title: s27_S27_ME_L001_case_minus6

description:
Library name: s27_S27_ME_L001
Plasma derived extracellular vesicle RNA


title: s26_S26_ME_L001_control_minus6

status: Public on Jan 20 2026

type: SRA

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

description:
Library name: s26_S26_ME_L001
Plasma derived extracellular vesicle RNA

library_source: transcriptomic

data_processing:
RNAseq reads were quantified using Salmon
EdgeR was used to normalize read counts for sequencing depth and gene length
Assembly: Homo Sapiens GRch38.104
Supplementary files format and content: supplementary file containing data in the units of counts per million (CPM)

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
RNA was extracted using Isolate II RNA kit (Bioline) following Manufacturer’s instructions
Library preparation was performed using NEBNext Ultra II FS DNA Library Prep Kit following manufacturer’s instructions

tag: tissue

value: Plasma

tag: treatment


title: 1646a1576c0fa12f;PLACEBO

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 1646a1576c0fa12f

data_processing:
Reads from all samples were processed using the MoTrPAC RNA-Seq pipeline
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts for each sample

source_name: Whole Blood

extract_protocol:
Human total RNA from blood (collected in PAXgene tubes, http://www.bdbiosciences.com/us/applications/blood-collection/cell-biomarker-preservation/paxgenereg-blood-rna-tube/p/762165) was extracted using the Agencourt RNAdvance blood kit (Beckman Coulter) on an automated Biomek Fxp workstation (Beckman Coulter).The purity of the RNA was assessed using a NanoDrop (Thermo Fisher Scientific) and quantified with the Quant-iT RiboGreen RNA Assay kit (Thermo Fisher Scientific). RNA integrity (RIN) was measured using the RNA Nano 6000 Assay kit on an Agilent Bioanalyzer 2100 system (Agilent Technologies) and the samples with RIN above 7.0 were processed to libraries.
The mRNA libraries were prepared using the Universal Plus mRNA-Seq Library preparation kit (NuGEN) on an automated Biomek i7 workstation (Beckman Coulter). In brief, mRNA was purified from 400 ng of total RNA using oligo-dT beads, and cDNA was synthesized according to NuGEN’s protocol. The AnyDeplete kit (NuGEN) was used to remove ribosomal RNA (rRNA) and globin transcripts before library amplification. The purified libraries were quantified with the Qubit dsDNA HS kit (Thermo Fisher Scientific), and their size and distribution were analyzed using a Bioanalyzer with the High Sensitivity DNA kit (Agilent). After library preparation, samples were pooled, and library integrity was verified by sequencing on an Illumina MiSeq. Deep sequencing was then conducted on a NovaSeq 6000 (Illumina, Inc., San Diego, CA), with an average depth of 30 million 100 bp paired-end reads per sample.

value: Whole Blood

value: PLACEBO


title: s25_S25_ME_L001_control_minus6

description:
Library name: s25_S25_ME_L001
Plasma derived extracellular vesicle RNA


title: s24_S24_ME_L001_control_minus6

description:
Library name: s24_S24_ME_L001
Plasma derived extracellular vesicle RNA


title: 15e42366369da6c9;MVA-NP+M1

description: Library name: 15e42366369da6c9


title: 197e1f3a10d58439;PLACEBO

description: Library name: 197e1f3a10d58439


title: s22_S22_ME_L001_control_minus6

description:
Library name: s22_S22_ME_L001
Plasma derived extracellular vesicle RNA


title: 15a8c2d2a9fca0d5;PLACEBO

description: Library name: 15a8c2d2a9fca0d5


title: s23_S23_ME_L001_control_minus6

description:
Library name: s23_S23_ME_L001
Plasma derived extracellular vesicle RNA


title: s2_S2_ME_L001_case_minus6

description:
Library name: s2_S2_ME_L001
Plasma derived extracellular vesicle RNA


title: 151e80df75e5200f;PLACEBO

description: Library name: 151e80df75e5200f


title: 143e296c8f2db6c8;MVA-NP+M1

description: Library name: 143e296c8f2db6c8


title: 147197092062681e;MVA-NP+M1

description: Library name: 147197092062681e


title: 1562d8499d605599;PLACEBO

description: Library name: 1562d8499d605599


title: 175275783c5e6f05;MVA-NP+M1

description: Library name: 175275783c5e6f05


title: 16bae7ddc6151b83;PLACEBO

description: Library name: 16bae7ddc6151b83


title: 13f1446e037c28f8;PLACEBO

description: Library name: 13f1446e037c28f8


title: s18_S18_ME_L001_control_minus6

description:
Library name: s18_S18_ME_L001
Plasma derived extracellular vesicle RNA


title: 15d2c225505ec6be;MVA-NP+M1

description: Library name: 15d2c225505ec6be


title: s17_S17_ME_L001_control_minus6

description:
Library name: s17_S17_ME_L001
Plasma derived extracellular vesicle RNA


title: 135185ef80fe9190;MVA-NP+M1

description: Library name: 135185ef80fe9190


title: 131bb9a6e3fe11ae;MVA-NP+M1

description: Library name: 131bb9a6e3fe11ae


title: s19_S19_ME_L001_case_minus6

description:
Library name: s19_S19_ME_L001
Plasma derived extracellular vesicle RNA


title: 1319cfda94302523;PLACEBO

description: Library name: 1319cfda94302523


title: 12fda1d05619b4a4;PLACEBO

description: Library name: 12fda1d05619b4a4


title: s16_S16_ME_L001_case_minus3

description:
Library name: s16_S16_ME_L001
Plasma derived extracellular vesicle RNA


title: s14_S14_ME_L001_control_minus6

description:
Library name: s14_S14_ME_L001
Plasma derived extracellular vesicle RNA


title: 12fa1f3ec21f9dab;MVA-NP+M1

description: Library name: 12fa1f3ec21f9dab


title: s20_S20_ME_L001_control_minus6

description:
Library name: s20_S20_ME_L001
Plasma derived extracellular vesicle RNA


title: 11d4f2c6c2c1f07e;MVA-NP+M1

description: Library name: 11d4f2c6c2c1f07e


title: s15_S15_ME_L001_case_minus6

description:
Library name: s15_S15_ME_L001
Plasma derived extracellular vesicle RNA


title: s11_S11_ME_L001_control_minus6

description:
Library name: s11_S11_ME_L001
Plasma derived extracellular vesicle RNA


title: 114e82e4b1851bd4;PLACEBO

description: Library name: 114e82e4b1851bd4


title: s10_S10_ME_L001_control_minus6

description:
Library name: s10_S10_ME_L001
Plasma derived extracellular vesicle RNA


title: s1_S1_ME_L001_control_minus6

description:
Library name: s1_S1_ME_L001
Plasma derived extracellular vesicle RNA


title: 119c7937ce225cff;MVA-NP+M1

description: Library name: 119c7937ce225cff


title: s21_S21_ME_L001_control_minus6

description:
Library name: s21_S21_ME_L001
Plasma derived extracellular vesicle RNA


title: 1073b0b631b9ca12;PLACEBO

description: Library name: 1073b0b631b9ca12


title: s13_S13_ME_L001_control_minus6

description:
Library name: s13_S13_ME_L001
Plasma derived extracellular vesicle RNA


title: 10781c329e54f0d7;MVA-NP+M1

description: Library name: 10781c329e54f0d7


title: 109cbcd0c71bb448;MVA-NP+M1

description: Library name: 109cbcd0c71bb448


title: 0febaa76a12a5fae;MVA-NP+M1

description: Library name: 0febaa76a12a5fae


title: 1030ad00d7f1ca46;PLACEBO

description: Library name: 1030ad00d7f1ca46


title: SR_Tumor

type: RNA

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

hyb_protocol: Hybridization was carried out following manufacturer's instructions.

data_processing: Data were analyzed using ROSALIND Platform for nCounter Analysis software (ROSALIND, San Diego, CA)

organism: Canis lupus familiaris

source_name: Primary bladder tumor

label_protocol: Purified RNA samples were submitted for hybridization nCounter analysis at the Stark Neurosciences Research Institute Biomarker Core (SNRI) at the Indiana University School of Medicine (Indianapolis, Indiana). Briefly, samples were hybridized with gene-specific reporter and capture probes comprising the 800-gene nCounter Canine Immuno-oncology (IO) Panel code sets (NanoString Technologies, Seattle, WA).

extract_protocol: All canine samples were collected with the approval of the Purdue Animal Care and Use Committee (protocol approval #1111000124). Tumor tissues and urine samples were obtained via cystoscopy from dogs with histologically confirmed InvUC. Paired tumor and urine samples from each individual were collected concurrently during the procedure. Control bladder mucosa samples had been collected immediately post-mortem from dogs euthanized with no evidence of urinary tract disease as part of an earlier study.  Free catch control urine sediment samples were collected from healthy dogs, all of which were screened for urinary tract disease with urinalysis and urinary tract ultrasound. Tumor samples were stored in trizol at -80o and urine sediment samples were snap frozen and stored at -80.tal RNA was isolated and purified from all tissue and urine sediment samples according to manufacturer instructions using the AllPrep DNA/RNA Micro Kit (Qiagen, Valencia, CA).

value: InvUC tumor sample


title: 104459e43b97ca4a;PLACEBO

description: Library name: 104459e43b97ca4a


title: 1199e9b0858826be;MVA-NP+M1

description: Library name: 1199e9b0858826be


title: 124c461e040719d0;MVA-NP+M1

description: Library name: 124c461e040719d0


title: 0fb2da4f4bd4a775;PLACEBO

description: Library name: 0fb2da4f4bd4a775


title: SS_Tumor


title: FT_Urine

value: urine sediment from dogs with InvUC


title: s12_S12_ME_L001_case_minus6

description:
Library name: s12_S12_ME_L001
Plasma derived extracellular vesicle RNA


