title: OE2

city: Xiamen

first: Wanhong

last: Han

address: No.  55, Zhenhai Road, Siming District

institute: the First Affiliated Hospital of Xiamen University,School of Medicine, Xiamen University

description:
Library name: sample5
FPKM.OE2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: glioma cell line

value: overexpressed tau


title: OE1

status: Public on Dec 01 2025

type: SRA

country: China

description:
Library name: sample4
FPKM.OE1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: OE3

description:
Library name: sample6
FPKM.OE3


title: Con3

description:
Library name: sample3
FPKM.Con3

value: transfected with contrl vector


title: LNCAP_control_DHT+GDC0941_rep2

city: Baltimore

first: Yangzhenyu

last: Gao

state: MD

address: 2917 Saint Paul

department: Oncology

country: USA

institute: johns hopkins university

description: Library name: LNCAP_control_DHT+GDC0941_rep2

data_processing:
Adaptor sequences were removed using Trimmomatic v0.39 and aligned to the hg38 human genome using STAR2.6.0. The reads that are uniquely mapped are counted using HTSeq0.9.1. The reads per kilobase per million (RPKM) was calculated for each gene and normalized to obtain gene expression levels.
Differential expression analysis of shKMT2D versus control was performed using DESeq2. Heatmaps of shKMT2D and control samples were then generated using the ComplexHeatmap package in R.
Assembly: hg38
Supplementary files format and content: fastq

source_name: Prostate

growth_protocol: LNCaP cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin in plates coated with 0.01% poly L-lysine.

extract_protocol:
Qiagen RNeasy Mini Kit
NEBNext Ultra™ II RNA Library Prep Kit for Illumina

treatment_protocol: LNCaP cells were androgen deprived and cultured in DMSO or 1µg/ml doxycycline for 72h and treated with 10nM DHT, 1µM PI3K inhibitor GDC0941 or both for 24h, before processing for RNA-Seq.

tag: tissue

value: Prostate

value: LNCaP

value: prostate cancer

value: DMSO, DHT+GDC0941


title: LG-P

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

description: Library name: step3_6q_2

library_source: transcriptomic single cell

data_processing:
10X Genomic
genome build: GRCh38
Supplementary files format and content: mtx, barcodes, features

source_name: retina

extract_protocol:
Macular and peripheral explants were dissociated into single cells following light treatment using Papain Dissociation System (Worthington Biochem, NJ, USA) according to the manufacturer’s protocol.Then The single-cell suspension was combined with barcoded gel beads in a microfluidic chip and run on the Chromium Controller (10X Genomics) to create gel bead-in-emulsion (GEMs) droplets (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268, 10×Genomics). The GEMs were incubated, enabling mRNA reverse transcription into cDNA.
The barcoded cDNA was then amplified using PCR to construct a library according to users guide of Chromium Single Cell 3ʹ Reagent Kits v3

treatment_protocol: Macular and peripheral explants were dissociated into single cells following light  treatment. In brief,We employed a custom-built light exposure system situated within the tissue culture incubator to induce light stress in retinal explants.Light stress was accomplished by subjecting explants to intense light at 32k lux, while the control group were exposed to 5k lux light. Retinal explant tissues were placed on 12-well plate transwell inserts (#3460, Corning) with neurobasal medium (#21103049, Gibco), 2% B27 (#17504044, Gibco), 1% N2 (#17502048, Gibco), 1% fetal bovine serum (FBS, #F9423, Sigma‐Aldrich), 1% GlutaMax (#35050, Gibco), 1%ITS (#51500056, Gibco) and 1% penicillin-streptomycin (P/S, #P4333, Sigma‐Aldrich). Macular and peripheral neural retinal explants were exposed to light exposure for 4 hr.Single cell dissociation was achieved using the Papain Dissociation System (Worthington Biochem, NJ, USA) according to the manufacturer’s protocol.

value: retina


title: MBP-WRKY36-3_1

city: Kunming

first: Lirong

last: Zhao

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

institute: Chinese Academy of Sciences

description: Library name: MBP-WRKY36-3_1

library_source: genomic

data_processing:
Sequencing quality assessment, including the proportion of Clean Reads and base quality.
Evaluation of alignment results, including alignment rate and TSS enrichment analysis.
Peak identification, including Peak distribution and intra-group data repeatability evaluation.
Peak analysis, including annotation and enrichment analysis of associated genes and motifs.
Assembly: Oryza sativa genome (rice.uga.edu, version 7.0)
Supplementary files format and content: Gene annotation was performed on the grouping Peak, and the gene represented by the TSS closest to the grouping Peak was defined as the associated gene of the grouping Peak. Functional annotation and enrichment analysis of GO and KEGG were performed on the grouped associated gene sets. Including: seqnames, start, end, width, strand, peakName, colorScore (The q value is -log10 multiplied by 10 and rounded; larger values are more significant), annotation, geneChr, geneStart, geneEn, geneLength, geneStrand, geneId, transcriptId, distanceToTSS, gene_name, gene_biotype, geneG, geneKEGG, geneDescription, geneNR, geneSwissprot, geneTrEMB

molecule: genomic DNA

organism: Oryza sativa

source_name: Shoot

extract_protocol:
The main reference of DAP-seq experimental process is: Bartlett A, O’Malley RC, Huang SC, et al.,  Mapping genome-wide transcription-factor binding sites using DAP-seq. Nature Protocl, 2017. (1) DNA was extracted from 10-day rice seedlings, then genomic DNA was broken into ~200bp fragments, and the DNA library was prepared by adding the linker. (2) The expression vector containing the target protein coding sequence was constructed and the Halo-target protein fusion protein was expressed in vitro.
The HaloTag-TF fusion protein was incubated with the DNA library, the DNA was recovered, and the second generation library was constructed after PCR amplification.

value: Shoot

tag: sample group


title: HG-P

description: Library name: step3_6q_4


title: LG-M

description: Library name: step3_6q_1


title: Con2

description:
Library name: sample2
FPKM.Con2


title: MBP-1

description: Library name: MBP-1

value: MBP


title: MBP-WRKY36-2_1

description: Library name: MBP-WRKY36-2_1


title: Con1

description:
Library name: sample1
FPKM.Con1


title: MSKPCA2_shKMT2D_rep1

description: Library name: MSKPCA2_shKMT2D_rep1

data_processing:
Adaptor sequences were removed using Trimmomatic v0.39 and aligned to the hg38 human genome using STAR2.6.0. The reads that are uniquely mapped are counted using HTSeq0.9.1. The reads per kilobase per million (RPKM) was calculated for each gene and normalized to obtain gene expression levels.
Differential expression analysis of shKMT2D versus control was performed using DESeq2. Heatmaps of shKMT2D and control samples were then generated using the ComplexHeatmap package in R. The top 5,000 peaks were selected based on adjusted p-values.
Assembly: hg38
Supplementary files format and content: fastq, bam

growth_protocol: MSKPCA2 organoids were grown as per established protocols (Gao et al. Science 2014)

treatment_protocol: Organoids were androgen deprived and cultured in DMSO or 1µg/ml doxycycline for 72h and treated with 10nM DHT for 24h, before processing for RNA-Seq.

value: prostate cancer organoid

value: Doxycycline


title: MSKPCA2_control_rep1

description: Library name: MSKPCA2_control_rep1

value: DMSO


title: Control 2

city: Jinan

first: Xiaofang

last: Huang

state: Shandong Province

address: 107 Western of Wenhua Road

institute: Qilu Hospital of Shandong University

description:
Library name: C_2
Biological replicate 2 of vehicle-treated control mice. Intestinal epithelial cell-derived extracellular vesicles.

library_source: other

data_processing:
Raw sequencing reads were quality-checked with bcl2fastq. Adapters were trimmed and low-quality bases were removed using cutadapt (v1.7.1) with parameters: -m 18 -q 20. Cleaned reads were aligned to the Mus musculus GRCm38 genome using STAR (v2.7.10a) with --outFilterMultimapNmax 10. miRNA quantification was performed with featureCounts (v2.0.1) using the miRBase v22 annotation and parameters: -t miRNA -g gene_id. The final output is a raw count matrix of miRNA expression.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: other

organism: Mus musculus

source_name: Intestine

extract_protocol:
Total RNA, including small RNAs, was extracted from the purified EVs using the miRNeasy Micro Kit from Qiagen. This kit is specifically designed for efficient recovery of small RNAs.
A sequencing library was constructed from the total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina] following the manufacturer's protocol.

treatment_protocol: IEC-EVs were isolated from enzymatically digested mouse intestinal tissue through a series of differential centrifugations, followed by ultracentrifugation and purification on a discontinuous OptiPrep™ density gradient.

tag: age

value: 6-8 weeks old

tag: Sex

value: male

tag: stain

value: Intestine

value: Primary cells

value: intestinal epithelial cell

tag: genotype

value: WT

tag: batch


title: 36_MYC

description: Library name: 36_MYC

data_processing:
Sequencing quality assessment, including the proportion of Clean Reads and base quality.
Evaluation of alignment results, including alignment rate and TSS enrichment analysis.
Peak identification, including Peak distribution and intra-group data repeatability evaluation.
Peak analysis, including annotation and enrichment analysis of associated genes and motifs.
Assembly: Oryza sativa genome (rice.uga.edu, version 7.0)
Supplementary files format and content: Gene annotation was performed on the grouping Peak, and the gene represented by the TSS closest to the grouping Peak was defined as the associated gene of the grouping Peak. Functional annotation and enrichment analysis of GO and KEGG were performed on the grouped associated gene sets.

extract_protocol:
A total of 2 g of seedling shoots from transgenic 35S:OsWRKY36-Myc plants were harvested and fixed in a crosslinking solution containing 1% (w/v) formaldehyde under vacuum for 30 min on ice. crosslinking was terminated by treating with 0.125 mM glycine under vacuum for 5 min. ChIP assay was performed using the EpiQuik™ Plant ChIP Kit (Epigentek).
The DNA precipitated by ChIP was purified. Purified DNA was amplified by PCR using two primers that could anneal with both ends of the linker.

tag: chip antibody

value: anti-Myc


title: Dithizone treated 2

description:
Library name: D_2
Biological replicate 2 of dithizone-treated mice with Paneth cell ablation. Intestinal epithelial cell-derived extracellular vesicles.

value: Dithizone


title: RNA-seq_PC3_control_rep3

description: Library name: PC3_control_rep3

data_processing:
Transcript quantification was performed using Salmon. Differential expression analysis was conducted using DESeq2, and genes were classified as upregulated (log2FC ≥ 0.5, padj < 0.05) or downregulated (log2FC ≤ -0.5, padj < 0.05). DESeq2-normalized expression values of these differentially expressed genes were scaled to z-scores, and heatmaps were generated using the ComplexHeatmap package to visualize expression patterns across samples.
Assembly: hg38
Supplementary files format and content: fastq

growth_protocol: PC3 cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin

treatment_protocol: Cells were cultured in DMSO or 1µg/ml doxycycline for 72h before processing for RNA-Seq

value: Prostate


title: RNA-seq_PC3_shKMT2D_rep2

description: Library name: PC3_shKMT2D_rep2

value: prostate cancer


title: RNA-seq_PC3_control_rep2

description: Library name: PC3_control_rep2


title: RNA-seq_PC3_control_rep1

description: Library name: PC3_control_rep1


title: Dithizone treated 3

description:
Library name: D_3
Biological replicate 3 of dithizone-treated mice with Paneth cell ablation. Intestinal epithelial cell-derived extracellular vesicles.


