hours and transduced (ZsGreen+) were FACS-sorted for RNA-Seq.

value: patient-derived human AML cells

tag: source patient id

value: sample #88


title: con2

value: control


title: MUT-3

value: Fbxw7 KO


title: mESC_HPRT1R_clone2_H3K27me3_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, H3K27me3 ChIP, rep 1

value: Embryonic stem cells


title: mESC_HPRT1R_clone1_H3K27me3_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, H3K27me3 ChIP, rep 2


title: CCMCL, PRMT5 Sensitive Untreated 2

description:
CCMCL DMSO 2
CSU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

source_name: lymphoma

value: CCMCL

value: Mantle Cell Lymphoma

value: MCL

value: DMSO


title: MUT-2


title: con1

value: embryos


title: CCMCL, PRMT5 Sensitive Untreated 1

description:
CCMCL DMSO 1
CSU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: mESC_HPRT1R_clone2_H3K4me3_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, H3K4me3 ChIP, rep 1


title: mESC_HPRT1R_clone1_H3K27ac_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, H3K27ac ChIP, rep 2


title: CCMCL, PRMT5 Resistant Treated 3

description:
CCMCL PR PRT 3
CRPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: WT-3

value: WT


title: CCMCL, PRMT5 Resistant Treated 2

description:
CCMCL PR PRT 2
CRPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Patient-derived AML sample #88_transduced with XBP1-encoding lentivirus_rep3


title: mESC_HPRT1R_clone1_IgG_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, IgG ChIP, rep 2


title: mESC_HPRT1R_clone1_H3K4me3_ChIP_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, H3K4me3 ChIP, rep 2


title: CCMCL, PRMT5 Resistant Untreated 1

description:
CCMCL PR DMSO 1
CRU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: WT-H3K4me3-2

data_processing:
Library strategy: Cut&Run
Cleaned sequencing reads by Cut&Run were mapped to the mm10 genome of mouse by using Bowtie2 (v2-2.2.4) with parameters “-q --phred33  --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”. Then, we removed duplicated reads using SAMtools (v1.5). Fragments of sizes ≤ 120 bp for PRDM16 Cut&Run were selected for downstream analysis while fragments of sizes > 120 bp for H3K4 methylation Cut&Run were selected for downstream analysis.
Filtered BAM files of mapping results were merged for the same sample using SAMtools and converted to BED format by using BEDTools. Peaks regions were called for each sample by using MACS2 from BAM files of Cut&Run with parameters  -f BAMPE -g mm -B -q 0.01 --extsize 147 --keep-dup auto”. The ucsc-tool “bedGraphToBigWig” was used to convert the bedgraph files generated by MACS2 to bigwig files. Ratio values of treat_pileup versus control_lambda for visualization in IGV were generated by bigwigCompare in deepTools2 from bigwig files generated by ucsc-tool “bedGraphToBigWig”.
We mapped the paired-end reads to both mouse and fly genomes and normalized mouse profiles using the number of fly reads. Differential peaks between groups were called by MACS2 subcommand “bdgdiff”.
Homer v4.10 was employed to perform gene annotation of peaks and differential peaks. Heatmap of signals of PRDM16 and H3K4 methylation were plotted by deepTools. Violin plots of PRDM16 and H3K4 methylation were performed by R package ggpubr.
Genome_build: mm10
Supplementary_files_format_and_content: peaks in text format

source_name: Mouse Embryonic Fibroblast

growth_protocol: MEF were cultured in  DMEM  supplemented with 15%  FBS ,1% NEAA

extract_protocol:
Cut & Run experiments were performed using 2X106 cells for MLL4,H3K4me1 or H3K4me3 antibodies, according to Cut & Run protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

tag: antibody


title: Patient-derived AML sample #88_transduced with XBP1-encoding lentivirus_rep1


title: CCMCL, PRMT5 Resistant Untreated 3

description:
CCMCL PR DMSO 3
CRU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Patient-derived AML sample #88_transduced with control lentivirus_rep3

value: transduced with control lentivirus


title: CCMCL, PRMT5 Resistant Untreated 2

description:
CCMCL PR DMSO 2
CRU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: PDX MCL, PRMT5 Resistant treated 1

description:
P6-1
PRTR1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: PDX AA MCL


title: mESC_HPRT1R_clone1_PolII_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, PolII ChIP, rep 1


title: Patient-derived AML sample #88_transduced with control lentivirus_rep2


title: CCMCL, PRMT5 Resistant Treated 1

description:
CCMCL PR PRT 1
CRPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: KO-H3K4me3-2

value: fbxw7 KO


title: mESC_HPRT1R_clone1_IgG_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, IgG ChIP, rep 1

value: BL6xCAST with synHPRT1R integrated on chrX


title: Patient-derived AML sample #88_transduced with control lentivirus_rep1


title: KO-H3K4me3-1


title: mESC_HPRT1_clone2_PolII_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, PolII ChIP, rep 2

value: BL6xCAST with synHPRT1 integrated on chrX


title: mESC_HPRT1R_clone1_H3K4me3_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, H3K4me3 ChIP, rep 1


title: Patient-derived AML sample #41_transduced with XBP1-encoding lentivirus_rep3

value: sample #41


title: WT-MLL4-2

value: Mouse Embryonic Fibroblast


title: mESC_HPRT1R_clone1_H3K27me3_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, H3K27me3 ChIP, rep 1


title: PDX MCL, PRMT5 Short-term treated 3

description:
C3
PRTS3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: lymphoma


title: WT-H3K4me1-1


title: WT-H3K4me3-1


title: Patient-derived AML sample #41_transduced with XBP1-encoding lentivirus_rep2

value: patient-derived human AML cells


title: WT-H3K4me1-2


title: WT-MLL4-1


title: PDX MCL, Untreated 2

description:
A2
U2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: Vehicle Control


title: PDX MCL, PRMT5 Short-term treated 2

description:
C2
PRTS2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: KO-H3K4me1-2


title: Patient-derived AML sample #41_transduced with XBP1-encoding lentivirus_rep1


title: PDX MCL, Untreated 1

description:
A1
U1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: KO-H3K4me1-1


title: mESC_HPRT1_clone2_H3K27ac_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, H3K27ac ChIP, rep 2

value: Embryonic stem cells


title: PDX MCL, PRMT5 Short-term treated 1

description:
C1
PRTS1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: mESC_HPRT1_clone2_IgG_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, IgG ChIP, rep 2


title: Patient-derived AML sample #41_transduced with control lentivirus_rep2


title: KO-MLL4-1


title: PDX MCL, Untreated 3,

description:
A3
U3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: PDX MCL, PRMT5 Resistant treated 2

description:
P7-53
PRTR2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Patient-derived AML sample #41_transduced with control lentivirus_rep3


title: mESC_HPRT1_clone2_PolII_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, PolII ChIP, rep 1


title: Patient-derived AML sample #41_transduced with control lentivirus_rep1


title: mESC_HPRT1R_clone1_H3K27ac_ChIP_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, H3K27ac ChIP, rep 1


title: mESC_HPRT1_clone2_H3K4me3_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, H3K4me3 ChIP, rep 2


title: COLO320DM_INPUT

city: Chennai

first: Samson

last: Mani

state: Tamilnadu

address: 38, Sardar Patel Road

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

data_processing:
library strategy: meRIP-seq
The raw reads were processed using cutadapt for trimming the adapter sequences and the sequence quality was checked with FASTQC.
The reads were aligned with human reference genome hg19 using bwa-mem algorithm.
MACS2 peak calling was performed with a p-value of 0.05 to obtain the peaks from the colon cancer cell line samples.
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

growth_protocol: DMEM, 10% fetal bovine serum, 1X pencillin/streptomycin. Cells were cultured at 37°C at 5% CO2

extract_protocol:
300µg of total RNA was extracted from the cell lines using Trizol and Nucleospin RNA extraction kit(macherey nagel-GMBH)
Approximately 300µg of total RNA was initially used for the fragmentation process to achieve the fragment length of ~100 nucleotides. The fragmented RNA was further enriched using Magna MeRIP™ m6A Kit- Transcriptome-wide Profiling kit (Cat. no: 17-10499, Sigma-Aldrich, USA) according to the manufacturer’s instructions to get m6A enriched RNA. About 10% of the fragmented RNA was saved as Input control.