title: ToMe_Tumor


title: B

value: normal canine bladder mucosa


title: CR_Tumor


title: 0faba4d38d2222f8;PLACEBO

description: Library name: 0faba4d38d2222f8


title: A


title: 0eca07d97abb1b9f;PLACEBO

description: Library name: 0eca07d97abb1b9f


title: 0d8277e38162ec17;PLACEBO

description: Library name: 0d8277e38162ec17


title: D


title: 0d37fe6299d3eeb8;PLACEBO

description: Library name: 0d37fe6299d3eeb8


title: 0d6a9e09785618ce;MVA-NP+M1

description: Library name: 0d6a9e09785618ce


title: TM_Urine


title: C


title: 0ff334c7cead1d4d;MVA-NP+M1

description: Library name: 0ff334c7cead1d4d


title: 0cbf1e04801d6422;MVA-NP+M1

description: Library name: 0cbf1e04801d6422


title: 0ccdb3d92d944be4;MVA-NP+M1

description: Library name: 0ccdb3d92d944be4


title: FT_Tumor


title: FH_Tumor


title: JL_Urine


title: 0c8745b41b897fee;PLACEBO

description: Library name: 0c8745b41b897fee


title: 0c18067bcba2ab20;MVA-NP+M1

description: Library name: 0c18067bcba2ab20


title: ToMe_Urine


title: 0baf9ba5e9f23cd3;MVA-NP+M1

description: Library name: 0baf9ba5e9f23cd3


title: RA_Urine


title: 09cf8937ebfbba4d;MVA-NP+M1

description: Library name: 09cf8937ebfbba4d


title: 0b5c1e9933cf80fb;MVA-NP+M1

description: Library name: 0b5c1e9933cf80fb


title: SR_Urine


title: BL_Urine


title: CS_Urine


title: Bf_Urine


title: 089d687a754370dc;MVA-NP+M1

description: Library name: 089d687a754370dc


title: PB_Urine


title: 084a8cd1616beb02;MVA-NP+M1

description: Library name: 084a8cd1616beb02


title: FH_Urine


title: 081c04b0b4542c9b;MVA-NP+M1

description: Library name: 081c04b0b4542c9b


title: TF

value: normal canine urine sediment


title: 0b1aced867721eb3;MVA-NP+M1

description: Library name: 0b1aced867721eb3


title: 06572c2f69e913fb;MVA-NP+M1

description: Library name: 06572c2f69e913fb


title: 09c09356b26dfcde;MVA-NP+M1

description: Library name: 09c09356b26dfcde


title: HA_Tumor


title: 0747f3fbb31dd106;MVA-NP+M1

description: Library name: 0747f3fbb31dd106


title: MS_Urine


title: MW_Urine


title: 061455084e2d2691;PLACEBO

description: Library name: 061455084e2d2691


title: 05e1bbe87158bfb8;PLACEBO

description: Library name: 05e1bbe87158bfb8


title: 06e4c24e47ce5df2;MVA-NP+M1

description: Library name: 06e4c24e47ce5df2


title: 0640e05f437dcbf3;PLACEBO

description: Library name: 0640e05f437dcbf3


title: HA_Urine


title: 0789448ff8f6c49c;MVA-NP+M1

description: Library name: 0789448ff8f6c49c


title: BMc_Urine


title: TT_Tumor


title: ZP_Tumor


title: 05b925b49f2c5d5c;MVA-NP+M1

description: Library name: 05b925b49f2c5d5c


title: BD_Urine


title: 058abb1d9ac129aa;MVA-NP+M1

description: Library name: 058abb1d9ac129aa


title: 04e4f62d9bf4312d;MVA-NP+M1

description: Library name: 04e4f62d9bf4312d


title: RA_Tumor


title: SS_Urine


title: ZP_Urine


title: CR_Urine


title: 04647d61b617cc48;MVA-NP+M1

description: Library name: 04647d61b617cc48


title: PB_Tumor


title: 04803d20b3673502;MVA-NP+M1

description: Library name: 04803d20b3673502


title: 04fdbee96b2f481c;MVA-NP+M1

description: Library name: 04fdbee96b2f481c


title: 03ad899c27769efd;MVA-NP+M1

description: Library name: 03ad899c27769efd


title: Mc


title: Ez


title: 03356cac9ead2d01;MVA-NP+M1

description: Library name: 03356cac9ead2d01


title: Bo


title: 03a388c3810c13ad;MVA-NP+M1

description: Library name: 03a388c3810c13ad


title: 02eb9f2a99714382;MVA-NP+M1

description: Library name: 02eb9f2a99714382


title: Ch


title: 022f93c976ffa227;MVA-NP+M1

description: Library name: 022f93c976ffa227


title: 0187ef0ed3d8e480;PLACEBO

description: Library name: 0187ef0ed3d8e480


title: BD_Spiked_75_WBC

source_name: Primary bladder tumor_Spiked_75,920_WBC

value: InvUC tumor sample_Spiked_75,920_WBC


title: IB


title: CE


title: 015aca736e7f72ca;PLACEBO

description: Library name: 015aca736e7f72ca


title: Tw


title: 009fd7380abe4bc9;PLACEBO

description: Library name: 009fd7380abe4bc9


title: BD_Tumor)Unspiked

source_name: Primary bladder tumor_UnSpiked

value: InvUC tumor sample_UnSpiked


title: Gb


title: MS_Tumor


title: BD_Spiked_23_WBC

source_name: Primary bladder tumor_Spiked with 23,360_WBC

value: InvUC tumor sample_Spiked with 23,360_WBC


title: 007d361bbbaa0f0e;MVA-NP+M1

description: Library name: 007d361bbbaa0f0e


title: 006c1ffe74d25779;MVA-NP+M1

description: Library name: 006c1ffe74d25779


title: 0056cd3b25759d67;PLACEBO

description: Library name: 0056cd3b25759d67


title: 002758a3d112d3b1;MVA-NP+M1

description: Library name: 002758a3d112d3b1


title: 033173d5ba0d7740;PLACEBO

description: Library name: 033173d5ba0d7740


title: Post

city: Seoul

first: So-Jung

last: Choi

state: --- Select One ---

address: 103, Daehak-ro, Jongno-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National university

description:
Library name: SAMPLE1_P
10x Genomics

library_source: transcriptomic single cell

data_processing:
I used Cell Ranger software version 7.0.1.
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Skin

extract_protocol: Library was performed according to the manufacturer’s instructions (10x Genomics, Chromium Next GEM Single Cell 5' v2 protocol). Briefly, single cells, reagents, and 5' gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-scale Gel Beads-in-emulsion (GEMs). Within each GEM, cDNA was synthesized with a 5' gene expression library prep, which contains an Illumina R1 sequence, 10x Barcode, and Unique Molecular Identifier (UMI). Following GEM-RT, the barcoded cDNA was cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate size fragments were selected with SPRIselect reagent for library construction. During the library construction, P5 and P7 sequences, along with a sample index, were added, resulting in a final 5' gene expression library.

treatment_protocol: 1. Prepare Liberase dissociation solution (350 μl PBS, 50 μl 2 mg/ml Liberase TL) into 1.5 ml Eppendorf tube 2. Prepare 70 μm cell strainer over the 50 ml conical tube containing the 5 ml of FBS 3. Slice tissue into small pieces with scalpel in a petri-dish (remove subcutaneous tissue) 4. Transfer biopsy material into dissociation solution using a pipet tip or forcep 5. Sample and digestion buffer are combined with an incubation of 60 min in a 37°C water bath (1.5 ml) 6. Remove the tube from the water bath and using a 1 ml pipette with a wide bore to carefully pipette the biopsy up and down approximately 10 times to disperse the tissue. 7. Carefully remove all of the 400 μl of dissociation solution containing cells and small debris from the biopsy and strain on the strainer sited on the 50 ml conical tube containing 5 ml of FBS. 8. Apply 500 μl of PBS solution three times to the strainer and place 50ml tube on the ice 9. Repeat steps 3-9.  10. Prepare Trypsin dissociation solution (350 μl PBS, 50 μl 0.25% Trypsin or 400 ul 0.05% Trypsin) in 1.5 mL eppendorf tube 11. Add to residual biopsy tissue into Trypsin solution and incubate for 30 min in a 37 °C water bath. 12. Carefully remove the 400 μl of dissociation solution from the tube containing the biopsy and strain into the 50 ml conical tube containing FBS. Do not remove the partially digested biopsy from the tube. 13. Wash the strainer with 500 μl of PBS three times 14. Transfer the FBS from 50 mL tubes to 15 mL tubes 15. Centrifuge at 1140 rpm (300G) for 5 min, 4C 16. Suction leaving the pellet cells (100 uL), leave the supernatant in a separate tube. 17. Resuspend with 1ml of RPMI 18. Centrifuge at 980 rpm (220G) for 5 min-, 4C 19. Suction leaving the pellet cells (remove all supernatant) 20. Resuspend in 110 μl 0.04% BSA containing RPMI and transfer to a 1.5 ml Eppendorf tube.

value: Skin

tag: cell type

value: tisssue

value: treatment (guselkumab)

tag: batch


title: Bf_Tumor


title: 02978ad977ba5956;PLACEBO

description: Library name: 02978ad977ba5956


title: MW_Tumor


title: Non lesion

description:
Library name: SAMPLE1_NL
10x Genomics

value: non treatment


title: Lesion

description:
Library name: SAMPLE1_L
10x Genomics


title: TT_Urine


title: CS_Tumor


title: BL_Tumor


title: TM_Tumor


title: ARID1B_OE_3

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Library name: mr819t

data_processing:
Raw fastq files were aligned using STAR v2.6.0. Raw counts were calculated by STAR, FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt files of raw counts and FPKM values

source_name: Breast

growth_protocol: MDA-MB-468 breast cancer cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin sodium (100 U/mL), and streptomycin sulfate (100 µg/mL).

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA) following the manufacturer’s instructions.
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: MDA-MB-468 cells were treated with either DMSO, IPZ (10µM) for 24 hours, or BRMi (1µM) for 72 hours and then collected for RNA analysis.

value: Breast

tag: cell line

value: Breast cancer cell

tag: genotype


title: ARID1B_OE_2

description: Library name: mr818t


title: BMc_Tumor


title: ARID1B_OE_1

description: Library name: mr817t


title: ARID1B_KO_2

description: Library name: mr815t


title: Ak_Spiked_InvUCcells_WBC

source_name: Normal_Spiked_1 million InvUC cells_100k_WBC

value: Normal urine from control dogs_Spiked_1 million InvUC cells_100k_WBC


title: BD_Tumor


title: ARID1B_KO_3

description: Library name: mr816t


title: JL_Tumor


title: Ak_Spiked_InvUCcells

source_name: Normal_Spiked_1 million InvUC cells_0WBC

value: Normal urine from control dogs_Spiked_1 million InvUC cells_0WBC


title: Ak_Spiked_InvUCcells_10_WBC

source_name: Normal_Spiked_1 million InvUC cells_1 million_WBC

value: Normal urine from control dogs_Spiked_1 million InvUC cells_1 million_WBC


title: Ak_Unspiked

value: Normal urine from control dogs_Spiked_0T_0W


title: Macrophage, HFD, Ly6c- /Cd9-, rep 3

city: Philadelphia

first: David

last: Hill

state: PA

address: Abramson Research Building, 1208B, 3615 Civic Center Blvd.

department: Division of Allergy and Immunology

institute: Children's Hospital of Philadelphia

description: Library name: Sample 3

data_processing:
Bulk RNAseq reads were aligned to the GRCmm39/mm10 genome using the nf-core RNAseq pipeline version 3.14.0. In brief, FastQC was used to assess the quality of reads and Trim Galore! was used for adapter and quality trimming. Alignment was performed with STAR version 2.7.10a followed by quantification with RSEM version 1.3.1. Duplicates were removed using Picard MarkDuplicates. Low expression genes were filtered with the R package edgeR, followed by differential expression analysis
Assembly: GRCmm39/mm10 genome
Supplementary files format and content: CSV file containing log normalized counts per million (cpm) for each sample

organism: Mus musculus

source_name: ex vivo Adipose tissue macrophages

growth_protocol: Experiments were performed using sex and age-matched littermate controls. Mice were provided with ad libitum access to water and diet. Mice were fed a high fat diet containing 60 kcal% fat (Research Diets D12492, New Brunswick, NJ) from 6 to 18 weeks of age.

extract_protocol:
[ex vivo adipose tissue macrophages] For bulk RNA-seq of sort-purified cell populations, RNA was isolated using standard Trizol protocol.  [whole eWAT] Total RNA was isolated from snap-frozen tissue samples. RNA extraction was performed using the Maxwell RSC simply RNA Tissue Kit (Promega, AD1340). Briefly, tissue was homogenized in a Thioglycerol Homogenization Solution using the Maxwell RSC Instrument (Promega).
[ex vivo adipose tissue macrophages] For bulk RNA-seq of sort-purified cell populations, libraries were prepared using the SMARTer Stranded RNA-seq kit (Clontech) and TruSeq RNA library prep kit (Illumina).   [whole eWAT] RNA libraries were prepared using the standard Illumina protocol.

treatment_protocol: [ex vivo adipose tissue macrophages] Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL of MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA) for cell sorting, cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.  [whole eWAT] whole eWAT was isolated amd snap-frozen.