title: MSKPCA2_shKMT2D_rep2

description: Library name: MSKPCA2_shKMT2D_rep2


title: Control 1

description:
Library name: C_1
Biological replicate 1 of vehicle-treated control mice. Intestinal epithelial cell-derived extracellular vesicles.


title: I35H5_LNinguinal_B16_ACTaPD1a41BB_TCR

city: Boston

first: Liang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Library name: I35H5_LNinguinal_B16_ACTaPD1a41BB_TCR

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v8.0.1.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v8.0.1. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Library strategy: TCR-seq

source_name: inguinal lymph node

extract_protocol:
Single-cell suspensions from the uterus were prepared using collagenase XI and DNase I. TCRβ/γδ+ T cells were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

value: inguinal lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: T cells in B16.gp33 melanoma with adoptive cell therapy and checkpoint blockade

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and pmel > wt

tag: age weeks

tag: pool of_mice

tag: treat agent

value: anti PD-1 (clone J43) and anti 4-1BB (clone 3H3); P14 T cells (CD45.1.2) and pmel (CD45.1)

tag: treat dose

value: B16.gp33, subcutaneous, at D0; 2.5x10E6 pmel and 2.5x10E6 P14, intravenous, at D7; 200ug anti PD1 and 50ug anti 4-1BB at D9, D11 and D13

tag: tumor

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

value: all T including P14 and pmel

tag: gating strategy

value: CD3e+ CD45.2+ enriched with transgenic CD3+ CD45.2- CD8+ CD45.1+ or CD45.1.2+

tag: mouse comments

value: ACT/CBI; pool of 10 mice

value: T cells


title: HL1,rep2

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

description: Library name: Sample 2

data_processing:
Reads were mapped to mouse genome mm10 from UCSC using BWA v0.7.17 with settings - 5SP -T036. Aligned reads with a mapping quality of at least 40 were used to identify valid ligation events with pairtools parse module (0.3.0 –min-map 40 –walks-policy 5unique – max-inter-align-gap 30). Paired reads were sorted by position and deduplicated with pairtools with default settings 37. Paired reads were converted to contact matrix with cooler tools38. Multi-resolution file mcool was generated with cooler tools v0.8.7 before Mustache v1.2.0 with settings -r 1kb -pt 0.1 was used to generate bedpe file with loop calls
Assembly: mm10
Supplementary files format and content: .hic and .mcool files

extract_protocol:
Following reverse crosslinking, DNA was extracted using phenol:chloroform:isoamyl alcohol, and the aqueous phase was transferred to a new tube with glycogen and sodium acetate added. The DNA was then precipitated with ethanol at -20°C for 4 hours, pelleted by centrifugation, air-dried, resuspended in TE buffer, and purified using a DNA Clean & Concentrator kit with final elution in 100 μL.
Library preparation was performed on HL-1 cells grown in Claycomb media following the Micro-C-XL method, with the elision of the gel-based sizing of the library (n=2).

tag: cell line

tag: cell type

value: cardiomyocyte


title: I35H5_LNinguinal_B16_ACTaPD1a41BB_GEX

description: Library name: I35H5_LNinguinal_B16_ACTaPD1a41BB_GEX

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v8.0.1.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v8.0.1. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: Sex

value: male


title: HL1,rep1

description: Library name: Sample 1


title: MSKPCA2_control_rep2

description: Library name: MSKPCA2_control_rep2

value: prostate cancer organoid

tag: treatment

value: DMSO


title: Dithizone treated 1

description:
Library name: D_1
Biological replicate 1 of dithizone-treated mice with Paneth cell ablation. Intestinal epithelial cell-derived extracellular vesicles.

tag: age

value: 6-8 weeks old

tag: stain

value: Intestine

value: Primary cells

value: intestinal epithelial cell

tag: genotype

value: WT

value: Dithizone

tag: batch


title: I35H5_LNinguinal_B16_ACTaPD1a41BB_FBC

description: Library name: I35H5_LNinguinal_B16_ACTaPD1a41BB_FBC

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v8.0.1.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v8.0.1. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Library strategy: CITE-seq

value: inguinal lymph node

value: TRUE

value: T cells in B16.gp33 melanoma with adoptive cell therapy and checkpoint blockade

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and pmel > wt

tag: age weeks

tag: pool of_mice

tag: treat agent

value: anti PD-1 (clone J43) and anti 4-1BB (clone 3H3); P14 T cells (CD45.1.2) and pmel (CD45.1)

tag: treat dose

tag: tumor

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy


title: ATAC-seq_PC3_shKMT2D_rep2

description: Library name: PC3_shKMT2D_rep2

data_processing:
Sequencing adaptors were removed using Trimmomatic v0.39. Trimmed reads were aligned to the hg38 human genome using Bowtie 2.4. Duplicate PCR and optical reads were removed using Picard MarkDuplicates v2.18.16. Aligned reads were extracted using SAMtools v1.9. Peaks were identified using a pipeline that adheres to standards set by ENCODE.  This includes initial peak calling with MACS2 v2.1.3 with a liberal p value threshold of 0.1 normalized to the input. Replicate peaks were then assessed using an irreproducible discovery rate (p value<0.05). Those peaks passing IDR were then merged to form a peak atlas. Peak intensity was calculated using the countOverlaps function in the GenomicAlignments section of R. Peaks were annotated using ChIPseeker in the R package. The differential analysis of each condition compared to the control was done using DESeq2. For each pairwise comparison, only those peaks that were reproducible were considered for differential analysis. Moreover, peaks were required to have an FDR<0.05 (FDR, false discovery rate) to be considered statistically significantly different between comparisons. Normalized DESeq2 bigwig files were used for plotting tornado plots using DeepTools.
Assembly: hg38
Supplementary files format and content: fastq, bigwig

extract_protocol:
Omni-ATAC protocol (Corces et al. Nature Methods 2017)
Illumina-compatible high diversity, single index library primers were utilized

treatment_protocol: Cells were cultured in DMSO or 1µg/ml doxycycline for 72h before start of experiment.

tag: tissue

value: Prostate

tag: cell line

tag: cell type

value: prostate cancer

tag: treatment

value: Doxycycline


title: Control 3

description:
Library name: C_3
Biological replicate 3 of vehicle-treated control mice. Intestinal epithelial cell-derived extracellular vesicles.

tag: age

tag: Sex

value: male

tag: stain

tag: genotype

tag: batch


title: INPUT-36

description: Library name: INPUT-36

value: Shoot

tag: chip antibody


title: I35H4_B16_ACTaPD1a41BB_TCR

description: Library name: I35H4_B16_ACTaPD1a41BB_TCR

source_name: skin of body

value: skin of body

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: age weeks

tag: pool of_mice

tag: treat agent

tag: treat dose

value: B16.gp33, subcutaneous, at D0; 2.5x10E6 pmel and 2.5x10E6 P14, intravenous, at D7; 200ug anti PD1 and 50ug anti 4-1BB at D9, D11 and D13

value: collagenase I

value: all T including P14 and pmel

value: CD3e+ CD45.2+ enriched with transgenic CD3+ CD45.2- CD8+ CD45.1+ or CD45.1.2+

tag: mouse comments

value: ACT/CBI; pool of 10 mice

value: T cells


title: ATAC-seq_PC3_control_rep3

description: Library name: PC3_control_rep3

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: DMSO


title: I35H4_B16_ACTaPD1a41BB_FBC

description: Library name: I35H4_B16_ACTaPD1a41BB_FBC

tag: immgent igt_10xlane_id

tag: hashtag number

value: TRUE

value: T cells in B16.gp33 melanoma with adoptive cell therapy and checkpoint blockade

tag: Sex

tag: tumor

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy


title: ATAC-seq_PC3_shKMT2D_rep1

description: Library name: PC3_shKMT2D_rep1


title: ATAC-seq_PC3_control_rep1

description: Library name: PC3_control_rep1


title: ATAC-seq_MSKPCA3_shKMT2D_GDC0941_rep3

description: Library name: MSKPCA3_shKMT2D_GDC0941_rep3

growth_protocol: MSKPCA3 organoids were grown as per established protocols (Gao et al. Science 2014)

treatment_protocol: Organoids were androgen deprived and cultured in DMSO or 1µg/ml doxycycline for 72h and treated with 1µM GDC0941 for 24 hours, before processing for ATAC-Seq.

value: MSKPCA3 organoid

value: Doxycycline, GDC0941


title: I35H4_B16_ACTaPD1a41BB_GEX

description: Library name: I35H4_B16_ACTaPD1a41BB_GEX

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and pmel > wt

tag: age weeks

tag: pool of_mice

value: anti PD-1 (clone J43) and anti 4-1BB (clone 3H3); P14 T cells (CD45.1.2) and pmel (CD45.1)


title: I35H3_LNinguinal_B16_ACT_GEX

description: Library name: I35H3_LNinguinal_B16_ACT_GEX

tag: tissue

value: inguinal lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

value: male

tag: treat agent

value: armenian Hamster IgG and Rat IgG2a; P14 T cells (CD45.1.2) and pmel (CD45.1)

tag: treat dose

value: B16.gp33, subcutaneous, at D0; 2.5x10E6 pmel and 2.5x10E6 P14, intravenous, at D7; 200ug Armenian Hamster IgG and 50ug Rat IgG2a, intraperitoneal, at D9, D11 and D13

value: mechanical dissociation alone

tag: mouse comments

value: ACT; pool of 10 mice

tag: cell type


title: ATAC-seq_MSKPCA3_shKMT2D_GDC0941_rep1

description: Library name: MSKPCA3_shKMT2D_GDC0941_rep1

value: Prostate

tag: cell line

value: prostate cancer

tag: treatment


title: RNA-seq_PC3_shKMT2D_rep1

description: Library name: PC3_shKMT2D_rep1

value: Doxycycline


title: I35H3_LNinguinal_B16_ACT_FBC

description: Library name: I35H3_LNinguinal_B16_ACT_FBC

tag: condition detailed_organ

tag: cite seq

tag: Sex

tag: tumor

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: all T including P14 and pmel

tag: gating strategy

value: CD3e+ CD45.2+ enriched with transgenic CD3+ CD45.2- CD8+ CD45.1+ or CD45.1.2+

value: T cells


title: I35H2_B16_ACT_GEX

description: Library name: I35H2_B16_ACT_GEX

tag: tissue

value: skin of body

tag: immgent igt_10xlane_id

value: TRUE

tag: exp name

value: T cells in B16.gp33 melanoma with adoptive cell therapy and checkpoint blockade