value: Colon


title: DLC16011027401_low IMF

first: xuewen

last: xu

address: Shizishan street, No.1

data_processing:
Clean reads were obtained from the released raw reads through the following quality control steps: 1) remove reads containing adaptor; 2) remove reads containing more than 5% N; 3) remove low-quality reads
Alignment of RNA-seq data was conducted using Hisat2 V2.0.5 with the genome assembly Sscrofa11.1 (GCA_000003025) as the reference.
The aligned reads for each sample were then assembled into transcripts with StringTie v1.3.3 .
The generated transcripts from different samples were merged using the “merge” function of StringTie and yielded the final annotation file (the merged.gtf file)
The differential expression analysis was conducted with Ballgown.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values and raw fragment counts for each sample

source_name: longissimus dorsi muscle

growth_protocol: The experimental population was composed of 265 F1 animals from the crossing of 8 Duroc boars and 112 Luchuan sows, which were fed with the same diets at the same farm. All animals were slaughtered by a standardized procedure at the age of 210 days ± 6 days at the same abattoir.

extract_protocol:
Total RNA was extracted from longissimus dorsi muscle samples with Trizol reagent according to the product instructions. RNA samples were quantified using NanoDrop-2000 spectrophotometers (Thermo Scientific) and checked for purity and integrity using Agilent 2100 bioanalyzer.
The 150-bp paired-end RNA sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep kit for Illumina® (NEB, USA) according to the manufacturer’s protocols and sequenced on the Illumina Hiseq 4000 platform.

treatment_protocol: Twenty-five minutes postmortem, samples of the longissimus dorsi muscle at the thoracolumbar junction were taken for meat quality trait measurements and RNA extraction.

tag: breed

value: Duroc x Luchuan crossed pigs

value: longissimus dorsi muscle

tag: imf content

value: low


title: DLC16012935001_low IMF


title: mESC_HPRT1_clone2_H3K27me3_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, H3K27me3 ChIP, rep 2


title: KO-MLL4-2


title: COLO205_INPUT


title: HT29_INPUT

value: Colorectum


title: mESC_HPRT1_clone2_IgG_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, IgG ChIP, rep 1


title: Yeast_HPRT1R_integrated_IgG_ChIP_rep2

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000.
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAMPE -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of ChIP-seq signal enrichment (for H3K4me3 ChIP only)

organism: Saccharomyces cerevisiae

source_name: Yeast, synHPRT1R integrated on chrXI, IgG ChIP, rep 2

growth_protocol: Yeast were cultured overnight at 30C in SC-Leu for YAC strains and YPD for integrated strains. In the morning, cultures were diluted to OD 0.1 and cultured for another 6 hours to reach  mid-log phase at an OD of ~0.6.

extract_protocol:
Cells were pelleted at 3,000 rcf for 5 minutes, washed twice with water, and resuspended in spheroplasting buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2, 0.5 mM 2-mercaptoethanol). Spheroplasting was performed by adding 0.125 U/μL Zymolyase (Zymo Research E1004) and incubating at 37oC for 45 minutes on a rotator. Nuclei were prepared as previously described (Orsi, G.A., et al., Curr Protoc Mol Biol, 2015). Resuspended nuclei were split into aliquots of ~108 nuclei each and snap frozen in liquid nitrogen.
~10^8 frozen nuclei were thawed and processed for CUT&RUN using the CUTANA™ ChIC/CUT&RUN kit (EpiCy-pher 14-1048) according to the manufacturer’s protocol. Antibodies were  used at 0.5 μg: rabbit IgG negative control (EpiCypher 13-0042), H3K4me3 (EpiCypher 13-0041). Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs E7645L) according to the manufacturer's protocol.

value: BY4741 with synHPRT1R integrated on chrXI

value: Yeast


title: Yeast_HPRT1R_YAC_IgG_ChIP_rep2

source_name: Yeast, synHPRT1R YAC, IgG ChIP, rep 2

value: BY4741 with synHPRT1R YAC


title: Yeast_HPRT1R_integrated_H3K4m3_ChIP_rep2

source_name: Yeast, synHPRT1R integrated on chrXI, H3K4me3 ChIP, rep 2


title: Yeast_HPRT1R_integrated_IgG_ChIP_rep1

source_name: Yeast, synHPRT1R integrated on chrXI, IgG ChIP, rep 1


title: Yeast_HPRT1R_integrated_H3K4m3_ChIP_rep1

source_name: Yeast, synHPRT1R integrated on chrXI, H3K4me3 ChIP, rep 1


title: HCT15_INPUT


title: mESC_HPRT1_clone2_H3K27me3_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, H3K27me3 ChIP, rep 1


title: mESC_HPRT1_clone2_H3K4me3_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, H3K4me3 ChIP, rep 1


title: Yeast_HPRT1R_YAC_IgG_ChIP_rep1

source_name: Yeast, synHPRT1R YAC, IgG ChIP, rep 1


title: mESC_HPRT1_clone2_H3K27ac_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, H3K27ac ChIP, rep 1


title: mESC_HPRT1_clone1_PolII_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, PolII ChIP, rep 2


title: DLC15123130306_low IMF


title: COLO320DM_MeRIP

value: N6-Methyladenosine, 5′-monophosphate sodium salt (m6 A)


title: DLC15121638107_low IMF


title: Yeast_HPRT1R_YAC_H3K4me3_ChIP_rep1

source_name: Yeast, synHPRT1R YAC, H3K4me3 ChIP, rep 1


title: DLC15120925905_low IMF


title: mESC_HPRT1_clone1_IgG_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, IgG ChIP, rep 2


title: COLO205_MeRIP


title: HCT15_MeRIP


title: Yeast_HPRT1R_YAC_H3K4me3_ChIP_rep2

source_name: Yeast, synHPRT1R YAC, H3K4me3, rep 2


title: mESC_HPRT1_clone1_H3K4me3_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, H3K4me3 ChIP, rep 2


title: DLC15120925901_low IMF

source_name: longissimus dorsi muscle


title: DLC16012334404_low IMF


title: DLC16010837810_low IMF


title: Yeast_HPRT1_integrated_H3K4m3_ChIP_rep2

source_name: Yeast, synHPRT1 integrated on chrXI, H3K4me3 ChIP, rep 2

value: BY4741 with synHPRT1 integrated on chrXI


title: HT29_MeRIP


title: mESC_HPRT1_clone1_H3K27me3_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, H3K27me3 ChIP, rep 2

value: BL6xCAST with synHPRT1 integrated on chrX


title: HCT116_INPUT


title: Yeast_HPRT1_integrated_IgG_ChIP_rep1

source_name: Yeast, synHPRT1 integrated on chrXI, IgG ChIP, rep 1


title: DLC16010928102_low IMF


title: mESC_HPRT1_clone1_H3K27ac_ChIP_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, H3K27ac ChIP, rep 2