value: ex vivo Adipose tissue macrophages

value: Wild-type C57BL/6J

value: High fat diet (12 weeks)


title: ARID1A_KO_2

description: Library name: mr812t


title: ARID1A_KO_1

description: Library name: mr811t


title: Macrophage, HFD, Ly6c- /Cd9-, rep 1

description: Library name: Sample 1


title: ARID1A_KO_3

description: Library name: mr813t


title: Macrophage, HFD, Ly6c- /Cd9-, rep 2

description: Library name: Sample 2


title: Young-PKO

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Single small intestinal cells pooled from 3 mice were analyzed by scRNA-seq

data_processing:
Demultiplexed FASTQ files (paired-end,Read 1: 30bp, Read 2:100bp) were generated using the CellRanger mkfastq command. The primary data analyses which included alignment, filtering, barcode counting and UMI quantification, quality control, clustering and statistical analysis were performed using CellRanger count command. Gene positions were annotated using Ensembl build 93 and filtered for biotype. Raw gene expression matrices were imported into R (version 3.6.1) and converted to a Seurat object using the Seurat R package (version 3.1.0). To remove dead cells and doublets, the total number of UMIs and genes and the percentage of UMIs derived from the mitochondrial genome for each cell were counted.  The upper and lower bounds were defined as the mean +/- two standard deviations for both the total UMIs and genes, respectively. Cells which had over 10% UMIs derived from mitochondrial genome were discarded. Finally, cells with total UMIs or genes outside of the upper and lower bounds were removed. For the remaining 5534 out of 6290 cells, gene expression matrices were normalized to the total cellular read count and to mitochondrial read count. Highly variably genes (HVG) were selected from the normalized data using Seurat SCTransform function. The top 3000 HVGs were used as features for dimensionality reduction and clustering. The Seurat RunPCA and JackStraw functions were performed to calculate and to select significant (P-value <0.05) principal components (PCs), respectively.  The RunUMAP function was then applied to plot the selected significant PCs. The FindNeighbors constructed a Shared Nearest Neighbor (SNN) Graph, and FindClusters function with “resolution = 0.1” parameter was carried out to cluster cells into different groups. Marker genes were defined based on the following criteria: 1) the average expression value in the cluster of interest was at least 1.2-fold higher than the average expression in the rest of clusters; 2) there are greater than 10% of cells in the cluster of interest which were detectable; and 3) marker genes should have the highest mean expression in the cluster of interest compared to the rest of clusters. Canonical marker genes were used to annotate cell clusters.
Assembly: mm10
Supplementary files format and content: hd5 file, data matrix from cell ranger export

source_name: Small intestine

growth_protocol: Young and aged Flox and SIRT1 PKO mice were housed in regular growth condition

extract_protocol:
Small intestines were removed and the fat/mesentery was dissected away. The intestinal lumen was washed with ice cold PBS (Mg2-Ca2-) using a 18G feeding needle (Roboz FN- 7905) until the intestines appeared white/pink. They were then opened longitudinally. The mucous was removed by gently rubbing the intestine between fingers in cold PBS. The intestines were cut into 3–5-mm fragments and placed into 50-ml conical tubes that were filled with ice-cold 30 ml of PBS (Mg2-Ca2-/)EDTA (10 mM). The samples were incubated and shook intermittently on ice for 30 min continuously discarding and replacing (at least three times) the supernatant. The fragments were then continually re-suspended with ice-cold 30 ml PBS (Mg2-Ca2-)EDTA (10mM) and intermittently shook on ice for 10 min, discarding the supernatant again for three times. The fragments were re-suspended again with ice-cold 30 ml PBS (Mg2-Ca2-)/EDTA (10mM) and incubated and intermittently shook while waiting on ice for 30 min. The samples were then triturated with a 10-ml pipette 1 to 2 times, and the contents were filtered twice through a 70- m mesh (BD Falcon) into a 50-ml conical tube to remove villous material and tissue fragments. The tissue suspensions were centrifuged for 5 min at 300g (4 C or room temperature), and the pellets were gently re-suspended in 1.0 ml of undiluted TrypLE Express (Invitrogen), 120 l of DNase I (10U/l, Roche) and transferred to 15-ml conical tubes. The samples were incubated in a 32 C water bath for 3 min (placed 15ml tubes inside water filled 50 ml tube on 32 C heat block), were not titurated, and were then placed on ice. Twelve millilitres of cold SMEM was added to each sample and were gently triturated twice. The samples were then centrifuged for 5 min at 300g.   The pellets were re-suspended and incubated for 15 min on ice in 0.5–1 ml SMEM that contained an antibody cocktail consisting of CD45-PE (eBioscience, 30-F11), CD31-PE (Biolegend, Mec13.3), Ter119-PE (Biolegend, Ter119), CD24-Pacific Blue (Biolegend, M1/69) and EPCAM-APC (eBioscience, G8.8).  Use 10l of each antibody. Do not add 7AAD to unstained samples. 15 ml tubes: No GFP unstained, PE antibodies only. CD24 Pac. Blue only, EPCAM only, 7AAD only, GFP unstained, 7AAD with all stains GFP. Twelve millilitres of SMEM were added and the samples were centrifuged for 5 min at 250g. The pellets were resuspended with 0.5–2 ml (depending on the size of the pellet) of SMEM/7-AAD (7-aminoactinomycin D) solution (1:500 dilution). 150l of 7-AAD in 1~2ml of MEM medium. Stained samples were filtered through a 40- m mesh/ filter (FLOW tubes) before cell sorting.
Single cell libraries were prepared on a 10x Genomics Chromium controller (10x Genomics, Pleasanton, CA) using the version 3 reagent kit according to the manufacturer’s instructions. The reagent mixture was calculated for capturing 6000 cells. The libraries were sequenced on a NovaSeq (Illumina, San Diego, CA) by the NIEHS Epigenomics core laboratory. Raw read processing was carried out using the Cell Ranger Single-Cell Software Suite (version 3.0.1, 10X Genomics).

value: Small intestine

tag: age

value: Young (2-3 months old)

value: SIRT1 Paneth cell-specific KO mice

value: No


title: Aged-Flox

description: Single small intestinal cells pooled from 2 mice were analyzed by scRNA-seq

value: Aged (12-14 months old)

value: Flox control mice


title: Young-Flox


title: KPNB1_KO_3

description: Library name: mr810t


title: Aged-PKO


title: Control_6

description: Library name: mr807t

value: WT


title: ARID1B_KO_1

description: Library name: mr814t


title: Control_5

description: Library name: mr806t


title: 5xFAD;Bmp4-WT mice, cortex, replicate 2

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

institute: Korea Brain Research Institute

description: inDropTM

data_processing:
The previously published pipeline in Python available at [https://github.com/indrops/indrops] was used to read raw sequencing data under modified settings (Bowtie 1.2.3, m = 200, n = 1, l = 15, e = 1000) and align them to the Ensembl mouse reference genome (GRCm38 release 102) to obtain a cell-gene expression matrix.
Seurat package (version 4.3) (Butler et al., 2018;Stuart et al., 2019;Hao et al., 2021) in R environment (version 4.3.0) were used to filter cells, reduce dimensionality, cluster with Louvain, and project cells with UMAP. We removed cells with low quality (less than 1,000 reads and 500 UMI-filtered mapped read) and doublets using ScDblFinder package (Germain et al., 2021). The G2M phase score, S-phase score, UMI count, and mitochondrial gene proportion were regressed out using the SCTransform wrapper. cells were annotated using the top most significant upregulated cluster-specific genes. Microglia was isolated preferentially expressed markers of microglia or macrophages. The subset of microglia was processed though dimensionality reduction, Louvain clustering, and projection into UMAP.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortex

extract_protocol:
Mice were deeply euthanized by CO2 asphyxiation and subsequently transcardially perfused with ice-cold PBS, pH 7.4. The brain tissues were dissected, and the cortical tissues were collected. The tissues were cut into 1mm slices and then dissociated enzymatically by 1 mg/ml collagenase type II (Worthington, 4176) and 2 mg/ml DNase 1 (Sigma-Aldrich, DN25) in 20 ml neurobasal media (Gibco, 21103049) at 37°C for 30 min.  Tissue slices were pelleted by centrifugation at 300g for 10 min and dissociated once more in a papain solution [1 mg/ml papain (Worthington, LS003119) and 2 mg/ml DNase 1 (Sigma-Aldrich, DN25) in 20 ml neurobasal media (Gibco, 21103049)] at 37°C for 30 min. The enzymes were then inactivated by adding 20 μg/ml ovoicoid protease inhibitor (OIA) (Worthington, 50-592-486). Dissociated cells were filtered through a 70um filter and spun down at 300 g for 10 min.
Single-cell barcoding and complementary DNA (cDNA) library preparation were performed according to the previously published  protocol (Zilionus,R et al.,Nat protoc, 2017.) with following modification. A home-made microfluidic device was connected to the Drop-seq apparatus in the  Korea Brain Research Institute.  Amplified cDNA was not fragmented, and cDNA clean up and size selection was performed using SPRIselect beads (Beckman Coulter, B23317).  Single-cell libraries were sequenced on an Illumina NovaSeq 6000 system though a sequencer company (Macrogen).

value: Cortex

tag: strain


title: 5xFAD;Bmp4-cKO mice, cortex, replicate 2

description: inDropTM


title: ARID1B OE - ARID1A ChIP

description: Library name: M1867

library_source: genomic

data_processing:
FastQC was used to check data quality. ChIP-seq reads were aligned to the Human Reference Genome hg38 using Bowtie2. PCR duplicate reads were removed with picard. Adaptors were trimmed with Trimmomatic. ChIP-seq peak identification, overlapping, subtraction, and feature annotation of enriched regions were performed using the HOMER (Hypergeometric Optimization of Motif EnRichment) suite.
Assembly: hg38
Supplementary files format and content: bigwig files generated by deepTools using CPM values

molecule: genomic DNA

extract_protocol:
50,000 cells were washed once with 1 × PBS and resuspended in 100 μl lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP 40, 0.1% Tween-20, 0.01% Digitonin) for 3min on ice, followed by adding 1ml of wash buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) to remove cytoplasm and mitochondria fraction.
The nuclei were resuspended in 25 μl transposition mix (12.5 ul 2x TD buffer, 2.5 μl Tn5 Transposome, 8.25 μl 1xPBS, 0.25 μl 1% digitonin, 0.25 μl 10% Tween-20, 1.25 μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 300 r.p.m. mixing. The tagmented DNA was purified using the DNA Clean & Concentrator-5 kit (ZYMO Research). Libraries were amplified and adapter dimers and primer dimers were cleaned up. Paired-end reads (50 bp) were sequenced using an Illumina HiSeq 4000.

value: Breast

value: ARID1B OE


title: ARID1A KO - ARID1A ChIP

description: Library name: M1861

value: Breast cancer cell

value: ARID1A KO


title: 5xFAD;Bmp4-WT mice, cortex, replicate 1

description: inDropTM


title: ARID1B KO - ARID1A ChIP

description: Library name: M1864

value: ARID1B KO


title: P14, XMLC2(+)Casp2(fl/fl), replicate 3

city: Freiburg

first: Katharina

last: Moos

address: Breisacherstr. 153

department: Medical Faculty

country: Germany

institute: University of Freiburg

data_processing:
Raw RNA sequencing reads were quality-controlled with FastQC (v0.11.8) and preprocessed with cutadapt (v4.0) to trim poly-G stretches resembling sequencing artefacts, trim low-quality bases from the 3’end, trim adapter and poly-A sequences introduced by the sequencing strategy, remove low-quality reads (more than 1 expected error and/or more than 30% N-bases) and remove short reads (less than 20 nucleotides).
Processed reads were aligned against the mouse reference genome GRCm39 from Ensembl (v108) using STAR (v2.6.1e).
The number of reads per gene (considering the full gene, i.e. both exonic and intronic sequences) was counted with HTSeq (v2.0.3).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file of raw read counts per gene

source_name: heart

extract_protocol:
Nuclei pellets were processed for RNA extraction, which was performed with Quick-RNA MicroPrep Kit (R1050, Zymo Research, USA) following the manufacturer’s protocol.
RNA-sequencing libraries were prepared by Lexogen NGS Services (Vienna, Austria) using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and following the low-input protocol. Sequencing was preformed on an Illumina NextSeq 2000 at Lexogen NGS Services to produce 100bp single-end reads for each sample.