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: age weeks

tag: pool of_mice

value: collagenase I


title: I35H2_B16_ACT_TCR

description: Library name: I35H2_B16_ACT_TCR

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: Goldrath

value: P14 and pmel > wt

tag: treat agent

tag: treat dose

tag: mouse comments

tag: cell type


title: ATAC-seq_MSKPCA3_shKMT2D_DATAC-seq_MSO_rep2

description: Library name: MSKPCA3_shKMT2D_DMSO_rep2

tag: cell line

value: MSKPCA3 organoid

tag: treatment

value: Doxycycline, DMSO


title: ATAC-seq_MSKPCA3_shKMT2D_DATAC-seq_MSO_rep3

description: Library name: MSKPCA3_shKMT2D_DMSO_rep3

tag: tissue


title: I35H2_B16_ACT_FBC

description: Library name: I35H2_B16_ACT_FBC

tag: immgent igt_10xlane_id

tag: exp name

tag: Sex

value: male

value: armenian Hamster IgG and Rat IgG2a; P14 T cells (CD45.1.2) and pmel (CD45.1)

value: B16.gp33, subcutaneous, at D0; 2.5x10E6 pmel and 2.5x10E6 P14, intravenous, at D7; 200ug Armenian Hamster IgG and 50ug Rat IgG2a, intraperitoneal, at D9, D11 and D13

tag: tumor

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy


title: ATAC-seq_MSKPCA3_control_GDC0941_rep3

description: Library name: MSKPCA3_control_GDC0941_rep3

value: Prostate

value: DMSO, GDC0941


title: I35H1_spleen_TCR

description: Library name: I35H1_spleen_TCR

source_name: spleen

value: spleen

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: lab

tag: organism name

tag: strain

tag: genetics

value: wt

tag: age weeks

tag: pool of_mice

value: FALSE

value: mechanical dissociation alone

value: splenocytes


title: ATAC-seq_PC3_shKMT2D_rep3

description: Library name: PC3_shKMT2D_rep3

tag: tissue

tag: cell line

tag: cell type

value: prostate cancer

tag: treatment

value: Doxycycline


title: ATAC-seq_MSKPCA3_control_GDC0941_rep1

description: Library name: MSKPCA3_control_GDC0941_rep1


title: I35H1_spleen_GEX

description: Library name: I35H1_spleen_GEX

tag: immgent igt_10xlane_id

value: TRUE

tag: exp name

value: T cells in B16.gp33 melanoma with adoptive cell therapy and checkpoint blockade

tag: Sex

tag: prep description

tag: organ

value: T cells


title: ATAC-seq_MSKPCA3_control_DATAC-seq_MSO_rep3

description: Library name: MSKPCA3_control_DMSO_rep3

value: MSKPCA3 organoid

value: DMSO


title: I35H1_spleen_FBC

description: Library name: I35H1_spleen_FBC

tag: hashtag number

tag: condition detailed_organ

value: Goldrath

value: male

tag: organ uberon_id

tag: target cells

tag: gating strategy


title: ATAC-seq_MSKPCA3_control_DATAC-seq_MSO_rep1

description: Library name: MSKPCA3_control_DMSO_rep1


title: ATAC-seq_MSKPCA3_control_GDC0941_rep2

description: Library name: MSKPCA3_control_GDC0941_rep2


title: ATAC-seq_MSKPCA3_control_DATAC-seq_MSO_rep2

description: Library name: MSKPCA3_control_DMSO_rep2


title: I35H3_LNinguinal_B16_ACT_TCR

description: Library name: I35H3_LNinguinal_B16_ACT_TCR

value: inguinal lymph node

tag: cite seq

tag: lab

tag: organism name

tag: strain

tag: genetics

value: P14 and pmel > wt

tag: treat agent

value: armenian Hamster IgG and Rat IgG2a; P14 T cells (CD45.1.2) and pmel (CD45.1)

tag: treat dose

value: B16.gp33, subcutaneous, at D0; 2.5x10E6 pmel and 2.5x10E6 P14, intravenous, at D7; 200ug Armenian Hamster IgG and 50ug Rat IgG2a, intraperitoneal, at D9, D11 and D13

tag: tumor

value: all T including P14 and pmel

value: CD3e+ CD45.2+ enriched with transgenic CD3+ CD45.2- CD8+ CD45.1+ or CD45.1.2+

tag: mouse comments

value: ACT; pool of 10 mice


title: Control_scRNAseq

city: Chengdu

first: Long

middle: Qian

last: Kang

state: Sichuan Province

address: 新川路2222号

department: Biotherapeutics

institute: Sichuan University

description:
Library name: Control
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/piplines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tissues were digested with neutral protease, collagenase IV, and DNase I at 37°C for 30 min, filtered through 40 μm mesh, and RBCs were lysed. Subsequently, CD45+ cells were isolated using magnetic bead sorting.
Cd45+ cells were loaded onto the 10X Genomics Chromium 3′ v3 platform. Libraries were sequenced on Illumina Novaseq 6000.

tag: tissue

value: Tumor

tag: cell type

value: CD45+ Cells


title: ATAC-seq_MSKPCA3_shKMT2D_GDC0941_rep2

description: Library name: MSKPCA3_shKMT2D_GDC0941_rep2

value: Prostate

tag: cell line

value: prostate cancer

tag: treatment

value: Doxycycline, GDC0941


title: Arg_scRNAseq

description:
Library name: Arg
10x Genomics


title: ATAC_LNCAP_GDC0941_rep2

description: Library name: LNCAP_GDC0941_rep2

data_processing:
Sequencing adaptors were removed using Trimmomatic v0.39. Trimmed reads were aligned to the hg38 human genome using Bowtie 2.4. Duplicate PCR and optical reads were removed using Picard MarkDuplicates v2.18.16. Aligned reads were extracted using SAMtools v1.9. Peaks were identified using a pipeline that adheres to standards set by ENCODE.  This includes initial peak calling with MACS2 v2.1.3 with a liberal p value threshold of 0.1 normalized to the input. Replicate peaks were then assessed using an irreproducible discovery rate (p value<0.05). Those peaks passing IDR were then merged to form a peak atlas. Peak intensity was calculated using the countOverlaps function in the GenomicAlignments section of R. Peaks were annotated using ChIPseeker in the R package. The differential analysis of each condition compared to the control was done using DESeq2. For each pairwise comparison, only those peaks that were reproducible were considered for differential analysis. Moreover, peaks were required to have an FDR<0.05 (FDR, false discovery rate) to be considered statistically significantly different between comparisons. Normalized DESeq2 bigwig files were used for plotting tornado plots using DeepTools.
Assembly: hg38
Supplementary files format and content: bam, bigwig

growth_protocol: LNCaP cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin streptomycin in plates coated with 0.01% poly L-lysine.

treatment_protocol: LNCaP cells were cultured in DMSO or 1µg/ml doxycycline for 72h followed by treatment with 1µM PI3K inhibitor GDC0941 for 24 hours, before processing for ATAC-Seq.

value: LNCaP


title: Control5_RNA

description:
Library name: Control5
60

data_processing:
Raw RNA-seq reads were first subjected to quality control using FastQC and trimmed to remove low-quality bases and adapter sequences. Clean reads were aligned to the reference genome using STAR, and gene-level read counts were obtained with featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen), quantified by NanoDrop, and library preparation was performed using Illumina protocols. cDNA was synthesized, fragmented, ligated with adaptors, amplified by PCR, and quality-checked using Agilent Bioanalyzer 2100.
Libraries were sequenced on Illumina platforms.


title: Control4_RNA

description:
Library name: Control4
58


title: ATAC_LNCAP_GDC0941_rep1

description: Library name: LNCAP_GDC0941_rep1


title: Control3_RNA

description:
Library name: Control3
56


title: ATAC_LNCAP_DMSO_rep2

description: Library name: LNCAP_DMSO_rep2


title: ATAC-seq_MSKPCA3_shKMT2D_DATAC-seq_MSO_rep1

description: Library name: MSKPCA3_shKMT2D_DMSO_rep1

value: MSKPCA3 organoid

value: Doxycycline, DMSO


title: RNA-seq_DU145_control_rep3

description: Library name: DU145_control_rep3

growth_protocol: DU145 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

value: DMSO


title: Control2_RNA

description:
Library name: Control2
55


title: Arg5_RNA

description:
Library name: Arg5
81


title: Control1_RNA

description:
Library name: Control1
51


title: Arg4_RNA

description:
Library name: Arg4
79


title: RNA-seq_DU145_control_rep2

description: Library name: DU145_control_rep2


title: RNA-seq_DU145_shKMT2D_rep3

description: Library name: DU145_shKMT2D_rep3

value: Doxycycline


title: RNA-seq_DU145_control_rep1

description: Library name: DU145_control_rep1


title: Arg1_RNA

description:
Library name: Arg1
74


title: RNA-seq_DU145_shKMT2D_rep2

description: Library name: DU145_shKMT2D_rep2


title: RNA-seq_PC3_shKMT2D_rep3

description: Library name: PC3_shKMT2D_rep3


title: Arg3_RNA

description:
Library name: Arg3
77


title: ATAC_LNCAP_DMSO_rep1

description: Library name: LNCAP_DMSO_rep1


title: Arg2_RNA

description:
Library name: Arg2
76


title: RNA-seq_DU145_shKMT2D_rep1

description: Library name: DU145_shKMT2D_rep1


title: DU145_control_rep2

description: Library name: DU145_control_rep2


title: CD8_Control2_RNA

description: Library name: CD8_Control2

source_name: CD8 T cell

value: CD8 T cell


title: CD8_Control3_RNA

description: Library name: CD8_Control3


title: DU145_control_rep3

description: Library name: DU145_control_rep3


title: DU145_control_rep1

description: Library name: DU145_control_rep1


title: CD8_Control4_RNA

description: Library name: CD8_Control4


title: DU145_shKMT2D_rep2

description: Library name: DU145_shKMT2D_rep2


title: CD8_Arg5_RNA

description: Library name: CD8_Arg5


title: CD8_Control1_RNA

description: Library name: CD8_Control1


title: DU145_shKMT2D_rep1

description: Library name: DU145_shKMT2D_rep1


title: CD8_Arg4_RNA

description: Library name: CD8_Arg4


title: CD8_Arg3_RNA

description: Library name: CD8_Arg3


title: Multiome Day 7 KMT2D Knockdown ATAC

first: Taibo

last: Li

address: 1830 E Monument Street, Suite 2-300

institute: Johns Hopkins School of Medicine

description:
Library name: D7_KD_ATAC
D7_KD_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Single-cell multiomic data were processed using the 10x cellranger count pipeline
Assembly: hg38
Supplementary files format and content: Cellranger output files: filtered_feature_bc_matrix.h5

source_name: Prostate organoid

extract_protocol:
100,000 cells (viability 95%) were lysed for 4min and resuspended in Diluted Nuclei Buffer (10x Genomics, PN- 2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automated cell counter by trypan blue staining.  9,660 nuclei were loaded per transposition reaction, targeting recovery of 10,000 nuclei after encapsulation. After transposition reaction nuclei were encapsulated and barcoded.
Next-generation sequencing libraries were constructed following the User Guide, which were sequenced on an Illumina NovaSeq 6000 system at the same time.