title: HCT116_MeRIP


title: Yeast_HPRT1_integrated_H3K4m3_ChIP_rep1

source_name: Yeast, synHPRT1 integrated on chrXI, H3K4me3 ChIP, rep 1


title: mESC_HPRT1_clone1_PolII_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, PolII ChIP, rep 1


title: Yeast_HPRT1_integrated_IgG_ChIP_rep2

source_name: Yeast, synHPRT1 integrated on chrXI, IgG ChIP, rep 2


title: DLC15121638110_low IMF


title: Yeast_HPRT1_YAC_IgG_ChIP_rep2

source_name: Yeast, synHPRT1 YAC, IgG ChIP, rep 2


title: mESC_HPRT1_clone1_H3K4me3_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, H3K4me3 ChIP, rep 1


title: DLC16011128402_high IMF

value: high


title: DLC16011128502_high IMF


title: DLC15120526205_low IMF


title: DLC16011232508_low IMF


title: Yeast_HPRT1_YAC_H3K4me3_ChIP_rep2

source_name: Yeast, synHPRT1 YAC, H3K4me3, rep 2


title: mESC_HPRT1_clone1_H3K27ac_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, H3K27ac ChIP, rep 1


title: mESC_HPRT1_clone1_H3K27me3_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, H3K27me3 ChIP, rep 1


title: DLC15122831901_high IMF


title: mESC_HPRT1R_clone2_RNA_rep3

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
STAR (v2.5.2a) was used to align reads, without providing a gene annotation file, to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the GRCm38/mm10  genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --scaleFactor (-)TMM --filterRNAstrand forward/reverse. Scale factors for TMM normalization were calcualted using edgeR.
Assembly: GRCm38/mm10  + HPRT1/HPRT1R, GRCm38/mm10 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

source_name: mESC, synHPRT1R integrated on chrX, clone 2, rep 3

extract_protocol:
Cells were grown to medium confluency in 6-well plates. Cells were harvested by washing once with PBS, disso-ciating into single-cell suspending with TrypLE Express (ThermoFisher 12604013) and then neutralizing with mESC media. Cells were pelleted at 500 rcf for 5 minutes and RNA was isolated using Qiagen RNeasy Plus Mini kit, resuspending in 350 μL buffer RLT Plus + β-mercaptoethanol, with homogenization using QIAshredder columns (Qiagen 79654).
RNA-seq libraries were prepared from 1 μg total RNA using QIAseq FastSelect -rRNA HMR (Qiagen 334386) and QIAseq Stranded RNA kits (Qiagen 180743) according to the manufacturer’s protocol.

value: BL6xCAST with synHPRT1R integrated on chrX


title: DLC15121837310_high IMF


title: Yeast_HPRT1R_integrated_CAGE_rep2

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
5’ reads only were aligned using bowtie2 (v2.2.9) to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000 --filterRNAstrand forward/reverse --scaleFactor (-)1 --extendReads 100
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAM -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of CAGE-seq signal enrichment

source_name: Yeast, synHPRT1R integrated on chrXI, rep 2

extract_protocol:
Yeast were pelleted at 3,000 rcf for 5 minutes, washed once with water, pelleted again at 3,000 rcf for 5 minutes, and cell pellets were frozen at -80oC. Frozen pellets were resuspended in 200 μL lysis buffer (50 mM Tris-HCl pH 8, 100 mM NaCl) and lysed by disruption with an equal volume of acid washed glass beads, vortexing 10 x 15 seconds. 300 μL lysis buffer was added and samples were mixed by inversion followed by a short centrifugation to collect all liquid in the tube. 450 μL of supernatant was mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. 350 μL of the aqueous layer was then mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. RNA was precipitated from 300 μL of the aqueous phase by adding 30 μL of 3 M NaOAc and 800 μL of cold 99.5% ethanol, briefly vortexing, and centrifuging at max speed for 10 minutes. The pellet was rinsed with 70% ethanol and dried at room temperature before dissolving in 100 μL of RNase-free DNase set (Qiagen 79254) and incubating at room temperature for 10 minutes to remove DNA. RNA was purified using the RNeasy Plus Mini kit (Qiagen 74136) and eluted in 30 μL RNase-free water.
CAGE libraries were prepared as previously described (Murata, M., et al., Methods Mol Biol, 2014), starting with 5 μg RNA, with the following modifications. SuperScript™ IV Reverse Transcriptase (Invitrogen 18090010) was used for the reverse transcription step. AMPure XP beads (Beckman Coulter A63881) were used for all bead cleanup steps. We also used custom-made linker and primer oligos so that linkers are universal to all samples and primers contain sample-specific barcodes. Libraries were amplified using universal forward and reverse primers with 20 cycles of PCR


title: Yeast_HPRT1R_integrated_CAGE_rep1

source_name: Yeast, synHPRT1R integrated on chrXI, rep 1


title: Yeast_HPRT1_YAC_H3K4me3_ChIP_rep1

source_name: Yeast, synHPRT1 YAC, H3K4me3 ChIP, rep 1

value: BY4741 with synHPRT1 YAC


title: DLC15120625105_high IMF

source_name: longissimus dorsi muscle


title: mESC_HPRT1R_clone2_RNA_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 2, rep 2


title: Yeast_HPRT1R_YAC_CAGE_rep2

source_name: Yeast, synHPRT1R YAC, rep 2


title: mESC_HPRT1R_clone2_RNA_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, rep 1


title: mESC_HPRT1R_clone1_RNA_rep3

source_name: mESC, synHPRT1R integrated on chrX, clone 1, rep 3


title: DLC16011428801_high IMF


title: mESC_HPRT1_clone1_IgG_ChIP_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, IgG ChIP, rep 1


title: Yeast_HPRT1_YAC_IgG_ChIP_rep1

source_name: Yeast, synHPRT1 YAC, IgG ChIP, rep 1


title: Yeast_HPRT1R_YAC_CAGE_rep1

source_name: Yeast, synHPRT1R YAC, rep 1


title: DLC16011129805_high IMF


title: Yeast_HPRT1_integrated_CAGE_rep1

source_name: Yeast, synHPRT1 integrated on chrXI, rep 1


title: DLC16011328604_high IMF


title: mESC_HPRT1R_clone1_RNA_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, rep 2


title: Yeast_HPRT1_integrated_CAGE_rep2

source_name: Yeast, synHPRT1 integrated on chrXI, rep 2


title: Yeast_HPRT1_CAGE_RNA_rep2

source_name: Yeast, synHPRT1 YAC, rep 2


title: mESC_HPRT1_clone2_RNA_rep3

source_name: mESC, synHPRT1 integrated on chrX, clone 2, rep 3


title: DLC15122731808_high IMF


title: DLC15121622707_high IMF


title: mESC_HPRT1R_clone1_RNA_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, rep 1


title: mESC_HPRT1_clone2_RNA_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, rep 1


title: DLC15121622708_high IMF


title: mESC_HPRT1_clone2_RNA_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, rep 2


title: Yeast_HPRT1R_integrated_RNA_rep1

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
STAR (v2.5.2a) was used to align reads, without providing a gene annotation file, to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --scaleFactor (-)TMM --filterRNAstrand forward/reverse. Scale factors for TMM normalization were calcualted using edgeR.
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