value: heart

value: cardiomyocyte

value: Casp2 KO


title: Control_4

description: Library name: mr805t


title: KPNB1_KO_1

description: Library name: mr808t


title: P14, XMLC2(+)Casp2(fl/fl), replicate 4


title: KPNB1_KO_2

description: Library name: mr809t


title: P14, XMLC2(+)Casp2(fl/fl), replicate 2


title: Control - ARID1A ChIP

description: Library name: M1858


title: P14, XMLC2(+)Casp2(fl/fl), replicate 1


title: Sample_30

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: University of Kansas Medical Center, Dept. of Internal Medicine/Pulmonary Critical Care and Sleep Medicine

department: Internal Medicine

institute: University of Kansas Medical Center

description: Library name: 30_S16

data_processing:
Data were run through differential analysis using edgeR. Pathway analysis was run using QIAGEN Ingenuity Pathway Analysis tool.
Assembly: hg38
Supplementary files format and content: non-normalized gene counts matrix CSV format

source_name: Lung fibroblasts

extract_protocol:
RNA from primary human lung fibroblasts was isolated using RNeasy mini kit (Qiagen).  Total RNA (500 ng) was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Universal Plus mRNA-seq with NuQuant stranded mRNA library preparation protocol according to the manufacturer’s instructions.

value: Lung fibroblasts


title: P14, XMLC2(-)Casp2(fl/fl), replicate 4


title: P14, XMLC2(-)Casp2(fl/fl), replicate 2


title: Sample_29

description: Library name: 29_S15


title: Sample_28

description: Library name: 28_S14


title: P14, XMLC2(-)Casp2(fl/fl), replicate 3


title: Sample_25

description: Library name: 25_S13


title: P7, XMLC2(+)Casp2(fl/fl), replicate 4


title: P7, XMLC2(-)Casp2(fl/fl), replicate 4


title: Sample_22

description: Library name: 22_S11


title: P14, XMLC2(-)Casp2(fl/fl), replicate 1


title: Sample_24

description: Library name: 24_S12


title: Sample_12

description: Library name: 12_S8


title: P7, XMLC2(+)Casp2(fl/fl), replicate 2


title: P7, XMLC2(+)Casp2(fl/fl), replicate 3


title: P7, XMLC2(+)Casp2(fl/fl), replicate 1


title: Sample_19

description: Library name: 19_S9


title: Sample_7

description: Library name: 7_S5


title: Sample_8

description: Library name: 8_S6


title: Sample_4

description: Library name: 4_S3

value: Control


title: Sample_2

description: Library name: 2_S2


title: P7, XMLC2(-)Casp2(fl/fl), replicate 3


title: Sample_20

description: Library name: 20_S10


title: P1, XMLC2(+)Casp2(fl/fl), replicate 1


title: Sample_6

description: Library name: 6_S4


title: Sample_10

description: Library name: 10_S7


title: P1, XMLC2(+)Casp2(fl/fl), replicate 4


title: P1, XMLC2(+)Casp2(fl/fl), replicate 2


title: PGO, 18week

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

institute: Yale University

description:
Library name: scRNA-seq sample2
10x Genomics

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in)
Assembly: GRCh38
Supplementary files format and content: For RNA-seq, csv file including TPM. For scRNA-seq, matrix, features and barcode files.

source_name: brain organoid

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 10,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P standard  v3.1 (Next GEM)  protocol (10X Genomics)

value: brain organoid


title: PGO, 6week

description:
Library name: scRNA-seq sample1
10x Genomics


title: P1, XMLC2(-)Casp2(fl/fl), replicate 4


title: P1, XMLC2(-)Casp2(fl/fl), replicate 3


title: ECD+ERBB2_3

city: Omaha

first: Vimla

last: Band

state: Nebraska

address: 601 Saddle Creek road

department: Department of Genetics, Cell Biology & Anatomy,

institute: University of Nebraska Medical Center

description: Library name: SAMPLES 12

data_processing:
RNA-seq of tumors: Raw FASTQ reads were trimmed using the Trim Galore v0.6.5 to remove the adapters, terminal unknown bases (Ns), and low-quality regions (Phred score < 33). The reads that passed the quality control were mapped to the mouse genome assembly (mm10) using STAR v2.7 and the gene level values were quantified using RSEM v1.3 based on GENCODE annotation (v35).
RNA-seq of 76NERT cell line transfectants: The RNA-seq reads underwent processing via the nf-core RNA-seq pipeline (version 3.9), accessed through Nextflow (version 22.10.3), and executed with Singularity to ensure reproducibility and portability. Utilizing paired-end sequencing reads, alignment to the human reference genome (GRCh38) was achieved using the Spliced Transcripts Alignment to a Reference (STAR) software (version 2.7.11a), integrating Ensembl gene annotations for precise mapping.
Assembly: mm10 and GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM and TPM values for each Sample of 76NERT cell line
Supplementary files format and content: csv files include TPM values for each tumor Sample

growth_protocol: 76NTERT cells expressing vector, ECD, ERBB2, and ECD+ERBB2 were cultured in triplicates in DFCI-3 starvation medium for 72 h.

extract_protocol:
Trizol-Chloroform RNA-extraction and RNA clean up using Qiagen Rneasy clean up microkit for both cell lines and tumors
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina)

value: Mammary epithelial Cells

value: ECD+ERBB2 Overexpression


title: Sample_1

description: Library name: 1_S1


title: P1, XMLC2(-)Casp2(fl/fl), replicate 1


title: P7, XMLC2(-)Casp2(fl/fl), replicate 1


title: P1, XMLC2(+)Casp2(fl/fl), replicate 3


title: ECD+ERBB2_2

description: Library name: SAMPLES 11


title: P1, XMLC2(-)Casp2(fl/fl), replicate 2


title: ERBB2_3

description: Library name: SAMPLES 9

value: ERBB2 Overexpression


title: ECD+ERBB2_1

description: Library name: SAMPLES 10


title: P7, XMLC2(-)Casp2(fl/fl), replicate 2


title: ERBB2_1

description: Library name: SAMPLES 7


title: ECD_3

description: Library name: SAMPLES 6

value: ECD Overexpression


title: H1299-DOX-DPPA2-Ms-1

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: H1299-DOX-DPPA2-Ms-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

data_processing:
Paired-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in paired-end mode (valid read pairs were only kept).
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files using bamCoverage (DeepTools v3.5.0) where reads were not extended (relying instead on the true fragment length determined by read-pairs).
The resultant BAM files were then input to EPIC2 (v0.0.52) (--bin-size 100 –gaps-allowed 1 –fragment-size 147 -- false-discovery-rate-cutoff 0.05) using species matched isotype controls (IgG) as the control. BAM files were also input to MACS2 (v2.27.1) for peak calling in paired-end mode with an FDR threshold of <0.05 (-f BAMPE -q 0.05) again using species matched isotype controls (IgG) as the control.
Assembly: GRCh38.p13
Supplementary files format and content: Bigwig files output by deepTools summarising read density across the genome with values as CPM/bp.
Supplementary files format and content: Peak files produced by MACS2.
Supplementary files format and content: Peak files produced by EPIC2.
Library strategy: CUT&Run

source_name: lung cancer

growth_protocol: Non-small cell lung cancer cell lines NCI-H661 and NCI-H1299 were cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). These cell lines was also STR profiled to ensure authenticity. NCI-H661 and NCI-H1299 were purchased from ATCC.

extract_protocol:
NCI-H661 or NCI-H1299 cells were harvested and counted after staining cells with 0.4% Trypan blue where 500,000 live cells were used per CUT&Run. Cells were washed with ice cold cell wash buffer (150mM NaCl, 20mM HEPES in H2O) and kept on ice. 11uL Concanavalin A beads (Epicypher) were washed twice with 100uL cold bead activation buffer (20mM HEPES, 50uL KCl, 1mM CaCl2, 1mM MnCl2 in H2O) and then resuspended in 11uL of the same buffer on ice. Cells were washed twice with NE buffer (20mM HEPES, 10mM KCl, 0.1% Triton X, 20% glycerol in H2O) to release nuclei with gentle pipetting and 300xg spins at 4C in between for 5 mins each. Nuclei were resuspended in 100uL of cold cell wash buffer and then incubated with 10uL of washed beads to allow for nuclei-bead adsorption for 10 mins at room temperature. Beads were then resuspended in 50uL of cold antibody buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 0.05% digitonin, 2mM EDTA in H2O) followed by the addition of 1ug of IgG controls (Mouse IgG (Invitrogen, #31903), Rabbit IgG (Invitrogen, #012-6102)) or antibodies (DPPA2 (Sigma, #MAB4356), DPPA4 (abcepta, #AP1438a, abcepta, #AP21202c, abcam, #ab154642), V5-tag (Invitrogen #46-0705), Flag-tag (Merck #F1084 (monoclonal), Invitrogen #740001 (superclonal), RING1B (CST #5694), PCGF1 (Santa Cruz Biotechnology #sc515371), MTF2 (Proteintech #16208-1-AP), EP300 (Aviva Systems Biology (#OAAF01891), SOX2 (abcam #97959)) (or 0.5ug for the H3K4me3 (CST, #9751) positive control) and incubation overnight at 4C on a nutator. Bead complexes were then washed twice with 200uL cold antibody buffer (same as above, but without EDTA) and then resuspended in 50uL of the same buffer. 1.5uL of Protein-A/G-MNase (CST) was added to each bead suspension, pipette mixed and incubated at room temperature for 10 mins. Beads were washed two times with cold 250uL of antibody buffer and resuspended in 50uL of the same buffer. 1uL of 100mM CaCl2 was added to each bead suspension to activate the bound MNase followed by incubation at 4C for 1hr on a thermalcycler to facilitate chromatin digestion. 38uL of stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNase A, 50ug/mL glycogen in H2O) containing 250pg of E.coli normalisation spike-in DNA (CST) was added to each suspension to inhibit MNase, degrade RNA and release digested chromatin into the supernatant by incubation at 37C for 10 mins in a thermalcycler. The supernatant containing digested chromatin was transferred to a new tube and treated with 1uL 20mg/mL proteinase K for 1hr at 37C. DNA was purified using a 1.8X bead cleanup (SergiLabs) and eluted in 30uL of H20 for DNA library preparation.
CUT&Run libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit (NEB) according to the manufacturer’s instruction. During library preparation the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) were used to enable library multiplexing. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and HSD1000 High Sensitivity DNA kit (Agilent) on the TapeStation 4150 (Agilent). Libraries were pooled and sequenced on the Illumina NextSeq2000 platform in a paired-end configurations with 100bp read lengths.

treatment_protocol: For inducible knockdown experiments, miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone, followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. For inducible overexpression experiments the above vector backbones were cloned to replace the (iRFP-shRNA) fragment downstream of the tet-response element (TRE) with cDNA encoding human DPPA2 (ORF:NM_138815) or DPPA4 (ORF:NM_018189) with additional N-terminal Flag or V5 tags respectively (gene fragments synthesised by IDT). Stable cell lines were generated in the same way as above for shRNA lines for the NCI-H1299 cell line (which does not express DPPA2/4). All cell sorting was undertaken on FACSAria Fusion flow cytometry instruments (BD). To induce either shRNA or cDNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days and knockdown or overexpression were confirmed by RT-qPCR or western blot analysis.

value: lung cancer

value: lung adenocarcinoma

value: DPPA2 and DPPA4 stable

value: 7 days doxycyline 2ug/mL

tag: replicate

tag: target

tag: antibody

value: Sigma #MAB4356


title: VEC_2

description: Library name: SAMPLES 2

value: WT


title: H1299-DOX-DPPA4-Rb-1

description:
Library name: H1299-DOX-DPPA4-Rb-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: abcam #ab154642


title: NCIH661_Dppa4_3

description:
Library name: NCIH661_Dppa4_3
Parental cells treated with siDPPA4

data_processing:
Paired-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in single-end or paired-end mode (valid read pairs were only kept).
Bismark (v0.22.3) was used to align reads to a bisulfite converted hg38 (GRCh38.p13) genome using bowtie2 internally, followed by read deduplication and methylated/unmethylated read counting.
The resultant methylation bedgraph was converted to the bigwig format using bedGraphToBigWig (UCSC.utils (v1.3.1) R package).
Assembly: GRCh38.p13
Supplementary files format and content: Bigwig files summarising DNA methylation percentage across the genome.
Supplementary files format and content: Coverage files output by bismark.
Supplementary files format and content: Bedgraph files in UCSC format output by bismark containing DNA methylation fractions across the genome, this file was used to generate bigwigs above.

