title: Case26_dsRNA-seq_IN

description: Library name: dsRNA-seq_Case26_IN

source_name: Frontal Cortex

value: Frontal Cortex

value: dsRNA-seq without J2 immunoprecipitation


title: Caco-2.batch2.PER.rep1.G02

status: Public on Jul 01 2026

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: Caco2_Batch2_PER_1_G02

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

organism: Homo sapiens

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

tag: tissue

value: colon

tag: cell line

tag: cell type

value: epithelial

tag: genotype

value: cell line

tag: treatment


title: CN from animal_53, rep2

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

country: USA

institute: Arizona State University

description:
Library name: NSM1475-b2
3 lvl sciRNAseq

library_source: transcriptomic single cell

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

molecule: nuclear RNA

organism: Macaca mulatta

source_name: caudate nucleus

growth_protocol: free-ranging population

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

value: caudate nucleus


title: Caco-2.batch2.PER.rep1.F02

description: Library name: Caco2_Batch2_PER_1_F02


title: Case65_dsRNA-seq_IP

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

description: Library name: dsRNA-seq_Case65_IP

library_source: transcriptomic

data_processing:
For RNA-seq and dsRNA-seq experiments, the fastq files were analyzed using NF-Core. For eCLIP-seq experiments, Skipper was used to analyze the sequencing files. For Riboseq, the xtail package was used to determine footprinting reads and calculate translation efficiency.
Assembly: hg38
Supplementary files format and content: For RNA-seq and dsRNA-seq experiments, the .tsv or .csv file contains the gene counts for each sample as analyzed by NF-Core. For eCLIP-seq, the .tsv file contains the reproducible enriched windows identified by Skipper.

molecule: total RNA

extract_protocol:
For RNA-seq and dsRNA-seq experiments, RNA was extracted using Trizol and purified using Rneasy or ethanol precipitation. For eCLIP-seq and Riboseq experiments, RNA was purified using lysis buffer and gel-extracted.
For RNA-seq experiments, librarires were prepared using the Illumina Stranded mRNA Prep (Ligation). For eCLIP-seq experiments, libraries were prepared using an in-house amplification procedure that closely follows the Illumina Stranded protocol.

value: Apparently Healthy

value: dsRNA-seq with J2 immunoprecipitation

tag: batch


title: MEL Mtg16 H3K4me1 DMSO B

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

description: Library name: CUTRUN_H3K4me1 DMSO B

library_source: genomic

data_processing:
Adaptor trimming was performed using TrimmomaticPE, and trimmed reads were aligned to concatenated mm39+ec (CUT&RUN) or mm39+dm3 (ChIP-Seq) genomes. Resulting alignments were then processed with samtools (v. 1.16.1) to remove low quality reads, count reads aligned to mm39, ec, and dm3 genomes, and remove spike-in reads. Peak calling was performed using MACS2 (v. 2.2.9.1), q 0.01. Read quantification was performed with DiffBind (v. 3.16.0). Differential analysis was performed using DESeq2 (v. 1.46.0) with built-in normalization.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: MEL Mtg16-FKBP-2XHA

growth_protocol: MEL cells were grown in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1% penicillin/streptomycin, and 1% L-glutamine.

extract_protocol:
CUT&RUN experiments were performed in biological triplicate. Samples were harvested by centrifugation, washed (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 1X Roche Complete Protease Inhibitor tablet), and adsorbed to activated Concavalin A beads for 10min at room temperature. Samples were then incubated with primary antibody diluted in digitonin buffer + 2mM EDTA (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 0.2% digitonin, 1X Roche Complete Protease Inhibitor tablet) overnight at 4C. The next day, samples were washed and incubated with secondary antibody diluted in digitonin buffer + 2mM EDTA for 1hr at 4C. After secondary antibody incubation, pAG-MNase was added to the samples, then activated with CaCl2 and incubated at 4C for 2hrs. After MNase incubation, the reaction stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNase A, 50ug/mL glycogen, supplemented with 0.5ng E. coli gDNA per sample) was added and samples incubated for 10min at 37C. Samples were then cleaned using NEB Monarch DNA Cleanup Kit according to manufacturer instructions prior to library preparation. ChIP-Seq experiments were performed in biological triplicate. All buffers were filter sterilized and supplemented with protease inhibitors immediately prior to use (2uL aprotinin and 20uL 0.1M PMSF per 1mL buffer). 10 million cells per immunoprecipitation sample were harvested by centrifugation, washed in PBS, and fixed for 10min at room temperature in 1% methanol-free formaldehyde, then quenched with 0.125M glycine. All subsequent steps were performed on ice or at 4C. Fixed cells were lysed in cell lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X-100) that was supplemented with 0.5 million crosslinked S2 cells per sample. After lysis, cells were washed in wash buffer (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) and then sonicated for 20 cycles with a Bioruptor water bath sonicator (30s on/30s off) in sonication buffer (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% SDS, 0.5% sarkosyl). Successful sonication (DNA fragments between 100-500bp) were verified via agarose gel electrophoresis for every sample prior to IP. After sonication, samples were quantified using Qubit HS, supplemented with 1% Triton-X-100, and antibody was added, followed by overnight incubation at 4C with rotation. After overnight antibody incubation, samples were incubated with equilibrated Protein A/G Dynabeads (50:50 mix) for 1hr at 4C, followed by 5 successive washes: low salt (20mM Tris pH 8.0, 150mM NaCl, 2mM EDTA, 1% Triton-X-100), high salt (20mM Tris pH 8.0, 500mM NaCl, 2mM EDTA, 1% Triton-X-100), LiCl (10mM Tris pH 8.0, 25mM LiCl, 2mM EDTA, 1% Triton X-100), TE (10mM Tris pH 8.0, 1mM EDTA), and TE. After the final wash, elution buffer (1X TE pH 8.0. 0.1% SDS, 200mM NaCl, 0.8ug/uL proteinase K) was added directly to the beads and samples were de-crosslinked overnight at 65C prior to PCR clean up.
ChIP-Seq and CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit according to manufacturer instructions with minor modifications. The end prep reaction for both library types was performed under the following conditions: 20C 30min, 50C 1hr. ChIP-Seq libraries were prepared with size selection. CUT&RUN libraries were prepared without size selection.

treatment_protocol: 250nM dTAGV1

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: Case65_dsRNA-seq_IN

description: Library name: dsRNA-seq_Case65_IN


title: MEL Mtg16 H3K4me1 dTAGV1 15m A

description: Library name: CUTRUN_H3K4me1 dTAGV1 15m A


title: MEL Mtg16 H3K4me1 DMSO A

description: Library name: CUTRUN_H3K4me1 DMSO A


title: Caco-2.batch2.PER.rep1.D02

description: Library name: Caco2_Batch2_PER_1_D02


title: CN from animal_52

description:
Library name: NSM1474
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_2hWO_C

description: Library name: ChIP_H3K27ac-ChIP_2hWO_C

data_processing:
Adaptor trimming was performed using TrimmomaticPE, and trimmed reads were aligned to concatenated mm39+ec (CUT&RUN) or mm39+dm3 (ChIP-Seq) genomes. Resulting alignments were then processed with samtools (v. 1.16.1) to remove low quality reads, count reads aligned to mm39, ec, and dm3 genomes, and remove spike-in reads. Peak calling was performed using MACS2 (v. 2.2.9.1), q 0.01. Read quantification was performed with DiffBind (v. 3.16.0). Differential analysis was performed using DESeq2 (v. 1.46.0) with built-in normalization.
Assembly: mm39
Supplementary files format and content: bigwig


title: Case103_dsRNA-seq_IN

description: Library name: dsRNA-seq_Case103_IN


title: CN from animal_51, rep2

description:
Library name: NSM1473-b2
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_2hWO_B

description: Library name: ChIP_H3K27ac-ChIP_2hWO_B


title: CN from animal_51

description:
Library name: NSM1473
3 lvl sciRNAseq


title: Case131_dsRNA-seq_IN

description: Library name: dsRNA-seq_Case131_IN


title: CN from animal_50, rep2

description:
Library name: NSM1472-b2
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_2hWO_A

description: Library name: ChIP_H3K27ac-ChIP_2hWO_A


title: Caco-2.batch2.MBZ.rep3.H08

description: Library name: Caco2_Batch2_MBZ_3_H08


title: CN from animal_50

description:
Library name: NSM1472
3 lvl sciRNAseq


title: Tdiff.1_dsRNA-seq_IP_Replicate3

description:
Library name: dsRNA-seq_Tdiff.1_IP-3
Alias is J2_3_IP

source_name: Transdifferentiated Neurons

value: Transdifferentiated Neurons


title: Case103_dsRNA-seq_IP

description: Library name: dsRNA-seq_Case103_IP


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_1hWO_C

description: Library name: ChIP_H3K27ac-ChIP_1hWO_C


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_1hWO_B

description: Library name: ChIP_H3K27ac-ChIP_1hWO_B


title: CN from animal_49, rep2

description:
Library name: NSM1471-b2
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_1hWO_A

description: Library name: ChIP_H3K27ac-ChIP_1hWO_A


title: Caco-2.batch2.MBZ.rep3.F08

description: Library name: Caco2_Batch2_MBZ_3_F08


title: iPSC-diff.1_PKR-eCLIP-seq_5nMAA_IN_Replicate1

description: Library name: eCLIP_iPSC-diff.1_5nMAA_PKR_IN-1

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: eCLIP-seq without PKR immunoprecipitation, 5 nM antimycin A for 6 h


title: Tdiff.1_dsRNA-seq_IP_Replicate1

description:
Library name: dsRNA-seq_Tdiff.1_IP-1
Alias is J2_1_IP


title: Caco-2.batch2.MBZ.rep3.E08

description: Library name: Caco2_Batch2_MBZ_3_E08


title: Tdiff.1_dsRNA-seq_IN_Replicate3

description:
Library name: dsRNA-seq_Tdiff.1_IN-3
Alias is J2_3_IN


title: CN from animal_48, rep2

description:
Library name: NSM1470-b2
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_30mWO_B

description: Library name: ChIP_H3K27ac-ChIP_30mWO_B


title: CN from animal_49

description:
Library name: NSM1471
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_30mWO_C