source_name: Yeast, synHPRT1R integrated on chrXI, rep 1

extract_protocol:
Yeast were pelleted at 3,000 rcf for 5 minutes, washed once with water, pelleted again at 3,000 rcf for 5 minutes, and cell pellets were frozen at -80oC. Frozen pellets were resuspended in 200 μL lysis buffer (50 mM Tris-HCl pH 8, 100 mM NaCl) and lysed by disruption with an equal volume of acid washed glass beads, vortexing 10 x 15 seconds. 300 μL lysis buffer was added and samples were mixed by inversion followed by a short centrifugation to collect all liquid in the tube. 450 μL of supernatant was mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. 350 μL of the aqueous layer was then mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. RNA was precipitated from 300 μL of the aqueous phase by adding 30 μL of 3 M NaOAc and 800 μL of cold 99.5% ethanol, briefly vortexing, and centrifuging at max speed for 10 minutes. The pellet was rinsed with 70% ethanol and dried at room temperature before dissolving in 100 μL of RNase-free DNase set (Qiagen 79254) and incubating at room temperature for 10 minutes to remove DNA. RNA was purified using the RNeasy Plus Mini kit (Qiagen 74136) and eluted in 30 μL RNase-free water.
RNA-seq libraries were prepared from 1 μg total RNA using the QIAseq FastSelect -rRNA Yeast kit (Qiagen 334217) and QIAseq Stranded RNA Library kit (Qiagen 180743) according to the manufacturer’s protocol.


title: mESC_HPRT1_clone1_RNA_rep3

source_name: mESC, synHPRT1 integrated on chrX, clone 1, rep 3


title: mESC_HPRT1_clone1_RNA_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, rep 2


title: Yeast_HPRT1_CAGE_RNA_rep1

source_name: Yeast, synHPRT1 YAC, rep 1


title: Yeast_HPRT1R_YAC_RNA_rep3

source_name: Yeast, synHPRT1R YAC, rep 3


title: Yeast_HPRT1R_YAC_RNA_rep2

source_name: Yeast, synHPRT1R YAC, rep 2


title: mESC_HPRT1_clone1_RNA_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, rep 1


title: Yeast_HPRT1R_integrated_RNA_rep2

source_name: Yeast, synHPRT1R integrated on chrXI, rep 2


title: mESC_HPRT1R_clone2_ATAC_rep3

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the GRCm38/mm10  genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 2652783500
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAMPE -g 1.87e9 --keep-dup all
Assembly: GRCm38/mm10  + HPRT1/HPRT1R, GRCm38/mm10 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of ATAC-seq signal enrichment

source_name: mESC, synHPRT1R integrated on chrX, clone 2, rep 3

extract_protocol:
Cells were grown to medium confluency in 6-well plates. Cells were harvested by washing once with PBS, disso-ciating into single-cell suspending with TrypLE Express (ThermoFisher 12604013) and then neutralizing with mESC media. Cells were counted and 50,000 were taken for tagmentation. Cells were pelleted at 500 rcf for 5 minutes at 4oC, washed with 50 μL cold PBS, resuspended in 50 μL cold ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), spun down at 500 rcf for 10 mins at 4oC, resuspended in 50 μL TDE mix.
Tagmentation was performed at 37oC on a rotator for 30 mins and DNA was purified using the DNA Clean and Concentrator 5 kit (Zymo Research D4004). PCR was performed as previously described (Buenrostro, J.D., et al., Curr Protoc Mol Biol, 2015) using barcoded primers for 10 total cycles.


title: Yeast_HPRT1R_YAC_RNA_rep1

source_name: Yeast, synHPRT1R YAC, rep 1


title: mESC_HPRT1R_clone2_ATAC_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 2, rep 2


title: Yeast_HPRT1_integrated_RNA_rep3

source_name: Yeast, synHPRT1 integrated on chrXI, rep 3


title: Yeast_HPRT1_integrated_RNA_rep2

source_name: Yeast, synHPRT1 integrated on chrXI, rep 2


title: Yeast_HPRT1_integrated_RNA_rep1

source_name: Yeast, synHPRT1 integrated on chrXI, rep 1


title: mESC_HPRT1R_clone1_ATAC_rep3

source_name: mESC, synHPRT1R integrated on chrX, clone 1, rep 3


title: Yeast_HPRT1R_integrated_RNA_rep3

source_name: Yeast, synHPRT1R integrated on chrXI, rep 3


title: DLC16011328302_high IMF

source_name: longissimus dorsi muscle


title: mESC_HPRT1R_clone1_ATAC_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 1, rep 1


title: mESC_HPRT1_clone2_ATAC_rep3

source_name: mESC, synHPRT1 integrated on chrX, clone 2, rep 3


title: Yeast_HPRT1_YAC_RNA_rep2

source_name: Yeast, synHPRT1 YAC, rep 2


title: Yeast_HPRT1_YAC_RNA_rep1

source_name: Yeast, synHPRT1 YAC, rep 1


title: mESC_HPRT1_clone2_ATAC_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 2, rep 2


title: mESC_HPRT1_clone2_ATAC_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 2, rep 1


title: Yeast_HPRT1R_integrated_ATAC_rep3

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000.
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAMPE -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bam - sequence alignment data
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of ATAC-seq signal enrichment

extract_protocol:
~5x106 cells were taken from each culture, pelleted at 3,000 rcf for 5 minutes, washed twice with 500 μL spheroplasting buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2), resuspended in 100 μL spheroplasting buffer with 0.2 U/μL zymolyase (Zymo Research E1004), then incubated for 30 minutes at 30°C on a rotator. Spheroplasts were washed twice with 500 μL spheroplasting buffer then resuspended in 50 μL 1x TD buffer with TDE (Illumina 20034197).
Tagmentation was performed for 30 minutes at 37oC on a rotator and DNA was purified using the DNA Clean and Concentrator 5 kit (Zymo Research D4004). PCR was performed as previously described (Buenrostro, J.D., et al., Curr Protoc Mol Biol, 2015) using barcoded primers for 11 total cycles.


title: mESC_HPRT1_clone1_ATAC_rep3

source_name: mESC, synHPRT1 integrated on chrX, clone 1, rep 3


title: mESC_HPRT1_clone1_ATAC_rep2

source_name: mESC, synHPRT1 integrated on chrX, clone 1, rep 2


title: Yeast_HPRT1R_integrated_ATAC_rep2

source_name: Yeast, synHPRT1R integrated on chrXI, rep 2


title: mESC_HPRT1R_clone2_ATAC_rep1

source_name: mESC, synHPRT1R integrated on chrX, clone 2, rep 1


title: glp-1 D1 3

city: Chongqing

first: Yuxi

last: Dai

address: Daxuecheng west street, Huxi town, Shapingba

institute: Chongqing university

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality and quantity of the libraries were determined using an Agilent Bioanalyzer 2100 (Agilent) and NanoDrop 2000 (Thermo Fisher Scientific), respectively.
he libraries were sequenced at a paired-end 150 bp read length on an Illumina NovaSeq 6000 RNA-seq reads were aligned to the reference genome WBcel235 using HISAT2 v.2.0.4 (Kim et al., 2015).
The differential gene and transcript expression analysis was performed using DESeq2 v.1.6.3 (Love et al., 2014)
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Synchronized L1 worms were cultured on an NGM plate seeded with OP50 bacteria.

extract_protocol:
Total RNA was extracted using TRIzol reagent and used to generate sequencing libraries using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Growing the worms cultured at 25°C to D1 adult  and are kept at 20°C to D6, respectively.