growth_protocol: Non-small cell lung cancer cell line NCI-H661 was cultured in RPMI-1640 (Gibco) and Cov318 with DMEM (Gibco) growth medium, each supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). NSCLC cell lines were also STR profiled to ensure authenticity. NCI-H661 and Cov318 were purchased from ATCC.

extract_protocol:
Cells were harvested, washed once with PBS, stored in RLT+ lysis buffer (Qiagen) and snap frozen. gDNA was extracted from cells using an AllPrep RNA/DNA extraction kit (Qiagen #80204) according to the manufacturer’s instructions
DNA libraries were generated using the NEBNext End Prep kit (NEB E7370, E7535) and bisulfite converted using the EZ DNA Methylation Gold Kit (Zymo Research #D5005, D5006) according to the manufacturer’s instructions. Libraries were amplified using KAPA HiFi Uracil+ (KK2801/2) using NEBNext Universal and Index primers, cleaned up using 0.8x Ampure beads and pooled for sequencing

treatment_protocol: For NCI-H661 and Cov318 siRNA knockdowns, 10uL Lipofectamine 2000 (ThermoFisher, #11668027) and 200pmol of non-targeted and DPPA2/4 targeted siRNA twice over 96 hours (first dose at day 0, second dose at day 2, collection on day 4) using SMARTpool siRNA (containing 4 siRNAs per pool) (Horizon/Dharmacon, Non-targeting; #D-001810-10-05, DPPA2; #L-018977-01-0005, DPPA4; #L-020766-01-0005). Lipofectamine 2000 and siRNA complexes were first formed with reduced-serum OptiMEM medium (Gibco) for 20 mins at room temperature, prior to addition to cells grown in complete medium.

value: lung large cell carcinoma

value: Parental

value: siDPPPA4 4 days


title: ECD_2

description: Library name: SAMPLES 5


title: H1299-DOX-DPPA4n-Rb-1

description:
Library name: H1299-DOX-DPPA4n-Rb-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: DPPA4n (N-terminal)

value: abcepta #AP1438a


title: ERBB2_2

description: Library name: SAMPLES 8


title: NCIH661_Dppa2_4_3

description:
Library name: NCIH661_Dppa2_4_3
Parental cells treated with both siDPPA2 and siDPPA4

value: siDPPA2+siDPPA4 4 days


title: VEC_1

description: Library name: SAMPLES 1

value: Mammary epithelial Cells


title: ECD_1

description: Library name: SAMPLES 4


title: H1299-DOX-DPPA2-Ms-2

description:
Library name: H1299-DOX-DPPA2-Ms-2
double inducible Flag-DPPA2 and V5-DPPA4 expression


title: VEC_3

description: Library name: SAMPLES 3


title: Cov318_Dppa4_4

description:
Library name: Cov318_Dppa4_4
Parental cells treated with siDPPA4

source_name: ovarian cancer

value: ovarian cancer


title: Patient 12 second CSF sample TCR

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

description: Library name: P12-T2_VDJ-T

data_processing:
Sequencing reads were processed with 10X Genomics' software CellRanger version 7.0.0
All CSF cell count matrices (all patients and samples) were combined to construct the joint count matrix.
Assembly: GRCh38
Supplementary files format and content: CSF_all_cells_counts.txt contains all CSF raw counts merged.
Supplementary files format and content: CSF_all_cells_metadata.txt contains cell and patient level metadata of all merged CSF cells.
Library strategy: scTCR-seq

source_name: CSF

extract_protocol:
CSF samples were collected during routine clinical care, primarily through lumbar puncture, except for four samples collected by ventricular CSF sampling. Cells were cryopreserved prior to sequencing.
Libraries were prepared following 10x Genomics’ 5-prime protocol.

value: CSF

tag: diagnosis

value: leptomeningeal disease (LMD)


title: Patient 12 third CSF sample TCR

description: Library name: P12-T3_VDJ-T


title: H1299-DOX-DPPA4n-Rb-2

description:
Library name: H1299-DOX-DPPA4n-Rb-2
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: lung cancer


title: Patient 10 second CSF sample TCR

description: Library name: P10-T2_VDJ-T


title: Cov318_Dppa4_3

description:
Library name: Cov318_Dppa4_3
Parental cells treated with siDPPA4


title: Patient 7 second CSF sample TCR

description: Library name: P07-T2_VDJ-T


title: Cov318_control_3

description:
Library name: Cov318_control_3
Parental cells treated with siControl

value: siControl 4 days


title: NCIH661_Dppa2_4_2

description:
Library name: NCIH661_Dppa2_4_2
Parental cells treated with both siDPPA2 and siDPPA4


title: NCIH661_Dppa2_3

description:
Library name: NCIH661_Dppa2_3
Parental cells treated with siDPPA2

value: siDPPPA2 4 days


title: NCIH661_control_3

description:
Library name: NCIH661_control_3
Parental cells treated with siControl


title: Cov318_control_4

description:
Library name: Cov318_control_4
Parental cells treated with siControl


title: Patient 15 CSF sample TCR

description: Library name: P15_VDJ-T


title: Patient 16 CSF sample TCR

description: Library name: P16_VDJ-T


title: NCIH661_control_2

description:
Library name: NCIH661_control_2
Parental cells treated with siControl


title: Patient 12 first CSF sample TCR

description: Library name: P12_VDJ-T


title: Patient 11 CSF sample TCR

description: Library name: P11_VDJ-T


title: NCIH661_Dppa2_2

description:
Library name: NCIH661_Dppa2_2
Parental cells treated with siDPPA2


title: Patient 13 CSF sample TCR

description: Library name: P13_VDJ-T


title: NCIH661_Dppa2_4_1

description:
Library name: NCIH661_Dppa2_4_1
Parental cells treated with both siDPPA2 and siDPPA4


title: Patient 10 first CSF sample TCR

description: Library name: P10_VDJ-T


title: Patient 14 CSF sample TCR

description: Library name: P14_VDJ-T


title: NCIH661_Dppa4_2

description:
Library name: NCIH661_Dppa4_2
Parental cells treated with siDPPA4


title: Patient 9 CSF sample TCR

description: Library name: P09_VDJ-T


title: NCIH661_control_1

description:
Library name: NCIH661_control_1
Parental cells treated with siControl


title: NCIH661_Dppa2_1

description:
Library name: NCIH661_Dppa2_1
Parental cells treated with siDPPA2


title: NCIH661_Dppa4_1

description:
Library name: NCIH661_Dppa4_1
Parental cells treated with siDPPA4


title: Patient 6 CSF sample TCR

description: Library name: P06_VDJ-T


title: Patient 7 first CSF sample TCR

description: Library name: P07_VDJ-T


title: Patient 8 CSF sample TCR

description: Library name: P08_VDJ-T


title: Cov318_control_2

description:
Library name: Cov318_control_2
Parental cells treated with siControl


title: Patient 3 CSF sample TCR

description: Library name: P03_VDJ-T


title: Patient 5 CSF sample TCR

description: Library name: P05_VDJ-T


title: shREN-DOX-R3

description:
Library name: shREN-DOX-R3
shREN inducible

data_processing:
Paired-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in paired-end mode (valid read pairs were only kept).
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. We additionally shifted reads by -4bp on the + strand and +5 bp on the -strand to account for Tn5 insertions using alignmentSieve (DeepTools v3.5.0). bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files using bamCoverage (DeepTools v3.5.0) where reads were not extended (relying instead on the true fragment length determined by read-pairs).
The resultant BAM files were then input to MACS2 (v2.27.1) for peak calling in paired-end mode with an FDR threshold of <0.05 (-f BAMPE -q 0.05).
Assembly: GRCh38.p13
Supplementary files format and content: Narrowpeak files output by MACS2.
Supplementary files format and content: Bigwig files output by deepTools summarising Tn5 insertions (chromatin accessibility) across the genome with values as CPM/bp.

growth_protocol: Non-small cell lung cancer cell line NCI-H661 was cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). NSCLC cell lines were also STR profiled to ensure authenticity. NCI-H661 was purchased from ATCC.

extract_protocol:
NCI-H661 cells were harvested and counted after staining cells with 0.4% Trypan blue where 500,000 live cells were used for each ATAC assay. Cells were washed with ice cold PBS once and then lysed in 500uL NE buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20) on ice by gentle pipetting to isolate nuclei. 50uL of nuclei (50,000 cells), were then pelleted at 1500xg for 10mins at 4C followed by supernatant aspiration. Nuclei were gently resuspended directly in tagmentation mix (1.75uL Tn5 transposase (Illumina), 17uL TD buffer (Illumina), 21.25uL H2O) on ice and then allowed to tagment for 37C for 30 mins in a thermalcycler.
Tagmented DNA was then purified using Ampure XP beads at a 1.8X ratio and eluted in 21uL of H2O for library preparation as previously described using 15 cycles of PCR to incorporate i7/i5 indices followed by a final 1.8X Ampure XP bead cleanup and elution in 22uL of H2O.

treatment_protocol: For NCI-H661 inducible shRNA knockdowns miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone3 , followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. To induce shRNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days.

value: shREN stable

value: Doxycyline 2ug/mL 7 days


title: Patient 4 CSF sample TCR

description: Library name: P04_VDJ-T


title: shDPPA4-DOX-R3

description:
Library name: shDPPA4-DOX-R3
shDPPA4 inducible

value: shDPPA4 stable


title: Patient 2 CSF sample TCR

description: Library name: P02_VDJ-T


title: shDPPA4-CTRL-R3

description:
Library name: shDPPA4-CTRL-R3
shDPPA4 inducible

value: H20 7 days


title: shDPPA2-DOX-R3

description:
Library name: shDPPA2-DOX-R3
shDPPA2 inducible

value: lung large cell carcinoma

value: shDPPA2 stable


title: Patient 1 CSF sample TCR

description: Library name: P01_VDJ-T

library_source: other

molecule: other


title: Cov318_Dppa4_2

description:
Library name: Cov318_Dppa4_2
Parental cells treated with siDPPA4

value: Parental

value: siDPPPA4 4 days


title: shDKD-DOX-R3

description:
Library name: shDKD-DOX-R3
double shDPPA2 and shDPPA4 inducible

value: shDKD stable


title: shDKD-CTRL-R3

description:
Library name: shDKD-CTRL-R3
double shDPPA2 and shDPPA4 inducible


title: shDPPA4-DOX-R2

description:
Library name: shDPPA4-DOX-R2
shDPPA4 inducible


title: shREN-CTRL-R3

description:
Library name: shREN-CTRL-R3
shREN inducible


title: Patient 10 second CSF sample gene expression

description: Library name: P10-T2_cDNA

data_processing:
Sequencing reads were processed with 10X Genomics' software CellRanger version 7.0.0
All CSF cell count matrices (all patients and samples) were combined to construct the joint count matrix.
Assembly: GRCh38
Supplementary files format and content: CSF_all_cells_counts.txt contains all CSF raw counts merged.
Supplementary files format and content: CSF_all_cells_metadata.txt contains cell and patient level metadata of all merged CSF cells.