description: Library name: ChIP_H3K27ac-ChIP_30mWO_C


title: Caco-2.batch2.MBZ.rep3.D08

description: Library name: Caco2_Batch2_MBZ_3_D08


title: Tdiff.1_dsRNA-seq_IN_Replicate2

description:
Library name: dsRNA-seq_Tdiff.1_IN-2
Alias is J2_2_IN


title: CN from animal_48

description:
Library name: NSM1470
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_30mWO_A

description: Library name: ChIP_H3K27ac-ChIP_30mWO_A


title: Caco-2.batch2.MBZ.rep3.C08

description: Library name: Caco2_Batch2_MBZ_3_C08


title: Tdiff.1_dsRNA-seq_IN_Replicate1

description:
Library name: dsRNA-seq_Tdiff.1_IN-1
Alias is J2_1_IN


title: CN from animal_47, rep2

description:
Library name: NSM1469-b2
3 lvl sciRNAseq


title: Caco-2.batch2.MBZ.rep3.B08

description: Library name: Caco2_Batch2_MBZ_3_B08


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_2h_C

description: Library name: ChIP_H3K27ac-ChIP_2h_C


title: DSP-1001660014797-G-H09

city: Bethesda

first: Laurie

middle: T

last: Krug

state: Maryland

address: 10 Center Drive

institute: National Cancer Institute

description:
Library name: DSP-1001660014797-G-H09
GEOMX RNA-seq

data_processing:
*library strategy: Spatial Transcriptomics by NanoString GeoMx
The raw DCC files were generated from converting raw FASTQ files from an Illumina NextSeq2000 using the GeoMx NGS Pipeline.
DCC files, a PKC probe mapping file for the Human Whole Transcriptome Analysis (WTA) Panel, and an annotation excel file including all AOIs were combined into a common R object, with probe IDs mapped to gene IDs, using the GeoMx R package function “readNanoStringGeoMxSet()”.
All AOIs were checked for QC parameters including minimum read counts (>1000), percentage trimmed (>80%), percentage aligned (>75%), percentage stitched (>80%), saturation (>50%), nuclei (>20), area (>1000), negative probe count (>1), max NTC counts (<9000).
All probes were checked for QC parameters for minimum probe ratio (>0.1) and whether they are an outlier using the Grubb’s outlier test.  AOIs and probes were filtered out if they did not meet a QC parameter or if they had detection of <10% of overall AOIs (for probes) or <10% of the probe set (for AOIs).
Quartile-3 normalization was applied to all filtered AOI read counts using the GeoMx R package function “normalize()”.
Assembly: GRCh38-p13
Supplementary files format and content: DCC files
Supplementary files format and content: CXCR4.csv: Gene expression of different areas with their metadata.

source_name: cutaneous KS tumor

growth_protocol: Spatial Transcriptomics were performed on both eight donor biopsies and four PDX that corresponded to four matched patient biopsies. KS tumors were isolated as a punch biopsy. We engrafted four cutaneous KS donor biopsy tumors in immunodeficient mice to generate KS PDX. KS was maintained in the PDX of recipient mice for long periods, up to 262 days, supporting the consistent expansion of KSHV-infected endothelial cells across multiple donors with diverse clinical features.

extract_protocol:
Areas of illumination (AOI) were defined by fluorescently-conjugated antibodies for endothelial cells (CD31) and KSHV latency-associated nuclear antigen (LANA) as vessel region of interest (ROI) (CD31+LANA-), tumor ROI (CD31+LANA+), and segmented KSHV LANA+ nuclei in tumor ROI.
Oligonucleotide barcodes from each ROI were UV-photocleaved, collected into 96-well plates, followed by library preparation and sequencing as recommended by the NanoString GeoMx protocol.  Sequencing was performed on NextSeq2000 using an P3 flow cell kit (27 x 27 and index 8 x 8).

treatment_protocol: KS-PDX were treated with rituximab to deplete input CD20+ B cells.

value: cutaneous KS tumor

tag: biopsy/pdx

value: Biopsy

tag: slide name

tag: scan name

value: WTA slide#2 071323

tag: segment name_label

value: Full ROI

tag: segment

tag: region

value: vessel

tag: scan id

tag: sample id

tag: paired sample

value: TRUE


title: Case26_dsRNA-seq_IP

description: Library name: dsRNA-seq_Case26_IP

value: Frontal Cortex


title: CN from animal_54

description:
Library name: NSM1476
3 lvl sciRNAseq


title: CN from animal_47

description:
Library name: NSM1469
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 DMSO C

description: Library name: CUTRUN_H3K4me1 DMSO C


title: Caco-2.batch2.MBZ.rep3.A08

description: Library name: Caco2_Batch2_MBZ_3_A08

value: colon

value: epithelial


title: DSP-1001660014797-G-H08

description:
Library name: DSP-1001660014797-G-H08
GEOMX RNA-seq

value: tumor


title: Caco-2.batch2.PER.rep1.E02

description: Library name: Caco2_Batch2_PER_1_E02

value: cell line


title: CN from animal_46, rep2

description:
Library name: NSM1468-b2
3 lvl sciRNAseq

value: caudate nucleus


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_2h_B

description: Library name: ChIP_H3K27ac-ChIP_2h_B

value: MEL Mtg16-FKBP-2XHA


title: DSP-1001660014797-G-H07

description:
Library name: DSP-1001660014797-G-H07
GEOMX RNA-seq

value: PDX

value: Segment 1


title: Caco-2.batch2.PER.rep1.C02

description: Library name: Caco2_Batch2_PER_1_C02


title: CN from animal_53

description:
Library name: NSM1475
3 lvl sciRNAseq


title: CN from animal_52, rep2

description:
Library name: NSM1474-b2
3 lvl sciRNAseq


title: CN from animal_46

description:
Library name: NSM1468
3 lvl sciRNAseq


title: Caco-2.batch2.MBZ.rep2.H09

description: Library name: Caco2_Batch2_MBZ_2_H09


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_1h_C

description: Library name: ChIP_H3K27ac-ChIP_1h_C

value: murine erythroleukemia


title: Caco-2.batch2.MBZ.rep2.G09

description: Library name: Caco2_Batch2_MBZ_2_G09


title: DSP-1001660014797-G-H06

description:
Library name: DSP-1001660014797-G-H06
GEOMX RNA-seq


title: Caco-2.batch2.PER.rep1.A02

description: Library name: Caco2_Batch2_PER_1_A02


title: Case131_dsRNA-seq_IP

description: Library name: dsRNA-seq_Case131_IP

value: Apparently Healthy

value: dsRNA-seq with J2 immunoprecipitation


title: Caco-2.batch2.PER.rep1.B02

description: Library name: Caco2_Batch2_PER_1_B02


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_1h_B

description: Library name: ChIP_H3K27ac-ChIP_1h_B


title: Caco-2.batch2.MBZ.rep2.F09

description: Library name: Caco2_Batch2_MBZ_2_F09


title: DSP-1001660014797-G-H05

description:
Library name: DSP-1001660014797-G-H05
GEOMX RNA-seq

value: cutaneous KS tumor


title: CN from animal_45, rep2

description:
Library name: NSM1467-b2
3 lvl sciRNAseq


title: Caco-2.batch2.MBZ.rep2.E09

description: Library name: Caco2_Batch2_MBZ_2_E09


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_1h_A

description: Library name: ChIP_H3K27ac-ChIP_1h_A


title: Caco-2.batch2.MBZ.rep2.D09

description: Library name: Caco2_Batch2_MBZ_2_D09


title: CN from animal_44, rep2

description:
Library name: NSM1466-b2
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_30m_C

description: Library name: ChIP_H3K27ac-ChIP_30m_C


title: CN from animal_44

description:
Library name: NSM1466
3 lvl sciRNAseq


title: CN from animal_45

description:
Library name: NSM1467
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_30m_B

description: Library name: ChIP_H3K27ac-ChIP_30m_B


title: DSP-1001660014797-G-H03

description:
Library name: DSP-1001660014797-G-H03
GEOMX RNA-seq

value: WTA slide#2 071323


title: Caco-2.batch2.MBZ.rep3.G08

description: Library name: Caco2_Batch2_MBZ_3_G08


title: Caco-2.batch2.MBZ.rep2.C09

description: Library name: Caco2_Batch2_MBZ_2_C09


title: CN from animal_43, rep2

description:
Library name: NSM1465-b2
3 lvl sciRNAseq


title: DSP-1001660014797-G-H04

description:
Library name: DSP-1001660014797-G-H04
GEOMX RNA-seq

value: Full ROI


title: DSP-1001660014797-G-H02

description:
Library name: DSP-1001660014797-G-H02
GEOMX RNA-seq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_30m_A

description: Library name: ChIP_H3K27ac-ChIP_30m_A


title: Caco-2.batch2.MBZ.rep2.B09

description: Library name: Caco2_Batch2_MBZ_2_B09


title: Tdiff.1_dsRNA-seq_IP_Replicate2

description:
Library name: dsRNA-seq_Tdiff.1_IP-2
Alias is J2_2_IP

value: Transdifferentiated Neurons


title: CN from animal_43

description:
Library name: NSM1465
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_15m_C

description: Library name: ChIP_H3K27ac-ChIP_15m_C


title: DSP-1001660014797-G-H01

description:
Library name: DSP-1001660014797-G-H01
GEOMX RNA-seq

value: Biopsy

value: TRUE


title: Caco-2.batch2.MBZ.rep2.A09

description: Library name: Caco2_Batch2_MBZ_2_A09

value: colon


title: CN from animal_42, rep2

description:
Library name: NSM1464-b2
3 lvl sciRNAseq


title: DSP-1001660014797-G-G12

description:
Library name: DSP-1001660014797-G-G12
GEOMX RNA-seq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_15m_B