tag: developmental stage

value: D1 adult

tag: culture temperature

tag: e. coli b strain for diet


title: glp-1 D6 2

value: D6 adult

value: 25°C to D1, then keep at 21°C


title: glp-1 D6 1

value: 25°C to D1, then keep at 20°C


title: glp-1 D6 3

value: 25°C to D1, then keep at 22°C


title: 2D10_Prostratin_24hr_ATACseq

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

description:
Prostratin: -2 designation at end of cell-barcode
all processed data contained within filtered_feature_bc_matrix.h5 and in barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

data_processing:
cellranger-arc version v2.0.1 count command with default settings was used to perform alignment, demultiplexing, barcode processing, peak calling, and counting RNA/ATAC reads in single cells.
cellranger-arc version v2.0.1 aggr command with option normalization=none used to combine datasets into combined count matrices. Sample designation is appended to the end of each cell-barcode in the aggregated matrix is as follows: DMSO: -1, Prostratin: -2, iBET151:-3, SAHA:-4.
Assembly: GRCh38 with the HIV proviral genome appended as an additional chromosome. 5' and 3' LTRs were combined into a single 5' LTR to prevent multi-mapping issues.
Supplementary files format and content: filtered_feature_bc_matrix.h5 > file containing all RNAseq and ATAC peak features allocated to cells by cellranger-arc count. File is in hdf5 format.
Supplementary files format and content: features.tsv.gz ; barcodes.tsv.gz ; matrix.mtx.gz > files containing feature and cell-barcode data. Files are in plain text [.tsv and .mtx] formats.

growth_protocol: Cells were cultured in RPMI supplemented with 10% FCS, L-Glutamine, HEPES, PenStrep, and Sodium Pyruvate.

extract_protocol: 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338 Rev D)

treatment_protocol: Cells were treated with DMSO (1:10^4 dilution), 500nM SAHA, 75nM Prostratin and 75nM iBET151 for 24hrs

value: Latently infected Jurkat T cell line

value: Prostratin


title: Yeast_HPRT1R_integrated_ATAC_rep1

source_name: Yeast, synHPRT1R integrated on chrXI, rep 1


title: Yeast_HPRT1R_YAC_ATAC_rep1

source_name: Yeast, synHPRT1R YAC, rep 1


title: Yeast_HPRT1_YAC_RNA_rep3

source_name: Yeast, synHPRT1 YAC, rep 3


title: hippocampus,DIVI7, scRNA-seq, rep1

city: Beijing

first: Ran

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

description:
10x Genomics
Sample_DIV7_rep1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Primary Hippocampal neuronal culture were prepared from postnatal 0 (P0) mice. Briefly, hippocampi were dissected and digested with 0.25% trypsin (Gibco, 25200072) at 37℃ for 15 min. After wash twice with HBS solution (Hanks buffer (Sigma H2387), 1mM HEPES, 4mM NaHCO3) containing 5% FBS, neurons were isolated by pipette up and down for 20-25 times in culture medium containing MEM (Gibco 61100-061), 0.5% glucose, 1.3μM transferrin, 26.19mM, 2% B-27 supplement, 5% FBS, and then plated on glass coverslips pre-coated by poly-D-lysine at a density of 80,000 neurons per well in 48-well plate. Neurons were cultured at 37℃ in 5% CO2 before use. For single cell sequencing, cultured neurons were washed once with opti-MEM, and digested with 0.25% trypsin-EDTA containing DNase I for 5 min. Then neurons were pipetted up and down for 10 times, and centrifuged at 300 g for 2 min. Finally, neurons were recompensed in opti-MEM and pipetted up and down for several times to gain single cell suspensions for further sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: hippocampus

value: Neurons, radial glia cells, ciliated cells, mural cells,oligodendrocytes,microglia,endothelial cells,Cajal-Retzius cells

tag: time

value: Day 7 in vitro


title: Yeast_HPRT1R_YAC_ATAC_rep3

source_name: Yeast, synHPRT1R YAC, rep 3

value: BY4741 with synHPRT1R YAC

value: Yeast


title: mESC_HPRT1_clone1_ATAC_rep1

source_name: mESC, synHPRT1 integrated on chrX, clone 1, rep 1

value: Embryonic stem cells


title: glp-1 D1 2


title: 2D10_iBET151_24hr_ATACseq

description:
iBET151: -3 designation at end of cell-barcode
all processed data contained within filtered_feature_bc_matrix.h5 and in barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.


title: Yeast_HPRT1_integrated_ATAC_rep3

source_name: Yeast, synHPRT1 integrated on chrXI, rep 3

value: BY4741 with synHPRT1 integrated on chrXI


title: Yeast_HPRT1R_YAC_ATAC_rep2

source_name: Yeast, synHPRT1R YAC, rep 2


title: WT D6 2


title: glp-1 D1 1


title: 2D10_SAHA_24hr_ATACseq

description:
SAHA: -4 designation and end of cell-barcode.
all processed data contained within filtered_feature_bc_matrix.h5 and in barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

value: SAHA


title: WT D6 3


title: hippocampus,DIVI7, scRNA-seq, rep2

description:
10x Genomics
Sample_DIV7_rep2

tag: tissue


title: hippocampus,DIVI5, scRNA-seq, rep2

description:
10x Genomics
Sample_DIV5_rep2

value: Day 5 in vitro


title: 2D10_DMSO_24hr_ATACseq

description:
DMSO: -1 designation at end of cell-barcode
all processed data contained within filtered_feature_bc_matrix.h5 and in barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

value: DMSO


title: Yeast_HPRT1_integrated_ATAC_rep2

source_name: Yeast, synHPRT1 integrated on chrXI, rep 2

tag: genotype


title: hippocampus,DIVI5, scRNA-seq, rep1

description:
10x Genomics
Sample_DIV5_rep1


title: Yeast_HPRT1_YAC_ATAC_rep3

value: BY4741 with synHPRT1 YAC


title: 2D10_iBET151_24hr_nuclei_scRNAseq

molecule: nuclear RNA

tag: treatment


title: WT D1 2

value: D1 adult


title: WT D1 3


title: WT D1 1


title: hippocampus,DIVI3, scRNA-seq, rep1

description:
10x Genomics
Sample_DIV3_rep1

value: Day 3 in vitro


title: 2D10_DMSO_24hr_nuclei_scRNAseq


title: WT D6 1

value: D6 adult

value: 25°C to D1, then keep at 20°C


title: Yeast_HPRT1_integrated_ATAC_rep1

source_name: Yeast, synHPRT1 integrated on chrXI, rep 1


title: Yeast_HPRT1_YAC_ATAC_rep2

source_name: Yeast, synHPRT1 YAC, rep 2


title: patient9 C8

type: RNA

first: chuanjue

last: cui

address: No.167th Beilishi Road, Xicheng District

department: Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease,

institute: Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: CAP-negative control_PWBCs

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: subject status

value: carotid atherosclerotic plaque (CAP)-negative control patient

value: peripheral white blood cells (PWBCs)


title: 2D10_SAHA_24hr_nuclei_scRNAseq

value: Latently infected Jurkat T cell line


title: mESC_HPRT1R_clone1_ATAC_rep2

source_name: mESC, synHPRT1R integrated on chrX, clone 1, rep 2

value: BL6xCAST with synHPRT1R integrated on chrX


title: hippocampus, DIVI1, scRNA-seq

description:
10x Genomics
Sample_DIV1

value: hippocampus

value: Neurons, radial glia cells, ciliated cells, mural cells,oligodendrocytes,microglia,endothelial cells,Cajal-Retzius cells

value: Day 1 in vitro


title: patient7 C5


title: patient10 C4-2


title: Yeast_HPRT1_YAC_ATAC_rep1

source_name: Yeast, synHPRT1 YAC, rep 1

value: Yeast


title: ms1156_IgG2c

status: Public on Dec 29 2023

type: protein

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.