title: shDPPA2-CTRL-R3

description:
Library name: shDPPA2-CTRL-R3
shDPPA2 inducible


title: Patient 7 second CSF sample gene expression

description: Library name: P07-T2_cDNA


title: Patient 12 third CSF sample gene expression

description: Library name: P12-T3_cDNA


title: shREN-CTRL-R2

description:
Library name: shREN-CTRL-R2
shREN inducible


title: shDKD-DOX-R1

description:
Library name: shDKD-DOX-R1
double shDPPA2 and shDPPA4 inducible


title: Patient 12 second CSF sample gene expression

description: Library name: P12-T2_cDNA


title: Patient 11 CSF sample gene expression

description: Library name: P11_cDNA


title: Patient 10 first CSF sample gene expression

description: Library name: P10_cDNA


title: shDPPA2-DOX-R2

description:
Library name: shDPPA2-DOX-R2
shDPPA2 inducible


title: Patient 13 CSF sample gene expression

description: Library name: P13_cDNA


title: Patient 16 CSF sample gene expression

description: Library name: P16_cDNA


title: Patient 15 CSF sample gene expression

description: Library name: P15_cDNA


title: shDPPA4-CTRL-R2

description:
Library name: shDPPA4-CTRL-R2
shDPPA4 inducible


title: Patient 14 CSF sample gene expression

description: Library name: P14_cDNA


title: shDPPA2-CTRL-R2

description:
Library name: shDPPA2-CTRL-R2
shDPPA2 inducible


title: Patient 6 CSF sample gene expression

description: Library name: P06_cDNA


title: Patient 12 first CSF sample gene expression

description: Library name: P12_cDNA


title: MCF10A shScr, rep1

city: Oslo

first: Fabiana

last: Patalano

address: Blindernveien 31

country: Norway

institute: University of Oslo

description: Library name: Sample 16

data_processing:
Samples were processed using nf-core/hic v2.1.0 and nf-core/rnaseq version 3.14.0
Assembly: hg38
Supplementary files format and content: .mcool files are HiC contact matrix bigWig with read coverage (reverse) bigWig with read coverage (forward)

source_name: mammary gland

growth_protocol: MCF10A cell lines were maintained in Dulbecco's modified Eagle's medium/Nutrient F12 (DMEM/F12) (Sigma-Aldrich) supplemented with 5% horse serum (MCF10A), 14 mM NaHCO3, 10 μg/mL insulin, 2 mM L-glutamine, 20 ng/mL human epidermal growth factor, 500 ng/mL Hydrocortisone and 100 ng/mL cholera Toxin.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Plus kit following manufacturer’s instructions. HiC Libraries were prepared in duplicates for each cell type using the Arima-HiC+ kit (Arima Genomics, USA) according to manufacturer instructions. For each cell line, 1 million cells were used per HiC reaction. Cells were fixed with 1.2% formaldehyde for 12 min. All subsequent steps were carried out according to the Arima protocol. Resulting libraries were amplified with 5 PCR cycles and sequenced on an Illumina NovaSeq 6000 instrument in paired-end run with 2×101 bp.
Total RNA was isolated using the Qiagen RNeasy Plus kit following manufacturer’s instructions. HiC Libraries were prepared in duplicates for each cell type using the Arima-HiC+ kit (Arima Genomics, USA) according to manufacturer instructions. For each cell line, 1 million cells were used per HiC reaction. Cells were fixed with 1.2% formaldehyde for 12 min. All subsequent steps were carried out according to the Arima protocol. Resulting libraries were amplified with 5 PCR cycles and sequenced on an Illumina NovaSeq 6000 instrument in paired-end run with 2×101 bp.

treatment_protocol: To generate lentiviral particles, HEK293T cells were co-transfected using the calcium phosphate method with 20 µg of the pGFP-C-shLenti shHP1α plasmid (OriGene Technologies), 15 µg of psPAX2 (a gift from Didier Trono (Addgene plasmid # 12260; http://n2t.net/addgene:12260; RRID:Addgene_12260)), and 6 µg of pMD2.G (a gift from Didier Trono (Addgene plasmid # 12259; http://n2t.net/addgene:12259; RRID:Addgene_12259)). Viral supernatant was collected 48 hours after transfection and filtered through a 0.45 µm membrane. MCF10A cells were then transduced with the viral mixture supplemented with 4 µg/mL polybrene and 10 mM HEPES (pH 7.5). Following a 24-hour incubation, the viral medium was replaced with fresh growth media. The cells were cultured for an additional 24 hours to allow GFP expression, after which fluorescence-activated cell sorting (FACS) was performed to isolate a fully transduced cell population for downstream assays. For EMT induction, MCF10A cells were treated with 5 ng/mL TGF-β1 (R&D Systems) for 8 days.

value: mammary gland

value: epithelial cell


title: Patient 5 CSF sample gene expression

description: Library name: P05_cDNA


title: Patient 8 CSF sample gene expression

description: Library name: P08_cDNA


title: MCF10A shHPA, rep3

description: Library name: Sample 12

value: HP1a knockdown


title: Patient 3 CSF sample gene expression

description: Library name: P03_cDNA

value: CSF


title: Pancreatic islet, high fat diet-fed, scRNAseq

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

address: 333 Cedar Street

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using CellRanger software 3.0.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic islet

extract_protocol:
Dead cells were removed using a Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101). Cell concentration and viability were determined using a Countess II Automated Cell Counter (ThermoFisher Scientific).
Library was prepared according to manufacturer's instructions (Single Cell 3' v3 protocol, 10x Genomics).

treatment_protocol: High fat diet-fed mice were fed 60% kcal fat diet (Research Diets 124932) for 10 weeks starting at 6 weeks of age

value: Pancreatic islet

value: 16 weeks old

tag: Sex

value: Male

value: high fat diet-fed


title: Pancreatic islet, wild-type, scRNAseq

description: 10x Genomics

value: wild-type


title: shDKD-CTRL-R1

description:
Library name: shDKD-CTRL-R1
double shDPPA2 and shDPPA4 inducible

value: lung cancer


title: MCF10A shScr, rep3

description: Library name: Sample 18


title: MCF10A TGFB, rep3

description: Library name: Sample 15

value: TGFB treatment


title: MCF10A shHPA, rep1

description: Library name: Sample 10


title: Patient 9 CSF sample gene expression

description: Library name: P09_cDNA

value: leptomeningeal disease (LMD)


title: Patient 7 first CSF sample gene expression

description: Library name: P07_cDNA


title: MCF10A rep2

description: Library name: Sample 8

value: WT


title: Anti-H3K27ace_GSK2879552_rep2

city: chiba

first: YINGBO

last: GONG

department: Medicine

country: Japan

institute: CHIBA University

data_processing:
The reads were mapped to the human genome assembly (GRCh37.p13 (hg19)) using the Bowtie 2 mapping tool with default settings. Peaks were called using MACS2 software with the broad option, and those identified in three replicates were used for further analyses. Data quantification was conducted using the “Annotate Peaks” command in Partek Flow software (https://www.partek.com/). DARs were detected using the “Gene-Specific Analysis” command in Partek Flow software. IGV was used for visualization.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: NCI-1417 [H1417] (Cat. No. CRL-5869) cell line were purchased from the American Type Culture Collection and were cultured in RPMI1640 medium (Cat#: 189-02025, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% FBS (Cat#: 10270106, GIBCO Thermo Fisher Scientific, San Jose, CA)

extract_protocol:
NCI-H1417 cells were cross-linked at 37°C for 10 min with 1% formaldehyde. After quenching the cross-linking reaction with 1.25 M glycine, cells were lysed in swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, and 0.1% (v/v) NP-40) containing a protease inhibitor cocktail (Nacalai Tesque). The mixture was subsequently centrifuged at 5000×g for 5 min at 4°C. Pelleted nuclei were re-suspended in sonication buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) SDS and 0.1 (w/v) Na-deoxycholate containing a protease inhibitor cocktail, ~5x106 cell/mL), sonicated on a Q700 (QSONICA, Newtown, CT) for 20–25 cycles of 15 s of sonication, followed by 45 s rest, at an amplitude of 60 (total 6000 J).
ChIP-seq libraries were constructed using an NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) according to the manufacturer’s protocols.

treatment_protocol: NCI-H1417 were seeded in plates. LSD1 inhibitors were serially diluted with DMSO and mixed with the culture medium. The mixtures were then added to each well on the plates. The final concentration of DMSO was set at 0.075 %. Cells were maintained with the inhibitors without any medium change. Cells were treated with DMSO or 300 nM LSD1 inhibitor (TAS1440, ORY-1001, GSK2879552) for 5 days

value: small-cell lung cancer

tag: chip antibody


title: MCF10A shScr, rep2

description: Library name: Sample 17


title: shREN-DOX-R2

description:
Library name: shREN-DOX-R2
shREN inducible

value: lung large cell carcinoma

value: shREN stable

value: Doxycyline 2ug/mL 7 days


title: Anti-H3K27ace_GSK2879552_rep3


title: Patient 4 CSF sample gene expression

description: Library name: P04_cDNA


title: MCF10A TGFB, rep1

description: Library name: Sample 13

value: mammary gland


title: UTL-148PS

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

description:
Library name: UTL-148PS
UTL-148PS

data_processing:
Raw small RNA sequencing reads were trimmed to remove adapter sequences using Cutadapt (v5.1). Adapter-trimmed reads were then mapped and annotated using Unitas (v1.7.3), a specialized tool for comprehensive small RNA annotation. For liver biopsy samples, read count matrices generated by Unitas were imported into DESeq2 (v1.44.0) in R for normalization and differential expression analysis. Prior to analysis, RNAs with zero counts in more than 80% of samples were excluded to reduce low-abundance noise. Data visualization was performed in R using ggplot2 (v3.5.1) and ggpubr (v0.6.0). For perfusate samples, read count matrices generated by Unitas were imported into R and normalized to reads per million (RPM). Given the lower complexity of perfusate libraries relative to biopsy samples, differential expression analysis was performed using Student’s t-tests on RPM values. Data visualization was carried out in R with ggplot2 (v3.5.1) and ggpubr (v0.6.0), and receiver operating characteristic (ROC) curves were generated using the ROCR package (v1.0-11).
Assembly: hg38
Supplementary files format and content: count table including microRNA and tRNA fragments

source_name: liver

extract_protocol:
Total RNA was extracted from needle biopsies using the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. #R2062) according to the manufacturer’s instructions, including on-column DNase I treatment to remove genomic DNA contamination. For DOPS samples, RNA was isolated from 500 μl of solution using the same kit, following the manufacturer’s protocol for liquid samples, and eluted in 15 μl of RNase-free water. Purified RNA was stored at –80 °C, and repeated freeze–thaw cycles were avoided to minimize RNA degradation.
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat. #E7330) following the manufacturer’s instructions. For each sample, 100 ng of tissue RNA or 5 μl of DOPS RNA was used as input. Indexing was performed using the NEBNext Multiplex Oligos for Illumina, with PCR amplification carried out for 15 cycles for tissue RNA libraries and 18 cycles for perfusate RNA libraries. Amplified products were resolved on an 8% polyacrylamide gel (Thermo Fisher Scientific, Cat. #EC6215BOX), and target bands were excised and purified. Equal amounts of libraries were pooled and sequenced on an Illumina NextSeq 500 platform, generating approximately 10 million 75 bp single-end reads per sample.