description: Library name: ChIP_H3K27ac-ChIP_15m_B


title: CN from animal_42

description:
Library name: NSM1464
3 lvl sciRNAseq


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_2h_A

description: Library name: ChIP_H3K27ac-ChIP_2h_A


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_15m_A

description: Library name: ChIP_H3K27ac-ChIP_15m_A


title: CN from animal_41, rep2

description:
Library name: NSM1463-b2
3 lvl sciRNAseq


title: DSP-1001660014797-G-G11

description:
Library name: DSP-1001660014797-G-G11
GEOMX RNA-seq


title: Caco-2.batch2.MBZ.rep1.H09

description: Library name: Caco2_Batch2_MBZ_1_H09

value: epithelial


title: Caco-2.batch2.MBZ.rep1.F09

description: Library name: Caco2_Batch2_MBZ_1_F09


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_DMSO_C

description: Library name: ChIP_H3K27ac-ChIP_DMSO_C


title: Caco-2.batch2.MBZ.rep1.G09

description: Library name: Caco2_Batch2_MBZ_1_G09


title: DSP-1001660014797-G-G09

description:
Library name: DSP-1001660014797-G-G09
GEOMX RNA-seq

value: vessel


title: DSP-1001660014797-G-G10

description:
Library name: DSP-1001660014797-G-G10
GEOMX RNA-seq

value: tumor


title: Caco-2.batch2.MBZ.rep1.E09

description: Library name: Caco2_Batch2_MBZ_1_E09

value: cell line


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_DMSO_B

description: Library name: ChIP_H3K27ac-ChIP_DMSO_B

value: MEL Mtg16-FKBP-2XHA


title: CN from animal_40, rep2

description:
Library name: NSM1462-b2
3 lvl sciRNAseq

value: caudate nucleus


title: DSP-1001660014797-G-G08

description:
Library name: DSP-1001660014797-G-G08
GEOMX RNA-seq

value: PDX


title: MEL_Mtg16-FKBP_H3K27ac-ChIP_DMSO_A

description: Library name: ChIP_H3K27ac-ChIP_DMSO_A

value: murine erythroleukemia


title: CN from animal_41

description:
Library name: NSM1463
3 lvl sciRNAseq


title: Caco-2.batch2.MBZ.rep1.D09

description: Library name: Caco2_Batch2_MBZ_1_D09


title: MEL Mtg16 LBH 1hWO C

description:
Library name: PROSeq_LBH589_1hWO_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
13173-JE_deseq_results_table_normcounts.txt
13173-JE_dREG_deseq_results_alltimepoints.txt

data_processing:
Adaptors were trimmed from the R1 file from paired-end PRO-Seq experiments using TrimmomaticSE. Reverse complements were generated using FASTX Toolkit (v. 0.0.13). Trimmed reverse complement reads were then aligned to a concatenated mm39+dm3 genome using Bowtie2 (v. 2.2.2). Resulting alignments were then processed with samtools (v. 1.16.1) to remove low quality reads, count reads aligned to mm39 and dm3 genomes, and remove spike-in reads. Differential expression of protein coding genes was assessed using NRSA. Regions with non-coding transcriptional activity for all samples were identified using dREG. To generate a set of enhancer regions, raw peak files from all samples were concatenated using bedtools, filtered for only intergenic or intronic regions using Homer. Only regions with a maximum RPM over 10 across all samples were carried forward. FeatureCounts (v. 2.0.1) was used to quantify reads in each of the final enhancer regions. Differential expression of enhancers was determined using DESeq2 (v. 1.46.0). Both built-in and spike-in normalization (minimum read count) was performed for all PRO-Seq experiments. Built-in DESeq2 normalization was used for all analyses presented, except for PRO-Seq experiments with A485, where spike-in normalization was used.
Assembly: mm39
Supplementary files format and content: count tables for genes and enhancers
Library strategy: PRO-Seq

extract_protocol:
Total RNA from nuclei was isolated by Trizol LS extraction, hydrolyzed in 0.2 N NaOH, and biotin-CTP containing nascent RNAs were isolated by streptavidin bead (Invtirogen) pulldown.
RNA was reverse transcribed and amplified following 3′ adaptor ligation, 5′ cap removal and triphosphate repair, 5′ hydroxyl repair, and 5′ adapter ligation. PAGE purified cDNA libraries were provided to the Vanderbilt University Medical Center VANTAGE Core for sequencing. Libraries were sequenced on a NovaSeq 6000 or NovaSeq X (50 x 106 reads per sample).

treatment_protocol: 250nM dTAGV1, 10uM A485, 5nM LBH589

value: LBH 1hWO


title: CN from animal_40

description:
Library name: NSM1462
3 lvl sciRNAseq


title: DSP-1001660014797-G-G07

description:
Library name: DSP-1001660014797-G-G07
GEOMX RNA-seq


title: CN from animal_39, rep2

description:
Library name: NSM1461-b2
3 lvl sciRNAseq


title: DSP-1001660014797-G-G02

description:
Library name: DSP-1001660014797-G-G02
GEOMX RNA-seq


title: DSP-1001660014797-G-G03

description:
Library name: DSP-1001660014797-G-G03
GEOMX RNA-seq


title: MEL Mtg16 LBH 1hWO B

description:
Library name: PROSeq_LBH589_1hWO_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
13173-JE_deseq_results_table_normcounts.txt
13173-JE_dREG_deseq_results_alltimepoints.txt


title: DSP-1001660014797-G-G01

description:
Library name: DSP-1001660014797-G-G01
GEOMX RNA-seq


title: Caco-2.batch2.MBZ.rep1.A09

description: Library name: Caco2_Batch2_MBZ_1_A09


title: Caco-2.batch2.MBZ.rep1.B09

description: Library name: Caco2_Batch2_MBZ_1_B09


title: MEL Mtg16 LBH 1hWO A

description:
Library name: PROSeq_LBH589_1hWO_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
13173-JE_deseq_results_table_normcounts.txt
13173-JE_dREG_deseq_results_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep3.H01

description: Library name: Caco2_Batch2_DIQ_3_H01


title: MEL Mtg16 LBH 30mWO C

description:
Library name: PROSeq_LBH589_30mWO_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
13173-JE_deseq_results_table_normcounts.txt
13173-JE_dREG_deseq_results_alltimepoints.txt

value: LBH 30mWO


title: CN from animal_37

description:
Library name: NSM1460
3 lvl sciRNAseq


title: DSP-1001660014797-G-F12

description:
Library name: DSP-1001660014797-G-F12
GEOMX RNA-seq

value: cutaneous KS tumor

value: Segment 1


title: MEL Mtg16 LBH 30mWO B

description:
Library name: PROSeq_LBH589_30mWO_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
13173-JE_deseq_results_table_normcounts.txt
13173-JE_dREG_deseq_results_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep3.F01

description: Library name: Caco2_Batch2_DIQ_3_F01


title: DSP-1001660014797-G-F10

description:
Library name: DSP-1001660014797-G-F10
GEOMX RNA-seq

value: WTA slide#2 071323


title: DSP-1001660014797-G-F11

description:
Library name: DSP-1001660014797-G-F11
GEOMX RNA-seq


title: Caco-2.batch2.DIQ.rep3.E01

description: Library name: Caco2_Batch2_DIQ_3_E01


title: DSP-1001660014797-G-F09

description:
Library name: DSP-1001660014797-G-F09
GEOMX RNA-seq

value: Full ROI


title: MEL Mtg16 LBH 1h C

description:
Library name: PROSeq_LBH589_1h_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: LBH 1h


title: MEL Mtg16 LBH 1h B

description:
Library name: PROSeq_LBH589_1h_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep3.D01

description: Library name: Caco2_Batch2_DIQ_3_D01


title: CN from animal_35

description:
Library name: NSM1458
3 lvl sciRNAseq


title: DSP-1001660014797-G-F08

description:
Library name: DSP-1001660014797-G-F08
GEOMX RNA-seq

value: Biopsy

value: TRUE


title: MEL Mtg16 LBH 1h A

description:
Library name: PROSeq_LBH589_1h_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep3.C01

description: Library name: Caco2_Batch2_DIQ_3_C01

value: colon

value: epithelial


title: CN from animal_35, rep2

description:
Library name: NSM1458-b2
3 lvl sciRNAseq


title: DSP-1001660014797-G-F03

description:
Library name: DSP-1001660014797-G-F03
GEOMX RNA-seq

value: vessel


title: CN from animal_34, rep2

description:
Library name: NSM1457-b2
3 lvl sciRNAseq


title: MEL Mtg16 LBH 30m C

description:
Library name: PROSeq_LBH589_30m_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: LBH 30m


title: Caco-2.batch2.DIQ.rep3.B01

description: Library name: Caco2_Batch2_DIQ_3_B01

value: cell line


title: DSP-1001660014797-G-E10

description:
Library name: DSP-1001660014797-G-E10
GEOMX RNA-seq

value: tumor


title: CN from animal_34

description:
Library name: NSM1457
3 lvl sciRNAseq

value: caudate nucleus


title: MEL Mtg16 LBH 30m B

description:
Library name: PROSeq_LBH589_30m_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: Caco-2.batch2.DIQ.rep3.A01

description: Library name: Caco2_Batch2_DIQ_3_A01


title: DSP-1001660014797-G-E07

description:
Library name: DSP-1001660014797-G-E07
GEOMX RNA-seq


title: CN from animal_33, rep2

description:
Library name: NSM1456-b2
3 lvl sciRNAseq


title: Caco-2.batch2.DIQ.rep2.H01

description: Library name: Caco2_Batch2_DIQ_2_H01


title: DSP-1001660014797-G-E05

description:
Library name: DSP-1001660014797-G-E05
GEOMX RNA-seq

value: WTA slide#1B 071323


title: MEL Mtg16 DMSO I

description:
Library name: PROSeq_dTAGV1_0h_9
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: DMSO


title: CN from animal_33

description:
Library name: NSM1456
3 lvl sciRNAseq


title: MEL Mtg16 LBH 30m A

description:
Library name: PROSeq_LBH589_30m_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep2.G01

description: Library name: Caco2_Batch2_DIQ_2_G01


title: CN from animal_32, rep2

description:
Library name: NSM1455-b2
3 lvl sciRNAseq


title: DSP-1001660014797-G-E01

description:
Library name: DSP-1001660014797-G-E01
GEOMX RNA-seq

value: cutaneous KS tumor


title: MEL Mtg16 DMSO H

description:
Library name: PROSeq_dTAGV1_0h_8
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep2.F01