value: Prostate organoid

value: MSKPCA3 patient-derived organoids

tag: time point/genotype

value: Day 7 KMT2D Knockdown

value: KMT2D knockdown by siRNA

tag: library type

value: ATAC


title: CD8_Arg2_RNA

description: Library name: CD8_Arg2


title: CD8_Arg1_RNA

description: Library name: CD8_Arg1


title: Multiome Day 7 Control ATAC

description:
Library name: D7_Control_ATAC
D7_Control_filtered_feature_bc_matrix.h5

value: Day 7 Control


title: Multiome Day 7 KMT2D Knockdown RNA

description:
Library name: D7_KD_RNA
D7_KD_filtered_feature_bc_matrix.h5

value: mRNA


title: CD8_Control5_RNA

description: Library name: CD8_Control5


title: Multiome Day 0 ATAC

description:
Library name: D0_ATAC
D0_filtered_feature_bc_matrix.h5

value: Day 0 control


title: Multiome Day 7 Control RNA

description:
Library name: D7_Control_RNA
D7_Control_filtered_feature_bc_matrix.h5


title: Multiome Day 0 RNA

description:
Library name: D0_RNA
D0_filtered_feature_bc_matrix.h5


title: Three pooled e17.5 eye cups from Myrf humWT/humWT strain

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

description: Library name: e17.5_MyrfhumWT/humWT_eye_cup

data_processing:
Sequencing outputs were demultiplexed using 10x Genomics Cell Ranger 7.1.0 software and FASTQ files were aligned to the Genome Reference Consortium Mouse Build 38, mm10 genome (Church et al., 2009; Mouse Genome Sequencing et al., 2002; Zheng et al., 2017, https://genomes.ucsc.edu).
Seurat/4.1.1 (Butler et al., 2018; Stuart et al., 2019) scRNAseq software was utilized to normalize data using the NormalizeData and FindVariableFeatures commands with nfeatures set to 2000. Poor quality cells were removed using cutoffs of nFeature_RNA < 200 and % mitochondrial RNA >15%. Doublet cells were considered those with nCounts > 2000 and removed from the study.
Data from all time points and genotypes was anchored and integrated prior to scaling, principal component analysis and Uniform Manifold Approximation and Projection (UMAP) clustering.
Assembly: Genome Reference Consortium Mouse Build 38, mm10 genome
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)

molecule: polyA RNA

source_name: eye cup

extract_protocol:
Eyes were collected from e17.5 litters, the cornea, lens, and optic nerve were removed, and the eyecups were place on ice in 1 X HBSS (Invitrogen, 14175095) while samples were genotyped using a rapid genotyping protocol (Truett et al., 2000). Three Myrffl/fl and three Rx>cre Myrffl/fl samples were pooled for each time point.  Eyecups were dissociated into single cells in a Papain solution containing 5mM L Cysteine (Sigma, C7352), 1mM EDTA (Sigma, E4884), 0.6 mM 2-mercaptoethanol (Sigma, M6250), and 1mg/ml Papain (Roche, 10108014001) for 10 minutes at 37°C with trituration every 2 minutes.  The dissociation was stopped using Neurobasal Media (Invitrogen, 12348017) with 10% Fetal Bovine Serum (FBS) (Corning, MT35010CV), single cells were collected by centrifugation for 5 minutes at 300 RCF at 4°C.  The supernatant was aspirated, and the single cells were resuspended in cold Neurobasal Media with 3% FBS.
Single cell libraries were prepared by the University of Michigan Advanced Genomics Core and sequencing was performed using the 10X Genomics Chromium platform using manufacturer’s protocol for 10x Single Cell Expression 3’ and sequenced on the NovaSeq (S4) 300 cycle (Illumina, San Diego, CA).

value: eye cup

value: Total eye cup cells

tag: genotype

value: Myrf humWT/humWT


title: DU145_shKMT2D_rep3

description: Library name: DU145_shKMT2D_rep3

value: Prostate

value: prostate cancer


title: pooling of sorted CD4+ T cells obtained from BM848, BM720, BM668

city: Seoul

first: Sojeong

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Blood Cancer Research Institute

country: South Korea

institute: Yonsei University College of Medicine

description:
Library name: BM_CHS5
Chromium Next GEM Single Cell 5' HT v2 Reagents

data_processing:
To demultiplex the sequenced RNA data, the ‘mkfastq’ function (Cell Ranger, 10X Genomics, v3.0.1) was used to generate fastq files
Demultiplexed fastq files for gene expression were aligned to the reference human genome (GRCh38; 10X Cell Ranger reference GRCh38 v3.0.0) using Cell Ranger (v6.1.1).
The sequenced TCR data were aligned to the reference human genome (vdj_GRCh38_alts_ensembl-5.0.0)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz for scRNAseq
Supplementary files format and content: features.tsv.gz  for scRNAseq
Supplementary files format and content: matrix.mtx.gz  for scRNAseq
Supplementary files format and content: TCR.csv for scTCRseq
Supplementary files format and content: best_cluster.tsv for demultiplexing

source_name: primary cells

growth_protocol: Primary human BMMCs were cryopreserved and subsequently thawed for use

extract_protocol:
BMMCs were isolated from bone marrow aspirates using Ficoll, cryopreserved, thawed, stained with anti-CD4 antibody, and sorted by FACS
Performed according to the manufacturer's protocol using Chromium Next GEM Single Cell 5' HT v2 Reagents
Single-cell RNA sequencing (scRNA-seq) and single-cell T-cell receptor sequencing (scTCR-seq) were performed simultaneously using multiplexing techniques.

treatment_protocol: No treatment

value: bone marrow

value: mononuclear cells

value: No treatment


title: pooling of sorted CD4+ T cells obtained from BM694, BM37, BM678-1

description:
Library name: BM_CHS6
Chromium Next GEM Single Cell 5' HT v2 Reagents


title: pooling of sorted CD4+ T cells obtained from BM474-1, BM_900, BM33

description:
Library name: BM_CHS7
Chromium Next GEM Single Cell 5' HT v2 Reagents


title: pooling of sorted CD4+ T cells obtained from SMM_3, Healthy_4, MGUS_3

description:
Library name: BM_CHS3
Chromium Next GEM Single Cell 5' HT v2 Reagents


title: miRNA-Seq, Zeb1_200M_pituitary_2_youngCohort

city: Cambridge

first: David

middle: P

last: Bartel

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute / MIT

description:
Library name: Zeb1_200M_pituitary_2_youngCohort
small RNA

data_processing:
Adaptor sequences were trimmed from reads using cutadapt (Martin 2011). Reads were filtered for quality using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters “-q 30 –p 100” to ensure that all bases had an accuracy of 99.9%. To assign processed sequencing reads to miRNAs, the first 19nt of each read were matched to a dictionary of miRNA sequences downloaded from TargetScanMouse Release 7, requiring no mismatches between the read and the miRNA dictionary. Reads mapping to the internal size standards and spike-in miRNAs were removed for further analysis. Differential expression analysis was performed using DESeq2 v1.38.3 without use of the lfcShrink() function.
Assembly: TargetScanMouse Release 7
Supplementary files format and content: tab-delimited text file of DESeq2 output includes miRNA name (mirna), baseMean, log2 fold change, lfcSE, stat, p-value, adjusted p-value, raw counts, and normalized counts

source_name: pituitary

extract_protocol:
Total RNA was extracted from mouse tissues using TRI Reagent (ThermoFisher) according to the manufacturer’s protocol with the following modifications. Mouse tissues were rapidly dissected after CO2-based euthanasia and flash frozen in Eppendorf tubes in liquid N2. Tissue was transferred to a 15 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized with a TissueRuptor (Qiagen) and disposable probes. Samples were transferred to Eppendorf tubes (1 mL per tube) and phase separated with 200 μL chloroform (J.T. Baker Analytical). After isopropanol precipitation and two 70% ethanol washes, total RNA was resuspended in water.
Each small-RNA sequencing libraries was prepared with 0.5 μg of total RNA extracted from mouse pituitary. To minimize loss due to low starting input, 3 ug of total RNA from the budding yeast Naumovozyma castelli was added to each sample prior to size-selection. In addition, 0.5 fmoles of miR-427-5p (X. tropicalis) and 0.5 fmoles of miR-14 (D. melanogaster) were added as spike-ins. From each sample, RNAs that co-migrated within the range of 18 and 32 nt radiolabeled internal standards were isolated on a 15% polyacrylamide urea gel. Purified RNA was ligated to a preadenylated 3′ adapter (AppNNNNTCGTATGCCGTCTTCTGCTTGddC) using T4 RNA Ligase 2 KQ mutant (NEB) in a reaction supplemented with 10% polyethylene glycol (PEG 8000, NEB). To reduce ligation biases, this 3′ adapter had 4 random-sequence positions at its 5′ end. After gel purification on a 8% polyacrylamide urea gel, RNA was ligated to a 5′ adapter (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) using T4 RNA Ligase I (NEB) in a reaction supplemented with 10% PEG. To reduce ligation biases, this adapter had 4 random-sequence positions at its 3′ end. After gel purification on an 8% polyacrylamide urea gel, RNA was reverse transcribed with SuperScript III (Invitrogen), and the cDNA was amplified ~12 cycles with KAPA HiFi DNA polymerase (Kapa Biosystems). Amplified DNA was purified on a 3% metaphor agarose gel and submitted for sequencing. A step-by-step protocol for constructing libraries for small-RNA sequencing is available at http://bartellab.wi.mit.edu/protocols.html.

value: pituitary

tag: Sex

value: female

tag: age

value: 8–12 weeks old


title: miRNA-Seq, Zeb1_200M_pituitary_3_youngCohort

description:
Library name: Zeb1_200M_pituitary_3_youngCohort
small RNA


title: miRNA-Seq, Zeb1_200M_pituitary_4_youngCohort

description:
Library name: Zeb1_200M_pituitary_4_youngCohort
small RNA


title: pooling of sorted CD4+ T cells obtained from Healthy_5, SMM_4, MGUS_4

description:
Library name: BM_CHS4
Chromium Next GEM Single Cell 5' HT v2 Reagents


title: miRNA-Seq, Zeb1_200M_pituitary_1_youngCohort

description:
Library name: Zeb1_200M_pituitary_1_youngCohort
small RNA


title: miRNA-Seq, Zeb1_200H_pituitary_4_youngCohort

description:
Library name: Zeb1_200H_pituitary_4_youngCohort
small RNA


title: pooling of sorted CD4+ T cells obtained from Healthy_2, SMM_1, MGUS_1

description:
Library name: BM_CHS1
Chromium Next GEM Single Cell 5' HT v2 Reagents


title: miRNA-Seq, Zeb1_200H_pituitary_3_youngCohort

description:
Library name: Zeb1_200H_pituitary_3_youngCohort
small RNA


title: pooling of sorted CD4+ T cells obtained from SMM_2, Healthy_3, MGUS_2

description:
Library name: BM_CHS2
Chromium Next GEM Single Cell 5' HT v2 Reagents


title: RNA-seq of KS stimulated monocytes

city: Beijing

first: Xingxian

last: Liu

address: 30 Shuangqing Rd, Haidian District

institute: Tsinghua University

description: Library name: KS_RNA

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: hg38
Supplementary files format and content: csv file including TPM values for each sample

source_name: CD14-positive monocytes

extract_protocol:
RNA using Trizol, RFP in Ribo-seq using Qiagen miRNeasy Mini Kit.
RNA-seq library construction using SMARTER-seq Library Prep Kit following manufacturers' protocol. Ribo-seq library construction following Ingolia et al, Nat. Prot. 2012.

value: CD14-positive monocytes

value: KS stimulated for 120h


title: RNA-seq of untreated monocytes

description: Library name: No_treatment_RNA


title: miRNA-Seq, Zeb1_200H_pituitary_2_youngCohort

description:
Library name: Zeb1_200H_pituitary_2_youngCohort
small RNA


title: miRNA-Seq, Zeb1_WT_pituitary_4_youngCohort

description:
Library name: Zeb1_WT_pituitary_4_youngCohort
small RNA


title: miRNA-Seq, Zeb1_200H_pituitary_1_youngCohort

description:
Library name: Zeb1_200H_pituitary_1_youngCohort
small RNA


title: Three pooled e17.5 eye cups from Myrf humdG/humdG strain

description: Library name: e17.5_MyrfhumdG/humdG_eye_cup

value: Myrf humdG/humdG


title: Control1_ATAC

description: Library name: Control1

data_processing:
Raw ATAC-seq reads were subjected to quality control and adapter trimming, followed by alignment to the reference genome using Bowtie2. Duplicate reads, mitochondrial reads, and low-quality fragments were removed, and accessible chromatin peaks were called using MACS2. Peak counts were quantified and normalized, and downstream analyses including differential accessibility and functional enrichment were performed.
Assembly: mm10
Supplementary files format and content: bw file

extract_protocol:
CD8+ T cells were treated with or without arginine, nuclei were isolated, and ATAC-seq libraries were prepared using 50,000 nuclei per reaction. Transposition was performed at 37°C for 30 min, followed by purification, PCR amplification, and sequencing on Illumina Novaseq.
Libraries were sequenced on Illumina platforms.