value: liver

tag: transplant outcome

value: EAD


title: Anti-H3K27ace_ORY1001_rep1


title: Anti-H3K27ace_TAS1440_rep2


title: Anti-H3K27ace_GSK2879552_rep1


title: MCF10A rep3

description: Library name: Sample 9

value: epithelial cell


title: MCF10A TGFB, rep2

description: Library name: Sample 14


title: UTL-139PS

description:
Library name: UTL-139PS
UTL-139PS


title: Anti-H3K27ace_TAS1440_rep1


title: Patient 2 CSF sample gene expression

description: Library name: P02_cDNA

value: CSF


title: MCF10A rep1

description: Library name: Sample 7


title: Anti-H3K27ace_DMSO_rep1

value: DMSO


title: UTL-145PS

description:
Library name: UTL-145PS
UTL-145PS

value: NF


title: UTL-138PS

description:
Library name: UTL-138PS
UTL-138PS


title: Anti-H3K27ace_ORY1001_rep2


title: UTL-125PS

description:
Library name: UTL-125PS
UTL-125PS


title: Patient 1 CSF sample gene expression

description: Library name: P01_cDNA


title: UTL-141PS

description:
Library name: UTL-141PS
UTL-141PS


title: Anti-H3K4me3_GSK2879552_rep2


title: UTL-129PS

description:
Library name: UTL-129PS
UTL-129PS


title: Anti-H3K27ace_TAS1440_rep3


title: Anti-H3K4me3_GSK2879552_rep1


title: UTL-131PS

description:
Library name: UTL-131PS
UTL-131PS


title: UTL-124PS

description:
Library name: UTL-124PS
UTL-124PS


title: Anti-H3K4me3_GSK2879552_rep3


title: UTL-112PS

description:
Library name: UTL-112PS
UTL-112PS


title: Anti-H3K4me3_ORY1001_rep1


title: Anti-H3K27ace_DMSO_rep2


title: UTL-104PS

description:
Library name: UTL-104PS
UTL-104PS


title: UTL-117PS

description:
Library name: UTL-117PS
UTL-117PS


title: UTL-100PS

description:
Library name: UTL-100PS
UTL-100PS


title: UTL-143PS

description:
Library name: UTL-143PS
UTL-143PS


title: Anti-H3K27ace_DMSO_rep3


title: Anti-H3K4me3_TAS1440_rep1


title: Anti-H3K27ace_ORY1001_rep3


title: UTL-115PS

description:
Library name: UTL-115PS
UTL-115PS


title: Anti-H3K4me3_DMSO_rep2


title: Anti-H3K4me3_TAS1440_rep3


title: Anti-H3K4me3_DMSO_rep1


title: Anti-H3K4me3_ORY1001_rep2


title: UTL-097PS

description:
Library name: UTL-097PS
UTL-097PS


title: Anti-H3K4me3_TAS1440_rep2


title: Anti-H3K4me2_GSK2879552_rep3


title: UTL-096PS

description:
Library name: UTL-096PS
UTL-096PS


title: UTL-102PS

description:
Library name: UTL-102PS
UTL-102PS


title: UTL-103PS

description:
Library name: UTL-103PS
UTL-103PS


title: UTL-101PS

description:
Library name: UTL-101PS
UTL-101PS


title: UTL-093PS

description:
Library name: UTL-093PS
UTL-093PS


title: Anti-H3K4me3_DMSO_rep3


title: UTL-095PS

description:
Library name: UTL-095PS
UTL-095PS


title: Anti-H3K4me2_ORY1001_rep2


title: UTL-091PS

description:
Library name: UTL-091PS
UTL-091PS


title: Anti-H3K4me2_GSK2879552_rep2


title: UTL-090PS

description:
Library name: UTL-090PS
UTL-090PS


title: Anti-H3K4me3_ORY1001_rep3


title: MCF10A shHPA, rep2

description: Library name: Sample 11

value: HP1a knockdown


title: UTL-110PS

description:
Library name: UTL-110PS
UTL-110PS


title: Anti-H3K4me2_GSK2879552_rep1


title: UTL-094PS

description:
Library name: UTL-094PS
UTL-094PS


title: Anti-H3K4me2_TAS1440_rep3


title: Anti-H3K4me2_ORY1001_rep3


title: Anti-H3K4me2_ORY1001_rep1


title: Anti-H3K4me2_DMSO_rep3


title: Anti-H3K4me2_TAS1440_rep2


title: UTL-099PS

description:
Library name: UTL-099PS
UTL-099PS


title: Anti-H3K4me2_DMSO_rep2


title: Anti-H3K4me2_DMSO_rep1


title: UTL-087PS

description:
Library name: UTL-087PS
UTL-087PS


title: Anti-H3K4me1_GSK2879552_rep3


title: Anti-H3K4me2_TAS1440_rep1


title: Anti-H3K4me1_GSK2879552_rep1


title: UTL-083PS

description:
Library name: UTL-083PS
UTL-083PS


title: Anti-H3K4me1_GSK2879552_rep2


title: UTL-084PS

description:
Library name: UTL-084PS
UTL-084PS


title: UTL-088PS

description:
Library name: UTL-088PS
UTL-088PS


title: UTL-086PS

description:
Library name: UTL-086PS
UTL-086PS


title: UTL-082PS

description:
Library name: UTL-082PS
UTL-082PS


title: UTL-089PS

description:
Library name: UTL-089PS
UTL-089PS


title: UTL-079PS

description:
Library name: UTL-079PS
UTL-079PS


title: Anti-H3K4me1_ORY1001_rep3


title: Anti-H3K4me1_ORY1001_rep2


title: UTL-085PS

description:
Library name: UTL-085PS
UTL-085PS


title: UTL-080PS

description:
Library name: UTL-080PS
UTL-080PS


title: UTL-081PS

description:
Library name: UTL-081PS
UTL-081PS


title: Anti-H3K4me1_TAS1440_rep1


title: Anti-H3K4me1_TAS1440_rep2


title: Anti-H3K4me1_ORY1001_rep1


title: Anti-H3K4me1_TAS1440_rep3


title: UTL-074PS

description:
Library name: UTL-074PS
UTL-074PS


title: Anti-H3K4me1_DMSO_rep2


title: UTL-078PS

description:
Library name: UTL-078PS
UTL-078PS


title: UTL-092PS

description:
Library name: UTL-092PS
UTL-092PS


title: UTL-077PS

description:
Library name: UTL-077PS
UTL-077PS


title: UTL-075PS

description:
Library name: UTL-075PS
UTL-075PS


title: UTL-073PS

description:
Library name: UTL-073PS
UTL-073PS


title: Anti-H3K4me1_DMSO_rep3


title: INPUT_GSK2879552_rep4


title: UTL-071PS

description:
Library name: UTL-071PS
UTL-071PS


title: Anti-H3K4me1_DMSO_rep1


title: INPUT_GSK2879552_rep3


title: UTL-072PS

description:
Library name: UTL-072PS
UTL-072PS


title: INPUT_ORY1001_rep2


title: INPUT_ORY1001_rep4


title: INPUT_TAS1440_rep1


title: INPUT_TAS1440_rep2


title: INPUT_TAS1440_rep3


title: UTL-058PS

description:
Library name: UTL-058PS
UTL-058PS


title: UTL-063PS

description:
Library name: UTL-063PS
UTL-063PS


title: UTL-069PS

description:
Library name: UTL-069PS
UTL-069PS


title: UTL-062PS

description:
Library name: UTL-062PS
UTL-062PS


title: INPUT_GSK2879552_rep2


title: UTL-067PS

description:
Library name: UTL-067PS
UTL-067PS


title: INPUT_ORY1001_rep3


title: UTL-056PS

description:
Library name: UTL-056PS
UTL-056PS


title: UTL-055PS

description:
Library name: UTL-055PS
UTL-055PS


title: UTL-066PS

description:
Library name: UTL-066PS
UTL-066PS


title: UTL-064PS

description:
Library name: UTL-064PS
UTL-064PS


title: UTL-061PS

description:
Library name: UTL-061PS
UTL-061PS


title: UTL-059PS

description:
Library name: UTL-059PS
UTL-059PS


title: INPUT_DMSO_rep2


title: UTL-052PS

description:
Library name: UTL-052PS
UTL-052PS


title: INPUT_TAS1440_rep4


title: UTL-053PS

description:
Library name: UTL-053PS
UTL-053PS


title: INPUT_ORY1001_rep1


title: UTL-057PS

description:
Library name: UTL-057PS
UTL-057PS


title: H1417_KO_TAS1440DAY7_3

data_processing:
Deep sequencing was performed on an Illumina NovaSeq 6000 (paired-end reads) according to the manufacturer’s protocols. Sequenced reads from the RNA-seq experiments were aligned using the Bowtie 2 and TopHat (version 1.3.2), and Cufflinks (version 2.0.2) was used for transcriptome assembly. Gene expression levels were expressed as fragments per kilobase of exons per million mapped sequence reads. DEGs were identified using the R software package (version 4.2.0). Heatmaps and dendrograms were generated using R, GraphPad Prism 9.0, or https://www.chiplot.online/. DEG-related and terms of the KEGG were analyzed by gene set enrichment analysis software (GSEA, version 4.2.3).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: NCI-1417 [H1417] (Cat. No. CRL-5869), NCI-H209 [H209] (HTB-172), SHP-77 (Cat. No. CRL-2195), NCI-H211 (Cat. No. CRL-5824), NCI-H196 (Cat. No. CRL-5823), NCI-H146 (Cat. No. HTB-173), NCI-H187 (Cat. No. CRL-5804), NCI-H69 (Cat. No. HTB-119), NCI-H446 [H446] (Cat. No. HTB-171), DMS 79 (Cat. No. CRL-2049), NCI-H510A [H510A, NCI-H510] (Cat. No. HTB-184), DMS 114 (Cat. No. CRL-2066), DMS 53 (Cat. No. CRL-2062), NCI-H2081 (Cat. No. CRL-5920), NCI-H524 [H524] (Cat. No. CRL-5831), NCI-H128 (Cat. No. HTB-120), NCI-H526 (Cat. No. CRL-5811), and NCI-H1694 (Cat. No. CRL-5888) cell lines were purchased from the American Type Culture Collection. Lu-135 (Cat. No. JCRB0170), COR-L51 (Cat. No. 92031916), CPC-N (Cat. No. ACC 306), and SBC-5 (Cat. No. JCRB0819) cell lines were obtained from the Japanese Collection of Research Bioresources, European Collection of Authenticated Cell Cultures, German Collection of Microorganisms and Cell Cultures GmbH, and Health Science Research Resources Bank, respectively. All of these are small-cell lung cancer cell lines and were cultured in RPMI1640 medium (Cat#: 189-02025, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% FBS (Cat#: 10270106, GIBCO Thermo Fisher Scientific, San Jose, CA) (NCI-1417, NCI-H209, SHP-77, NCI-H211, NCI-H196, Lu-135, and COR-L51), in conditioned, high-glucose RPMI1640 (Wako, Cat#: 187-02705) with 10% FBS (NCI-H146, NCI-H187, NCI-H69, NCI-H446, NCI-H526, NCI-H524, and DMS 79), in McCoy’s 5A (GIBCO, Cat#: 16600-082) with 10% FBS (CPC-N), in minimum essential medium (Cat#: 21442-25, Nacalai Tesque, Kyoto, Japan) with 10% FBS (SBC-5), in F-12K medium (GIBCO, Cat#: 11765-054) with 10% FBS (NCI-H510A), in Waymouth’s medium (GIBCO, Cat#: 11220-035) with 10% FBS (DMS 114 and DMS 53), in IMDM medium (GIBCO, Cat#: 12440-053) with 20% FBS (NCI-H128), or in HITES medium (GIBCO, 11330-032) with 10% FBS, Insulin (FUJIFILM, Cat#: 093-06351), Transferrin (Cat#: 10652202001, Roche Diagnostics, Rotkreuz, Switzerland), Hydrocortisone (Cat#: H6909-10ML, SIGMA-Aldrich, St. Louis, MO, USA), GlutaMAX (GIBCO, Cat#: 35050-061), Sodium Selenite (FUJIFILM, Cat#: 190-10844), and -Estradiol (SIGMA-Aldrich, Cat#: E2758-250MG) (NCI-H2081 and NCI-H1694). INSM1 knockout NCI-H1417 and NCI-H146 cells were generated using CRISPR‒Cas9 genome editing as previously described (Ochiiwa et al., 2021).

extract_protocol:
SCLC cell lines were treated, for the indicated durations, with different LSD1 inhibitors. Total cellular RNA was extracted using a modified chloroform/phenol procedure (TRIzol™, Invitrogen Thermo Fisher Scientific). RNA integrity and concentration were measured using a 4200 TapeStation system for high-throughput automated electrophoresis (Agilent, Santa Clara, CA, USA)
RNA-Seq libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) following the manufacturers’ protocols.

treatment_protocol: The SCLC cell lines were seeded in plates. The following day, LSD1 inhibitors were serially diluted with DMSO and mixed with the culture medium. The mixtures were then added to each well on the plates. The final concentration of DMSO was set at 0.075 %. Cells were maintained with the inhibitors without any medium change.