description: Library name: Caco2_Batch2_DIQ_2_F01


title: DSP-1001660014797-G-D09

description:
Library name: DSP-1001660014797-G-D09
GEOMX RNA-seq

value: PDX


title: Caco-2.batch2.DIQ.rep2.E01

description: Library name: Caco2_Batch2_DIQ_2_E01


title: CN from animal_32

description:
Library name: NSM1455
3 lvl sciRNAseq


title: CN from animal_31

description:
Library name: NSM1454
3 lvl sciRNAseq


title: Caco-2.batch2.DIQ.rep2.C01

description: Library name: Caco2_Batch2_DIQ_2_C01


title: MEL Mtg16 dTAGV1+A485 1h B

description:
Library name: PROSeq_dTAGV1_A485_1h_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1+A485 1h


title: Caco-2.batch2.DIQ.rep2.B01

description: Library name: Caco2_Batch2_DIQ_2_B01


title: DSP-1001660014797-G-D03

description:
Library name: DSP-1001660014797-G-D03
GEOMX RNA-seq

value: Segment 1


title: DSP-1001660014797-G-D02

description:
Library name: DSP-1001660014797-G-D02
GEOMX RNA-seq

value: Full ROI


title: CN from animal_30

description:
Library name: NSM1453
3 lvl sciRNAseq


title: MEL Mtg16 A485 1h F

description:
Library name: PROSeq_A485_1h_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: Caco-2.batch2.DIQ.rep2.A01

description: Library name: Caco2_Batch2_DIQ_2_A01


title: CN from animal_29

description:
Library name: NSM1452
3 lvl sciRNAseq


title: DSP-1001660014797-G-C12

description:
Library name: DSP-1001660014797-G-C12
GEOMX RNA-seq

value: TRUE


title: Caco-2.batch2.DIQ.rep3.G01

description: Library name: Caco2_Batch2_DIQ_3_G01

value: colon


title: MEL Mtg16 A485 1h E

description:
Library name: PROSeq_A485_1h_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: UOCB_CART19_Rep2

city: Philadelphia

first: Rawan

last: Shraim

state: PA

address: 3501 Civic Center Blvd

department: Oncology

institute: Children's Hospital of Philadelphia

description: Library name: HTS114_08_B2_UOCB_CART19_Rep2_S8

data_processing:
Bulk RNA-sequencing - Fastq files were aligned to the human reference genome (GRCh38) using the STAR aligner (v2.7.11b). Per gene read counts for Ensembl gene annotations were computed using the subread package in R. Gene counts were normalized for library sizes, voom transformed and represented as log2CPM( counts per million)  using the edgeR R package (v 4.2.2).
scRNA-sequencing - Samples were processed using cellranger-7.1.0. For non-multiplexed samples, cellranger count was used to obtain the single-cell matrix and .h5 file. For multiplexed samples, cellranger multi was used in additional to supplementary files corresponding to the sample names. After obtaining the .h5 file, Seurat was used for downstream analyses.
Assembly: HG38
Supplementary files format and content: scRNA-sequencing - Files are in .h5 format and can be read into R using Seurat library.
Supplementary files format and content: Bulk RNA-sequencing - csv files with voom transformed log2 CPM per sample

growth_protocol: Bulk RNA-sequencing - NALM6 or UOCB cell lines transduced to express GFP were co-cultured with CART cells at an effector:target ratio of 1:8 in RPMI supplemented with 20% fetal bovine serum (FBS) and 1% penicillin/streptomycin, 1% HEPES, 1% non-essential amino acids, and 1% L-glutamine.

extract_protocol:
Bulk RNA-sequencing  -  Pellets were transformed to total RNA using Qiagen’s QiaShredder (Cat no. 79656) and RNeasy Mini RNA extraction kit
scRNA-sequencing - Cryopreserved peripheral blood mononuclear cells (PBMCs) or bone marrow mononuclear cells (BMMC) were thawed and resuspended in media. Suspensions were centrifuged at 300 x g for 5 minutes at 4°C and resuspended in Dulbecco's phosphate-buffered saline (DPBS, Gibco, PN 14190-144) with 1% bovine serum albumin (BSA, Miltenyi Biotec, PN 130-091-376). Cell suspensions were then centrifuged at 500 x g for 5 minutes at 4°C and resuspended in 50 µL of cell staining buffer (Biolegend Inc, PN 420201) followed by addition of 5 µL of Human TruStain FcX™ blocking reagent (Biolegend Inc, PN 422301) if the cell count per sample in DPBS + 1% BSA was > 200,000 cells. Cells were incubated in Fc block for 10 minutes at 4°C. During incubation, hashtag antibodies were prepared by adding 2.2 µL (1.5 µg) of each of the TotalSeq™ anti-human Hashtag to 52.8 µL cell staining buffer and centrifuged at 14000 x g for 10 minutes at 4°C. At the end of incubation in Fc block, each cell suspension was labelled with 50 µL TotalSeq™ anti-human Hashtag antibody and incubated for 30 minutes at 4°C. Cells were then washed thrice in cell staining buffer at 500 x g for 5 minutes at 4°C and resuspended in DPBS + 0.04% BSA. If cell counts in DPBS + 1% BSA were < 200, 000 cells, cells were centrifuged at 300 x g for 5 minutes at 4°C and resuspended in DPBS + 0.04% BSA.
Bulk RNA-sequencing - Complementary DNA libraries were prepared with Illumina’s Stranded mRNA poly-A enrichment kit following the standard protocol. Individual library QC was performed on Agilent TapeStation prior to pooling. Pooled libraries were sequenced on NextSeq2000 on a P4 XLEAP SBS flow cell to collect 20 million reads per sample.
scRNA-sequencing - Hashed and pooled cell suspensions or individual cell suspensions were subsequently processed to generate single cell RNA-seq libraries using chromium Next GEM single cell 3’ reagent kits v3.1 Dual Index (10x Genomics, PN-1000268) with 3’ feature barcode technology (10x Genomics, PN-1000262) for cell surface protein using chromium controller as per manufacturer’s instructions. Library fragment size was determined using the Bioanalyzer Agilent 2100 with the High Sensitivity DNA chip (Agilent Technologies, 5067-4626) and libraries were quantified using Kapa qPCR quantification kit (Roche Diagnostics, PN 501965234). After pooling, libraries were sequenced on an Illumina NovaSeq 6000 using sequencing parameters read1: i7: i5: read2 :: 28:10:10:90 bp at an average sequencing depth of 50,000 read pairs per cell.

treatment_protocol: Bulk RNA-sequencing - Cells were incubated with or without IL-10 added at a concentration of 15 ng/mL.

value: without IL10


title: DSP-1001660014797-G-C11

description:
Library name: DSP-1001660014797-G-C11
GEOMX RNA-seq


title: CN from animal_28

description:
Library name: NSM1451
3 lvl sciRNAseq


title: MEL Mtg16 A485 1h D

description:
Library name: PROSeq_A485_1h_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: UOCB_CART19_Rep1

description: Library name: HTS114_07_B1_UOCB_CART19_Rep1_S7


title: MEL Mtg16 dTAGV1 1h C

description:
Library name: PROSeq_dTAGV1_1h_6
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 1h


title: CN from animal_27

description:
Library name: NSM1450
3 lvl sciRNAseq


title: UOCB_CART22_IL10_Rep3

description: Library name: HTS114_06_A6_UOCB_CART22_IL10_Rep3_S6

value: with IL10


title: DSP-1001660014797-G-C09

description:
Library name: DSP-1001660014797-G-C09
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1 1h B

description:
Library name: PROSeq_dTAGV1_1h_5
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: CN from animal_26

description:
Library name: NSM1449
3 lvl sciRNAseq


title: UOCB_CART22_IL10_Rep2

description: Library name: HTS114_05_A5_UOCB_CART22_IL10_Rep2_S5


title: DSP-1001660014797-G-C08

description:
Library name: DSP-1001660014797-G-C08
GEOMX RNA-seq


title: DSP-1001660014797-G-D05

description:
Library name: DSP-1001660014797-G-D05
GEOMX RNA-seq

value: Biopsy


title: MEL Mtg16 DMSO G

description:
Library name: PROSeq_dTAGV1_0h_7
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12663-AJ_deseq_results_table_normcounts.txt
12663-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: CN from animal_25

description:
Library name: NSM1448
3 lvl sciRNAseq


title: DSP-1001660014797-G-D04

description:
Library name: DSP-1001660014797-G-D04
GEOMX RNA-seq

value: vessel


title: Caco-2.batch2.DIQ.rep2.D01

description: Library name: Caco2_Batch2_DIQ_2_D01

value: epithelial

value: cell line


title: UOCB_CART22_IL10_Rep1

description: Library name: HTS114_04_A4_UOCB_CART22_IL10_Rep1_S4


title: CN from animal_24

description:
Library name: NSM1447
3 lvl sciRNAseq

value: caudate nucleus


title: DSP-1001660014797-G-C07

description:
Library name: DSP-1001660014797-G-C07
GEOMX RNA-seq

value: WTA slide#1B 071323

value: tumor


title: MEL Mtg16 dTAGV1+A485 30m B

description:
Library name: PROSeq_dTAGV1_A485_30m_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia

value: dTAGV1+A485 30m


title: MEL Mtg16 dTAGV1 1h A

description:
Library name: PROSeq_dTAGV1_1h_4
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: UOCB_CART19_IL10_Rep3

description: Library name: HTS114_03_A3_UOCB_CART19_IL10_Rep3_S3


title: DSP-1001660014797-G-C05

description:
Library name: DSP-1001660014797-G-C05
GEOMX RNA-seq

value: cutaneous KS tumor

value: PDX


title: CN from animal_23

description:
Library name: NSM1446
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1+A485 30m A

description:
Library name: PROSeq_dTAGV1_A485_30m_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: UOCB_CART19_IL10_Rep2

description: Library name: HTS114_02_A2_UOCB_CART19_IL10_Rep2_S2


title: CN from animal_22

description:
Library name: NSM1445
3 lvl sciRNAseq


title: MEL Mtg16 A485 30m B

description:
Library name: PROSeq_A485_30m_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014797-G-C04