value: CD8 T cell


title: Control 5 fibroblast cells, galactose

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Library name: control_5

data_processing:
RNA-seq data were then aligned using STAR against GRCH38 (hg38) version of the human genome. Raw read counts were quantified using RSEM.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw counts, tpm, and fpkm for each sample

source_name: fibroblast

extract_protocol:
RNA was extracted from human-derived fibroblast cells using the Qiagen RNeasy Plus Mini Kit (cat. # 74104) following the manufacturer’s protocol.
Libraries were generated the RNAeq NETFLEX Rapid Directional kit version 1.0 from PerkinElmer.

value: fibroblast

tag: disease state

value: Healthy

value: Male

tag: age at_biopsy

tag: growth media

value: galactose


title: Ribo-seq of KS stimulated monocytes

description: Library name: KS_Ribo

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: hg38
Supplementary files format and content: csv file including TPM values for each sample
Library strategy: Ribo-Seq


title: miRNA-Seq, Zeb1_WT_pituitary_2_youngCohort

description:
Library name: Zeb1_WT_pituitary_2_youngCohort
small RNA

tag: strain


title: Control 6 fibroblast cells, galactose

description: Library name: control_6

value: Female


title: Control 7 fibroblast cells, galactose

description: Library name: control_7


title: Zeb1_200M_ovary_4_youngCohort

description:
Library name: Zeb1_200M_ovary_4_youngCohort
stranded

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR v2.7.1a with the parameters “--outFilterType BySJout --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonicalUnannotated”. Aligned reads were assigned to genes using featureCounts (Liao et al. 2014) with the parameter “-s 0” and annotations from Gencode (m38.p6 gencode.vM25.basic.annotation.gtf; downloaded 7/10/24). Count files were merged to generate tables of counts for each tissue organized by genotype. Differential expression was determined using DESeq2 v1.38.3 without the lfcShrink function (Love et al. 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text file of DESeq2 output includes ENSEMBL gene name (ENSEMBL), baseMean, log2 fold change, lfcSE, stat, p-value, adjusted p-value, raw counts, and normalized counts

source_name: ovary

extract_protocol:
Total RNA was extracted from mouse tissues using TRI Reagent (ThermoFisher) according to the manufacturer’s protocol with the following modifications. Mouse tissues were rapidly dissected after CO2-based euthanasia and flash frozen in Eppendorf tubes in liquid N2. Tissue was transferred to a 15 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized with a TissueRuptor (Qiagen) and disposable probes. Samples were transferred to Eppendorf tubes (1 mL per tube) and phase separated with 200 μL chloroform (J.T. Baker Analytical). After isopropanol precipitation and two 70% ethanol washes, total RNA was resuspended in water.
Prior to library preparation, ribosomal RNA depletion was performed using QIAseq FastSelect -rRNA HMR KIT oligos (Qiagen) by mixing 14 μL of RNA input (containing 0.5 μg of hypothalamus, pituitary, or ovary total RNA), 1 μL FastSelect reagent (Qiagen), and 10 μL Frag & Prime Buffer (Watchmaker Genomics) and incubating under the following conditions: 85°C 10 minutes, 75°C 2 minutes, 70°C 2 minutes, 65°C 2 minutes, 60°C 2 minutes, 55°C 2 minutes, 37°C 2 minutes, 25°C 2 minutes, 4°C. Samples were then carried forward to the First Strand Synthesis step of the Watchmaker RNA Library Prep Kit (Watchmaker Genomics). Libraries were sequenced on the Illumina NovaSeq platform with 50 nt paired-end reads.

value: ovary

tag: background


title: Zeb1_200M_ovary_2_youngCohort

description:
Library name: Zeb1_200M_ovary_2_youngCohort
stranded


title: Control 3 fibroblast cells, galactose

description: Library name: control_3


title: Control 1 fibroblast cells, galactose

description: Library name: control_1


title: Zeb1_200H_ovary_4_youngCohort

description:
Library name: Zeb1_200H_ovary_4_youngCohort
stranded


title: Zeb1_200M_ovary_3_youngCohort

description:
Library name: Zeb1_200M_ovary_3_youngCohort
stranded


title: miRNA-Seq, Zeb1_WT_pituitary_1_youngCohort

description:
Library name: Zeb1_WT_pituitary_1_youngCohort
small RNA


title: Control 4 fibroblast cells, galactose

description: Library name: control_4


title: Zeb1_200H_ovary_2_youngCohort

description:
Library name: Zeb1_200H_ovary_2_youngCohort
stranded


title: Patient 2 fibroblast cells, galactose

description: Library name: patient_2

value: Complex I Primary Mitochondrial Disorder


title: Zeb1_200M_ovary_1_youngCohort

description:
Library name: Zeb1_200M_ovary_1_youngCohort
stranded


title: Control 2 fibroblast cells, galactose

description: Library name: control_2


title: Zeb1_200H_ovary_3_youngCohort

description:
Library name: Zeb1_200H_ovary_3_youngCohort
stranded


title: Zeb1_WT_ovary_4_youngCohort

description:
Library name: Zeb1_WT_ovary_4_youngCohort
stranded


title: WT, vent, d23, ATAC, rep2

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: WT, vent, d23, ATAC, rep2
10X Genomics

data_processing:
Raw fastq files were processed with Cellranger (v2) atac count
Assembly: Human hg38
Supplementary files format and content: The fragments.tsv.gz contains one line per unique fragment
Supplementary files format and content: The fragments.tsv.gz.tbi file is a tabix index of the fragment intervals facilitating random access to records from an arbitrary genomic interval

source_name: WTC11 iPSC parental line

growth_protocol: iPSCs were maintained in mTeSR Plus media on growth factor-reduced (GFR) matrigel

extract_protocol:
Cells on day 20 or day 23 were singularized using 0.25%Trypsin, nuclei were harvested, counted and loaded on a 10X Chromium chip according to manufacturer's instructions
Next GEM Single Cell ATAC v1.1

treatment_protocol: iPSC lines were differentiated to cardiomyocytes using the Stemdiff Atrial Cardiomyocyte or Ventricular Cardiomyocyte Differentiation Kits

tag: timepoint

value: Day 23

value: WTC11 iPSC parental line

value: Ventricular cardiomyocyte

value: Wildtype

tag: batch

value: batch 3


title: Zeb1_200H_ovary_1_youngCohort

description:
Library name: Zeb1_200H_ovary_1_youngCohort
stranded

value: female

value: 8–12 weeks old


title: Zeb1_WT_ovary_3_youngCohort

description:
Library name: Zeb1_WT_ovary_3_youngCohort
stranded


title: Patient 1 fibroblast cells, galactose

description: Library name: patient_1

value: NDUFS1 mutation (c.592_594delACA:p.T198del and c.1727G>A:p.G576E)


title: Ribo-seq of untreated monocytes

description: Library name: No_treatment_Ribo

value: CD14-positive monocytes

value: No treatment


title: Zeb1_WT_ovary_2_youngCohort

description:
Library name: Zeb1_WT_ovary_2_youngCohort
stranded


title: WT, vent, d23, ATAC, rep1

description:
Library name: WT, vent, d23, ATAC, rep1
10X Genomics


title: TBX5 Het, atrial, d20, ATAC, rep1

description:
Library name: TBX5 Het, atrial, d20, ATAC, rep1
10X Genomics

value: Day 20

value: Atrial cardiomyocyte

value: TBX5 Heterozygous mutant

value: batch 1


title: Zeb1_WT_ovary_1_youngCohort

description:
Library name: Zeb1_WT_ovary_1_youngCohort
stranded


title: Zeb1_200M_pituitary_4_youngCohort

description:
Library name: Zeb1_200M_pituitary_4_youngCohort
stranded

value: pituitary


title: humanDLPFC_Schizophrenia_7

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

institute: unc-chapel hill

data_processing:
Salmon (v1.6.0) quantification with GC bias and positional bias corrections
Assembly: custom
Supplementary files format and content: tsv file with rows as isoforms and columns as samples

source_name: dorsolateral prefrontal cortex (BA 8/9)

extract_protocol:
The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
TruSeq stranded mRNA library preparation kit (Cat# 20020595, Illumina Inc.) to prepare barcoded sequencing libraries from 300 ng of total RNA, which included polyA selection. Unique dual indices (catalog number 20022371, Illumina Inc.) were used. The library preparation was performed following the manufacturer’s protocol (#1000000040498). The pooled libraries were sequenced using the NovaSeq 6000 system (Illumina Inc.) with a S4 flowcell and v1.5 sequencing chemistry, resulting in approximately 80 million reads per sample with paired-end 150 bp read length

value: dorsolateral prefrontal cortex (BA 8/9)

value: Schizophrenia


title: WT, atrial, d20, ATAC, rep1

description:
Library name: WT, atrial, d20, ATAC, rep1
10X Genomics


title: Zeb1_200M_pituitary_2_youngCohort

description:
Library name: Zeb1_200M_pituitary_2_youngCohort
stranded


title: humanDLPFC_Schizophrenia_5


title: Zeb1_200M_pituitary_3_youngCohort

description:
Library name: Zeb1_200M_pituitary_3_youngCohort
stranded


title: Zeb1_200H_pituitary_4_youngCohort

description:
Library name: Zeb1_200H_pituitary_4_youngCohort
stranded


title: Arg1_ATAC

description: Library name: Arg1

value: CD8 T cell


title: humanDLPFC_Schizophrenia_3


title: Zeb1_200H_pituitary_3_youngCohort

description:
Library name: Zeb1_200H_pituitary_3_youngCohort
stranded


title: Zeb1_200H_pituitary_2_youngCohort

description:
Library name: Zeb1_200H_pituitary_2_youngCohort
stranded


title: humanDLPFC_Schizophrenia_1


title: Zeb1_WT_pituitary_4_youngCohort

description:
Library name: Zeb1_WT_pituitary_4_youngCohort
stranded


title: Zeb1_200M_pituitary_1_youngCohort

description:
Library name: Zeb1_200M_pituitary_1_youngCohort
stranded


title: Zeb1_200H_pituitary_1_youngCohort

description:
Library name: Zeb1_200H_pituitary_1_youngCohort
stranded


title: humanDLPFC_Control_10

value: Control


title: humanDLPFC_Control_9


title: Zeb1_WT_pituitary_2_youngCohort

description:
Library name: Zeb1_WT_pituitary_2_youngCohort
stranded


title: TBX5 Hom, atrial, d20, ATAC, rep1

description:
Library name: TBX5 Hom, atrial, d20, ATAC, rep1
10X Genomics

value: WTC11 iPSC parental line

value: TBX5 Homozygous mutant


title: Zeb1_WT_pituitary_1_youngCohort

description:
Library name: Zeb1_WT_pituitary_1_youngCohort
stranded


title: humanDLPFC_Schizophrenia_6


title: humanDLPFC_Control_8


title: Zeb1_200M_hypothalamus_3_youngCohort

description:
Library name: Zeb1_200M_hypothalamus_3_youngCohort
stranded

source_name: hypothalamus

value: hypothalamus


title: Zeb1_200M_hypothalamus_2_youngCohort

description:
Library name: Zeb1_200M_hypothalamus_2_youngCohort
stranded

value: female


title: humanDLPFC_Control_6


title: humanDLPFC_Control_5


title: Zeb1_200H_hypothalamus_4_youngCohort

description:
Library name: Zeb1_200H_hypothalamus_4_youngCohort
stranded

value: 8–12 weeks old


title: Zeb1_200M_hypothalamus_4_youngCohort

description:
Library name: Zeb1_200M_hypothalamus_4_youngCohort
stranded


title: humanDLPFC_Control_3


title: Zeb1_200H_hypothalamus_1_youngCohort

description:
Library name: Zeb1_200H_hypothalamus_1_youngCohort
stranded


title: Zeb1_200H_hypothalamus_3_youngCohort

description:
Library name: Zeb1_200H_hypothalamus_3_youngCohort
stranded


title: humanDLPFC_Control_11


title: Human corneal epthelial cells, blue light, 48 h-3

first: KUANGQI

last: Chen

address: Qingchun Road 79th

institute: Zhejiang University School of Medicine First Affiliated Hospital

data_processing:
The raw data in fastq format were processed offline using Cutadapt software (cutadapt-1.9) to remove adapter sequences.
more details in the 'readme.txt'
Assembly: The clean data were aligned to the genome using HISAT2 (hisat2-2.0.4), followed by preliminary assembly using StringTie
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: corneal epithelium