hyb_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen.

label: R-PE conjugated goat anti-mouse IgG2c secondary antibody

molecule: protein

source_name: Serum/plasma

extract_protocol: Blood was collected from mice. The blood was then processed into serum or plasma which was then run on our arrays.

treatment_protocol: Retrogenic chimeras were made by reconsitution of irradiated mice with RAG bone marrow transduced with candidate TCRs

value: Serum/plasma

tag: condition


title: patient3 J5

source_name: CAP-positive patient_PWBCs

value: carotid atherosclerotic plaque (CAP)-positive patient

tag: cell type


title: patient1 J2-2


title: ms637_IgG2c

label_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.


title: patient2 4-2


title: ms630_IgG2c


title: ms1044_IgG2c


title: patient4 J7


title: patient5 J9


title: ms477_IgG2c


title: ms1181_IgG2c


title: ms324_IgG2c


title: patient8 C6


title: ms1041_IgG2c


title: ms636_IgG2c


title: ms474_IgG2c


title: ms1527_IgG2c


title: ms1526_IgG2c


title: ms1541_IgG2c


title: ms1529_IgG2c


title: ms1549_IgG2c


title: ms1535_IgG2c


title: ms326_IgG2c


title: patient6 C3


title: ms1546_IgG2c


title: ms321_IgG2c


title: ms1473_IgG2c


title: ms1470_IgG2c


title: ms1466_IgG2c


title: 2D10_Prostratin_24hr_nuclei_scRNAseq

tag: cell line

value: Prostratin


title: ms1341_IgG2c


title: ms1339_IgG2c


title: ms1336_IgG2c


title: ms1334_IgG2c


title: ms1544_IgG2c


title: ms1525_IgG2c


title: ms1331_IgG2c


title: ms1183_IgG2c


title: ms1539_IgG2c


title: ms1542_IgG2c


title: ms1463_IgG2c


title: ms1468_IgG2c


title: ms1472_IgG2c


title: ms1543_IgG2c


title: ms1531_IgG2c


title: ms1467_IgG2c


title: ms1548_IgG2c


title: ms1547_IgG2c


title: ms1537_IgG2c


title: ms1545_IgG2c


title: ms1534_IgG2c


title: ms1533_IgG2c


title: ms1532_IgG2c


title: ms1538_IgG2c


title: ms1465_IgG2c


title: ms1471_IgG2c


title: ms1464_IgG2c


title: ms1154_IgG2c


title: ms1530_IgG2c


title: ms1540_IgG2c


title: ms1340_IgG2c


title: ms1330_IgG2c


title: ms1335_IgG2c


title: ms1153_IgG2c


title: ms1500_IgG2c


title: ms1528_IgG2c


title: ms1499_IgG2c


title: ms1497_IgG2c


title: ms1469_IgG2c


title: ms1495_IgG2c


title: ms1343_IgG2c


title: ms1337_IgG2c


title: ms1498_IgG2c


title: ms1304_IgG2c


title: ms1302_IgG2c


title: ms1180_IgG2c


title: ms1496_IgG2c


title: ms1479_IgG2c


title: ms1442_IgG2c


title: ms1440_IgG2c


title: ms1438_IgG2c


title: ms1494_IgG2c


title: ms1436_IgG2c


title: ms1296_IgG2c


title: ms1482_IgG2c


title: ms1488_IgG2c


title: ms1298_IgG2c


title: ms1490_IgG2c


title: ms1026_IgG2c


title: ms1487_IgG2c


title: ms1444_IgG2c


title: ms1403_IgG2c


title: ms1400_IgG2c


title: ms1329_IgG2c


title: ms1282_IgG2c


title: ms1265_IgG2c


title: ms1074_IgG2c


title: ms1448_IgG2c


title: ms1149_IgG2c


title: ms1041_IgG2a

data_processing:
Sample replicate MFI values were averaged for each antigen.
Raw values were used without normalization.