description:
Library name: DSP-1001660014797-G-C04
GEOMX RNA-seq

value: Full ROI

value: TRUE


title: UOCB_CART19_IL10_Rep1

description: Library name: HTS114_01_A1_UOCB_CART19_IL10_Rep1_S1


title: DSP-1001660014797-G-C03

description:
Library name: DSP-1001660014797-G-C03
GEOMX RNA-seq

value: Segment 1


title: MEL Mtg16 A485 30m A

description:
Library name: PROSeq_A485_30m_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: CN from animal_21

description:
Library name: NSM1444
3 lvl sciRNAseq


title: BM9_BM11_CSP

description:
Library name: BM9_BM11_CSP
Hashtag oligos for Multiplexed samples

source_name: BM

value: BM


title: DSP-1001660014797-G-C02

description:
Library name: DSP-1001660014797-G-C02
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1 30m F

description:
Library name: PROSeq_dTAGV1_30m_6
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 30m


title: CN from animal_20

description:
Library name: NSM1443
3 lvl sciRNAseq


title: BM9_BM11_GEX

description:
Library name: BM9_BM11_GEX
Multiplexed samples


title: CN from animal_19

description:
Library name: NSM1442
3 lvl sciRNAseq


title: DSP-1001660014797-G-C01

description:
Library name: DSP-1001660014797-G-C01
GEOMX RNA-seq

value: Biopsy


title: BM8

description: Library name: BM8


title: DSP-1001660014797-G-B12

description:
Library name: DSP-1001660014797-G-B12
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1 30m E

description:
Library name: PROSeq_dTAGV1_30m_5
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: CN from animal_18

description:
Library name: NSM1441
3 lvl sciRNAseq


title: DSP-1001660014797-G-C10

description:
Library name: DSP-1001660014797-G-C10
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1 30m D

description:
Library name: PROSeq_dTAGV1_30m_4
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: BM7

description: Library name: BM7


title: DSP-1001660014797-G-B11

description:
Library name: DSP-1001660014797-G-B11
GEOMX RNA-seq

value: vessel


title: CN from animal_17

description:
Library name: NSM1440
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1+A485 15mC

description:
Library name: PROSeq_dTAGV1_A485_15m_6
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1+A485 15m


title: BM6

description: Library name: BM6


title: DSP-1001660014797-G-B10

description:
Library name: DSP-1001660014797-G-B10
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1+A485 15m B

description:
Library name: PROSeq_dTAGV1_A485_15m_5
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: BM5

description: Library name: BM5


title: CN from animal_16

description:
Library name: NSM1439
3 lvl sciRNAseq


title: DSP-1001660014797-G-B08

description:
Library name: DSP-1001660014797-G-B08
GEOMX RNA-seq


title: CN from animal_15

description:
Library name: NSM1438
3 lvl sciRNAseq


title: DSP-1001660014797-G-B07

description:
Library name: DSP-1001660014797-G-B07
GEOMX RNA-seq


title: BM4_HTO

description:
Library name: BM4_HTO
Hashtag oligos for Multiplexed samples


title: CN from animal_14

description:
Library name: NSM1437
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1+A485 15m A

description:
Library name: PROSeq_dTAGV1_A485_15m_4
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: MEL Mtg16 A485 15m C

description:
Library name: PROSeq_A485_15m_6
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: BM4_GEX

description:
Library name: BM4_GEX
Multiplexed samples


title: DSP-1001660014797-G-B06

description:
Library name: DSP-1001660014797-G-B06
GEOMX RNA-seq


title: MEL Mtg16 A485 15m B

description:
Library name: PROSeq_A485_15m_5
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: BM2

description: Library name: BM2


title: CN from animal_13

description:
Library name: NSM1436
3 lvl sciRNAseq


title: CN from animal_12

description:
Library name: NSM1435
3 lvl sciRNAseq


title: MEL Mtg16 A485 15m A

description:
Library name: PROSeq_A485_15m_4
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014797-G-B03

description:
Library name: DSP-1001660014797-G-B03
GEOMX RNA-seq


title: BM1

description: Library name: BM1


title: CN from animal_11

description:
Library name: NSM1434
3 lvl sciRNAseq


title: APH8_APH9_HTO

description:
Library name: APH8_APH9_HTO
Hashtag oligos for Multiplexed samples

source_name: PBMC

value: PBMC


title: MEL Mtg16 dTAGV1 15m E

description:
Library name: PROSeq_dTAGV1_15m_5
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 15m


title: DSP-1001660014797-G-B01

description:
Library name: DSP-1001660014797-G-B01
GEOMX RNA-seq

value: WTA slide#1B 071323


title: Caco-2.batch2.MBZ.rep1.C09

description: Library name: Caco2_Batch2_MBZ_1_C09

value: colon

value: epithelial

value: cell line


title: CN from animal_10

description:
Library name: NSM1433
3 lvl sciRNAseq

value: caudate nucleus


title: DSP-1001660014797-G-B05

description:
Library name: DSP-1001660014797-G-B05
GEOMX RNA-seq

value: cutaneous KS tumor


title: MEL Mtg16 dTAGV1 15m F

description:
Library name: PROSeq_dTAGV1_15m_6
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: CN from animal_39

description:
Library name: NSM1461
3 lvl sciRNAseq


title: APH8_APH9_GEX

description:
Library name: APH8_APH9_GEX
Multiplexed samples


title: DSP-1001660014797-G-A11

description:
Library name: DSP-1001660014797-G-A11
GEOMX RNA-seq

value: tumor

value: TRUE


title: CN from animal_37, rep2

description:
Library name: NSM1460-b2
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 15m D

description:
Library name: PROSeq_dTAGV1_15m_4
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: APH7_APH10_HTO

description:
Library name: APH7_APH10_HTO
Hashtag oligos for Multiplexed samples


title: CN from animal_9

description:
Library name: NSM1432
3 lvl sciRNAseq


title: MEL Mtg16 LBH 30mWO A

description:
Library name: PROSeq_LBH589_30mWO_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
13173-JE_deseq_results_table_normcounts.txt
13173-JE_dREG_deseq_results_alltimepoints.txt

value: LBH 30mWO


title: CN from animal_36, rep2

description:
Library name: NSM1459-b2
3 lvl sciRNAseq


title: CN from animal_8

description:
Library name: NSM1431
3 lvl sciRNAseq


title: DSP-1001660014797-G-A10

description:
Library name: DSP-1001660014797-G-A10
GEOMX RNA-seq

value: Segment 1


title: MEL Mtg16 DMSO F

description:
Library name: PROSeq_dTAGV1_0h_6
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: DMSO


title: APH7_APH10_GEX

description:
Library name: APH7_APH10_GEX
Multiplexed samples


title: CN from animal_7

description:
Library name: NSM1430
3 lvl sciRNAseq


title: MEL Mtg16 DMSO E

description:
Library name: PROSeq_dTAGV1_0h_5
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014797-G-A09

description:
Library name: DSP-1001660014797-G-A09
GEOMX RNA-seq

value: Biopsy


title: CN from animal_36

description:
Library name: NSM1459
3 lvl sciRNAseq


title: DSP-1001660014797-G-A03

description:
Library name: DSP-1001660014797-G-A03
GEOMX RNA-seq

value: PDX


title: APH6

description: Library name: APH6

value: PBMC


title: CN from animal_6

description:
Library name: NSM1429
3 lvl sciRNAseq


title: MEL Mtg16 DMSO D

description:
Library name: PROSeq_dTAGV1_0h_4
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014797-G-A01

description:
Library name: DSP-1001660014797-G-A01
GEOMX RNA-seq

value: No Template Control


title: APH2

description: Library name: APH2


title: CN from animal_5, rep2

description:
Library name: NSM1428-b2
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 2hWO C

description:
Library name: PROSeq_dTAGV1_2hWO_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 2hWO


title: CN from animal_5

description:
Library name: NSM1428
3 lvl sciRNAseq


title: DSP-1001660014796-H-G12

description:
Library name: DSP-1001660014796-H-G12
GEOMX RNA-seq

value: WTA slide#4 071323

value: Full ROI

value: vessel

value: FALSE


title: MEL Mtg16 dTAGV1 2hWO B

description:
Library name: PROSeq_dTAGV1_2hWO_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: APH1

description: Library name: APH1


title: SP_4

city: Shanghai

first: Jian

last: Wang

address: Pujian Load 160th, Pudong New Aera

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 8

data_processing:
Trimmomatic software
Sequence reads were trimmed for adapter and low-quality reads.
Assembly: hg38
Supplementary files format and content: tabe-delimited text file includes raw counts for each sample

source_name: blood vessel

extract_protocol:
RNA was harvested using Trjzol (Thermo Fisher). 5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by NEBNext UltraTM RNA Library Prep Kit following the manufacturers' protocols.