extract_protocol:
Total RNA from the samples was extracted and purified using TRIzol reagent following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Sqa library Prepared Kit following manufacturer's protocols

value: corneal epithelium

value: Human corneal epithelial cells

value: WT

value: blue light, 48 h


title: humanDLPFC_Schizophrenia_4


title: Human corneal epthelial cells, blue light, 48 h-2


title: Zeb1_WT_hypothalamus_3_youngCohort

description:
Library name: Zeb1_WT_hypothalamus_3_youngCohort
stranded


title: humanDLPFC_Control_2


title: humanDLPFC_Schizophrenia_2


title: Human corneal epthelial cells, control-3

value: control


title: Zeb1_WT_hypothalamus_2_youngCohort

description:
Library name: Zeb1_WT_hypothalamus_2_youngCohort
stranded


title: Human corneal epthelial cells, control-2


title: humanDLPFC_Control_7


title: humanDLPFC_Control_1


title: Zeb1_200M_hypothalamus_1_youngCohort

description:
Library name: Zeb1_200M_hypothalamus_1_youngCohort
stranded


title: Zeb1_WT_hypothalamus_1_youngCohort

description:
Library name: Zeb1_WT_hypothalamus_1_youngCohort
stranded


title: Zeb1_200H_hypothalamus_2_youngCohort

description:
Library name: Zeb1_200H_hypothalamus_2_youngCohort
stranded


title: ATAC-seq_PC3_control_rep2

description: Library name: PC3_control_rep2

source_name: Prostate

value: Prostate

value: prostate cancer

value: DMSO


title: humanDLPFC_Control_4

value: dorsolateral prefrontal cortex (BA 8/9)


title: Zeb1_WT_hypothalamus_4_youngCohort

description:
Library name: Zeb1_WT_hypothalamus_4_youngCohort
stranded


title: Human corneal epthelial cells, control-1


title: CBX5_control

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. atacseq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp atacseq reads were aligned to the UCSC hg38 genome using Bowtie version 2. Only uniquely mapping reads with at most two mismatches were retained. To create atacseq coverage plots, the locations of the mapped atacseq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format. Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.05
Assembly: hg38 or mm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample, bw

source_name: liver

extract_protocol:
ATAC-seq was performed according to ATAC-seq protocol by Shanghai Jiayin Biotechnology Ltd. In brief, cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA).
Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150

value: liver

value: hepatocellular carcinoma

value: siNC


title: Tumour, vaccine, rep3, 2 dose

city: Liverpool

first: Grace

last: Tan

address: 6 West Derby Street

department: MCCM

country: United Kingdom

institute: University of Liverpool

description:
Library name: TB8
Column names in raw counts All samples Prime.csv

data_processing:
The principal component analysis (PCA) plot was used to determine the principal components using the DEGs list and visualized using the “ggplot2” R package  (v 3.5.2). The clustering analysis of DEGs was carried out using the “tidyheatmaps” package (v 0.2.1) of R86. The enrichment of pathways was identified by GSEA method using clusterProfiler (v 4.16.0)
Counts normalisation and differential gene expression analysis were performed using the DESeq2 package (v 1.48.0) in R (v 4.5.0) statistical software84. Differentially expressed genes (DEGs) were defined by a fold change (FC) ≥ 1.5 and an adjusted P-value (padj) < 0.1
Assembly: Mus musculus reference genome mm39 NCBI Refseq GCF_000001635.27
Supplementary files format and content: csv files includes raw counts for each sample
Supplementary files format and content: csv files include TPM values for each sample

source_name: Tumour

growth_protocol: Mouse oral cancer 2 (MOC-2) were cultured in IMDM/F12 (2:1) supplemented with 10 % foetal bovine serum (FBS; Gibco), penicillin streptomycin (100 U/mL) (P/S; Gibco), 5μg/mL insulin (Sigma, I6634), 400 ng/mL hydrocortisone (Sigma, H0135), 5ng/mL epidermal growth factor (EMD Milipore, 01-107) at 37°C, 5 % CO2 in a humidified incubator. To establish a homogenous MAGED4B- and FJX1- expressing cell line, MOC-2 cells were transduced with retrovirus particles generated from the pBABE-MAGED4B-FJX1-puro vector and HEK293T gag-pol packaging cells (Takara Bio, 631458). Transduced cells were selected and maintained in 4 μg/mL puromycin (Gibco). Mice were subcutaneously (s.c) injected with 2.0 x 10^5 cells of  MOC-2 cells

extract_protocol:
Tumours were excised from mice and dissociated using the Mouse Tumor Dissociation Kit (Miltenyi Biotec, 130-096-730) with the gentleMACS Dissociator (Miltenyi Biotec). CD45+ tumour-infiltrating lymphocytes (TILs) were isolated from tumours of control and vaccinated mice using Mouse CD45 TIL MicroBeads (Miltenyi Biotec, 130-110-618). The sample are biological replicates consisted of distinct tumours harvested from different tumour-bearing mice in each treatment group. Total RNA sample was extracted from isolated TILs from mice in each experimental group using the RNeasy mini-Kit (QIAGEN) per the manufacturer’s protocol. RNA purity, concentration, and integrity were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific), Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. Only samples meeting quality thresholds (e.g., RIN ≥ 4) were used for library preparation
RNA libraries were constructed using quantified RNA samples, pooled, and sequenced on the Illumina NovaSeq 6000 platform in paired-end 150 bp (PE150) mode (Novogene), targeting a minimum depth of 6 Gb reads per sample. Raw reads were aligned to the Mus musculus reference genome (mm39, NCBI RefSeq GCF_000001635.27) using HISAT2 (version 2.0.5)

treatment_protocol: For day15, mice were randomised into treatment groups: not receiving vaccine or receiving one dose of combined vaccines of high dose (10μg) dbDNA of dHD and Flt3L-FJX1 (TGL-100 OPT) vaccines at day-3 post innoculation. For day30 mice were randomised into treatment groups: receiving control vaccine or receiving two doses of combined vaccines of high dose (10μg) dbDNA of dHD and Flt3L-FJX1 (TGL-100 OPT) vaccines at day-3 and day-24 post innoculation.

value: Tumour

value: mouse oral carcinoma

value: transduced with human MAGED4B and human FJX1

value: vaccinated


title: Tumour, vaccine, rep2, 2 dose

description:
Library name: TB4
Column names in raw counts All samples Prime.csv


title: Tumour, vaccine, rep4, 2 dose

description:
Library name: TB9
Column names in raw counts All samples Prime.csv


title: Tumour, vaccine, rep1, 2 dose

description:
Library name: TB2
Column names in raw counts All samples Prime.csv


title: CBX5_treat


title: Hep3b

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&tag reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp CUT&tag reads were aligned to the UCSC hg38 genome using Bowtie version 2. Only uniquely mapping reads with at most two mismatches were retained. To create CUT&tag coverage plots, the locations of the mapped CUT&tag reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format. Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.05
Assembly: hg38 or mm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample, bw
Library strategy: CUT&Tag

extract_protocol:
cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris). CUT&tag libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler.
Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: wt


title: Tumour, control vaccine, rep3, 2 dose

description:
Library name: TA8
Column names in raw counts All samples Prime.csv

value: no treatment


title: Human corneal epthelial cells, blue light, 48 h-1

value: corneal epithelium

value: Human corneal epithelial cells


title: Tumour, control vaccine, rep2, 2 dose

description:
Library name: TA6
Column names in raw counts All samples Prime.csv


title: Molt4-IK-KO, CUT&Tag for H3K27me3

city: Hershey

first: Bing

last: He

address: 500 University Dr

institute: Penn State University

data_processing:
Sequencing reads were mapped to the human genome (hg38) using Bowtie2 (v2.2.2) with default parameter setting
Samtools and PICARD were used for QC of mapped reads (MAPQ>30).
ChIP-Seq peaks were called by MACS2 using default parameter setting
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Molt4, T-ALL cell line, CRISPR KO Ikaros

growth_protocol: Cells were cultured in RPMI1640 with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
CUT&Tag for Molt4 cells was performed according to EpiCypher CUTANA Direct-to-PCR CUT&Tag Protocol.

treatment_protocol: The IKZF1 gene was deleted in human T-ALL cells MOLT4 using the CRISPR-Cas system to create MOLT-4 IKZF1-null cells

value: Leukemia cells

tag: antibody


title: Molt4-IK-KO, CUT&Tag for HDAC1


title: Tumour, vaccine, rep5, 1 dose

description:
Library name: TGB7
Column names in raw counts All samples Prime.csv

tag: tissue


title: Molt4-IK-KO, CUT&Tag for Ikaros

tag: cell type

value: Ikaros


title: Molt4-IK-KO, CUT&Tag for IgG

tag: cell line

value: IgG


title: Tumour, control vaccine, rep1, 2 dose

description:
Library name: TA5
Column names in raw counts All samples Prime.csv

tag: treatment


title: Molt4-wt, CUT&Tag for H3K27me3

source_name: Molt4, T-ALL cell line, CRISPR KO control


title: Tumour, vaccine, rep2, 1 dose

description:
Library name: TGB3
Column names in raw counts All samples Prime.csv


title: Molt4-wt, CUT&Tag for HDAC1


title: Tumour, control vaccine, rep4, 1 dose

description:
Library name: TGA8
Column names in raw counts All samples Prime.csv


title: Molt4-IK-KO, mRNA-seq, rep3

data_processing:
Sequencing reads were mapped to the human genome (hg38) using STAR (v2.6.1c) with default parameter setting
FPKM values were computed using Cufflinks (v2.2.1)
Signal file were generated using HOMER (v4.10)
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep kit (Molt4) or NEXTflex Illumina Rapid Directional RNA-Seq Library Prep Kit (DN3)  following manufacturers' protocols.