label: R-PE conjugated goat anti-mouse IgG2a secondary antibody


title: ms1044_IgG2a


title: ms1156_IgG2a


title: ms1181_IgG2a


title: ms630_IgG2a


title: ms636_IgG2a


title: ms474_IgG2a


title: ms326_IgG2a


title: ms324_IgG2a


title: ms1546_IgG2a


title: ms1535_IgG2a


title: ms1529_IgG2a


title: ms1527_IgG2a


title: ms1541_IgG2a


title: ms1526_IgG2a


title: ms1466_IgG2a


title: ms1463_IgG2a


title: ms1470_IgG2a


title: ms1339_IgG2a


title: ms1473_IgG2a


title: ms321_IgG2a


title: ms1341_IgG2a


title: ms1334_IgG2a


title: ms637_IgG2a


title: ms477_IgG2a


title: ms1331_IgG2a


title: ms1336_IgG2a


title: ms1154_IgG2a


title: ms1539_IgG2a


title: ms1549_IgG2a


title: ms1183_IgG2a


title: ms1542_IgG2a


title: hippocampus,DIVI3, scRNA-seq, rep2

description:
10x Genomics
Sample_DIV3_rep2


title: ms1544_IgG2a


title: ms1467_IgG2a


title: ms1472_IgG2a


title: ms1468_IgG2a


title: ms1540_IgG2a


title: ms1538_IgG2a


title: ms1548_IgG2a


title: ms1545_IgG2a


title: ms1543_IgG2a


title: ms1547_IgG2a


title: ms1537_IgG2a


title: ms1534_IgG2a


title: ms1533_IgG2a


title: ms1471_IgG2a


title: ms1469_IgG2a


title: ms1464_IgG2a


title: ms1531_IgG2a


title: ms1340_IgG2a


title: ms1532_IgG2a


title: ms1528_IgG2a


title: ms1343_IgG2a


title: ms1335_IgG2a


title: ms1180_IgG2a


title: ms1465_IgG2a


title: ms1500_IgG2a


title: ms1153_IgG2a


title: ms1525_IgG2a


title: ms1337_IgG2a


title: ms1330_IgG2a


title: ms1496_IgG2a


title: ms1499_IgG2a


title: ms1497_IgG2a


title: ms1495_IgG2a


title: ms1302_IgG2a


title: ms1298_IgG2a


title: ms1026_IgG2a


title: ms1494_IgG2a


title: ms1530_IgG2a


title: ms1482_IgG2a


title: ms1479_IgG2a


title: ms1444_IgG2a


title: ms1442_IgG2a


title: ms1440_IgG2a


title: ms1304_IgG2a


title: ms1490_IgG2a


title: ms1296_IgG2a


title: ms1438_IgG2a


title: ms1436_IgG2a


title: ms1403_IgG2a


title: ms1329_IgG2a


title: ms1400_IgG2a


title: ms1265_IgG2a


title: ms1282_IgG2a


title: ms1498_IgG2a


title: ms1074_IgG2a


title: ms1149_IgG2a


title: ms1041

label: R-PE conjugated goat anti-mouse IgG secondary antibody


title: ms1181


title: ms636


title: ms630


title: ms474


title: ms637


title: ms1488_IgG2a


title: ms324


title: ms321


title: ms1156


title: ms1549


title: ms1487_IgG2a


title: ms477


title: ms1448_IgG2a


title: ms1546


title: ms1541


title: ms326


title: ms1535


title: ms1526


title: ms1527


title: ms1529


title: ms1334


title: ms1339


title: ms1466


title: ms1331


title: ms1463


title: ms1183


title: ms1341


title: ms1336


title: ms1154


title: ms1473


title: ms1544


title: ms1467


title: ms1525


title: ms1470


title: ms1542


title: ms1539


title: ms1468


title: ms1540


title: ms1543


title: ms1545


title: ms1547


title: ms1538


title: ms1537


title: ms1532


title: ms1531


title: ms1533


title: ms1044


title: ms1471


title: ms1469


title: ms1465


title: ms1528


title: ms1472


title: ms1548


title: ms1343


title: ms1340


title: ms1337


title: ms1335


title: ms1330


title: ms1534


title: ms1180


title: ms1495


title: ms1496


title: ms1497


title: ms1499


title: ms1494


title: ms1153


title: ms1500


title: ms1498


title: ms1482


title: ms1530


title: ms1464


title: ms1298


title: ms1304


title: ms1479


title: ms1296


title: ms1440


title: ms1026


title: ms1444


title: ms1442


title: ms1490


title: ms1436


title: ms1488


title: ms1438


title: ms1403


title: ms1487


title: ms1329


title: ms1302


title: ms1448


title: ms1400


title: ms1149


title: ms1282


title: LECs, AAV-VEGF-C treated mice, exp3

city: Paris

first: Ruchith

last: Singhabahu

address: 47 bd de l'Hôpital

country: France

institute: Institut du Cerveau

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.10.11) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: Dura mater

extract_protocol:
RNA extractions were performed using the Direct-zol™ RNA Microprep kit (R2061) according to the manufacturer’s instructions
RNA library preparation was realized following manufacturer’s recommendations (SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian from Takara).

value: Dura mater

value: Lymphatic endothelial cells

value: WT

value: AAV-VEGF-C


title: LECs, AAV-Control treated mice, exp3

value: AAV-Control


title: LECs, AAV-VEGF-C treated mice, exp1


title: LECs, AAV-Control treated mice, exp2


title: LECs, AAV-Control treated mice, exp1


title: ms1265


title: ms1074


title: Epithelial cells from anti-PD-L1+aoy treated mouse 4 day 12

city: Bellinzona

first: Fabio

last: Grassi

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
We used FastQC v0.11.9 to assess the quality of the reads.
Adapters sequences were removed using Trimmomatic v0.39
Reads were subsequently mapped to the mouse genome using HISAT2 v2.1.0
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Intestine

extract_protocol:
Total RNA was extracted from IECs using RNeasy Micro Kit and then digested with DNase I at 37 C for 15 min to remove any contaminating DNA
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) was employed with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® rRNA Depletion Kit v2 for cDNA synthesis with the addition of barcode sequences.

value: Intestine

value: Epithelial cells ex vivo


title: LECs, AAV-VEGF-C treated mice, exp2


title: Epithelial cells from anti-PD-L1 treated mouse 1, day 12


title: CD45+ TILs from mouse 3 treated with aPD-L1+E.colipApyr

description: 10x Genomics

data_processing:
The 10x Cell Ranger Count pipeline (version 3.1.0) was used to align reads to the reference transcriptome (mm10) and to calculate UMI counts from the mapped reads
Expression data were imported in R (version 4.0.3) and analyzed using Seurat (version 4.0.0) and popsicleR (version 0.2.1;) R packages.
For each sample, low quality cells were identified as outliers within the distribution of the number of genes, UMI counts, and percent of reads mapping on mitochondrial genes per cell, and subsequently discarded.
Doublets were identified and discarded using Scrublet (version 0.2.1;). Samples were integrated using the Seurat integration strategy . Prior to dimensional reduction with PCA, cell cycle scores were assigned to each cell and regressed out.
We selected 10 principal components for cluster analysis
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Tumor

extract_protocol:
Tumors were cut in small pieces and resuspended in RPMI1640 with 1.5 mg/mL Type I Collagenase (Sigma), 100 μg/mL DNase I (Roche), and 5% FBS, digested for 45 minutes at 37°C under gentle agitation. The digestion product was then passed through a 70 μm cell strainer to obtain a single-cell suspension. Cells were stained with Zombie Live/Dead and CD45 and immune cells were sorted using BDFACSAria and immediately processed for scRNA-Seq
scRNA-seq was performed immediately after FACS sorting of CD45+ TILs with the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1(10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Target number of captured cells ranged from 2,000 to 10,000 cells. Sequencing libraries were prepared per manufacturer’s protocol.

value: Tumor

value: CD45+ immune cells


title: Epithelial cells from anti-PD-L1+aoy treated mouse 3, day 12


title: Epithelial cells from anti-PD-L1+aoy treated mouse 1, day 12


title: Epithelial cells from anti-PD-L1 treated mouse 3, day 12


title: CD45+ TILs from mouse 1 treated with aPD-L1+E.colipApyr

description: 10x Genomics


title: Epithelial cells from anti-PD-L1 treated mouse 2 day 12


title: Epithelial cells from anti-PD-L1+aoy treated mouse 2, day 12


title: Epithelial cells from anti-PD-L1 treated mouse 5, day 12


title: CD45+ TILs from mouse 3 treated with aPD-L1+E.colipBAD28

description: 10x Genomics


title: CD45+ TILs from mouse 1 treated with aPD-L1+E.colipBAD28

description: 10x Genomics


title: CD45+ TILs from mouse 2 treated with aPD-L1+E.colipApyr

description: 10x Genomics


title: CD45+ TILs from mouse 2 treated with aPD-L1+E.colipBAD28

description: 10x Genomics


title: IL4

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

description: 10x Genomics

data_processing:
The analysis was performed with the Cell Ranger 7.1.0 software using the default parameters.
Souporcell (https://github.com/wheaton5/souporcell ) was used to separate the cells from CB6F1/J (Jax no. 100007) into BL/6 and BALB/c cells with singularity exec function.
Seurat (v3.2.3) R package to perform calculation of the number of unique genes detected in each cell (nFeature_RNA), the total number of molecules detected within a cell (nCount_RNA), and produce the UMAP.
pySCENIC (v0.10.) was used to explore the potential transcriptional regulators.
Assembly: mm10
Supplementary files format and content: HDF5 files are provied for further analyisis

source_name: Peritoneal cells

extract_protocol:
Peritoneal cells were isolated from CB6F1/J (Jax no. 100007)  mice after IL4 treatment.
10x Genomics Single Cell Gene Expression libraries were sequenced on a NextSeq 2000 run. The sequencing run was setup as a 28 cycles + 90 cycles non-symmetric run.

value: Peritoneal cells

tag: age

value: 6-8 weeks old


title: LPS

description: 10x Genomics

tag: strain


title: thymic_iNKT_ACC1KO_n2

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

data_processing:
Cell Ranger v7.0.0 was used to align the sequencing reads to the mm10 mouse transcriptome and quantify the expression of transcripts in each cell. This pipeline produced a gene expression matrix for each sample, which records the number of UMIs for each gene associated with each cell barcode.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thymus

extract_protocol:
For sample preparation of scRNA-seq, thymocytes were prepared from young adult mice (6–8 weeks old) and CD3+CD1d tetramer+ iNKT cells were collected with cell sorter.
Libraries were prepared using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 4 rxns (10× Genomics #PN-1000128) according to the manufacturer’s protocol.