value: blood vessel

value: HUVEC

value: umbilical vein endothelial cell


title: CN from animal_4, rep2

description:
Library name: NSM1427-b2
3 lvl sciRNAseq

value: caudate nucleus


title: DSP-1001660014796-H-G10

description:
Library name: DSP-1001660014796-H-G10
GEOMX RNA-seq

value: cutaneous KS tumor

value: tumor


title: CN from animal_4

description:
Library name: NSM1427
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 2hWO A

description:
Library name: PROSeq_dTAGV1_2hWO_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: SP_2

description: Library name: Sample 6


title: SP_3

description: Library name: Sample 7


title: CN from animal_3, rep2

description:
Library name: NSM1426-b2
3 lvl sciRNAseq


title: DSP-1001660014796-H-G11

description:
Library name: DSP-1001660014796-H-G11
GEOMX RNA-seq

value: Biopsy

value: Segment 1


title: MEL Mtg16 dTAGV1 1hWO B

description:
Library name: PROSeq_dTAGV1_1hWO_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 1hWO


title: DSP-1001660014796-H-G09

description:
Library name: DSP-1001660014796-H-G09
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1 1hWO A

description:
Library name: PROSeq_dTAGV1_1hWO_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: SP_1

description: Library name: Sample 5


title: CN from animal_3

description:
Library name: NSM1426
3 lvl sciRNAseq


title: Con_4

description: Library name: Sample 4


title: MEL Mtg16 dTAGV1 30mWO C

description:
Library name: PROSeq_dTAGV1_30mWO_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 30mWO


title: CN from animal_1, rep2

description:
Library name: NSM1425-b2
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 30mWO B

description:
Library name: PROSeq_dTAGV1_30mWO_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014796-H-G06

description:
Library name: DSP-1001660014796-H-G06
GEOMX RNA-seq


title: DSP-1001660014796-H-G08

description:
Library name: DSP-1001660014796-H-G08
GEOMX RNA-seq


title: DSP-1001660014796-H-G07

description:
Library name: DSP-1001660014796-H-G07
GEOMX RNA-seq


title: Con_3

description: Library name: Sample 3


title: CN from animal_1

description:
Library name: NSM1425
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 30mWO A

description:
Library name: PROSeq_dTAGV1_30mWO_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: Con_2

description: Library name: Sample 2


title: DSP-1001660014796-H-G05

description:
Library name: DSP-1001660014796-H-G05
GEOMX RNA-seq


title: MB from animal_55

description:
Library name: NSM1424
3 lvl sciRNAseq

source_name: midbrain

value: midbrain


title: MEL Mtg16 A485 2h B

description:
Library name: PROSeq_dTAGV1_2h_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: Con_1

description: Library name: Sample 1


title: CN from animal_31, rep2

description:
Library name: NSM1454-b2
3 lvl sciRNAseq


title: DSP-1001660014796-H-G04

description:
Library name: DSP-1001660014796-H-G04
GEOMX RNA-seq

value: WTA slide#4 071323


title: MB from animal_54

description:
Library name: NSM1423
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1+A485 1h C

description:
Library name: PROSeq_dTAGV1_A485_1h_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1+A485 1h


title: MEL Mtg16 A485 1h C

description:
Library name: PROSeq_dTAGV1_1h_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: V-3

description: Library name: Sample 7


title: MB from animal_52

description:
Library name: NSM1421
3 lvl sciRNAseq


title: Donor-4_Dome, Visium

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Donor-4_dome

data_processing:
The FASTQ files were processed using Space Ranger v. 4.1.0
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: Donor4_Dome.tif: image of tissue and spots that can be used to run spaceranger count
Supplementary files format and content: genecount_filtered_feature_bc_matrix.h5: HDF5 file with gene barcode matrices that contains only tissue-associated barcodes
Supplementary files format and content: genecounts_spatial_enrichment.csv: table of genes and their spatial enrichment
Supplementary files format and content: harmonized_peak_reference.gtf: peak reference used to generate peakcounts matrix and spatial enrichment table
Supplementary files format and content: peakcounts_filtered_feature_bc_matrix.h5: HDF5 file with peak barcode matrices that contains only tissue-associated barcodes
Supplementary files format and content: peakcounts_spatial_enrichment.csv: table of peaks and their spatial enrichment
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions.csv: table of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Bladder dome

extract_protocol:
Fresh frozen tissue was OCT embedded, and 10uM frozen section was cut with cryostat directly onto a Visium slide (Slide # V19B23-041, Slide area D1).
Spatial transcriptome sequencing library was prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer’s protocol.

value: Bladder dome


title: MEL Mtg16 A485 1h B

description:
Library name: PROSeq_dTAGV1_1h_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: V-2

description: Library name: Sample 6


title: MEL Mtg16 A485 1h A

description:
Library name: PROSeq_dTAGV1_1h_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014796-H-G01

description:
Library name: DSP-1001660014796-H-G01
GEOMX RNA-seq

value: Full ROI

value: vessel

value: FALSE


title: MB from animal_51

description:
Library name: NSM1420
3 lvl sciRNAseq


title: V-1

description: Library name: Sample 5

value: blood vessel

value: HUVEC

value: umbilical vein endothelial cell


title: DSP-1001660014796-H-F12

description:
Library name: DSP-1001660014796-H-F12
GEOMX RNA-seq

value: cutaneous KS tumor


title: MB from animal_50

description:
Library name: NSM1419
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 30m C

description:
Library name: PROSeq_dTAGV1_30m_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: dTAGV1 30m


title: F-4

description: Library name: Sample 4


title: DSP-1001660014796-H-F11

description:
Library name: DSP-1001660014796-H-F11
GEOMX RNA-seq

value: Biopsy

value: tumor


title: MB from animal_49

description:
Library name: NSM1418
3 lvl sciRNAseq


title: DSP-1001660014796-H-F10

description:
Library name: DSP-1001660014796-H-F10
GEOMX RNA-seq


title: F-3

description: Library name: Sample 3


title: MEL Mtg16 dTAGV1 30m A

description:
Library name: PROSeq_dTAGV1_30m_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: murine erythroleukemia


title: F-2

description: Library name: Sample 2


title: DSP-1001660014796-H-F09

description:
Library name: DSP-1001660014796-H-F09
GEOMX RNA-seq


title: MEL Mtg16 dTAGV1 15m C

description:
Library name: PROSeq_dTAGV1_15m_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: dTAGV1 15m


title: F-1

description: Library name: Sample 1


title: MB from animal_48

description:
Library name: NSM1417
3 lvl sciRNAseq

value: midbrain


title: MB from animal_47

description:
Library name: NSM1416
3 lvl sciRNAseq


title: MB from animal_46

description:
Library name: NSM1415
3 lvl sciRNAseq


title: MEL Mtg16 dTAGV1 15m B

description:
Library name: PROSeq_dTAGV1_15m_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: V-3-RIBO

description: Library name: Sample 7

data_processing:
The raw reads from the sequencer were subjected to quality control using fastp (https://github.com/OpenGene/fastp) to filter out low-quality data.
We used the reads alignment tool bowtie2 (version 2.2.8) to align the Clean Reads to the ribosomes of this species. We removed the reads that aligned to ribosomal RNA and retained the remaining data for subsequent analysis.
We will compare the reads after removing ribosomal RNA and perform BLAST comparisons with the GenBank and Rfam databases to identify and remove tRNAs, snRNAs, miRNAs, and snoRNAs from the samples as much as possible.
Assembly: hg38
Supplementary files format and content: tabe-delimited text file includes raw counts for each sample
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

extract_protocol:
Ribosome-bound nascent peptide chain complexes were treated with low-concentration RNase to degrade the RNA segments not covered by ribosomes, and then the ribosomes were removed.
RNA libraries were prepared by NEBNext UltraTM RNA Library Prep Kit following the manufacturers' protocols.

value: vector plasmid


title: MEL Mtg16 dTAGV1 15m A

description:
Library name: PROSeq_dTAGV1_15m_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014796-H-F07

description:
Library name: DSP-1001660014796-H-F07
GEOMX RNA-seq

value: WTA slide#4 071323


title: V-2-RIBO

description: Library name: Sample 6


title: DSP-1001660014796-H-F06

description:
Library name: DSP-1001660014796-H-F06
GEOMX RNA-seq


title: MB from animal_44

description:
Library name: NSM1413
3 lvl sciRNAseq


title: V-1-RIBO

description: Library name: Sample 5


title: DSP-1001660014796-H-E07

description:
Library name: DSP-1001660014796-H-E07
GEOMX RNA-seq

value: Segment 1


title: MB from animal_43

description:
Library name: NSM1412
3 lvl sciRNAseq


title: MEL Mtg16 DMSO B

description:
Library name: PROSeq_dTAGV1_0h_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: DMSO


title: F-4-RIBO

description: Library name: Sample 4

value: FTO overexpression


title: MEL Mtg16 DMSO C

description:
Library name: PROSeq_dTAGV1_0h_3
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: DSP-1001660014796-H-E01

description:
Library name: DSP-1001660014796-H-E01
GEOMX RNA-seq

value: FALSE


title: MB from animal_42

description:
Library name: NSM1411
3 lvl sciRNAseq


title: MEL Mtg16 DMSO A

description:
Library name: PROSeq_dTAGV1_0h_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt


title: F-3-RIBO

description: Library name: Sample 3

value: blood vessel


title: DSP-1001660014796-H-D12

description:
Library name: DSP-1001660014796-H-D12
GEOMX RNA-seq


title: MB from animal_41

description:
Library name: NSM1410
3 lvl sciRNAseq


title: D1 MOR FEMALE, BIO REPLICATE 4

first: Dana

last: Zeid

address: 1701 North 13th St

institute: Temple University

description: Library name: Blue17

data_processing:
Adaptors were trimmed from raw sequencing reads using TrimGalore software
Trimmed reads were mapped to the GRCr8 rat genome using Kallisto
Kallisto abundance estimates were imported into R software using the tximport package and analyzed using the DESeq2 package.
Assembly: GRCr8
Supplementary files format and content: tab delimited text file ("Normalized_counts.txt") contains normalized kallisto counts

organism: Rattus norvegicus

source_name: Brain tissue (ventral tegmental area)

extract_protocol:
Brain tissue was dissected from adult (postnatal day 60+) rats: Immediately after euthanasia via decapitation, whole brains were removed and sectioned on a 1mM brain block. VTA punches were quickly micro dissected & flash frozen on dry ice. Total RNA was isolated using a Qiazol/chloroform procedure and purified using the Qiagen RNeasy Micro kit.
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit per manufacturer instructions

value: Brain tissue (ventral tegmental area)

tag: Sex

value: Female

tag: experimental group

value: Day1 MOR ABS


title: DSP-1001660014796-H-D10

description:
Library name: DSP-1001660014796-H-D10
GEOMX RNA-seq

tag: tissue

value: cutaneous KS tumor


title: MB from animal_40

description:
Library name: NSM1409
3 lvl sciRNAseq


title: Saline FEMALE, BIO REPLICATE 6

description: Library name: Blue15

value: Saline


title: F-1-RIBO

description: Library name: Sample 1

tag: cell line

value: HUVEC

value: umbilical vein endothelial cell


title: F-2-RIBO

description: Library name: Sample 2

tag: cell type


title: DSP-1001660014796-H-D09

description:
Library name: DSP-1001660014796-H-D09
GEOMX RNA-seq

value: Biopsy

value: Full ROI

value: vessel


title: MB from animal_39

description:
Library name: NSM1408
3 lvl sciRNAseq

value: midbrain


title: F-4-IP

description:
Library name: Fto-4-IP
F.txt

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: hg38
Supplementary files format and content: tabe-delimited text file includes raw peaks for each sample
Library strategy: MeRIP-Seq

extract_protocol:
RNA was harvested using Trjzol (Thermo Fisher). 5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions.