value: INSM1 knockout


title: INPUT_DMSO_rep1


title: INPUT_GSK2879552_rep1


title: UTL-054PS

description:
Library name: UTL-054PS
UTL-054PS


title: INPUT_DMSO_rep4


title: UTL-048PS

description:
Library name: UTL-048PS
UTL-048PS


title: UTL-047PS

description:
Library name: UTL-047PS
UTL-047PS


title: UTL-051PS

description:
Library name: UTL-051PS
UTL-051PS


title: H1417_KO_TAS1440DAY7_1


title: H1417_KO_TAS1440DAY7_2


title: INPUT_DMSO_rep3


title: H1417_KO_DMSODAY7_2


title: H1417_KO_DMSODAY7_3


title: H146_KO_TAS1440DAY7_1


title: UTL-045PS

description:
Library name: UTL-045PS
UTL-045PS


title: H146_KO_DMSODAY7_3


title: H146_KO_TAS1440DAY7_2


title: UTL-038PS

description:
Library name: UTL-038PS
UTL-038PS


title: UTL-039PS

description:
Library name: UTL-039PS
UTL-039PS


title: UTL-044PS

description:
Library name: UTL-044PS
UTL-044PS


title: H1417_KO_DMSODAY7_1


title: H146_KO_DMSODAY7_2


title: UTL-040PS

description:
Library name: UTL-040PS
UTL-040PS


title: H146_KO_DMSODAY7_1


title: H1417_WT_TAS1440DAY7_3


title: UTL-034PS

description:
Library name: UTL-034PS
UTL-034PS


title: UTL-033PS

description:
Library name: UTL-033PS
UTL-033PS


title: UTL-035PS

description:
Library name: UTL-035PS
UTL-035PS


title: H1417_WT_TAS1440DAY7_2


title: H1417_WT_TAS1440DAY7_1


title: UTL-036PS

description:
Library name: UTL-036PS
UTL-036PS


title: H146_KO_TAS1440DAY7_3


title: UTL-031PS

description:
Library name: UTL-031PS
UTL-031PS


title: UTL-037PS

description:
Library name: UTL-037PS
UTL-037PS


title: H146_WT_TAS1440DAY7_3


title: H1417_WT_DMSODAY7_1


title: H146_WT_TAS1440DAY7_1


title: UTL-023PS

description:
Library name: UTL-023PS
UTL-023PS


title: UTL-019PS

description:
Library name: UTL-019PS
UTL-019PS


title: H146_WT_DMSODAY7_2


title: 20-6_NCI-H209_Day7_TAS1440_300nM


title: H1417_WT_DMSODAY7_2


title: UTL-041PS

description:
Library name: UTL-041PS
UTL-041PS


title: H146_WT_DMSODAY7_1


title: UTL-018PS

description:
Library name: UTL-018PS
UTL-018PS


title: UTL-017PS

description:
Library name: UTL-017PS
UTL-017PS


title: H146_WT_DMSODAY7_3


title: UTL-028PS

description:
Library name: UTL-028PS
UTL-028PS


title: 20-5_NCI-H209_Day7_TAS1440_300nM


title: UTL-012PS

description:
Library name: UTL-012PS
UTL-012PS


title: Brain, GL261-CAR, oAd, CP3

city: Chengdu

first: Zhang

last: Zongliang

address: People's South Road 17, Chengdu, P.R. China

department: State Key Laboratory of Biotherapy

country: China

institute: Sichuan University

description:
Library name: Smple 8
Fresh orthotopic GL261-CAR tumors scRNA-sequencing

data_processing:
The resulting feature‑barcode matrix was imported into Seurat (v4.3.0) in R (v4.2.2) for downstream quality control, normalization, clustering, and differential expression analysis. All computational analyses were performed using the SeekSoul Online platform (https://seeksoul.online/).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Mice bearing intracranial GL261‑CAR tumors were treated intratumorally with PBS (control), oAd, or oAd‑mCD47/PD‑L1‑mIL‑12 (1 × 10^9 pfu). Tumors were harvested three days after the second viral injection and dissociated into single‑cell suspensions using the SeekMate Tissue Dissociation Reagent Kit A Pro (SeekGene, K01801‑30) at 37 °C for 15 min. Erythrocytes were lysed with an erythrocyte removal reagent (Solarbio, R1010). Cell count and viability were determined using a SeekMate Tinitan Fluorescence Cell Counter (SeekGene, M002C) with AO/PI staining. Debris and dead cells were removed by sequential filtration through a 40‑μm cell strainer and a dead‑cell removal kit (Miltenyi Biotec, #130‑090‑101). Cells were washed twice in RPMI‑1640 medium and resuspended at 1 × 106 cells/mL.
Single‑cell RNA‑seq libraries were constructed using the SeekOne Digital Droplet Single‑Cell 3′ Library Preparation Kit (SeekGene, #K00202) according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq X Plus platform with 150‑bp paired‑end reads. Raw sequencing reads were processed with fastp (v0.23.2) to trim adapters and remove low‑quality bases. Cellular barcodes were demultiplexed and reads were aligned to the mouse reference genome (mm10) using SeekSoul tools (SeekGene, v1.2.1).

treatment_protocol: Single‑cell RNA sequencing (scRNA‑seq) of orthotopic tumors following oncolytic adenovirus treatment

value: Brain

value: Glioma

value: express the coxsackievirus–adenovirus receptor (CAR)

tag: sample group

value: oAd, CP


title: UTL-022PS

description:
Library name: UTL-022PS
UTL-022PS


title: H1417_WT_DMSODAY7_3

value: small-cell lung cancer

value: WT


title: UTL-030PS

description:
Library name: UTL-030PS
UTL-030PS


title: UTL-025PS

description:
Library name: UTL-025PS
UTL-025PS


title: UTL-029PS

description:
Library name: UTL-029PS
UTL-029PS


title: H146_WT_TAS1440DAY7_2


title: Brain, GL261-CAR, oAd, CP1

description:
Library name: Smple 7
Fresh orthotopic GL261-CAR tumors scRNA-sequencing


title: 20-3_NCI-H209_Day7_DMSO_0


title: UTL-024PS

description:
Library name: UTL-024PS
UTL-024PS


title: UTL-016PS

description:
Library name: UTL-016PS
UTL-016PS


title: UTL-015PS

description:
Library name: UTL-015PS
UTL-015PS


title: 20-4_NCI-H209_Day7_TAS1440_300nM


title: UTL-007PS

description:
Library name: UTL-007PS
UTL-007PS


title: Brain, GL261-CAR, oAd, CP4

description:
Library name: Smple 9
Fresh orthotopic GL261-CAR tumors scRNA-sequencing


title: UTL-003PS

description:
Library name: UTL-003PS
UTL-003PS


title: UTL-004PS

description:
Library name: UTL-004PS
UTL-004PS


title: UTL-027PS

description:
Library name: UTL-027PS
UTL-027PS


title: 20-1_NCI-H209_Day7_DMSO_0


title: UTL-020PS

description:
Library name: UTL-020PS
UTL-020PS


title: 19-6_NCI-H128_Day7_TAS1440_300nM


title: Brain, GL261-CAR, oAd, AD3

description:
Library name: Smple 6
Fresh orthotopic GL261-CAR tumors scRNA-sequencing

value: oAd, AD


title: UTL-010PS

description:
Library name: UTL-010PS
UTL-010PS


title: Brain, GL261-CAR, oAd, AD1

description:
Library name: Smple 4
Fresh orthotopic GL261-CAR tumors scRNA-sequencing


title: Brain, GL261-CAR, PBS, C3

description:
Library name: Smple 3
Fresh orthotopic GL261-CAR tumors scRNA-sequencing

value: PBS, C


title: LUT127PS

description:
Library name: LUT127PS
LUT127PS


title: Brain, GL261-CAR, oAd, AD2

description:
Library name: Smple 5
Fresh orthotopic GL261-CAR tumors scRNA-sequencing


title: 20-2_NCI-H209_Day7_DMSO_0


title: UTL-002PS

description:
Library name: UTL-002PS
UTL-002PS


title: UTL-009PS

description:
Library name: UTL-009PS
UTL-009PS


title: mpk_KO_cpd_6

city: Baltimore

first: Mackenzie

last: Kui

state: Maryland

address: 725 N Wolfe Street

department: Physiology

institute: Johns Hopkins

description:
Library name: 24_KOcpd2h
KO_cpd_6

data_processing:
Pooled libraries were sequenced on an Illumina® NovaSeqX Plus instrument using standard protocols for paired end sequencing. 24 samples were multiplexed for an estimated 89 million unique mapped reads per sample. Demultiplexed FASTQ files were generated using bcl-convert v3.7.5.
Transcriptomic data collected by RNA sequencing (RNA-seq) was analyzed to determine the genes that are present in each sample and condition, their expression levels, and the differences between expression levels among experiment conditions, as follows. Sequencing reads were mapped to the mouse genome version GRCm39 with the alignment tool STAR v.2.7.8a (ref-star), which allows for large ‘gaps’ in the alignment, representing introns.
Assembly: The aligned reads were assembled with PsiCLASS v.1.0.2 (ref-psiclass) to create gene and transcript models. Unlike traditional transcript assemblers that process each sample separately, PsiCLASS simultaneously analyzes all samples in the experiment to produce a unified set of transcript annotations to use in the subsequent differential analyses. Transcripts were then assigned to known genes from the GENCODE v.M28 reference gene set. Lastly, DESeq2 (ref-deseq) was used to quantify the expression levels and determine differentially expressed genes. P values were corrected for FDR.
Supplementary files format and content: csv files contain raw counts normalized by gene length

source_name: kidney cortical collecting duct

growth_protocol: Without transformation (WT) and Gpr39 knockout (KO) mpkCCD cells were seeded onto 12-well transwell inserts and cultured in complete media without dDAVP for 9 days to allow for full polarization. Cells were then switched to simple media for 24 hours prior to treatment.

extract_protocol:
Following treatment, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions. Samples were checked for quality/quantity on Fragment Analyzer and Qubit prior to library preparation.
NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat# E7775) were used to generate libraries. Specifically, Poly A RNAs were isolated from total RNAs and fragmented for cDNA synthesis. End repair was performed, and DNA fragments were ligated to sequencing adapters. Ligated fragments were subsequently size selected through purification using Sample Purification Beads PCR amplification was used to prepare the libraries. The Fragment Analyzer was used for quality control of the libraries to ensure adequate concentration and appropriate fragment size. The resulting library insert size was 200bp-500bp with a median size around 300bp. Libraries were barcoded using unique dual indexing (E6440S) and pooled for sequencing.

treatment_protocol: Cells were treated with either 1 µM cpd1324 + 10 µM ZnCl₂ or vehicle control (0.1% DMSO + 10 µM ZnCl₂) for 2 hours in the basolerateral compartment

value: kidney cortical collecting duct

value: mpkCCD

value: epithelial

value: KO

value: 1 µM cpd1324 + 10 µM ZnCl₂

tag: time

value: 2 hours


title: Brain, GL261-CAR, PBS, C1

description:
Library name: Smple 1
Fresh orthotopic GL261-CAR tumors scRNA-sequencing

tag: tissue


title: 19-5_NCI-H128_Day7_TAS1440_300nM

tag: treatment


title: Brain, GL261-CAR, PBS, C2

description:
Library name: Smple 2
Fresh orthotopic GL261-CAR tumors scRNA-sequencing

tag: cell type


title: LUT124PS

description:
Library name: LUT124PS
LUT124PS

value: liver

value: NF


title: LUT128PS

description:
Library name: LUT128PS
LUT128PS

value: EAD


title: LUT114PS

description:
Library name: LUT114PS
LUT114PS


title: LUT116-2PS

description:
Library name: LUT116-2PS
LUT116-2PS


title: 19-2_NCI-H128_Day7_DMSO_0

value: DMSO


title: UTL-001PS

description:
Library name: UTL-001PS
UTL-001PS


title: LUT125PS

description:
Library name: LUT125PS
LUT125PS


title: LUT117PS

description:
Library name: LUT117PS
LUT117PS


title: LUT106PS

description:
Library name: LUT106PS
LUT106PS