value: CRISPR KO Ikaros


title: Tumour, vaccine, rep1, 1 dose

description:
Library name: TGB2
Column names in raw counts All samples Prime.csv


title: Tumour, control vaccine, rep3, 1 dose

description:
Library name: TGA7
Column names in raw counts All samples Prime.csv


title: Molt4-wt, CUT&Tag for Ikaros


title: Tumour, control vaccine, rep2, 1 dose

description:
Library name: TGA6
Column names in raw counts All samples Prime.csv


title: Molt4-IK-KO, mRNA-seq, rep2


title: Hep3b_IgG

value: IgG(antibody)


title: Molt4-wt, mRNA-seq, rep3

value: CRISPR KO control


title: Tumour, control vaccine, rep4, 2 dose

description:
Library name: TA9
Column names in raw counts All samples Prime.csv


title: Molt4-IK-KO, mRNA-seq, rep1


title: Naïve CD44lowCD62+ CD8+ cells, rep1

city: Baltimore

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description: Library name: naïve_rep1

data_processing:
Reads were aligned to the mouse genome (GRCm39) using HiSat (version HISAT2-2.1.0)
and the number of reads aligned to coding regions was determined with HTSeq .
Significant differential expression was analyzed using DESeq2, with a false discovery rate (FDR) ≤ 0.05 and a fold-change greater than 2 (Anders and Huber, 2014).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: lymphoid tissue

growth_protocol: Foxp3+CD8+ Tregs or Foxp3+CD4+ Tregs were induced in Treg conditon medium for 3 days. Treg condition medium contains 10 ng/ml IL-2, 15 ng/ml TGFβ. The plates were pre-coated with 4 µg/ml anti-CD3 and 1 µg/ml anti-CD28 overnight at 4 degree. Then, the laminin α5 (1 µg/ml) were pre-coated at 37 degree for 2 hours.After washing, the plates were ready for seeding the cells. Each well started with 1x105 CD4 and CD8 T cells with 200 µl medium.

extract_protocol:
RNA was extracted with Rneasy Micro Kit (QIAGEN, Cat. #74004). 200 µg of total RNA was send out.
NEB Next II directional RNA kit was used for library preparation.

value: lymphoid tissue

value: Naïve CD44lowCD62+ CD8+


title: Foxp3+CD8+ Tregs, laminin α5, anti-IFNγ, rep3

description: Library name: CD8_Treg_Laminin_alpha_anti_IFNr_rep3

value: Foxp3+CD8+ Tregs, laminin α5,anti-IFNγ


title: Foxp3+CD4+ Tregs, rep1

description: Library name: Treg_rep1

value: Foxp3+CD4+ Tregs


title: Tumour, control vaccine, rep1, 1 dose

description:
Library name: TGA2
Column names in raw counts All samples Prime.csv

value: Tumour

value: mouse oral carcinoma


title: Molt4-wt, mRNA-seq, rep1


title: Foxp3+CD8+ Tregs, laminin α5, anti-IFNγ, rep2

description: Library name: CD8_Treg_Laminin_alpha_anti_IFNr_rep2


title: Tumour, vaccine, rep4, 1 dose

description:
Library name: TGB6
Column names in raw counts All samples Prime.csv

value: transduced with human MAGED4B and human FJX1

value: vaccinated


title: DSP-1001660019972-F-B04

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw_dcc.tar:  raw read counts in DCC of tar
Supplementary files format and content: processed_data.txt.gz:  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format
Library strategy: Spatial transcriptomic

source_name: AO 44120-1 is an AO CRC

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

value: AO 44120-1 is an AO CRC

tag: rnapanel

tag: cancer

value: Yes

tag: scan name

tag: roi

tag: segment

value: PanCK


title: Foxp3+CD8+ Tregs, laminin α5, rep3

description: Library name: CD8_Treg_Laminin_alpha5_rep3

value: Foxp3+CD8+ Tregs, laminin α5


title: Molt4-wt, CUT&Tag for IgG

value: Leukemia cells

tag: genotype


title: DSP-1001660019972-F-B02

value: Vimentin


title: Tumour, vaccine, rep3, 1 dose

description:
Library name: TGB5
Column names in raw counts All samples Prime.csv


title: DSP-1001660019972-F-B01


title: DSP-1001660019972-F-B05


title: Foxp3+CD8+ Tregs, laminin α5, anti-IFNγ, rep1

description: Library name: CD8_Treg_Laminin_alpha_anti_IFNr_rep1


title: Foxp3+CD8+ Tregs, laminin α5, rep1

description: Library name: CD8_Treg_Laminin_alpha5_rep1


title: DSP-1001660019972-F-A12


title: Foxp3+CD8+ Tregs, rep2

description: Library name: CD8_Treg_rep2

value: Foxp3+CD8+ Tregs


title: DSP-1001660019972-F-A11


title: Foxp3+CD8+ Tregs, rep3

description: Library name: CD8_Treg_rep3


title: DSP-1001660019972-F-A10


title: Foxp3+CD8+ Tregs, rep1

description: Library name: CD8_Treg_rep1


title: Molt4-wt, mRNA-seq, rep2


title: DSP-1001660019972-F-A09


title: DSP-1001660019972-F-A08


title: 6wk Bleo hBcl Tamox Rep 3

city: Denver

first: Elizabeth

last: Redente

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

description:
Library name: Sample19
6wkhBclTam19

data_processing:
raw sequencing reads were trimmed using skewer with parameters (end-quality=15, mean-quality=25, min=30). Trimmed reads were aligned to the mouse reference genome GRCm38 using Hisat2. Gene quantification was performed with htseq-count using GRCm38 ensembl v84 GTF. Differential expression analysis between groups was conducted with R package DESeq2.
Assembly: GPL24247
Supplementary files format and content: norm_count.txt
Supplementary files format and content: 211014_A00405_0476_BHW5MNDSX2_L1_Redente_demux.csv
Supplementary files format and content: vst_norm_count.txt

source_name: Lung

extract_protocol:
TRIzol followed by purification of aqueious layer with Rneasy Micro Kit from Qiagen
Nugen mRNA kit was used with a total of 100ng of total RNA for library construction

treatment_protocol: Mice treated with saline (time 0) or bleomycin (3wk, 6wk). Mice treated with Tamoxifen or Corn Oil

value: Lung

tag: age

value: Fibroblast

value: Cre+

value: Bleomycin + Tamoxifen


title: DSP-1001660019972-F-A07


title: 6wk Bleo hBcl Tamox Rep 2

description:
Library name: Sample18
6wkhBclTam18


title: 6wk Bleo hBcl Tamox Rep 4

description:
Library name: Sample20
6wkhBclTam20


title: DSP-1001660019972-F-A06


title: DSP-1001660019972-F-A05


title: DSP-1001660019972-F-A04

source_name: AO 40928-8 is an AO CRC

value: AO 40928-8 is an AO CRC


title: DSP-1001660019972-F-B03


title: 6wk Bleo hBcl CO Rep 3

description:
Library name: Sample15
6wkhBclCO15

value: Bleomycin + Corn Oil


title: 6wk Bleo hBcl CO Rep 2

description:
Library name: Sample14
6wkhBclCO14


title: 6wk Bleo hBcl CO Rep 4

description:
Library name: Sample16
6wkhBclCO16


title: DSP-1001660019972-F-A03


title: DSP-1001660019973-E-H12


title: Foxp3+CD8+ Tregs, laminin α5, rep2

description: Library name: CD8_Treg_Laminin_alpha5_rep2

value: lymphoid tissue


title: DSP-1001660019972-F-A02


title: DSP-1001660019973-E-H11


title: DSP-1001660019973-E-H10


title: 3wk Bleo hBcl Tamox Rep 2

description:
Library name: Sample10
3wkhBclTam10


title: DSP-1001660019973-E-H09


title: 3wk Bleo hBcl Tamox Rep 3

description:
Library name: Sample11
3wkhBclTam11


title: 3wk Bleo hBcl Tamox Rep 1

description:
Library name: Sample9
3wkhBclTam9


title: 3wk Bleo hBcl CO Rep 4

description:
Library name: Sample8
3wkhBclCO8


title: DSP-1001660019973-E-H08


title: DSP-1001660019973-E-H07


title: 3wk Bleo hBcl CO Rep 3

description:
Library name: Sample7
3wkhBclCO7


title: 3wk Bleo hBcl CO Rep 2

description:
Library name: Sample6
3wkhBclCO6


title: 6wk Bleo hBcl Tamox Rep 1

description:
Library name: Sample17
6wkhBclTam17


title: 3wk Bleo hBcl CO Rep 1

description:
Library name: Sample5
3wkhBclCO5


title: DSP-1001660019973-E-H05


title: DSP-1001660019973-E-H04

source_name: Corresponding normal to CA479

value: Corresponding normal to CA479

value: No


title: DSP-1001660019973-E-H06


title: DSP-1001660019973-E-H03


title: Naïve Rep 4

description:
Library name: Sample4
Naive4

value: Naive

value: Saline


title: DSP-1001660019973-E-H02


title: Naïve Rep 3

description:
Library name: Sample3
Naive3


title: 6wk Bleo hBcl CO Rep 1

description:
Library name: Sample13
6wkhBclCO13


title: Naïve Rep 2

description:
Library name: Sample2
Naive2


title: DSP-1001660019973-E-H01


title: Naïve Rep 1

description:
Library name: Sample1
Naive1


title: 3wk Bleo hBcl Tamox Rep 4

description:
Library name: Sample12
3wkhBclTam12


title: DSP-1001660019973-E-G11

source_name: CA479 is an AO CRC

value: CA479 is an AO CRC

value: AO  CA479

value: Yes


title: DSP-1001660019973-E-G12

value: PanCK


title: WT1

city: 合肥市

first: yawen

last: chen

state: 蜀山区

address: 稻香村街道

institute: USTC

description: Library name: WT1

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 75% clean reads for each sample were retained for subsequent analyses.The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
OECloud platform (https://cloud.oebiotech.com/task/)
Assembly: mm10
Supplementary files format and content: excel file include FPKM vakues for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
First, use the Single Cell Full Length mRNA-Amplification Kit to perform RNA reverse transcription and amplification. For the cDNA that passes quality inspection, use the cDNA TruePrep DNA Library Prep Kit V2 for Illumina according to the instructions to construct the library.

value: liver

value: WT

value: homeostasis


title: WT3

description: Library name: WT3


title: DSP-1001660019973-E-G10


title: KO2

description: Library name: KO2

value: Cd200r knockout


title: DSP-1001660019973-E-G09

value: Vimentin


title: Hippocampus, Male, P30, WT, replicate 4

city: New York

first: Jacquelyn

last: Salzbank

state: NY

institute: Columbia University Irving Medical Center

description: Library name: HP.CM847.P30.M.WT

data_processing:
rRNA abundance was measured by mapping with Bowtie2.
Quality control was performed using Picard (v1.83) and RSeQC (v2.6.1).
Assembly: The reads were aligned with STAR (version 2.5.2a), and genes annotated in Gencode vM16 and quantified with featureCounts (v1.4.3-p1).
Supplementary files format and content: .csv file called "Processed_Counts_Matrix" includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
From each mouse the somatosensory cortex, the cerebellum and the hippocampus were collected. Tissues were homogenized in TRIzol Reagent (Thermo Fisher Scientific); total RNA was extracted with the RNeasy Mini Kit. (Qiagen, no. 74104). A total of 500 ng of RNA was used for sequencing.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library prep (Illumina, catalog number 20020595) in accordance with manufacturer recommendations, and using IDT for Illumina TruSeq DNA UD Indices (Illumina, catalog number 20022370) for adapters.