title: MB from animal_37

description:
Library name: NSM1407
3 lvl sciRNAseq


title: DSP-1001660014796-H-D08

description:
Library name: DSP-1001660014796-H-D08
GEOMX RNA-seq

value: WTA slide#4 071323

value: tumor


title: D30 MOR MALE, BIO REPLICATE 7

description: Library name: 534

value: Male

value: Day30 MOR ABS


title: F-3-IP

description:
Library name: Fto-3-IP
F.txt

value: FTO overexpression


title: DSP-1001660014796-H-D07

description:
Library name: DSP-1001660014796-H-D07
GEOMX RNA-seq

value: FALSE


title: D30 MOR MALE, BIO REPLICATE 6

description: Library name: 510

value: Brain tissue (ventral tegmental area)


title: F-2-IP

description:
Library name: Fto-2-IP
F.txt

value: blood vessel


title: DSP-1001660014796-H-D06

description:
Library name: DSP-1001660014796-H-D06
GEOMX RNA-seq

value: Segment 1


title: MB from animal_53

description:
Library name: NSM1422
3 lvl sciRNAseq


title: DSP-1001660014796-H-G03

description:
Library name: DSP-1001660014796-H-G03
GEOMX RNA-seq

value: cutaneous KS tumor


title: DSP-1001660014796-H-G02

description:
Library name: DSP-1001660014796-H-G02
GEOMX RNA-seq


title: MEL Mtg16 A485 2h A

description:
Library name: PROSeq_dTAGV1_2h_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: Saline FEMALE, BIO REPLICATE 5

description: Library name: 484

value: Female

value: Saline


title: MB from animal_35

description:
Library name: NSM1405
3 lvl sciRNAseq


title: DSP-1001660014796-H-C06

description:
Library name: DSP-1001660014796-H-C06
GEOMX RNA-seq

value: Biopsy

value: WTA slide#3 071323

value: Full ROI


title: F-1-IP

description:
Library name: Fto-1-IP
F.txt

value: HUVEC

value: umbilical vein endothelial cell


title: Saline MALE, BIO REPLICATE 8

description: Library name: 468

value: Male


title: MB from animal_34

description:
Library name: NSM1404
3 lvl sciRNAseq

value: midbrain


title: MB from animal_33

description:
Library name: NSM1403
3 lvl sciRNAseq


title: D1 MOR MALE, BIO REPLICATE 9

description: Library name: 453

value: Day1 MOR ABS


title: DSP-1001660014796-H-C05

description:
Library name: DSP-1001660014796-H-C05
GEOMX RNA-seq

value: vessel

value: FALSE


title: V-4-IP

description:
Library name: Vec-4-IP
V.txt

value: blood vessel

value: vector plasmid


title: V-3-IP

description:
Library name: Vec-3-IP
V.txt


title: DSP-1001660014796-H-C04

description:
Library name: DSP-1001660014796-H-C04
GEOMX RNA-seq

value: cutaneous KS tumor


title: MEL Mtg16 dTAGV1 30m B

description:
Library name: PROSeq_dTAGV1_30m_2
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12168-JE_deseq_normcounts_table_fulltimecourse.txt
12168-JE_dREG_deseq_normcounts_alltimepoints.txt

value: MEL Mtg16-FKBP-2XHA

value: dTAGV1 30m


title: MB from animal_32

description:
Library name: NSM1402
3 lvl sciRNAseq


title: D1 MOR MALE, BIO REPLICATE 8

description: Library name: 451

value: Brain tissue (ventral tegmental area)


title: V-2-IP

description:
Library name: Vec-2-IP
V.txt


title: DSP-1001660014796-H-C03

description:
Library name: DSP-1001660014796-H-C03
GEOMX RNA-seq


title: MB from animal_31

description:
Library name: NSM1401
3 lvl sciRNAseq


title: Saline MALE, BIO REPLICATE 7

description: Library name: 437

value: Saline


title: DSP-1001660014796-H-C02

description:
Library name: DSP-1001660014796-H-C02
GEOMX RNA-seq

value: Biopsy

value: Segment 1

value: tumor


title: DSP-1001660014796-H-F08

description:
Library name: DSP-1001660014796-H-F08
GEOMX RNA-seq

value: WTA slide#4 071323

value: Full ROI


title: F-4-Input

description:
Library name: Fto-4-Input
F.txt

value: HUVEC

value: umbilical vein endothelial cell

value: FTO overexpression


title: Saline MALE, BIO REPLICATE 6

description: Library name: 435

value: Male


title: MB from animal_30

description:
Library name: NSM1400
3 lvl sciRNAseq

value: midbrain


title: MB from animal_29

description:
Library name: NSM1399
3 lvl sciRNAseq


title: DSP-1001660014796-H-C01

description:
Library name: DSP-1001660014796-H-C01
GEOMX RNA-seq

value: WTA slide#3 071323

value: FALSE


title: D30 MOR FEMALE, BIO REPLICATE 5

description: Library name: 430

value: Female

value: Day30 MOR ABS


title: F-3-Input

description:
Library name: Fto-3-Input
F.txt

value: blood vessel


title: DSP-1001660014796-H-B12

description:
Library name: DSP-1001660014796-H-B12
GEOMX RNA-seq

value: cutaneous KS tumor


title: MB from animal_28

description:
Library name: NSM1398
3 lvl sciRNAseq


title: Saline FEMALE, BIO REPLICATE 4

description: Library name: 429

value: Brain tissue (ventral tegmental area)

value: Saline


title: MB from animal_45

description:
Library name: NSM1414
3 lvl sciRNAseq


title: DSP-1001660014796-H-B11

description:
Library name: DSP-1001660014796-H-B11
GEOMX RNA-seq

value: Biopsy


title: Saline FEMALE, BIO REPLICATE 3

description: Library name: 427


title: MB from animal_27

description:
Library name: NSM1397
3 lvl sciRNAseq


title: F-1-Input

description:
Library name: Fto-1-Input
F.txt


title: MB from animal_26

description:
Library name: NSM1396
3 lvl sciRNAseq


title: DSP-1001660014796-H-B10

description:
Library name: DSP-1001660014796-H-B10
GEOMX RNA-seq

value: Segment 1

value: tumor


title: V-4-Input

description:
Library name: Vec-4-Input
V.txt

value: vector plasmid


title: Saline FEMALE, BIO REPLICATE 2

description: Library name: 413


title: DSP-1001660014796-H-B09

description:
Library name: DSP-1001660014796-H-B09
GEOMX RNA-seq


title: MB from animal_25

description:
Library name: NSM1395
3 lvl sciRNAseq


title: F-2-Input

description:
Library name: Fto-2-Input
F.txt

value: HUVEC


title: D30 MOR FEMALE, BIO REPLICATE 4

description: Library name: 406


title: V-3-Input

description:
Library name: Vec-3-Input
V.txt

value: umbilical vein endothelial cell


title: MB from animal_24

description:
Library name: NSM1394
3 lvl sciRNAseq


title: DSP-1001660014796-H-B08

description:
Library name: DSP-1001660014796-H-B08
GEOMX RNA-seq


title: V-1-IP

description:
Library name: Vec-1-IP
V.txt


title: D30 MOR FEMALE, BIO REPLICATE 3

description: Library name: 399


title: V-2-Input

description:
Library name: Vec-2-Input
V.txt


title: DSP-1001660014796-H-B07

description:
Library name: DSP-1001660014796-H-B07
GEOMX RNA-seq


title: D30 MOR FEMALE, BIO REPLICATE 2

description: Library name: 373


title: MB from animal_23

description:
Library name: NSM1393
3 lvl sciRNAseq


title: V-1-Input

description:
Library name: Vec-1-Input
V.txt


title: MB from animal_22

description:
Library name: NSM1392
3 lvl sciRNAseq


title: H-HIF_2-Hypoxia

description: Library name: Samples 2

data_processing:
We conducted bioinformatics analysis on the raw sequencing data obtained after sequencing completion, including sequencing data quality assessment, reference sequence alignment, identification of open chromatin sites peaks, and functional annotation analysis. The sequencing data quality assessment can quickly determine whether the data has quality issues, allowing for the selection of high-quality data for further analysis. Reference sequence alignment involves comparing the quality-controlled sequences to the reference genome, followed by statistical analysis of the alignment results. Then, open chromatin site peak identification is carried out, and subsequent functional annotation and motif analysis of the peaks are conducted. Further, differential peak analysis and annotation between groups and other subsequent analyses are performed.
Assembly: hg38
Supplementary files format and content: tabe-delimited text file includes raw peaks for each sample
Library strategy: CUT&Tag

extract_protocol:
After corresponding treatment, HUVEC at a density of 10^5 cells were collected.
HUVEC at a density of 10^5 cells were bound to magnetic beads, and digitonin was added to penetrate the cell membrane. Then the anti-HIF2α antibody, ChiTag goat anti-rabbit IgG antibody, and pAG-Tn5 were desiccated and segmented successively. The reaction products were collected by DNA Clean Beads and enriched by PCR to construct the next-generation sequencing library.