value: thymus

value: primary

value: iNKT cell

value: Knock Out


title: thymic_iNKT_ACC1KO_n1


title: macrophage_IL4

description: 10x Genomics


title: BL6_LPS_3

data_processing:
TheReal Time Analysis software (RTA 3.4.4) was used for processing raw data files, the Illumina bcl2fastq v2.20 was used to demultiplex and convert binary base calls and qualities to fastq format.
Reads were trimmed for adapters and low-quality bases using Cutadapt(1.18)
Alignment with the reference genome (mm10) and the annotated transcripts using STAR(2.6.0c)
Gene expression quantification analysis was performed for all samples using STAR/RSEM ( v1.3.2) tools
EBSeq (1.24.0)and DESeq2(1.24.0) were used to find differential RNA expression
Assembly: mm10
Supplementary files format and content: raw counts text files were produced by RSEM( v1.3.2)

source_name: Peritoneal Macrophage

growth_protocol: Macrophage cells were isolated from the peritoneal cells by using EasySep™ Mouse F4/80 Positive Selection Kit (100-0659, Stemcell Technologies)

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (74134, QIAGEN)
mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina Illumina® Stranded mRNA Prep and paired-end sequencing.

treatment_protocol: Mice were treated with IL4,H. polygyrus or LPS in vivo or in vitro

value: Macrophage

value: treated with LPS


title: BL6_LPS_2


title: Epithelial cells from anti-PD-L1 treated mouse 4, day 12


title: Ctrl

description: 10x Genomics


title: CD45+ TILs from mouse 4 treated with aPD-L1+E.colipApyr

description: 10x Genomics


title: 4OH-Tam injected Kir4.1 cKO

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12.
R1 (26p) corresponds to a 16bp cell barcode + 10bp UMI barcode and R2 (98bp) contains the biological read. I1 corresponds to the 8bp Illumina I7 index of each read.
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 2.1.0, GRCm38.84) using 10X Genomics Cellranger count version 2.2.0
Assembly: mm10
Supplementary files format and content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated genes.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

source_name: 4-OH tamoxifen injected Kir4.1 cKO mice

extract_protocol:
Brainstem slices were prepared using a vibratome in ice cold, high sucrose slicing solution. Slicing solution was equilibrated with a 5% CO2-95% O2 gas mixture before use. Transverse brainstem slices (300 μm thick) were prepared and then immediately enzymatically treated at 34°C with protease XVIII (6 mg/mL) for 6 minutes. After enzyme incubation, slices were washed three times in cold dissociation solution and then transferred to an enzyme inhibitor mix containing trypsin inhibitor (10 mg/mL) and bovine serum albumin (BSA, 10 mg/mL) in cold sucrose dissociation solution. Shortly thereafter, slices were transferred to a glass Petri dish on ice. Using a plastic transfer pipette and scalpel, each region of interest was micro-dissected out of the slices and manually separated into sterile microcentrifuge tubes. Tissue chunks were then warmed to 34°C for 10 minutes before trituration.
A single cell suspension was achieved by trituration using a 25 and 30 gauge needles sequentially, attached to a 2 mL syringe. Samples were triturated for an average of 5 minutes. Immediately after, the samples were placed back on ice and filtered through a 30-micron filter into sterile microcentrifuge tubes for cell viability assessment. Cell viability for each sample was assessed on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded for capture onto an individual lane of a Chromium Controller (10X Genomics). Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform according to the manufacturer’s protocol (#CG00052) using version 2 (V2) chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR. All libraries were sequenced on individual lanes of an Illumina HiSeq4000 targeting 6,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.

value: rostral ventrolateral medulla


title: NOX4

city: Leuven

first: Elizabeth

last: Jones

address: Herestraat 49

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

description: brain

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7.
Adapters were filtered with ea-utils fastq-mcf v1.05.
Alignment was accomplished using HISAT2 against the human reference genome hg38 using the default parameters.
Resulting BAM alignment files were handled with Samtools v1.5.
Count-based differential expression analysis was assessed with R-based Bioconductor package DESeq2.
Assembly: hg38
Supplementary files format and content: csv file with normalised counts.
Supplementary files format and content: txt file with significant genes.

source_name: CL 05008-CLTH

growth_protocol: Human immortalised pericytes (Celther, CL 05008-CLTH) are cultured in DMEM supplemented with penicillin/streptomycin and 10% fetal bovine serum.

extract_protocol:
RNA was extracted from cells using the Qiagen RNeasy mini kit (74104) and the Qiazol Lysis Reagent (79306).
Libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq Library prep kit according to the manufacturer's protocol. Library quality and size range was assessed using a Bioanalyzer.

treatment_protocol: Pericytes were treated with 100 µM H2O2 for 24 hours with one media change after 8 hours. Control cells also had their medium changed.

value: CL 05008-CLTH

value: pericytes

tag: donor sex

value: male

value: no treatment


title: BL6_IL4_S2

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: OX4

description: brain


title: BL6_IL4_LPS_2

value: treated with IL4+LPS


title: IL4_LPS

description: 10x Genomics


title: OX2

description: brain


title: NOX1

description: brain


title: NOX2

description: brain


title: BL6_IL4_S3


title: NOX3

description: brain


title: 1-8 MV

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS78-BS

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Saliva

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

value: Healthy Subject

tag: anatomical location

value: Oral cavity structure

tag: rna source

value: total cell-free biofluid RNA


title: OX3

description: brain


title: BL6_IL4_2


title: BL6_LPS_1


title: 1-6 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS67-BS


title: BL6_IL4_LPS_1


title: BL6_IL4_1


title: BL6_HP_S1

value: infected with H. polygyrus


title: 2-7 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS77-BS


title: 2-8 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS88-BS


title: BL6_IL4_3


title: 2-2 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS46-BS


title: BL6_HP_S2


title: 2-5 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS65-BS


title: 1-10 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS42-BS


title: BL6_IL4_LPS_3


title: OX1

description: brain


title: BL6_IL4_S1


title: 2-7 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS80-BS


title: BL6_2

value: untreated


title: BL6_Ctrl_S2


title: 2-8 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS90-BS


title: BL6_Ctrl_S1


title: 2-3 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS56-BS


title: BL6_3


title: BALBc_LPS_2

value: BALB/c


title: 1_8

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS98-BS


title: 2-2 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS52-BS


title: BL6_1


title: 1_6

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS87-BS


title: BALBc_LPS_3


title: 2-4 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS64-BS


title: BALBc_IL4_S3


title: BALBc_IL4_S2


title: BL6_Ctrl_S3


title: BALBc_IL4_S1


title: 2-6 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS66-BS


title: 2_1

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS71-BS


title: BALBc_IL4_LPS_3


title: BALBc_IL4_LPS_2


title: 1_7

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS97-BS


title: BALBc_IL4_3


title: 1_2

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS74-BS


title: 1-2 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS43-BS


title: 1-1 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS41-BS


title: BALBc_IL4_LPS_1


title: BALBc_IL4_2


title: BALBc_IL4_1


title: BALBc_HP_S2


title: 2_3

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS81-BS


title: 1_4

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS85-BS


title: 1-9 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS76-BS


title: BALBc_HP_S1


title: 2-1 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS44-BS


title: 1-8 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS75-BS


title: BALBc_Ctrl_S3


title: 1-3 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS53-BS


title: 2-10 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS51-BS


title: BALBc_Ctrl_S2


title: 2_2

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS72-BS


title: BALBc_Ctrl_S1


title: 2_4

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS82-BS


title: BALBc_3


title: 1_5

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS86-BS


title: 1_3

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS84-BS


title: 2_9

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS95-BS


title: BALBc_2