value: Hippocampus

tag: Sex

value: Male


title: Hippocampus, Male, P30, WT, replicate 3

description: Library name: HP.CM846.P30.M.WT


title: DSP-1001660019973-E-G07


title: DSP-1001660019973-E-G08


title: KO1

description: Library name: KO1


title: DSP-1001660019973-E-G06


title: Hippocampus, Male, P30, WT, replicate 2

description: Library name: HP.CM838.43472.M.WT


title: DSP-1001660019973-E-G05


title: Hippocampus, Female, P15, WT, replicate 4

description: Library name: HP.1892.P15.F.WT

value: Female


title: Hippocampus, Male, P30, KO, replicate 4

description: Library name: HP.CM839.P30.M.KO

value: KO


title: DSP-1001660019973-E-G04


title: Hippocampus, Female, P15, KO, replicate 4

description: Library name: HP.1891.P15.F.KO


title: DSP-1001660019973-E-G03


title: DSP-1001660019973-E-G02


title: Hippocampus, Male, P15, WT, replicate 4

description: Library name: HP.1547.P15.M.WT


title: DSP-1001660019973-E-G01


title: Hippocampus, Female, P15, KO, replicate 3

description: Library name: HP.1546.P15.F.KO


title: Hippocampus, Female, P15, WT, replicate 3

description: Library name: HP.1544.P15.F.WT


title: DSP-1001660019973-E-F12


title: Hippocampus, Male, P15, KO, replicate 4

description: Library name: HP.1540.P15.M.KO


title: Hippocampus, Male, P15, WT, replicate 3

description: Library name: HP.1542.P15.M.WT


title: Hippocampus, Female, P30, KO, replicate 4

description: Library name: HP.1467.P30.F.KO


title: DSP-1001660019973-E-F11

source_name: Normal counterpart for 45757

value: Normal counterpart for 45757

value: Se


title: DSP-1001660019973-E-F09

source_name: 45757 is an EO CRC

value: 45757 is an EO CRC


title: DSP-1001660019973-E-F10


title: DSP-1001660019973-E-F08


title: DSP-1001660019973-E-F07

source_name: Corresponding normal 44120

value: Corresponding normal 44120

value: No


title: Hippocampus, Female, P30, WT, replicate 4

description: Library name: HP.1466.P30.F.WT


title: DSP-1001660019973-E-F05


title: DSP-1001660019973-E-F06


title: Hippocampus, Female, P7, WT, replicate 4

description: Library name: HP.1410.P7.F.WT


title: DSP-1001660019973-E-F04

source_name: to the cancer which is on slide 4

value: to the cancer which is on slide 4


title: Hippocampus, Female, P7, KO, replicate 5

description: Library name: HP.1381.P7.M.KO


title: Hippocampus, Male, P7, WT, replicate 4

description: Library name: HP.1380.P7.M.WT


title: DSP-1001660019973-E-F03

source_name: this is the corresponding normal

value: this is the corresponding normal


title: Hippocampus, Male, P7, WT, replicate 3

description: Library name: HP.1370.43503.M.WT


title: Hippocampus, Male, P30, KO, replicate 3

description: Library name: HP.1341.P30.M.KO


title: Hippocampus, Female, P7, KO, replicate 4

description: Library name: HP.1344.43522.F.KO


title: Hippocampus, Male, P7, WT, replicate 2

description: Library name: HP.1330.P7.M.WT


title: DSP-1001660019973-E-F02

source_name: 44120 is an average onset cancer

value: 44120 is an average onset cancer


title: DSP-1001660019973-E-E11


title: Hippocampus, Male, P30, KO, replicate 2

description: Library name: HP.1266.P30.M.KO


title: DSP-1001660019973-E-E10


title: Hippocampus, Male, P30, WT, replicate 1

description: Library name: HP.1265.P30.M.WT


title: DSP-1001660019973-E-E09


title: Hippocampus, Female, P30, KO, replicate 3

description: Library name: HP.1264.P30.F.KO


title: Hippocampus, Male, P7, KO, replicate 3

description: Library name: HP.1414.P7.M.KO


title: DSP-1001660019973-E-E08

source_name: 45757 is an early onset cancer

value: 45757 is an early onset cancer

value: Yes


title: Hippocampus, Female, P7, WT, replicate 3

description: Library name: HP.1336.43522.F.WT

value: WT


title: Hippocampus, Female, P30, WT, replicate 3

description: Library name: HP.1263.P30.F.WT


title: Hippocampus, Female, P30, WT, replicate 2

description: Library name: HP.1262.P30.F.WT


title: Hippocampus, Female, P30, WT, replicate 1

description: Library name: HP.1258.P30.F.WT


title: DSP-1001660019973-E-E06


title: DSP-1001660019973-E-E04


title: DSP-1001660019973-E-E05


title: Hippocampus, Female, P30, KO, replicate 2

description: Library name: HP.1257.P30.F.KO


title: DSP-1001660019973-E-E03


title: Hippocampus, Female, P30, KO, replicate 1

description: Library name: HP.1254.P30.F.KO


title: Hippocampus, Male, P30, KO, replicate 1

description: Library name: HP.1255.P30.M.KO


title: DSP-1001660019973-E-E01


title: DSP-1001660019973-E-E12


title: Hippocampus, Male, P15, WT, replicate 2

description: Library name: HP.1233.P15.M.WT


title: DSP-1001660019973-E-F01


title: DSP-1001660019973-E-D12


title: Hippocampus, Male, P15, KO, replicate 3

description: Library name: HP.1231.P15.M.KO


title: Hippocampus, Female, P15, KO, replicate 2

description: Library name: HP.1225.P15.F.KO


title: DSP-1001660019973-E-E07


title: DSP-1001660019973-E-D10


title: Hippocampus, Male, P15, KO, replicate 2

description: Library name: HP.1223.P15.M.KO


title: Hippocampus, Female, P15, KO, replicate 1

description: Library name: HP.1215.P15.F.KO


title: DSP-1001660019973-E-D08


title: DSP-1001660019973-E-D07


title: Hippocampus, Female, P15, WT, replicate 1

description: Library name: HP.1212.P15.F.WT


title: Hippocampus, Female, P15, WT, replicate 2

description: Library name: HP.1221.P15.F.WT


title: DSP-1001660019973-E-D09


title: DSP-1001660019973-E-D04

source_name: EO CA43718-3 is an EO CRC

value: EO CA43718-3 is an EO CRC

value: YES

value: Slide2_43718-3_ NL462C_Vimentin 1:150  and CD45-AF647(5 ug/mL), Pan CK and SYTO13


title: Hippocampus, Female, P7, WT, replicate 2

description: Library name: HP.1196.P7.F.WT

value: Hippocampus


title: DSP-1001660019973-E-D06

value: Vimentin


title: Hippocampus, Female, P7, KO, replicate 3

description: Library name: HP.1193.P7.F.KO

value: KO

value: Female


title: DSP-1001660019973-E-D05


title: Hippocampus, Male, P7, KO, replicate 2

description: Library name: HP.1191.P7.M.KO

value: Male


title: DSP-1001660019973-E-D01


title: Hippocampus, Male, P15, WT, replicate 1

description: Library name: HP.1220.P15.M.WT


title: Hippocampus, Male, P15, KO, replicate 1

description: Library name: HP.1210.P15.M.KO


title: Hippocampus, Female, P7, KO, replicate 2

description: Library name: HP.1183.P7.F.KO


title: DSP-1001660019973-E-D02


title: DSP-1001660019973-E-D03


title: DSP-1001660019973-E-E02


title: DSP-1001660019973-E-C12

value: PanCK


title: Hippocampus, Female, P7, WT, replicate 1

description: Library name: HP.1181.P7.F.WT


title: DSP-1001660019973-E-C11


title: DSP-1001660019973-E-C10


title: DSP-1001660019973-E-C09


title: Hippocampus, Male, P7, WT, replicate 1

description: Library name: HP.1171.P7.M.WT


title: DSP-1001660019973-E-D11


title: DSP-1001660019973-E-C08


title: Hippocampus, Female, P7, KO, replicate 1

description: Library name: HP.1170.P7.F.KO


title: DSP-1001660019973-E-C06


title: DSP-1001660019973-E-C07


title: Somatosensory Cortex, Male, P30, WT, replicate 2

description: Library name: S1.CM838.P30.M.WT

source_name: Somatosensory Cortex

value: Somatosensory Cortex


title: DSP-1001660019973-E-C05


title: Somatosensory Cortex, Male, P30, KO, replicate 4

description: Library name: S1.CM839.P30.M.KO


title: Somatosensory Cortex, Male, P30, WT, replicate 4

description: Library name: S1.CM847.P30.M.WT


title: DSP-1001660019973-E-C03

source_name: 42444 is an early onset cancer

value: 42444 is an early onset cancer

value: Slide1_S21-26292 A7_42444-4_Vimentin 1:150  and CD45-AF647(5 ug/mL), Pan CK and SYTO13


title: Somatosensory Cortex, Female, P15, WT, replicate 4

description: Library name: S1.1892.P15.F.WT


title: DSP-1001660019973-E-C02


title: Hippocampus, Male, P7, KO, replicate 1

description: Library name: HP.1185.P7.M.KO


title: DSP-1001660019973-E-C04


title: Somatosensory Cortex, Female, P0, KO, replicate 4

description: Library name: S1.1742.P0.F.KO


title: Somatosensory Cortex, Male, P0, WT, replicate 4

description: Library name: S1.1741.P0.M.WT


title: Somatosensory Cortex, Female, P0, WT, replicate 3

description: Library name: S1.1734.P0.F.WT


title: Somatosensory Cortex, Female, P15, KO, replicate 3

description: Library name: S1.1891.P15.F.KO


title: DSP-1001660019973-E-C01

source_name: 42444-NL is the normal counterpart of 42444 cancer

value: No


title: Somatosensory Cortex, Female, P0, KO, replicate 3

description: Library name: S1.1733.P0.F.KO


title: DSP-1001660019973-E-B11

value: 42444-NL is the normal counterpart of 42444 cancer


title: DSP-1001660019973-E-B12


title: Somatosensory Cortex, Male, P0, WT, replicate 3

description: Library name: S1.1713.P0.M.WT


title: Somatosensory Cortex, Female, P0, WT, replicate 4

description: Library name: S1.1743.P0.F.WT


title: DSP-1001660019973-E-B08


title: DSP-1001660019973-E-B07


title: DSP-1001660019973-E-B10


title: Somatosensory Cortex, Male, P0, KO, replicate 3

description: Library name: S1.1704.P0.M.KO


title: Somatosensory Cortex, Male, P0, KO, replicate 4

description: Library name: S1.1712.P0.M.KO


title: Somatosensory Cortex, Female, P0, KO, replicate 2

description: Library name: S1.1654.P0.F.KO


title: Somatosensory Cortex, Male, P0, WT, replicate 2

description: Library name: S1.1700.P0.M.WT


title: Somatosensory Cortex, Male, P0, KO, replicate 1

description: Library name: S1.1650.P0.M.KO


title: DSP-1001660019973-E-B01


title: DSP-1001660019973-E-B04


title: DSP-1001660019973-E-B05


title: DSP-1001660019973-E-B03


title: DSP-1001660019973-E-B06


title: DSP-1001660019973-E-B02


title: Somatosensory Cortex, Male, P0, KO, replicate 2

description: Library name: S1.1702.P0.M.KO