value: stroke plasma collected from patients with ischemic stroke at 1 day

tag: cut&tag antibody


title: D1 MOR MALE, BIO REPLICATE 7

description: Library name: 333

value: Male

value: Day1 MOR ABS


title: DSP-1001660014796-H-B06

description:
Library name: DSP-1001660014796-H-B06
GEOMX RNA-seq

value: WTA slide#3 071323


title: DSP-1001660014796-H-B05

description:
Library name: DSP-1001660014796-H-B05
GEOMX RNA-seq

value: Full ROI

value: FALSE


title: MB from animal_21

description:
Library name: NSM1391
3 lvl sciRNAseq

value: midbrain


title: Saline MALE, BIO REPLICATE 5

description: Library name: 330


title: H-HIF_2-Normal

description: Library name: Samples 1

value: blood vessel

tag: treatment

value: control


title: DSP-1001660014796-H-B03

description:
Library name: DSP-1001660014796-H-B03
GEOMX RNA-seq

value: cutaneous KS tumor


title: MB from animal_20

description:
Library name: NSM1390
3 lvl sciRNAseq


title: D1 MOR FEMALE, BIO REPLICATE 3

description: Library name: Blue14

value: Brain tissue (ventral tegmental area)

value: Female


title: Saline MALE, BIO REPLICATE 4

description: Library name: 329

value: Saline


title: Cytokines + Virus 2

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: CytVir2

data_processing:
We used HISAT2 [2] to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/.
Assembly: hg38
Supplementary files format and content: Microsoft Excel file contains raw counts for each sample

source_name: skin

extract_protocol:
Quagene meRnaeasy mini-kit
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.
RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification.
After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

value: skin

value: keratinocyte cell line 2

value: normal neonatal keratinocytes

value: Cytokines followed by Virus aplication


title: MB from animal_19

description:
Library name: NSM1389
3 lvl sciRNAseq


title: D1 MOR MALE, BIO REPLICATE 6

description: Library name: 323


title: DSP-1001660014796-H-B02

description:
Library name: DSP-1001660014796-H-B02
GEOMX RNA-seq

value: Biopsy

value: tumor


title: DSP-1001660014796-H-B01

description:
Library name: DSP-1001660014796-H-B01
GEOMX RNA-seq

value: vessel


title: Cytokines 2

description: Library name: Cyt2

value: Cytokines


title: Virus 2

description: Library name: Vir2

value: Lentivirus application


title: MB from animal_18

description:
Library name: NSM1388
3 lvl sciRNAseq


title: D1 MOR MALE, BIO REPLICATE 5

description: Library name: 322

value: Male

value: Day1 MOR ABS


title: DSP-1001660014796-H-A12

description:
Library name: DSP-1001660014796-H-A12
GEOMX RNA-seq

value: WTA slide#3 071323

value: Segment 1

value: FALSE


title: MB from animal_16

description:
Library name: NSM1387
3 lvl sciRNAseq

value: midbrain


title: MB from animal_36

description:
Library name: NSM1406
3 lvl sciRNAseq


title: Saline MALE, BIO REPLICATE 3

description: Library name: 321

value: Brain tissue (ventral tegmental area)


title: miRFP670nano-IL-1b_5

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw data were checked for quality, adapter content and duplication rates using FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: human umbilical vein endothelial cells

extract_protocol:
Cells were lysed in a lysis buffer containing Tris-HCl pH7.5 (50mM, Applichem, Germany), NaCl (150mM, Merck, Darmstadt, Germany), MgCl2,(10mM, Invitrogen, Schwerte, Germany), NP-40 (1%, Merck) dissolved in UltraPure DNase/RNase-free DW (Invitrogen) and supplemented with NaPPi (10mM, Merck), NaF (20mM, Applichem, Germany), okadaic acid (10nM, LC laboratory, USA), Na3VO4 (2mM, Sigma-Aldrich), protease inhibitor mix, (12µl/ml, Sigma-Aldrich), PMSF (4µl/ml, Carl Roth, Germany), SUPERase In RNase Inhibitor (200U/ml, Invitrogen), TURBO DNaseI (25U/ml, Invitrogen). Total RNA was purified using the miRNeasy Micro kit (QIAGEN), according to the manufacturer’s instructions.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 0.5-1µg of total RNA was used as input for Corall Total RNA-Seq Library Prep Kit following manufacture’s instructions (Lexogen). Sequencing was performed on the NextSeq2000 instrument (Illumina) using P3 flowcell and 1x72bp single end setup.

value: human umbilical vein endothelial cells

tag: overexpression


title: D1 MOR FEMALE, BIO REPLICATE 2

description: Library name: 285

value: Female


title: Cytokines + Virus 1

description: Library name: CytVir1

value: skin

value: keratinocyte cell line 1


title: MB from animal_14

description:
Library name: NSM1386
3 lvl sciRNAseq


title: MB from animal_12

description:
Library name: NSM1385
3 lvl sciRNAseq


title: D30 MOR MALE, BIO REPLICATE 5

description: Library name: 241

value: Day30 MOR ABS


title: Cytokines 1

description: Library name: Cyt1

value: normal neonatal keratinocytes


title: MB from animal_11

description:
Library name: NSM1384
3 lvl sciRNAseq


title: D1 MOR MALE, BIO REPLICATE 4

description: Library name: 233


title: miRFP670nano-IL-1b_2


title: Virus 1

description: Library name: Vir1


title: Control  1

description: Library name: Con1

value: Vehicle control (0.4% BSA)


title: D30 MOR MALE, BIO REPLICATE 4

description: Library name: 231


title: MB from animal_7

description:
Library name: NSM1382
3 lvl sciRNAseq


title: MB from animal_9

description:
Library name: NSM1383
3 lvl sciRNAseq


title: T26_0123

city: Tübingen

first: Daniel

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

description: Library name: 24048a026

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

source_name: meningioma

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

value: meningioma

tag: batch

value: METHhigh


title: D1 MOR FEMALE, BIO REPLICATE 1

description: Library name: 224


title: miRFP670nano-solvent_5

value: solvent


title: MB from animal_5

description:
Library name: NSM1381
3 lvl sciRNAseq


title: D30 MOR FEMALE, BIO REPLICATE 1

description: Library name: 222


title: T26_0058

description: Library name: 24048a025


title: miRFP670nano-solvent_4


title: MB from animal_4

description:
Library name: NSM1380
3 lvl sciRNAseq


title: T26_0072

description: Library name: 24048a022


title: D30 MOR MALE, BIO REPLICATE 3

description: Library name: 212

value: Male


title: miRFP670nano-solvent_3


title: D30 MOR MALE, BIO REPLICATE 2

description: Library name: 210


title: miRFP670nano-solvent_2


title: T26_0175

description: Library name: 24048a020


title: MB from animal_2

description:
Library name: NSM1378
3 lvl sciRNAseq


title: T26_0076

description: Library name: 24048a018


title: Saline MALE, BIO REPLICATE 2

description: Library name: 206

value: Saline


title: MB from animal_1

description:
Library name: NSM1377
3 lvl sciRNAseq


title: miP-PSTPIP2-IL-1b_4


title: Saline FEMALE, BIO REPLICATE 1

description: Library name: 195


title: mdTN from animal_55, rep2

description:
Library name: NSM1376-b2
3 lvl sciRNAseq

source_name: mediodorsal thalamic nucleus

value: mediodorsal thalamic nucleus


title: T26_0016

description: Library name: 24048a006

value: METHlow


title: D30 MOR MALE, BIO REPLICATE 1

description: Library name: 178


title: mdTN from animal_54, rep2

description:
Library name: NSM1375-b2
3 lvl sciRNAseq


title: Saline MALE, BIO REPLICATE 1

description: Library name: 190


title: miP-PSTPIP2-IL-1b_2


title: T26_0061

description: Library name: 24048a005


title: mdTN from animal_54

description:
Library name: NSM1375
3 lvl sciRNAseq


title: miP-PSTPIP2-IL-1b_1


title: D1 MOR MALE, BIO REPLICATE 2

description: Library name: 172

value: Day1 MOR ABS


title: miP-PSTPIP2-solvent_4


title: T26_0094

description: Library name: 24048a002


title: mdTN from animal_53, rep2

description:
Library name: NSM1374-b2
3 lvl sciRNAseq


title: D1 MOR MALE, BIO REPLICATE 1

description: Library name: 103


title: IPO5-2

city: Suzhou

first: Xingchen

last: Yao

state: Jiangsu

address: No 100 Chongwen Road Suzhou Industrial Park, Suzhou

institute: Suzhou Institute of Systems Medicine   Chinese Academy of Medical Sciences

description:
Library name: Semple4
RNA immunoprecipitation sequencing (RIP-seq) was performed in HeLa cells using IPO5 or IgG control antibodies. Total RNA enriched by RIP was fragmented and sequenced using small RNA library preparation. Libraries were sequenced on Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

data_processing:
Raw reads were quality-checked using FastQC (v0.11.9).
Adapter trimming and low-quality read removal were performed using Cutadapt (v3.4).
Clean reads were aligned to the human genome (GRCh38/hg38) using STAR aligner (v2.7.10a) with default parameters.
Read counts were generated using featureCounts (subread v2.0.3) based on GENCODE v38 gene annotations.
Counts were normalized to Reads Per Million (RPM) for downstream analysis.
Assembly: GRCh38 / hg38
Supplementary files format and content: The processed data file contains RIP-seq peak annotation results generated using the annotatePeaks.pl script from HOMER. The file is a tab-delimited text table listing peaks enriched in IPO5 RIP-seq samples mapped to the human transcriptome (hg38 assembly). Each row represents a peak and includes genomic coordinates, peak score, annotation details, and associated gene information. Column headers include: PeakID, chromosome (Chr), start and end positions, strand, peak score, focus ratio/region size, gene annotation, detailed annotation, distance to transcription start site (TSS), nearest promoter ID, Entrez ID, RefSeq and Ensembl gene IDs, gene symbol, gene alias, gene description, and gene type.

source_name: HeLa (a human cervical cancer cell line)

growth_protocol: HeLa cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
HeLa cells were lysed using IP lysis buffer (150 mM NaCl, 10 mM Tris-HCl pH 7.4, 1% NP-40, protease and RNase inhibitors). The lysates was then subjected to ultrasonic fragmentation at high power, 30 seconds on/30 seconds off for 10 cycles at 4°C. Cell lysates were incubated with antibody-conjugated magnetic beads overnight at 4°C. After immunoprecipitation, RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA fragments were end-repaired and ligated with 3' and 5' adapters using the Small RNA-seq Library Preparation Kit for Illumina V3 (ABclonal, RK20312) and indexed using the Small RNA Adapter Module 96 Index (ABclonal, RK20358), following the manufacturer's instructions. cDNA was synthesized and PCR-amplified to generate sequencing-ready libraries.

treatment_protocol: No treatment was applied prior to RIP. Cells were collected at 70–80% confluence for immunoprecipitation.


title: miP-PSTPIP2-solvent_3